< A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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() - Static method in class MAEPlugin.MAEPlugin
 
() - Static method in class MAEPlugin.analysis.FilterPlugin
 
() - Static method in class MAEPlugin.popup.PluginLoader
 
() - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
 

A

a_count - Variable in class WriteGifEncoder
 
abortFlag - Variable in class MAExplorer
Flag: set true by the STOP button.
accept(File, String) - Method in class EventMenu
accept() - filter used to test if file should be in directory list.
accept(File, String) - Method in class RevalBase
accept() - file browser filter used to test if file should be in directory list.
accept(File, String) - Method in class MAEPlugin.PluginFilenameFilter
accept() - Filter method for accepting a file.
accept(File, String) - Method in class MAEPlugin.popup.PluginLoader
accept() - implentation of FilenameFilter.
accum - Variable in class WriteGifEncoder
 
actionPerformed(ActionEvent) - Method in class ChooserGUI
actionPerformed() - handle action events buttons and text areas
actionPerformed(ActionEvent) - Method in class DrawClusterGram
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class ExprProfilePopup
actionPerformed() - event handler for button clicks
actionPerformed(ActionEvent) - Method in class Guesser
actionPerformed() - Handle Control button clicks.
actionPerformed(ActionEvent) - Method in class MenuBarFrame
actionPerformed() - handle action events for Buttons and menu commands.
actionPerformed(ActionEvent) - Method in class PopupBinOprDialogQuery
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupCondChooser
actionPerformed() - Handle Control panel button clicks
actionPerformed(ActionEvent) - Method in class PopupCondChooser.CondDialogBox
actionPerformed() - handle action events
actionPerformed(ActionEvent) - Method in class PopupCondChooser.PopupTextField
actionPerformed() - handle action events
actionPerformed(ActionEvent) - Method in class PopupCondChooser.ChoiceList
actionPerformed() - button handler
actionPerformed(ActionEvent) - Method in class PopupCondChooserGUI
actionPerformed() - handle action events buttons and text areas
actionPerformed(ActionEvent) - Method in class PopupDialogQuery
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupHPChooser
actionPerformed() - handle action events buttons and text areas.
actionPerformed(ActionEvent) - Method in class PopupLoginDialogQuery
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupOrderedCondChooser
actionPerformed() - Handle Control panel button clicks
actionPerformed(ActionEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
actionPerformed() - handle action events
actionPerformed(ActionEvent) - Method in class PopupOrderedCondChooser.PopupTextField
actionPerformed() - handle action events
actionPerformed(ActionEvent) - Method in class PopupOrderedCondChooser.ChoiceList
actionPerformed() - button handler
actionPerformed(ActionEvent) - Method in class PopupOrderedCondChooserGUI
actionPerformed() - handle action events buttons and text areas
actionPerformed(ActionEvent) - Method in class RtestBase
actionPerformed() - Handle Control panel button clicks
actionPerformed(ActionEvent) - Method in class PopupEditRscript
actionPerformed() - Handle Control panel button clicks
actionPerformed(ActionEvent) - Method in class PopupScrollableSelector
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class ShowExprProfilesPopup
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class ShowPlotPopup
actionPerformed() - Handle Control panel button clicks
actionPerformed(ActionEvent) - Method in class ShowSpreadsheetPopup
actionPerformed() - Handle Control panel button clicks
actionPerformed(ActionEvent) - Method in class ShowStringPopup
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class StateScrollers
actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class LogTextFrame
actionPerformed() - event handler for button press
actionPerformed(ActionEvent) - Method in class MAEPlugin.MenuPlugin
actionPerformed() - actionListener
actionPerformed(ActionEvent) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
actionPerformed() -
activeBin - Variable in class DrawHistogram
active bin idx [0:MAXBINS-1] else -1
activeBin - Variable in class DrawRatioHistogram
active bin # [0:nHist] else -1
activeClusterMethod - Static variable in class ClusterGenes
active instance, GC others
activeFilterNames - Variable in class Filter
names of active filters for drawing in pseudo array image [0:nActiveFilters-1]
activeFilterPluginList - Static variable in class MAEPlugin.analysis.FilterPlugin
pointer to the active FilterPlugin object.
activeGeneList - Variable in class Reval
list [0:maxGenes-1] booleans for genes passing data Filter
activeNormalization - Static variable in class MAEPlugin.analysis.NormalizationPlugin
Pointer to the current active Normalization object.
add(Component, int, int, int, int, double, double) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
add() - add component
add(String) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
 
addAllButton - Variable in class ChooserGUI
mv ALL Remainder entries to Selected
addAllButton - Variable in class PopupCondChooserGUI
Move ALL Remainder entries to Selected
addAllButton - Variable in class PopupOrderedCondChooserGUI
Move ALL Remainder entries to Selected
addAllCondForOCL(String, int) - Method in class PopupOrderedCondChooser
addAllCondForOCL() - Place cond data associated with new ordered condition list into ChooserGUI.
addAllObjs() - Method in class ChooserGUI
addAllObjs() - move all REMAINDER ta1 objects to SELECTED ta2.
addAllObjs() - Method in class PopupCondChooserGUI
addAllObjs() - move all REMAINDER remTextArea objects to SELECTED selTextArea.
addAllObjs() - Method in class PopupOrderedCondChooserGUI
addAllObjs() - move all REMAINDER remTextArea objects to SELECTED selTextArea.
addAllSamplesForCond(String, int) - Method in class PopupCondChooser
addAllSamplesForCond() - Place samples data associated with new condition into ChooserGUI.
addAnnButton - Variable in class PopupOrderedCondChooser
add annotation
addAnovaFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_ANOVA
addBoxplotFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_BOXPLOT
addButton - Variable in class ChooserGUI
mv Remainder entry to Selected
addButton - Variable in class PopupCondChooserGUI
Move the Remainder entry to Selected
addButton - Variable in class PopupOrderedCondChooserGUI
Move the Remainder entry to Selected
addButtonsCnt - Variable in class PopupDialogQuery
# of buttons to add.
addButtonsFlag - Variable in class ExprProfilePopup
flag: if false, don't add title or Close button
addButtonsToParent(ShowPlotPopup, Panel, Font) - Method in class DrawClusterGram
addButtonsToParent() - add buttons for this plot to parents's panel
addChangePosFlag - Variable in class ChooserGUI
if can move SELECTED entry up/down
addChangePosFlag - Variable in class PopupCondChooserGUI
if can move SELECTED entry up/down
addChangePosFlag - Variable in class PopupOrderedCondChooserGUI
if can move SELECTED entry up/down
addComponent(Component, int, int, int, int, int, int) - Method in class LogTextFrame
addComponent() - add a text component to the frame
addCondButton - Variable in class PopupCondChooser
Add condition
addConditionToOrderedCondList(Condition, String) - Method in class Condition
addConditionToOrderedCondList() - add condition to named ordered condition list.
addConditionToOrderedCondList(String, String) - Method in class MJAcondition
addConditionToOrderedCondList() - add condition to named ordered condition list.
addCondList(String, MaHybridSample[], int, int) - Method in class Condition
addCondList() - add conditionName Condition list with msList[] data
addCorFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_COR
addDelAllButtonPanel - Variable in class ChooserGUI
add,del,all buttons
addDelAllButtonPanel - Variable in class PopupCondChooserGUI
add,del,all buttons
addDelAllButtonPanel - Variable in class PopupOrderedCondChooserGUI
add,del,all buttons
addDensityFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_DENSITY
addExprProfFlag - Variable in class Report
 
addExprProfileFlag - Variable in class MAExplorer
set for EP ratios in gene REPORTS
addFormValue(Hashtable, String, String) - Method in class JavaCGIBridge
addFormValue() - adds a form variable, value pair to the passed Hashtable.
addGene(Gene) - Method in class GeneList
addGene() - add Gene to gene list bitSet, and mList[] if it exists.
addGeneByRegion(Gene) - Method in class EditedGeneList
addGenesByRegion() - add genes to editedCL if they are in the region in the pseudoarray image or scatterplot [TODO]
addGeneToEditedCL(Gene) - Method in class EditedGeneList
addGeneToEditedCL() - add gene to editedCL if not in CL by gene
addGeneToEditedCL(int) - Method in class EditedGeneList
addGeneToEditedCL() - add gene to editedCL if not in CL by mid
addGeneToGeneBitset(String, int) - Method in class MJAgeneList
addGeneToGeneBitset() - add gene MID to Gene bitset, ignore if already there
addGeneToGeneList(String, int, String[]) - Method in class MJAgeneList
addGeneToGeneList() - add gene MID to GeneList, ignore if already there
addHierClusterStatFlag - Variable in class Report
 
addHistFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_HIST
addHP_XYstatFlag - Variable in class MAExplorer
set for HP_XY statistics in gene REPORTS
addHP_XYstatFlag - Variable in class Report
 
addHPtoCondList(MaHybridSample) - Method in class Condition
addHPtoCondList() - add Sample to condition list.
addHPtoDB(MaHybridSample, int) - Method in class SampleSets
addHPtoDB() - set HP sample to active database entry i
addHPtoElist(MaHybridSample) - Method in class SampleSets
addHPtoElist() - add HP sample to end of HP-E list
addHPtoXset(MaHybridSample) - Method in class SampleSets
addHPtoXset() - add HP sample to HP-X set
addHPtoYset(MaHybridSample) - Method in class SampleSets
addHPtoYset() - add HP sample to HP-Y set
addItem(int) - Method in class GeneBitSet
addItem() - add Item (i.e.
addKmeansClusterStatFlag - Variable in class Report
 
addKmeansDataFlag - Variable in class ClusterGramCanvas
flag: if cdg.plotMode==mae.PLOT_KMEANS_CLUSTERGRAM)
addKmeansMnAndSDstatFlag - Variable in class Report
 
addLoessFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_LOESS
addMenuBar() - Method in class MenuBarFrame
addMenuBar() - add menubar with menus to the frame
addMenuStubToMenuStubList(String, Menu) - Method in class MenuBarFrame
addMenuStubToMenuStubList() - add menu position to Menu Stub List.
addNewCondition() - Method in class PopupCondChooser
addNewCondition() - add new condition to local chooser database and leave it as the selected condition
addNewCondition() - Method in class PopupOrderedCondChooser
addNewCondition() - add new condition to local chooser database and leave it as the selected condition
addNewHPtoDB(MaHybridSample) - Method in class SampleSets
addNewHPtoDB() - add new HP sample to end of active database list
addNewParameter() - Method in class PopupCondChooser
addNewParameter() - add a new parameter locally.
addNewParameter() - Method in class PopupOrderedCondChooser
addNewParameter() - add a new parameter locally.
addObj(Container, Object, int, int, int, int, double, double) - Method in class PopupHPChooser
addObj() - add object to GridBagLayout.
addObjGridBagLayout(Container, Object, int, int, int, int, double, double) - Method in class ChooserGUI
addObjGridBagLayout() - add object to GridBagLayout using x,y grid system.
addObjGridBagLayout(Container, Object, int, int, int, int, double, double) - Method in class PopupCondChooserGUI
addObjGridBagLayout() - add object to GridBagLayout using x,y grid system.
addObjGridBagLayout(Container, Object, int, int, int, int, double, double) - Method in class PopupOrderedCondChooserGUI
addObjGridBagLayout() - add object to GridBagLayout using x,y grid system.
addObjs(String) - Method in class ChooserGUI
addObjs() - move object to (remainder) TA1 from (selected) TA2.
addObjs(String) - Method in class PopupCondChooserGUI
addObjs() - move object to (remainder) remTextArea from (selected) selTextArea.
addObjs(String) - Method in class PopupOrderedCondChooserGUI
addObjs() - move object to (remainder) remTextArea from (selected) selTextArea.
addOCLButton - Variable in class PopupOrderedCondChooser
add ordered cond list
addOCLstatFlag - Variable in class MAExplorer
set for OCL statics statistics in gene REPORTS
addOCLstatFlag - Variable in class Report
 
addParamButton - Variable in class PopupCondChooser
add condition parameter
addPixels - Variable in class ScrollableImageCanvas
extra pixels for circles
addPlotFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_PLOT
addPopupWindowToReg(MAEUpdateListener, String, int) - Method in class MJApopupRegistry
addPopupWindowToReg() - register instance of MAEPlugin window with keyName
addPopupWindowToReg(MAEUpdateListener, String, int) - Method in class PopupRegistry
addPopupWindowToReg() - register MAEPlugin Instance Object window in maepList[]
addPopupWindowToReg(ShowExprProfilesPopup, String, int) - Method in class PopupRegistry
addPopupWindowToReg() - register ShowExprProfilesPopup window in seppList[]
addPopupWindowToReg(ShowPlotPopup, String, int) - Method in class PopupRegistry
addPopupWindowToReg() - register ShowPlotPopup window in sppList[]
addPopupWindowToReg(ShowSpreadsheetPopup, String, int) - Method in class PopupRegistry
addPopupWindowToReg() - register ShowSpreadsheetPopup window in ssspList[]
addPopupWindowToReg(ShowStringPopup, String, int) - Method in class PopupRegistry
addPopupWindowToReg() - register ShowStringPopup window in sspList[]
addQuotesIfSpace(String) - Static method in class MJAutil
addQuotesIfSpace() - add "..." around string if it contains a space but don't add quotes if it already has a leading ".
addQuotesIfSpace(String) - Static method in class Util
addQuotesIfSpace() - add "..." around string if it contains a space but don't add quotes if it already has a leading ".
addr1D(int, int) - Method in class ClusterGenes
addr1D() - lookup lower-diagonal addr1D(x,y) [y' + x'*(x'+1)/2] where:
addr1D(int, int) - Static method in class GeneGeneDist
addr1D() - lookup lower-diagonal addr1D(x,y) using [y' + x'*(x'+1)/2] address
addr1D(int, int) - Method in class HierClustNode
addr1D() - lookup lower-diagonal addr1D(x,y) [y' + x'*(x'+1)/2] where: x' = (yaddr1D(int, int) - Method in class MJAcluster
addr1D() - lookup lower-diagonal addr1D(x,y) [y' + x'*(x'+1)/2]
addRLO(String, String, String, String[], int[], int, int, String[], int[], String[], String[], int[], String) - Method in class MJAReval
addRLO() - add new R LayOut (RLO) instance to the RLO database.
addRLO(String, String, String, String[], int[], int, int, String[], int[], String[], String[], int[], String) - Method in class RevalBase
addRLO() - add new R LayOut (RLO) instance to the RLO database.
addRLO(String, String, String, String[], int[], int, int, String[], int[], String[], String[], int[], String) - Method in class RLO
addRLO() - add new R LayOut (RLO) instance to the RLO database.
addRLOsubmenuTree() - Method in class MenuBarFrame
addRLOsubmenuTree() - add RLO R scripts submenu tree to rloSmnu if RLOs exist.
addSampleToCondList(int, String) - Method in class MJAcondition
addSampleToCondList() - add sample to named condition list
addScroller(String) - Method in class StateScrollers
addScroller() - add a particular scroller by scroller name
addSetHP_XYEsubmenuTree(Menu, String) - Method in class MenuBarFrame
addSetHP_XYEsubmenuTree() - add HP sample submenu tree to submenu if submenus exist.
addSummaryFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_SUMMARY
addTtestFlag - Variable in class RgenDemo
RLO GenR test to add to R script: R_GENR_TTEST
addUniquePopupWindowToReg(MAEUpdateListener, String, int) - Method in class MJApopupRegistry
addUniquePopupWindowToReg() - register popupWindowInstance window with keyName
adjustAllButton - Variable in class StateScrollers
pop down current mode and popup adjust all sliders
adjustmentValueChanged(AdjustmentEvent) - Method in class ArrayScroller
adjustmentValueChanged() - handle ArrayScroller scroll events.
adjustmentValueChanged(AdjustmentEvent) - Method in class ExprProfileOverlay
adjustmentValueChanged() - handle scroll events and cause a repaint.
adjustmentValueChanged(AdjustmentEvent) - Method in class ExprProfileScrollPane
adjustmentValueChanged() - handle scroll events and cause repaint.
adjustmentValueChanged(AdjustmentEvent) - Method in class ShowPlotPopup
adjustmentValueChanged() - handle scroll events if plot supports scrollers.
adjustmentValueChanged(AdjustmentEvent) - Method in class SSscrollHorizontal
adjustmentValueChanged() - change spreadsheet cell positions via scrollers
adjustmentValueChanged(AdjustmentEvent) - Method in class SSscrollVertical
adjustmentValueChanged() - change spreadsheet cell positions via scrollers
adjustmentValueChanged(AdjustmentEvent) - Method in class StateScrollers
adjustmentValueChanged() - handle scroller state changed events
adjustRatioOrZscoreCounters() - Method in class StateScrollers
adjustRatioOrZscoreCounters() - adjust any sliders that depend on being in Zscore mode This is ONLY called when mae.isZscoreFlag is changed.
alertDone - Variable in class PopupDialogQuery
button pressed flag
alertOK - Variable in class ShowStringPopup
Flag: set true if popupName is "ALERT"
alertTimeout(String) - Method in class PopupDialogQuery
alertTimeout() - update the popup dialog msg - wait for "Continue"
ALL_BITS - Static variable in class GeneBitSet
0XFFFFFFFFFFFFFFFF is all 64-bits that is also 1's complement -1
allClBS - Variable in class GeneClass
working bit set of all genes
allConditionNames - Variable in class PopupOrderedCondChooser
list of all condition names
allGenesAndESTsCL - Variable in class GeneClass
special list of All genes and ESTs
allGenesCL - Variable in class GeneClass
special list of all genes
allGenesPlotButton - Variable in class ShowStringPopup
multipurpose button that toggles between: "Go 'Cluster gene counts' " for "allGenes" (cluster counts) and "Go 'Cluster single genes'" for "singleGene" (similar genes).
allNamedGenesCL - Variable in class GeneClass
special list of all named genes
allocateGeneLists() - Method in class Filter
allocateGeneLists() - create all of the gene lists if they were not previously created
allocateMapArrays() - Method in class Maps
allocateMapArrays() - Allocate the map arrays and hash tables
allocGeneBitSet(int, String, GeneList) - Method in class GeneBitSet
allocGeneBitSet() - create named GeneBitSet by allocating bit set structures.
allocGeneList(int, String, boolean) - Method in class GeneList
allocGeneList() - constructor to make new Gene named list with bitSet, but optional mList[].
allocLocalRLOstate() - Method in class PopupEditRscript
allocLocalRLOstate() - create empty local edit state variables for the RLO database.
allocSize - Variable in class MaHPquantTable
number of spots allocated as map.maxSpots+1.
allowNegQuantDataFlag - Variable in class MAExplorer
PARAM "allowNegQuantDataFlag"
allowPopdownOnWindowClosing - Variable in class StateScrollers
Flag: allow popdown if orig.
allSampleNames - Variable in class PopupCondChooser
list of ALL samples in the database
alog10(double) - Method in class MJAmath
alog10() - compute alog(x) base 10.
alog10(double) - Static method in class MathMAE
alog10() - compute alog(x) base 10.
alog2(double) - Method in class MJAmath
alog2() - compute alog(x) base 2.
alog2(double) - Static method in class MathMAE
alog2() - compute alog(x) base 2.
alphaList - Variable in class ChooserGUI.MouseEventHandler
alpha list if items in the list
alphaList - Variable in class Guesser
char text to be searched (GeneName)
alphaList - Variable in class KeyEventHandler
alpha list
alphaList - Variable in class MouseEventHandler
alpha list
alphaList - Variable in class PopupCondChooserGUI.MouseEventHandler
alpha list if items in the list
alphaList - Variable in class PopupOrderedCondChooserGUI.MouseEventHandler
alpha list if items in the list
alphaListMode - Variable in class Guesser
"GeneName", "GenBank", "dbEst" etc
alphaListSize - Variable in class ChooserGUI.MouseEventHandler
size of alphaList
alphaListSize - Variable in class Guesser
size of alphaList array
alphaListSize - Variable in class KeyEventHandler
size of alphaList array
alphaListSize - Variable in class PopupCondChooserGUI.MouseEventHandler
size of alphaList
alphaListSize - Variable in class PopupOrderedCondChooserGUI.MouseEventHandler
size of alphaList
alsoCalcEPdataFlag - Variable in class HPxyData
flag: use to also compute HP list statistics as well as XY stats
altFieldNames - Variable in class ShowSpreadsheetPopup
ARG: [maxCols] if ! null - same for all cells
analyses - Static variable in class RevalBase
List [0:nAnalyses-1] of R analysis procedures descriptions
analysisMenu - Variable in class MenuBarFrame
"Analysis" menu
AnalysisPlugin - class MAEPlugin.analysis.AnalysisPlugin.
This class is the analysis MAEPlugin base class and is used to implement specialized base classes based on CheckBoxMenuPlugin.
AnalysisPlugin() - Constructor for class MAEPlugin.analysis.AnalysisPlugin
AnalysisPlugin() - Constructor for new AnalysisPlugin with default label "Analysis Plugin".
AnalysisPlugin(String) - Constructor for class MAEPlugin.analysis.AnalysisPlugin
AnalysisPlugin() - Constructor for new AnalysisPlugin with label.
AnalysisPlugin(String, String) - Constructor for class MAEPlugin.analysis.AnalysisPlugin
AnalysisPlugin() - Constructor for new AnalysisPlugin with label and file name.
appendHistoryFlag - Static variable in class Util
Flag: set if appending command history to historyFile
appendLog(String) - Method in class LogTextFrame
appendLog() - save text into log area.
appendLogDataFlag - Variable in class LogTextFrame
Flag indicating that data is to be appended text area.
appendLogLn(String) - Method in class LogTextFrame
appendLogLn() - save text+"\n" into log area.
appendMsgFlag - Static variable in class Util
Flag: set if appending msg to historyFile
appendReport(String, boolean) - Method in class RtestBase
appendReport() - add text to report text area
appendTextFlag - Variable in class RtestBase
Flag for append text and resetting cursor to end of TextArea
appendToLogFile(String) - Method in class LogTextFrame
appendToLogFile() - append text to open log file
applet - Variable in class MAExplorer
"this" applet instance for MAExplorer main class
applyButton - Variable in class StateScrollers
Apply the parameters to the data filters.
area - Variable in class LogTextFrame
Text area for displaying the text
ArrayScroller - class ArrayScroller.
This class supports the scrollable clickable pseudoarray image.
ArrayScroller(MAExplorer, String, String, int, int, int, int, int) - Constructor for class ArrayScroller
ArrayScroller() - constructor.
ASCENDING - Static variable in class Report
flag: sort rows by assending column data
assignCLtoUserBS(String, GeneList) - Method in class GeneBitSet
assignCLtoUserBS() - assign GeneList ml to new user GeneBitSet userBS[] database.
assignCSbinOprToUserBS(String, String, String, String) - Method in class GeneBitSet
assignCSbinOprToUserBS() - assign GeneBitSet binary Boolean opr to new user GeneBitSet.
assignedBSname - Variable in class GeneBitSet
if this was assigned from another bitSet
assignGeneListToBestKmeansNodes(boolean) - Method in class ClusterGenes
assignGeneListToBestKmeansNodes() - assign genes for all complexClusterCL genes to the best N primary Nodes clusters.
assignGeneNames2StaticGeneList() - Method in class GeneClass
assignGeneNames2StaticGeneList() - assign Gene_Names' to map.midStaticCL list now that the gene lists exist in the map.midStaticCL list.
assignHPtoAxis(int, int, MaHybridSample) - Method in class SampleSets
assignHPtoAxis() - assign sample to current HP-X or HP-Y sample This is the default.
assignMasterGeneName(int) - Method in class Gene
assignMasterGeneName() - assign MasterGeneName using masterGeneNameMode for current database configuration.
assignMasterID(int) - Method in class Gene
assignMasterID() - assign Master_ID using masterIDmode using existing data.
aText - Variable in class Draw2Dplot
ARGS:
aTextOrig - Variable in class Draw2Dplot
copy of original aText disp below title3
aTitle - Variable in class MenuBarFrame
i.e.
autoStateScrPopupFlag - Variable in class MAExplorer
Auto state-scroller popup windown assoc w/Filters

B

b - Variable in class WriteGifEncoder
 
BAD_MODE - Static variable in class Guesser
used to set iMode
banner - Variable in class PopupCondChooser
Title banner for the main window
banner - Variable in class PopupOrderedCondChooser
Title banner for the main window
BANNER - Static variable in class PopupCondChooser
 
BANNER - Static variable in class PopupOrderedCondChooser
 
BANNER - Static variable in class RtestBase
 
base64encode(String) - Method in class JavaCGIBridge
base64encode() - return str encoded to base64 format.
base64Length(int) - Method in class JavaCGIBridge
base64Length() - compute# bytes it takes to store LEN bytes in base64.
baseCgiURLgeneClassNames - Variable in class Config
PARAM "baseCgiURLgeneClassNames"
baseCgiURLgeneIdNameClass - Variable in class Config
PARAM "baseCgiURLgeneIdNameClass"
baseCgiURLgipo - Variable in class Config
PARAM "baseCgiURLgipo"
baseCgiURLquant - Variable in class Config
PARAM "baseCgiURLquant"
baseCgiURLsamples - Variable in class Config
PARAM "baseCgiURLsamples"
basicAuthenticationEncode(String, String) - Method in class JavaCGIBridge
basicAuthenticationEncode() - create authentication header contents for the `Basic' scheme.
bDone - Variable in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
 
bestGene - Variable in class ExprProfileOverlay
gene if mouse event
bestGene - Variable in class ExprProfileScrollPane
gene if mouse event
bestHP - Variable in class ExprProfileOverlay
HP if mouse event
bestHP - Variable in class ExprProfileScrollPane
HP if mouse event
bestIntens - Variable in class ExprProfileOverlay
intensity if mouse event
bestIntens - Variable in class ExprProfileScrollPane
intensity if mouse event
bestKmeansForGene - Variable in class ClusterGenes
[0:nClist-1] best Kmeans node cluster in [1:maxKmeansNodes] for all genes in complexClusterCL
bestMid - Variable in class ExprProfileOverlay
gene clone ID if mouse event
bestMid - Variable in class ExprProfileScrollPane
gene clone ID if mouse event
BGAvgQ - Variable in class MaHybridSample
Average background for entire array
bgColor - Variable in class StateScrollers
optional background color ...
BGLowQ - Variable in class MaHybridSample
low background estimate for entire array
BGRmsQ - Variable in class MaHybridSample
RMS background for entire array
binDataValue - Variable in class DrawHistogram
[0:MAXBINS] bins actual value @start of bin for display
binFreq - Variable in class DrawHistogram
[0:MAXBINS] bins frequency for display
binIndex - Variable in class DrawRatioHistogram
corresponding hist bin index
bitData - Variable in class GeneBitSet
list of nWords bit words allocated [0:maxSize-1] and active [0:highMID-1]
bitIdx - Variable in class GeneBitSet
index within a bitWord right to left
BITS - Static variable in class WriteGifEncoder
 
bitSet - Variable in class GeneList
 
bitWord - Variable in class GeneBitSet
64 bit long subset of bits from bitData
bkgdCorrectFlag - Variable in class MAExplorer
calc: I'= Intensity - background
bkgrdQ - Variable in class MaHybridSample
raw background intensity, unscaled
bkgrdSpotQ - Variable in class MaHybridSample
list of raw background intensity data/spot, unscaled
bl - Variable in class PopupCondChooser.CondParamEditForm
main layout
bl - Variable in class PopupOrderedCondChooser.CondParamEditForm
main layout
blueBits(int) - Method in class MedianCut
blueBits() - Get 8-bit blue component of a 15-bit color 8-bit pixel with low 3 bits zero.
bLUT - Variable in class MedianCut
[0:255] Blue Color map look up table
bmax - Variable in class MC_Cube
 
bmin - Variable in class MC_Cube
 
bName - Variable in class GeneBitSet
name of bit set
botEdge - Variable in class ClusterGramCanvas
 
bottomSeparator - Variable in class JavaCGIBridge
The bottom of data separator.
boxHeight - Variable in class ClusterGramCanvas
size of a data box in the clustergram
boxWidth - Variable in class ClusterGramCanvas
bottom edge of box array
boxX - Variable in class ClusterGramCanvas
ULHC event hlr [0:nCols-1]
boxY - Variable in class ClusterGramCanvas
ULHC event hlr [0:nRows-1]
browserTitle - Static variable in class MAExplorer
browser title
bsEnum - Variable in class GeneBitSet
enumeration index 0 to length-1
bubbleSort(String[]) - Method in class MJAsort
bubbleSort() - Sort String array via bubble sort.
bubbleSort(String[]) - Static method in class SortMAE
bubbleSort() - Sort String array via bubble sort.
bubbleSort(String[], int) - Method in class MJAsort
bubbleSort() - Sort String array via bubble sort w/len specified
bubbleSort(String[], int) - Static method in class SortMAE
bubbleSort() - Sort String array via bubble sort w/len
bubbleSortIndex(float[], int, boolean) - Method in class MJAsort
bubbleSortIndex() - sort float data[0:len-1] copy w/bubble sort, return index[]
bubbleSortIndex(float[], int, boolean) - Static method in class SortMAE
bubbleSortIndex() - sort copy of float[0:len-1] data with bubble sort, return index[].
bubbleSortIndex(int[], int, boolean) - Method in class MJAsort
bubbleSortIndex() - sort int data[0:len-1] copy w/bubble sort, return index[]
bubbleSortIndex(int[], int, boolean) - Static method in class SortMAE
bubbleSortIndex() - sort copy of int[0:len-1] data with bubble sort, return index[].
bubbleSortIndex(short[], int, boolean) - Method in class MJAsort
bubbleSortIndex() - sort int data[0:len-1] copy w/bubble sort, return index[] Do NOT actually sort the original data[].
bubbleSortIndex(short[], int, boolean) - Static method in class SortMAE
bubbleSortIndex() - sort copy of short[0:len-1] data with bubble sort, return index[].
bubbleSortIndex(String[], int, boolean) - Static method in class MJAsort
bubbleSortIndex() - sort String data[0:len-1] copy w/bubble sort, return index[].
bubbleSortIndex(String[], int, boolean) - Static method in class SortMAE
bubbleSortIndex() - sort copy of String[0:len-1] data with bubble sort, return index[].
bufSize - Variable in class Table
size of input buffer when read file
buildAndRunGuesser(String) - Method in class Guesser
buildAndRunGuesser() - create the Guesser window GUI
buildChooserGUI() - Method in class ChooserGUI
buildChooserGUI() - create single instance GUI for Chooser
buildClusterGramLists() - Static method in class HierClustNode
buildClusterGramLists() - construct ordered ClusterGram lists
buildDataStructures() - Method in class PopupHPChooser
buildDataStructures() - build the data structures used by the popup chooser.
buildDendrogramLists() - Static method in class HierClustNode
buildDendrogramLists() - construct ordered ClusterGram and dendrogram lists.
buildGUI() - Method in class PopupCondChooser
buildGUI() - build the graphical user interface for PopupCondChooser.
buildGUI() - Method in class PopupCondChooser.CondDialogBox
buidlGUI() - Build GUI
buildGUI() - Method in class PopupOrderedCondChooser
buildGUI() - build the graphical user interface for PopupOrderedCondChooser.
buildGUI() - Method in class PopupOrderedCondChooser.CondDialogBox
buidlGUI() - Build GUI
buildGUI() - Method in class RtestBase
buildGUI() - build the graphical user interface
buildHPchooserGUI(String) - Method in class PopupHPChooser
buildHPchooserGUI() - create GUI for PopupHPChooser.
buildMenuGUI(int, int, int, int) - Method in class MenuBarFrame
buildMenuGUI() - build the GUI with pop up menus
buildParamEditGUI() - Method in class PopupCondChooser.CondParamEditForm
buildParamEditGUI() - create GUI for the condition form.
buildParamEditGUI() - Method in class PopupOrderedCondChooser.CondParamEditForm
buildParamEditGUI() - create GUI for the condition form.
buildPopupCondChooserGUI() - Method in class PopupCondChooserGUI
buildPopupCondChooserGUI() - create single instance GUI for Chooser.
buildPopupOrderedCondChooserGUI() - Method in class PopupOrderedCondChooserGUI
buildPopupOrderedCondChooserGUI() - create single instance GUI for Chooser.
bUnload - Variable in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
 
button_font - Variable in class LogTextFrame
control button font
buttonBkGrdColor - Variable in class LogTextFrame
background color of buttons
buttonFont - Variable in class PopupCondChooser
font for buttons
buttonFont - Variable in class PopupCondChooserGUI
button font
buttonFont - Variable in class PopupOrderedCondChooser
font for buttons
buttonFont - Variable in class PopupOrderedCondChooserGUI
button font
buttonFont - Variable in class ShowPlotPopup
cell label font
buttonFont - Variable in class ShowSpreadsheetPopup
cell label font
buttonFont - Variable in class SpreadSheet
ARG: cell label font
buttonFont - Variable in class SSspreadPanel
ARG: cell label font
buttonPanel - Variable in class ChooserGUI
buttons panel
buttonPanel - Variable in class Guesser
place for buttons
buttonPanel - Variable in class PopupCondChooserGUI
buttons panel
buttonPanel - Variable in class PopupOrderedCondChooserGUI
buttons panel
buttonPanel - Variable in class RtestBase
button control panel

C

c - Variable in class GridCoords
col #
C_ATCC_ID - Static variable in class Gene
Gene property: Clone is an ATCC numbered clone
C_BAD_DATA - Static variable in class Gene
property: gene has bad data
C_BAD_LOCAL_SPOT_BKGRD - Static variable in class Gene
Gene property: bad local spot background
C_BAD_MID - Static variable in class Gene
Gene property: the gene is bad, good gene name
C_BAD_SPOT - Static variable in class Gene
Gene property: non-analyzable gene (eg.
C_BAD_SPOT_GEOMETRY - Static variable in class Gene
Gene property: bad spot geometry
C_DUP_SPOT - Static variable in class Gene
Gene property: is duplicate of another gene on array
C_GOOD_MID - Static variable in class Gene
Gene property: the gene is good, good gene name.
C_IMAGE_ID - Static variable in class Gene
Gene property: Clone is an I.M.A.G.E.
C_IS_CUR_GENE - Static variable in class Gene
Gene property: is Current Gene (not normally used)
C_IS_EGL_GENE - Static variable in class Gene
Gene property: is an E.G.
C_IS_FILTERED - Static variable in class Gene
Gene property: is a gene that did pass data Filter
C_IS_KMEANS - Static variable in class Gene
Gene property: Is a K-means node gene
C_IS_NOT_FILTERED - Static variable in class Gene
Gene property: is a gene that did not pass data Filter
C_LOW_SPOT_REF_SIGNAL - Static variable in class Gene
Gene property: low spot reference signal
C_MARGINAL_SPOT - Static variable in class Gene
Gene property: Marginal spot
C_USE_GBID_FOR_CLONEID - Static variable in class Gene
Gene property: use GenBank ID for Clone ID
cacheDir - Variable in class MAExplorer
Standalone /Cache directory for saving data downloaded for array Web server.
cacheDistLR1Df - Static variable in class HierClustNode
lower-diagonal cache of distLR[L][R].
cacheDistLR1Ds - Static variable in class HierClustNode
lower-diagonal cache of distLR[L][R].
cacheFIOflag - Variable in class MAExplorer
Flag: if enabled, it first checks the /Cache directory for all http:// codebase files and if not in the cache, it saves the file in the cache after reading it from the Web.
cacheRead(String) - Method in class FileIO
cacheRead() - read data file from Cache file it it exists.
cacheSize - Static variable in class HierClustNode
size of cacheDistLR1D[] cache
cacheWrite(String, String) - Method in class FileIO
cacheWrite() - Write string into file in local cache.
calAllSamples() - Method in class CompositeDatabase
calAllSamples() - compute (meanCalDNA, stdDevCalDNA) calibration for all samples
calc2SampleCoefficientOfVariation(float, float) - Method in class MJAfilter
calc2SampleCoefficientOfVariation() - compute coeff.
calcAndGetSampleStats(int, boolean) - Method in class MJAhistogram
calcAndGetSampleStats() - get list of sample's global array statistics You map recompute the histogram.
calcEPstatistics() - Method in class HPxyData
calcEPstatistics() - compute the the EP statistics.
calcExprProfile(int) - Method in class MJAexprProfile
calcExprProfile() - compute expression profile of HP-E samples for MID The data is then returned using other methods.
calcF1F2CV(float, float) - Method in class Filter
calcF1F2CV() - compute 2 sample estimate the coefficient of variation as where CV is estimated as 2*|g1-g2|/(g1+g2).
calcFprobFromVariances(int, int, double, double) - Method in class MJAstatistics
calcFprobFromVariances() - calc 2-tailed f prob.
calcFprobFromVariances(int, int, double, double) - Method in class Statistics
calcFprobFromVariances() - calculate 2-tailed f probility that variables are same.
calcGeneGeneDists(float[], int, int) - Method in class GeneGeneDist
calcGeneGeneDists() - compute the gene-gene Euclidean distances for all dataCL genes in the lower diagonal matrix.
calcHierCluster(float[][], String[], int[], int) - Method in class HierClustNode
calcHierCluster() - compute the hierarchical clusters tree.
calcHistOfF1F2Ratios(GeneList, MaHybridSample) - Method in class CompositeDatabase
calcHistOfF1F2Ratios() - compute histogram of F1/F2 ratios for spots which are selected in the GeneList ml.
calcHistOfF1F2Ratios(int) - Method in class MJAhistogram
calcHistOfF1F2Ratios() - get Hashtable list of features for ratio histogram of the current HP sample F1/F2 spot data.
calcHistOfHP_XYRatios() - Method in class MJAhistogram
calcHistOfHP_XYRatios() - get Hashtable list of features of ratio histogram of HP-X/-Y spot data for the current HP-X and HP-Y samples.
calcHistOfHP_XYratios(GeneList, boolean) - Method in class CompositeDatabase
calcHistOfHP_XYRatios() - compute histogram of HP-X/-Y (or 'sets') spot ratios of filtered data
calcHistStats(String, int, float[], int) - Method in class MJAstatistics
calcHistStats() - compute and analyze histogram.
calcHistStats(String, int, float[], int) - Method in class Statistics
calcHistStats() - compute and analyze histogram generating statistics.
calcHistStats(String, int, float[], int, int[]) - Method in class MJAstatistics
calcHistStats() - compute and analyze histogram.
calcHistStats(String, int, float[], int, int[]) - Method in class Statistics
calcHistStats() - compute and analyze a histogram for whatever range of data is given.
calcHP_HPcorrelations() - Method in class CompositeDatabase
calcHP_HPcorrelations() - compute HP vs.
calcIntensHist() - Method in class MaHybridSample
calcIntensHist() - compute Filtered spot intensity histogram for this sample It gets the normalized data from SpotData.
calcIntensityHistogram(int) - Method in class MJAhistogram
calcIntensityHistogram() - compute intensity histogram for Sample for the current normalization.
calcIntensityScaleExtrema(float, float, float, float, int) - Method in class GenNormalizationPlugin
calcIntensityScaleExtrema() - compute scaled intensity extrema.
calcIntensityScaleExtrema(float, float, float, float, int) - Method in interface MAEPlugin.Normalization
calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample.
calcIntensityScaleExtrema(float, float, float, float, int) - Method in class MAEPlugin.analysis.NormalizationPlugin
calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample.
calcIntensityScaleExtrema(int) - Method in class MJAsample
calcIntensityScaleExtrema() - compute intensity scale extrema for Sample.
calcIntensScaleExtrema() - Method in class MaHybridSample
calcIntensScaleExtrema() - calculate intensity scale factor extrema for current normalization mode.
calcKStestStat(double[], int, double[], int) - Method in class Statistics
calcKStestStat() - calculate Kolmogorov-Smirnov ksD, pKS, dFks from (n1,data1) and (n2,data2).
calcMeanAndVariance(float[], int, int, boolean) - Method in class MJAstatistics
calcMeanAndVariance() - compute the mean and variance of dataS[] and save in mean[classK] and variance[classK] arrays.
calcMeanAndVariance(float[], int, int, boolean) - Method in class Statistics
calcMeanAndVariance() - compute the mean and variance of dataS[] for 1 condition and save the results inmean[conditionK] and variance[conditionK] arrays.
calcMeanCalDNA() - Method in class MaHybridSample
calcMeanCalDNA() - calculate mean and stdDev RAW intensity Calibration DNA.
calcMeanCalibrationDNA(int) - Method in class MJAsample
calcMeanCalibrationDNA() - compute (mean,StdDev) gene for Sample for calibration cDNA for the current normalization.
calcMeanClusterClusterDist(int, int) - Method in class ClusterGenes
calcMeanClusterClusterDist() - m,n cluster-cluster Euclidean distances.
calcMeanClusterVectors() - Method in class ClusterGenes
calcMeanClusterVectors() - compute meanClusterVector Kmeans nodes.
calcMeanDataVect(HierClustNode, HierClustNode) - Method in class HierClustNode
calcMeanDataVect() - compute mean intensity vector of 2 nodes.
calcMeanUseNormGeneSet() - Method in class MaHybridSample
calcMeanUseNormGeneSet() - calculate mean and stdDev RAW intensity.
calcMeanUseNormGeneSet(int) - Method in class MJAsample
calcMeanUseNormGeneSet() - compute (mean,StdDev) normalization gene set for Sample.
calcMedianClusterVectors() - Method in class ClusterGenes
calcMedianClusterVectors() - compute meanClusterVector as K-median nodes.
calcNbrActiveScrollers() - Method in class MJAfilter
calcNbrActiveScrollers() - calculate and get number of active-parameter State Scrollers and update the state variables from the scrollers.
calcNCondFtestStat(float[][], int[], int) - Method in class MJAstatistics
calcNCondFtestStat() - calc.
calcNCondFtestStat(float[][], int[], int) - Method in class Statistics
calcNCondFtestStat() - calc.
calcNearestGenes() - Method in class ClusterGenes
calcNearestGenes() - compute rank ordered sorted list of nearest genes
calcNormGeneVectors(GeneList, int) - Method in class GeneGeneDist
calcNormGeneVectors() - compute HP-E intensity vector for dataCL.mList[].
calcNormGeneVectors(String) - Method in class MJAcluster
calcNormGeneVectors() - compute HP-E intensity vector for geneList To Normalize.
calcOrderedCondListExprProfile(String, int) - Method in class MJAexprProfile
calcOrderedCondListExprProfile() - compute normalized ordered condition list EPs for MID.
calcPearsonCorrCoef(float[], float[], int, boolean) - Method in class MJAmath
calcPearsonCorrCoef() - compute Pearson correlation coefficient The data is data1[0:n-1] and data2[0:n-1].
calcPearsonCorrCoef(float[], float[], int, boolean) - Static method in class MathMAE
calcPearsonCorrCoef() - compute Pearson correlation coefficient The data is data1[0:n-1] and data2[0:n-1].
calcRatioHists(int, float[], float[], GeneList) - Method in class CompositeDatabase
calcRatioHists() - compute ratio histogram of d1List[]/d2List[] data.
calcRatioHistVal(float, float) - Method in class CompositeDatabase
calcRatioHistVal() - compute histogram bin value & increment ratio histogram
calcRemCond(String, int) - Method in class PopupOrderedCondChooser
calcRemCond() - compute remainder list of condition names (R = DB - Ci) where DB is all of the Conds in the database, and Ci are the Conds in condition Ci.
calcRemSamples(String, int) - Method in class PopupCondChooser
calcRemSamples() - compute remainder list of sample names (R = DB - Ci) where DB is all of the samples in the database, and Ci are the samples in condition Ci.
calcSampleIntensityHistogram(int) - Method in class MJAhistogram
calcSampleIntensityHistogram() - compute intensity histogram for current normalization method.
calcStandardizeMnStdDev() - Method in class HierClustNode
calcStandardizeMnStdDev() - calc global mnDataV[] and sdDataV[] over [0:nDataV-1] for all samples.
calcTandPvalues(int, int, double, double, double, double) - Method in class MJAstatistics
calcTandPvalues() - given (n1,m1,s1) and (n2,m2,s2), calc f, t, p, dF.
calcTandPvalues(int, int, double, double, double, double) - Method in class Statistics
calcTandPvalues() - calculate f, t, p, dF from (n1,m1,s1) and (n2,m2,s2).
calcWMWtestStat(int, int, double, double, double, double) - Method in class Statistics
calcWMWtestStat() - calculate WMW statistics from (n1,m1,s1) and (n2,m2,s2).
calcXYstat(int, float[], float[], int[], String, String) - Method in class MJAmath
calcXYstat() - compute correlation statistics string for display rSq=.., n=.., X(mn+-sd)=(..+-..), Y(mn+-sd)=(..+-..) If propList[] is not null, then test if filtered using IS_FILTERED property.
calcXYstat(int, float[], float[], int[], String, String) - Static method in class MathMAE
calcXYstat() - compute correlation statistics string for display rSq=.., n=.., X(mn+-sd)=(..+-..), Y(mn+-sd)=(..+-..) If propList[] is not null, then test if filtered using fc.IS_FILTERED value.
calcXYstatistics() - Method in class HPxyData
calcXYstatistics() - setup the data arrays depending on useHPxySetDataFlag.
calDNACL - Variable in class GeneClass
special list of calibration DNA
calDNAhybSamplesTable() - Method in class CompositeDatabase
calDNAhybSamplesTable() - calc.
calDNAname - Variable in class Config
PARAM "calDNAname" (opt) calibration DNA name
callAllStartupPlugins() - Method in class MenuBarFrame
callAllStartupPlugins() - call all Plugins initialized at Startup.
cancel() - Method in class PopupGeneGuesser
cancel() - cancel the guesser window
cancel() - Method in class PopupHPmenuGuesser
cancel() - cancel the HP sample guesser window
cancel() - Method in class PopupProjDirGuesser
cancel() - cancel the guesser window
cancelButton - Variable in class PopupCondChooser
cancel
cancelButton - Variable in class PopupCondChooser.PopupTextField
cancel button
cancelButton - Variable in class PopupCondChooser.ChoiceList
cancel w/o removing
cancelButton - Variable in class PopupOrderedCondChooser
cancel
cancelButton - Variable in class PopupOrderedCondChooser.PopupTextField
cancel button
cancelButton - Variable in class PopupOrderedCondChooser.ChoiceList
cancel w/o removing
cancelButton - Variable in class PopupEditRscript
"Cancel" window button
cancelButton - Variable in class PopupScrollableSelector
[0:nList-1] values
CANVAS_WRAPAROUND_BUG - Static variable in class MAExplorer
if debugging CANVAS_WRAPAROUND_BUG
canvasHSize - Static variable in class MAExplorer
PARAM "CanvasHorSize"
canvasVSize - Static variable in class MAExplorer
PARAM "CanvasVertSize"
cb - Variable in class ShowSpreadsheetPopup
Checkbox
cbsDbug - Static variable in class GeneBitSet
flag: selective debugging enable
cc - Variable in class PopupCondChooserGUI
instance of PopupCondChooser
cc - Variable in class PopupOrderedCondChooserGUI
instance of PopupOrderedCondChooser
ccd - Static variable in class ClusterGenes
link to global GeneGeneDist instance
ccd - Variable in class MAExplorer
Global instance of Gene-Gene distances
ccDist1D - Variable in class ClusterGenes
Gene-Gene distance matrix is a lower-diagonal ccDist[i][j] that is equivalent to ccDist1D[addr1D(i,j)]
ccGUI - Variable in class PopupCondChooserGUI
This is either the remote instance or 'this' instance of PopupCondChooserGUI for the instance of REMAINDER to use.
ccGUI - Variable in class PopupCondChooserGUI.MouseEventHandler
for event handling
ccGUI - Variable in class PopupOrderedCondChooserGUI
This is either the remote instance or 'this' instance of PopupOrderedCondChooserGUI for the instance of REMAINDER to use.
ccGUI - Variable in class PopupOrderedCondChooserGUI.MouseEventHandler
for event handling
ccGUIpanel - Variable in class PopupCondChooserGUI
main GUI panel
ccGUIpanel - Variable in class PopupOrderedCondChooserGUI
main GUI panel
cd - Variable in class PopupCondChooser
List [0:maxPossibleCond-1] of working condition data: name, selected and remainder samples, param form (name,value).
cd - Variable in class PopupCondChooser.CondParamEditForm
instance of condData
cdb - Variable in class Draw2Dplot
link to global CompositeDatabase instance
cdb - Variable in class DrawRatioHistogram
link to global instance
cdb - Variable in class DrawScatterPlot
link to global instance
cdb - Variable in class MAExplorer
Global instance of composite database object
cdb - Static variable in class MJAbase
link to global CompositeData instance
cdb - Variable in class MaHPquantTable
link to global CompositeDatabase instance
cdb - Static variable in class MaeJavaAPI
link to global CompositeData instance
cdb - Variable in class ScrollableImageCanvas
link to global instance of CompositeDatabase
cdb - Static variable in class SpotFeatures
link to global instance
cdList - Static variable in class EventMenu
link to global Condition instance
cdList - Variable in class MAExplorer
Global instance of condition list tables
cdList - Static variable in class MJAbase
link to global Condition instance
cdList - Static variable in class MaeJavaAPI
link to global Condition instance
cell - Variable in class SSstatusBar
 
CELL_EXPR_PROFILE - Static variable in class Report
 
CELL_EXPR_PROFILE - Static variable in class SpreadSheet
Spreadsheet Cell mode: Cell is an expression profile
CELL_NOP - Static variable in class Report
Spreadsheet Cell mode: cell has no associated action
CELL_NOP - Static variable in class SpreadSheet
Spreadsheet Cell mode: Cell is just data
CELL_URL - Static variable in class Report
 
CELL_URL - Static variable in class SpreadSheet
Spreadsheet Cell mode: Cell is a URL hypertext link
cellAdjust(MouseEvent) - Method in class SSspreadPanel
cellAdjust() - take action for mouse clicks on individual cells
cellClicked - Variable in class ShowSpreadsheetPopup
clicked color for cell color in spreadsheet
cellDataFont - Variable in class ShowSpreadsheetPopup
cell data font
cellDataFont - Variable in class SpreadSheet
ARG: cell data font
cellDataFont - Variable in class SSspreadPanel
ARG: cell data font
cellFormat - Variable in class ShowSpreadsheetPopup
ARG: cell type [0:maxCols] fields which are urls is Spreadsheet.CELL_NOP, .CELL_URL, or .CELL_EXPR_PROFILE
cellFormat - Variable in class SpreadSheet
ARG: cell type [cols] fields is CELL_xxxx
cellFormat - Variable in class SSspreadPanel
ARG: cell type fields[0:cols-1] one of CELL_NOP,CELL_URL, CELL_EXPR_PROFILE in user data space...
cellReg - Variable in class ShowSpreadsheetPopup
normal color for cell color in spreadsheet
cells - Variable in class SSspreadPanel
the array of SStextCell cells
cellUrlFont - Variable in class ShowSpreadsheetPopup
cell URL font
cellUrlFont - Variable in class SpreadSheet
ARG: cell URL font
cellUrlFont - Variable in class SSspreadPanel
ARG: cell URL font
centerPanel - Variable in class PopupEditRscript
Center Panel to hold the text area and the wizard panel.
cfg - Static variable in class ClusterGenes
link to global Config instance
cfg - Static variable in class EventMenu
link to global Config instance
cfg - Static variable in class Gene
link to global Config instance
cfg - Static variable in class GeneGeneDist
link to global Config instance
cfg - Variable in class GipoTable
link to global Config instance
cfg - Variable in class MAExplorer
Global instance of Configuration and state variables including top level file, URL configs, etc.
cfg - Static variable in class MJAbase
link to global Config instance
cfg - Variable in class MaHPquantTable
link to global Config instance
cfg - Static variable in class MaeJavaAPI
link to global Config instance
cfg - Variable in class Maps
link to global Config instance
cfg - Variable in class MenuBarFrame
link to global Config instance
cfg - Variable in class PopupRegistry
link to global Config instance
cfg - Variable in class Report
link to global Config instance
cfg - Variable in class ScrollableImageCanvas
link to global instance of Config
cfg - Static variable in class SpotFeatures
link to global instance of Config
cfg - Variable in class StateScrollers
link to global Config instance
cfgDB - Variable in class MAExplorer
Global instance of configuration data from MaExplorerConfig.txt file
cfNparams - Static variable in class Condition
# of condition parameters
cfParamNames - Static variable in class Condition
[0:cfNparams-1] list of condition parameter names for CondForm
cfParamValues - Static variable in class Condition
[0:nCondLists-1][0:cfNparams-1] list of condition parameter values for CondForm
cgC - Variable in class DrawClusterGram
Clustergram canvas
cgIdx - Variable in class PopupHPChooser
index of chooser instance in cgList[]
cgList - Variable in class PopupHPChooser
[0:nChooser-1] list of chooserGUIs
cGUI - Variable in class ChooserGUI
This is either the remote instance or 'this' instance of ChooserGUI for the instance of REMAINDER to use.
cGUI - Variable in class ChooserGUI.MouseEventHandler
for event handling
cGUIpanel - Variable in class ChooserGUI
main GUI panel
changeDefSample(int, boolean) - Static method in class EventMenu
changeDefSample() - switch to new msList[i] hybridized sample list
changeGeneButton(String, String, int) - Method in class ShowStringPopup
changeGeneButton() - change gene label
changeHPswapCy5Cy3Samples() - Method in class SampleSets
changeHPswapCy5Cy3Samples() - popup scrollable GUI array of checkbox to change cy3/Cy5 swap flags msList[0:nHP-1].swapCy5Cy3DataFlags
changePosPanel - Variable in class ChooserGUI
change up/down position panel
changePosPanel - Variable in class PopupCondChooserGUI
change up/down position panel
changePosPanel - Variable in class PopupOrderedCondChooserGUI
change up/down position panel
changeProjDir(String, String) - Method in class EventMenu
changeProjDir() - change the project name and path.
changeWizardMenuMode(boolean) - Method in class PopupEditRscript
changeWizardMenuMode() - change Wizard menu between Demo or non-demo RLO.
char_init() - Method in class WriteGifEncoder
char_init() - Set up the 'byte output' routine
char_out(byte, FileOutputStream) - Method in class WriteGifEncoder
char_out() - add char to end of current packet, and if it is 254 characters, flush the packet to disk.
check_dbID() - Method in class UserState
check_dbID() - get or create Unique Database ID ("DIDxxxxxx").
checkAndMakeMAEdirTree(String) - Method in class UserState
checkAndMakeMAEdirTree()- check for MAE prject directory tree.
checkBoxesSP - Variable in class PopupScrollableSelector
 
CheckBoxMenuPlugin - class MAEPlugin.CheckBoxMenuPlugin.
This class extends the MAEPlugin base class to implement a CheckBoxMenuPlugin base class.
CheckBoxMenuPlugin() - Constructor for class MAEPlugin.CheckBoxMenuPlugin
CheckBoxMenuPlugin() - constuctor to use default "CheckBoxPlugin" label name
CheckBoxMenuPlugin(String) - Constructor for class MAEPlugin.CheckBoxMenuPlugin
CheckBoxMenuPlugin() - constuctor with user supplied label
CheckBoxMenuPlugin(String, String) - Constructor for class MAEPlugin.CheckBoxMenuPlugin
CheckBoxMenuPlugin() - constuctor with user supplied label and plugin filename
checkBoxPanel - Variable in class PopupScrollableSelector
to put checkBoxPanel in so can scroll
checkCy3Cy5SamplesRange(float, float) - Method in class Filter
checkCy3Cy5SamplesRange() - test cy3/cy5 [CR1:CR2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
checkImagesDirExists() - Method in class MJAutil
checkImagesDirExists() - return true if images directory exists.<
checkImagesDirExists() - Static method in class Util
checkImagesDirExists() - check if images directory exists
checkSamplesRange(float, float, boolean) - Method in class Filter
checkSamplesRange() - for testing intensity[I1:I2] or ratio [R1:R2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
checkSpotIntensityCompareRange(int, int, boolean[], boolean[], float, float, float, float) - Method in class Filter
checkSpotIntensityCompareRange() - for testing spot intensity in [ST1:ST2] with compareMode COMPARE_ALL, COMPARE_ANY, COMPARE_PRODUCT, COMPARE_SUM.
checkSpotIntensityRange(float) - Method in class Filter
checkSpotIntensityRange() - test spot intensity in [ST1:ST2] for specified rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
checkStringPopupTimeouts(int) - Method in class PopupRegistry
checkPopupTimeouts() - check timeouts for all active popups and kill any that exceed the time.
checkWellFormedEditRLO() - Method in class PopupEditRscript
checkWellFormedEditRLO() - check if current edit RLO is well formed
chFirstTyped - Variable in class Guesser
first char typed
chkBoxMenuItemList - Static variable in class MenuBarFrame
[MAX_CHKBOX_CMDS] list of checkboxItem cmds menu items corresponding to names
chkBoxMenuLabelList - Static variable in class MenuBarFrame
[MAX_CHKBOX_CMDS] list of checkboxItem cmds menu labels
chkDirFinalSeparator(String, String) - Static method in class Util
chkDirFinalSeparator() - make dir path end in fileSeparator.
chkGetHP(int) - Static method in class MJAbase
chkGetHP() - check HP sample # to make sure it is legal and within the legal range and get MaHybidSample ms.
chkIfAbort() - Static method in class ClusterGenes
chkIfAbort() - check if abort, then shut down clustering.
chkIfCache() - Method in class MAExplorer
chkIfCache() - check if set up to cache from Web DB.
chkIfHPvisible(String) - Method in class SamplesTable
chkIfHPvisible() - check if allowed to view HP sample.
chkOtherCurGeneEffects(int, int) - Method in class MJApopupRegistry
chkOtherCurGeneEffects() - check for other current gene effects when change MID
chkOtherCurGeneEffects(int, int) - Method in class PopupRegistry
chkOtherCurGeneEffects() - check other gene effects when change current gene in ms.objXXX.
chkSwapCy5Cy3(String) - Method in class SampleSets
chkSwapCy5Cy3() - test if HP-X, HP-Y or HP-E list have Cy3/Cy5 swap flag set.
choiceList - Variable in class PopupCondChooser.ChoiceList
list of items to select from
choiceList - Variable in class PopupOrderedCondChooser.ChoiceList
list of items to select from
choiceStr - Variable in class PopupCondChooser.ChoiceList
item in list that was clicked on by user
choiceStr - Variable in class PopupOrderedCondChooser.ChoiceList
item in list that was clicked on by user
ChooserGUI - class ChooserGUI.
The ChooserGUI class is a base class for creating chooser GUIs.
ChooserGUI.MouseEventHandler - class ChooserGUI.MouseEventHandler.
 
ChooserGUI.MouseEventHandler(ChooserGUI, MAExplorer, ChooserGUI, TextArea, String[], int) - Constructor for class ChooserGUI.MouseEventHandler
MouseEventHandler() - constructor
ChooserGUI.MouseEventHandler(ChooserGUI, MAExplorer, TextArea) - Constructor for class ChooserGUI.MouseEventHandler
MouseEventHandler() - constructor
ChooserGUI(MAExplorer, ChooserGUI, int, int, Font, Font, Font, Object, boolean) - Constructor for class ChooserGUI
ChooserGUI() - constructor for base class of Chooser GUI
chooserPanel - Variable in class PopupCondChooser
Panel for condition data
chooserPanel - Variable in class PopupOrderedCondChooser
Panel for condition data
cIdx - Variable in class HierClustNode
Dynamic node: object cluster index if not -1
cityBlockDist(float[], float[], int, boolean) - Static method in class MathMAE
cityBlockDist() - compute city-block distance of 2 vectors.
cityBlockDistance(float[], float[], int, boolean) - Method in class MJAmath
cityBlockDistance() - compute city-block distance of 2 vectors.
cl_block(FileOutputStream) - Method in class WriteGifEncoder
cl_block() - table clear for block compress Clear out the hash table.
cl_hash(int) - Method in class WriteGifEncoder
cl_hash() - reset code table
classes - Variable in class MAEPlugin.JarClassLoader
Contains the loaded classes
classNameReplacementChar - Variable in class MAEPlugin.JarClassLoader
Utility Char
classNameX - Variable in class MAExplorer
"HP-X 'set'" name for msListX[] HPs
classNameY - Variable in class MAExplorer
"HP-Y 'set'" name for msListY[] HPs
cleanup() - Static method in class ClusterGenes
cleanup() - close up what needs to be closed and GC all structures.
cleanup() - Method in class CompositeDatabase
cleanup() - cleanup global static allocated variables in this class.
cleanup() - Method in class Condition
cleanup() - cleanup global static allocated variables in this class.
cleanup() - Method in class EventMenu
cleanup() - cleanup global static allocated variables in this class.
cleanup() - Method in class GeneBitSet
cleanup() - cleanup global static allocated variables in this class.
cleanup() - Method in class GeneGeneDist
cleanup() - cleanup global static allocated variables in this class.
cleanup() - Method in class GeneList
cleanup() - cleanup global static allocated variables in this class.
cleanup() - Static method in class HierClustNode
cleanup() - close up what needs to be close and GC all structures.
cleanup() - Method in class MAExplorer
cleanup() - close up what needs to be closed and GC all structures Reset to initial state so can restart it...
cleanup() - Method in class Util
cleanup() - cleanup global static allocated variables in this class If statics are added later to this class, then set them to null here.
clear_flg - Variable in class WriteGifEncoder
80% occupancy
clear() - Method in class GeneList
clear() - clear gene list length and bitSet, but keep mList[] data
clear() - Method in class PopupGeneGuesser
clear() - clear the text field in the main window
clear() - Method in class PopupHPmenuGuesser
clear() - clear the text field in the main window
clear() - Method in class PopupProjDirGuesser
clear() - clear the text field in the main window
clearActiveScrollers() - Method in class StateScrollers
clearActiveScrollers() - clear list of all active scrollers
clearButton - Variable in class LogTextFrame
clear button to clear the log and clear the log file is using a file
clearClusterDisplayState(CheckboxMenuItem) - Static method in class EventMenu
clearClusterDisplayState() - clear cluster display checkbox state.
ClearCode - Variable in class WriteGifEncoder
 
clearData() - Method in class Guesser
clearData() - clear TextField tf and TextArea ta data for switching to another list.
clearDynamicState() - Method in class MAExplorer
clearDynamicState() - reset dynamic state variables in MAE instance.
clearGeneBitset(String) - Method in class MJAgeneList
clearGeneBitset() - clear the gene bit set
clearGeneListBitSet(String, int, String[]) - Method in class MJAgeneList
clearGeneListBitSet() - clear the gene list bit set
clearGeneProperty(int) - Method in class Gene
clearGeneProperty() - clear C_xxxx gene properties.
clearGenRbit(int) - Method in class MJAReval
clearGenRbit() - clear specific GenR Bit(s) for current RLO.
clearHPglobalStats() - Method in class MaHybridSample
clearHPglobalStats() - clear global array statistics before compute actual ranges
clearInfo() - Method in class PopupCondChooser
clearInfo() - clear info for the 3 msg areas in the PopupCondChooser
clearInfo() - Method in class PopupCondChooserGUI
clearInfo() - clear info for the 3 msg areas in the PopupCondChooser
clearInfo() - Method in class PopupOrderedCondChooser
clearInfo() - clear info for the 3 msg areas in the PopupOrderedCondChooser
clearInfo() - Method in class PopupOrderedCondChooserGUI
clearInfo() - clear info for the 3 msg areas in the PopupOrderedCondChooser
clearLists() - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
 
clearLog() - Method in class LogTextFrame
clearLog() - clear the log area and delete old log file.
clearMlist() - Method in class GeneList
clearMlist() - clear gene mList[] entries to null.
clearNull() - Method in class GeneBitSet
clearNull() - clear gene bit set and set entries to null.
clearNull() - Method in class GeneList
clearNull() - clear bitSet and gene mList[], set entries to null.
clearPostProcessingFlags() - Method in class StateScrollers
clearPostProcessingFlags() - clear special post-processing flags that are then set by particular scroller changes
clearProcessBit(int) - Method in class MJAReval
clearProcessBit() - clear specific Process Bit(s) for current RLO.
clearReportButton - Variable in class RtestBase
"Clear report" to clear the text area
clearRLOdb() - Method in class MJAReval
clearRLOdb() - clear list of R LayOuts analyses in the database
clearRLOdb() - Method in class RevalBase
clearRLOdb() - clear list of R LayOuts analyses in the database
clearRLOdb() - Method in class RLO
clearRLOdb() - clear list of R LayOuts analyses in the database
clearXYdata() - Method in class HPxyData
clearXYdata() - clear X and Y mn, cv, stdDev data
clg - Variable in class MAExplorer
Global instance of Cluster Genes object
clg - Variable in class Report
link to ClusterGenes instance
clickedCellCol - Variable in class ShowSpreadsheetPopup
keep track of last clicked cell
clickedCellRow - Variable in class ShowSpreadsheetPopup
keep track of last clicked cell
clientBrowserTitle - Variable in class RtestBase
Client current browser title for this database
clientDatabase - Variable in class RtestBase
Client current database
clientName - Variable in class RevalBase
Name of the client program
clientName - Variable in class RtestBase
Name of the client
clientPrefixName - Variable in class RtestBase
Prefix Name of the client
clientPrjPath - Variable in class RtestBase
Client current project path.
clientRlibrBasePath - Static variable in class RevalBase
base path of where {client installation} R project RLORlibr/ directory lives
clientStateThrFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("State-thresholds")
clientStateValuesFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("Stat-flags-names")
clipCodeViewport(float, float) - Method in class Draw2Dplot
clip_code_viewport(x,y) - Return the clipping code of where (x,y) is w.r.t.
clipStrToWidth(String, int, int, Graphics, Font) - Method in class DrawPseudoImage
clipStrToWidth() - clip string to maxPixelWidth and font char width.
clipViewport(float, float, float, float) - Method in class Draw2Dplot
clipViewport(x1,x2,y1,y2) - Compute if (x1,x2,y1,y2) is inside of Viewport window.
clLst - Variable in class MAExplorer
Global instance of GeneList contains gene (clone) list tables
Clone_ID - Variable in class Gene
I.M.A.G.E clone id #, or "your plate", etc.
cloneID - Variable in class SpotFeatures
lookup I.M.A.G.E.
cloneIdIdx - Variable in class GipoTable
index for "Clone ID"
close() - Method in class DrawClusterGram
close() - close this popup and reset flags if keepFlagsOnClosing is false
close() - Method in class Guesser
close() - close the window.
close() - Method in class PopupCondChooser
close() - close this popup
close() - Method in class PopupCondChooser.CondDialogBox
close() - close this popup
close() - Method in class PopupCondChooser.PopupTextField
close() - close this popup
close() - Method in class PopupCondChooser.ChoiceList
close() - close this popup
close() - Method in class PopupHPChooser
close() - close the window.
close() - Method in class PopupOrderedCondChooser
close() - close this popup
close() - Method in class PopupOrderedCondChooser.CondDialogBox
close() - close this popup
close() - Method in class PopupOrderedCondChooser.PopupTextField
close() - close this popup
close() - Method in class PopupOrderedCondChooser.ChoiceList
close() - close this popup
close() - Method in class Report
close() - close this popup and reset flags if needed
close() - Method in class ShowPlotPopup
close() - close this popup and reset flags if needed
close() - Method in class ShowSpreadsheetPopup
close() - close this popup and reset flags if needed
close(boolean) - Method in class GenNormalizationPlugin
close() - close the plugin
close(boolean) - Method in interface MAEUpdateListener
close() - close the plugin
close(boolean) - Method in class ShowExprProfilesPopup
close() - close this popup and reset flags if needed
close(boolean) - Method in class ShowStringPopup
close() - close this popup and reset flags if needed
close(boolean) - Method in class MAEPlugin.analysis.NormalizationPlugin
close() - close the plugin
close(boolean) - Method in class MAEPlugin.connection.ConnectionPlugin
close() - close the plugin
close(boolean) - Method in class MAEPlugin.popup.PluginUnLoader
close() - close the plugin
close(int) - Method in class RtestBase
close() - exit with specified exit code.
closeButton - Variable in class RtestBase
"Close" window button
closeButton - Variable in class PopupEditRscript
"Close" window button
closeButton - Variable in class ShowExprProfilesPopup
 
closeButton - Variable in class ShowPlotPopup
close window button
closeGenRButton - Variable in class PopupEditRscript
"Close" window button for DEMO GenR edit
closeLogFile() - Method in class FileIO
closeLogFile() - close log file if it is open, but always reset the log state
closePopupTextReportWindow(Object) - Method in class MJAreport
closePopupTextReportWindow() - close Popup Report Window
closeRLOedit(boolean) - Method in class PopupEditRscript
closeRLOedit() - popdown the window and clear the edit state.
clstrSamp - Variable in class MAExplorer
Global instance of ClusterSamples class
clusterCL - Variable in class ClusterGenes.Cluster
optional list of genes in this cluster
clusterDistance(Gene, Gene) - Method in class GeneGeneDist
clusterDistance() - compute genes(I,J) cluster distance for HP-E samples.
clusterDistThr - Variable in class Config
Threshold PARAM: cluster distance Filter threshold
clusteredGenesCL - Variable in class Filter
"Tightly clustered genes"
ClusterGenes - class ClusterGenes.
Class to generate gene clusters from working data Filtered gene list.
ClusterGenes.Cluster - class ClusterGenes.Cluster.
[FUTURE] Class Cluster holds an ordered list of genes for a particular cluster.
ClusterGenes.Cluster(ClusterGenes, int, int, int, String, Gene[]) - Constructor for class ClusterGenes.Cluster
Cluster() - constructor.
ClusterGenes(GeneList, MaHybridSample[], int) - Constructor for class ClusterGenes
ClusterGenes() - constructor to create instance of new cluster method
ClusterGenes(MAExplorer) - Constructor for class ClusterGenes
ClusterGenes() - constructor to create instance of new cluster method
ClusterGramCanvas - class ClusterGramCanvas.
Create a ClusterGram canvas and display the colored green/red similarity table in a popup window.
ClusterGramCanvas(MAExplorer, DrawClusterGram, GeneList, HierClustNode) - Constructor for class ClusterGramCanvas
ClusterGramCanvas() - Constructor to display expresion profile in canvas
clusterHP_EfilterFlag - Variable in class MAExplorer
filter genes by cluster HP-E
clusterMenu - Variable in class MenuBarFrame
"Cluster" menu
clusterNodeNbr - Variable in class Gene
if >0, then this the cluster node in K-means clustering
clusterOnFilteredCLflag - Variable in class MAExplorer
cluster on Filtered/All genes
ClusterSamples - class ClusterSamples.
This class generates a cluster tree of HP samples from the active gene list.
ClusterSamples(MAExplorer, GeneList, MaHybridSample[], int) - Constructor for class ClusterSamples
ClusterSamples() - constructor
cmdHistoryNbr - Static variable in class Util
Command history number gets incremented each time a command is logged.
cName - Variable in class ClusterGenes.Cluster
optional cluster name
cName - Variable in class Condition
name of condition list
cName - Variable in class GeneList
instance: name of gene list
cnt - Variable in class MC_Cube
 
codeBase - Static variable in class MAExplorer
full codebase path for /mae/ on MAE svr
codetab - Variable in class WriteGifEncoder
 
colLabel - Variable in class ClusterGramCanvas
opt.
color_textHP - Variable in class CompositeDatabase
text HP labels shared colors
colorMax - Variable in class MedianCut
# of non-zero bins in hist15[]
cols - Variable in class ShowSpreadsheetPopup
cols
colSize - Variable in class PopupBinOprDialogQuery
# of columns to display
colSize - Variable in class PopupDialogQuery
# of columns to display
colSize - Variable in class PopupLoginDialogQuery
# of columns to use
comments - Variable in class Gene
--- options may or may not be used ---
COMPARE_ALL - Static variable in class MAExplorer
range-compare mode: spot intensity of samples - ALL samples must comply
COMPARE_ALL - Static variable in class MJAbase
range-compare mode: spot intensity of samples - ALL samples must comply
COMPARE_ANY - Static variable in class MAExplorer
range-compare mode: spot intensity of samples - ANY samples must comply
COMPARE_ANY - Static variable in class MJAbase
range-compare mode: spot intensity of samples - ANY samples must comply
COMPARE_AT_LEAST - Static variable in class MAExplorer
range-compare mode: spot intensity of samples - AT LEAST n samples must comply
COMPARE_AT_LEAST - Static variable in class MJAbase
range-compare mode: spot intensity of samples - AT LEAST n samples must comply
COMPARE_AT_MOST - Static variable in class MAExplorer
range-compare mode: spot intensity of samples - AT MOST n samples must comply
COMPARE_AT_MOST - Static variable in class MJAbase
range-compare mode: spot intensity of samples - AT MOST n samples must comply
COMPARE_PRODUCT - Static variable in class MAExplorer
range-compare mode: spot intensity of samples - PRODUCT of samples must comply
COMPARE_PRODUCT - Static variable in class MJAbase
range-compare mode: spot intensity of samples - PRODUCT of samples must comply
COMPARE_SUM - Static variable in class MAExplorer
range-compare mode: spot intensity of samples - SUM samples must comply
COMPARE_SUM - Static variable in class MJAbase
range-compare mode: spot intensity of samples - SUM samples must comply
complexClusterCL - Static variable in class ClusterGenes
ARG: list of genes to be clustered
CompositeDatabase - class CompositeDatabase.
Class to operate on composite sets of Hybridized Samples lists HP-X set, HP-Y set and HP-E list.
CompositeDatabase(MAExplorer) - Constructor for class CompositeDatabase
CompositeDatabase() - constructor to set up data structures.
compress(int, FileOutputStream) - Method in class WriteGifEncoder
compress() - GIF Image compression - modified 'compress'.
compressGeneList() - Method in class GeneList
compressGeneList() - compress the mList[] by removing nulls if any.
computeGeneGeneDistanceMatrix(String) - Method in class MJAcluster
computeGeneGeneDistanceMatrix() - return gene-gene cluster distance matrix.
computeGeneToMeanClusterDistance(int, int) - Method in class ClusterGenes
computeGeneToMeanClusterDistance() - gene to Mn-Cluster Euclidean distances
computeMaxCanvasSize() - Method in class Config
computeMaxCanvasSize() - compute the maximum pseudoArray Canvas size
computeMinMaxF1F2Data(boolean, boolean) - Method in class MJAgene
computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema returned as a float[] list for the current sample.
computeMinMaxF1F2Data(boolean, boolean) - Method in class MaHybridSample
computeMinMaxF1F2Data() - compute F1 F2 min and max raw intensity extrema.
computeWorkingGeneList() - Method in class Filter
computeWorkingGeneList() - run the data filter gene to compute the workingCL gene list.
computeWorkingGeneList() - Method in class MJAnormalization
computeWorkingGeneList() - run the data Filter and compute the working gene list.
condData - Variable in class Statistics
data[0:nConditions-1][sampleNbrInClass] for computations, set by calcMeanAndVariance()
condErrorMsgTf - Variable in class PopupCondChooser
error msg display
condErrorMsgTf - Variable in class PopupOrderedCondChooser
error msg display
condFont - Variable in class PopupCondChooser
font for conditions
condFont - Variable in class PopupOrderedCondChooser
font for conditions
Condition - class Condition.
This class represents an individual Condition list of hybridized sample entries.
Condition(MAExplorer, String, boolean) - Constructor for class Condition
Condition() - constructor to create a new named sample Condition list.
Condition(String) - Constructor for class Condition
Condition() - constructor to create a new empty named Condition list.
Condition(String, MaHybridSample[], int, int) - Constructor for class Condition
Condition() - constructor to create a new condition with list of samples.
condList - Static variable in class Condition
[0:nCondLists-1] list of condLists'
condList - Variable in class PopupCondChooser
The working list of conditions for GUI
condListNames - Variable in class PopupCondChooser
list of condition names
condName - Variable in class PopupCondChooser.CondData
Condition name
condName - Variable in class PopupOrderedCondChooser.OclListData
Condition name
condNames - Static variable in class Condition
[0:nCondLists-1] list of names of the conditions
condPanel - Variable in class PopupCondChooser
Panel to hold conditions list (LEFT) and Param Editor (RIGHT)
Config - class Config.
The class holds MAExplorer configuration variables that constitute par of the global state.
Config(MAExplorer, String) - Constructor for class Config
Config() - constructor to make it accessible.
configFile - Variable in class Config
Configuration file where we got the config data ...
configFile - Variable in class MAExplorer
Default Configuration file: "MaExplorerConfig.txt"
ConfigTable - class ConfigTable.
This reads the Config file as a tab-delimited table to define the initial Configi state.
ConfigTable(MAExplorer, String) - Constructor for class ConfigTable
ConfigTable() - constructor to read the configuration table file.
connect() - Method in class JavaCGIBridge
connect() - implements abstract method for HttpURLconnection.
ConnectionPlugin - class MAEPlugin.connection.ConnectionPlugin.
This class is the connection MAEPlugin base class and is be used to implement a connection base class.
ConnectionPlugin() - Constructor for class MAEPlugin.connection.ConnectionPlugin
ConnectionPlugin() - Constructor for creating new ConnectionPlugin
CONSOLE_FLAG - Static variable in class MAExplorer
Debugging flag - Always TRUE
CONSOLE_FLAG - Static variable in class PopupCondChooser
 
CONSOLE_FLAG - Static variable in class PopupOrderedCondChooser
 
CONSOLE_FLAG - Static variable in class RtestBase
Debug flags
constraints - Variable in class LogTextFrame
grid bag constraints
containsWildCard(String) - Method in class KeyEventHandler
containsWildCard() - return location of wildcard '*', -1 if not found.
content - Variable in class SSstatusBar
 
controlPanel - Variable in class ChooserGUI
control panel for main ok/reset buttons
controlPanel - Variable in class PopupCondChooserGUI
control panel for main ok/reset buttons
controlPanel - Variable in class PopupOrderedCondChooserGUI
control panel for main ok/reset buttons
controlPanel - Variable in class PopupEditRscript
Control Panel to hold buttons and GenR checkboxes in popup window.
controlPanel - Variable in class PopupScrollableSelector
to put checkBoxPanel in so can scroll
coordsNumber - Variable in class SSstatusBar
 
copy(GeneList, GeneList) - Method in class GeneList
copy() - copy GeneList mList[] and bitSets of c2 to c1.
copyArrayToSizedArray(String[], int) - Method in class Guesser
copyArrayToSizedArray() - resize copy tempList to outList [0:outLen-1].
copyBStoBS(GeneBitSet, GeneBitSet) - Static method in class GeneBitSet
copyBStoBS() - copy GeneBitSet b2Src to GeneBitSet b1Dst.
copyBStoCL(GeneList, GeneBitSet) - Method in class GeneBitSet
copyBStoCL() - copy GeneBitSet b2Src to GeneList c1Dst.mList[].
copyCLtoBS(GeneBitSet, GeneList, boolean) - Static method in class GeneBitSet
copyCLtoBS() - copy GeneList c2Src to GeneBitSet b1Dst.
copyCurClusterToEditedGeneList() - Static method in class ClusterGenes
copyCurClusterToEditedGeneList() - set EGL to K-means curCluster genes for the most similar genes.
copyFile(String, String, String, int) - Method in class FileIO
copyFile() - binary copy of one file or URL to a local file
copyFile(String, String, String, int) - Method in class MJAutil
copyFile() - binary copy of one file or URL toa local file
copyFile(String, String, String, int) - Method in class Reval
copyFile() - binary copy of one file or URL toa local file
copyFile(String, String, String, int) - Method in class RevalBase
copyFile() - binary copy of one file or URL toa local file
copyGBCTdataToStaticGeneDB() - Method in class GipoTable
copyGBCTdataToStaticGeneDB() - setupMaster_ID mid to GipoTable table row lookup table.
copyGeneNamesTableFile() - Method in class GipoTable
copyGeneNamesTableFile() - copy gene names into static Gene database map.midStaticCL.mList
copyGenesInSubtreeToEGL() - Method in class ClusterGramCanvas
copyGenesInSubtreeToEGL() - Copy terminal genes in dendrogram subtree to E.G.L for box that was selected at (selRow,selCol) such that terminal genes LEQ selDist GT 0.0F and dcg.drawDendroGramFlag.
copyOrigToWorkingData() - Method in class ChooserGUI
copyOrigToWorkingData() - copy original data to working data.
copyOrigToWorkingData() - Method in class PopupCondChooserGUI
copyOrigToWorkingData() - copy original data to working data.
copyOrigToWorkingData() - Method in class PopupOrderedCondChooserGUI
copyOrigToWorkingData() - copy original data to working data.
copySorted(GeneList, GeneList) - Method in class GeneList
copySorted() - copy GeneList mList[] sorted, and bitSets of c2 to c1.
copyStatesToValue() - Method in class PopupScrollableSelector
copyStatesToValue() - copy nameListCB[] state to valueList[]
copyTable(SimpleTable) - Method in class Table
copyTable() - copy SimpleTable data to this Table.
copyTempOutputFilesToReportDir() - Method in class RevalBase
copyTempOutputFilesToReportDir() - show plots generated if any with the last R eval.
copyValuesToMlistCy3Cy5Flags() - Method in class SampleSets
copyValuesToMlistCy3Cy5Flags() - copy nameListCB[] state to valueList[]
count - Variable in class GeneBitSet
# of ITEMS used in this GeneBitSet
count - Variable in class WriteGifEncoderHashitem
 
covDist - Variable in class ClusterGenes.Cluster
coefficient of variation computed as stDist/meanDist
cpef - Variable in class PopupCondChooser
CondParamEditForm instance
cpef - Variable in class PopupOrderedCondChooser
CondParamEditForm instance
cr1 - Variable in class MAExplorer
PARAM "CR1" MIN_RATIO range (i.e.
cr2 - Variable in class MAExplorer
PARAM "CR2" MAX_RATIO range
createCacheFileName(String) - Method in class FileIO
createCacheFileName() - create cache file name.
createClientDemoRscript(int) - Method in class RgenDemo
createClientDemoRscript() - create Demo R script in {MAExplorer installation}/R/ folder based on the RLO file specifications and the genRbits field.
createClusterMethod(GeneList, int, MaHybridSample[], int, int, boolean) - Method in class ClusterGenes
createClusterMethod() - create instance of new cluster method
createDialogQueryFrames() - Method in class MenuBarFrame
createDialogQueryFrames() - create all popup dialog frames
createFileTable(MAExplorer, String, String, String[], boolean) - Method in class Table
createFileTable() - create table from file on this Table.
createHPmeanAndVarTable() - Method in class CompositeDatabase
createHPmeanAndVarTable() - create table (HP,mn,stdDev,min,max,median) of raw intensity data.
createIndexToGridCoordMap() - Method in class GridCoords
createIndexToGridCoordMap() - once only FGRC <--> gid map creation.
createInputDataFiles(String) - Method in class Reval
createInputDataFiles() - create any input data files required for current analysis.
createInputDataFiles(String) - Method in class RevalBase
createInputDataFiles() - create any input data files required for current analysis.
createKmeansNodesPartition(int) - Method in class ClusterGenes
createKmeansNodesPartition() - setup primary K-means nodes partition.
createMAEstartupFileStr(boolean) - Method in class UserState
createMAEstartupFileStr() - create .mae startup DB File string.
createMontageTableOfCurGene(boolean) - Static method in class MJAutil
createMontageTableOfCurGene() - create montage table of current gene.
createMontageTableOfGene(int, boolean) - Static method in class MJAutil
createMontageTableOfGene() - create montage table of gene data across the HP-E sample conditions.
createNewCondList(String) - Method in class MJAcondition
createNewCondList() - create new named condition list
createNewNamedOrderedCondList(String) - Method in class Condition
createNewNamedOrderedCondList() - create new named ordered condition list if it does not already exist - in which case do nothing.
createNewNamedOrderedCondList(String) - Method in class MJAcondition
createNewNamedOrderedCondList() - create new named ordered condition list of conditions if it does not already exist - in which case do nothing.
createNewOverlayMap(String) - Static method in class MJAplot
createNewOverlayMap() - define a scatterplot named overlay map.
createNewOverlayMap(String) - Static method in class OverlayMap
createNewOverlayMap() - create a new scatterplot named overlay map.
createNewRLOdatabase(MaeJavaAPI, int) - Method in class MJAReval
createNewRLOdatabase() - constructor for initial database allocation
createPopupPlot() - Method in class ShowPlotPopup
createPopupPlot() - create the popup plot
createRunRscript() - Method in class RevalBase
createRunRscript() - create startup script to run R that is OS specific
createSample(int, String, String, String, String, String, String, String, boolean, boolean) - Method in class MAExplorer
createSample() - create and return a MaHybridSample hybridized sample object.
createSimilarGeneCountsClusters() - Method in class ClusterGenes
createSimilarGeneCountsClusters() - create similar gene counts clusters
createSimilarGenedCluster() - Method in class ClusterGenes
createSimilarGenedCluster() - create cluster of similar genes
createSpreadSheet() - Method in class ShowSpreadsheetPopup
createSpreadSheet() - create the the popup spreadsheet
createStateScrollers() - Method in class StateScrollers
createStateScrollers() - build the grid panel of popup scrollers
createStrReportOfOCL_FstatData(Gene[], int) - Method in class Report
createStrReportOfOCL_FstatData() - make String report of OCL F-test for mList[0:nC-1] If the OCL F-Test filter is active, then report F-test statistics.
createTableKmeansClusterStats(Gene[], int) - Method in class Report
createTableKmeansClusterStats() - make Table of Kmeans clusters for mList[0:nC-1]
createTableOfExprProfiles(Gene[], int, boolean) - Method in class Report
createTableOfExprProfiles() - make Table of expression profiles for mList[0:nC-1]
createTableOfHP_XYstat(Gene[], int) - Method in class Report
createTableOfHP_XYstat() - make Table of HP_XYstatistics for mList[0:nC-1] If the t-Test filter is active, then report t-test statistics If the KS-Test filter is active, then report KS-test statistics
createTableOfOCL_Fstat(Gene[], int) - Method in class Report
createTableOfOCL_Fstat() - make Table of OCL F-test for mList[0:nC-1] If the OCL F-Test filter is active, then report F-test statistics
createTempRscript(String) - Method in class RevalBase
createTempRscript() - create a copy of the .R script in /Temp/ for the current RLO database analysis currently selected.
createTotGeneRptTbl(Gene[], int, int, String, int, String, boolean, int) - Method in class Report
createTotGeneRptTbl() - generate total gene report table.
createTotURLgeneRptTbl(Table, Gene[], int, int, String, int, String, int[], boolean) - Method in class Report
createTotURLgeneRptTbl() - generate total URL gene report table
cTitle - Variable in class ExprProfileOverlay
titles [0:nGenes-1] "#Master_ID"
cTitle - Variable in class ExprProfileScrollPane
[0:nGenes-1] "#Master_ID"
ctrlMod - Variable in class ScrollableImageCanvas
CTRL/Mouse
cubeList - Variable in class MedianCut
list of cubes
cur_accum - Variable in class WriteGifEncoder
 
cur_bits - Variable in class WriteGifEncoder
 
CUR_GENE - Static variable in class PopupRegistry
Property bit type: Notify bit if CurGene changed
curAnalysis - Static variable in class RevalBase
Current analysis procedure being used from the analyses[] list
curCGmid - Variable in class DrawClusterGram
current mid of selected ClusterGram row
curCGrow - Variable in class DrawClusterGram
current selected row of ClusterGram
curClusterCL - Static variable in class ClusterGenes
ARG: current genes being clustered
curCond - Variable in class PopupCondChooser
The current condition name
curCond - Variable in class PopupOrderedCondChooser
The current condition name that is selected in the lower OCL list
curCondIdx - Static variable in class Condition
Current condition which was the last condition selected by the PopupConditionChooser.
curCondIdx - Variable in class PopupCondChooser
current cond index
curCondIdx - Variable in class PopupOrderedCondChooser
current cond index
curCondListName - Variable in class PopupCondChooser
show current condition name
curCondNameLabel - Variable in class PopupCondChooser
show current condition name
curCondNames - Variable in class PopupOrderedCondChooser
The current condition list of names
curCondSetDataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-cond-list")
curGene - Static variable in class ClusterGenes
current gene being clustered
curGeneClass - Variable in class GeneClass
current Gene class selected.
curGeneClassName - Static variable in class GeneClass
Name of current Gene Class
curGeneDistThr - Static variable in class ClusterGenes
Threshold distance for current gene cluster
curGeneTextButton - Variable in class MenuBarFrame
enter cur.
curHP - Static variable in class MAExplorer
Current hybridized sample index for hps.msList[]
curHP_X - Static variable in class MAExplorer
Current HP-X sample index for hps.msList[]
curHP_Y - Static variable in class MAExplorer
Current HP-Y sample index for hps.msList[]
curHPdataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-HP")
curOclDataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-OCL")
curOCLidx - Static variable in class Condition
Current OCL which was the last OCL selected by the PopupOrderedCondChooser.
curOclListName - Variable in class PopupOrderedCondChooser
show current condition name
curOclNameLabel - Variable in class PopupOrderedCondChooser
show current condition name
curPrjName - Static variable in class MAExplorer
current project being requested
currentHorzValue - Variable in class SSscrollHorizontal
upper bounds on scroller
currentValueH - Variable in class SSspreadPanel
 
currentValueV - Variable in class SSspreadPanel
 
cursorLoc - Variable in class PopupEditRscript
keep track of cursor location within textarea
curVertValue - Variable in class SSscrollVertical
keep track of oldvalue
curXbinIdx - Variable in class DrawRatioHistogram
index of X axis for data arrays
custGramReport - Variable in class DrawClusterGram
popup Report
cv - Variable in class Gene
optional computed coefficient of variation (CV) if doing statistical test
cv1Tmp - Static variable in class ClusterGenes
EP vector for CV1 computations
cv1Tmp - Static variable in class GeneGeneDist
temporary v1 vector[0:nEP-1] for computations
cv1TmpEP - Static variable in class ClusterGenes
EP vector for CV1 computations
cv1TmpEP - Static variable in class GeneGeneDist
temporary EP v1 vector[0:nEP-1] for computations
cv2Tmp - Static variable in class ClusterGenes
EP vector for CV2 computations
cv2Tmp - Static variable in class GeneGeneDist
temporary v2 vector[0:nEP-1] for computations
cv2TmpEP - Static variable in class ClusterGenes
EP vector for CV2 computations
cv2TmpEP - Static variable in class GeneGeneDist
temporary EP v2 vector[0:nEP-1] for computations
cvd2s(double, int) - Method in class MJAutil
cvd2s() - convert double to string with precision # of digits
cvd2s(double, int) - Static method in class Util
cvd2s() - convert double to string with precision # of digits If precision > 0 then limit # of digits in fraction
cvData - Variable in class ExprProfile
Coefficient of variation all HP-E samples
cvEdata - Variable in class HPxyData
Coefficient of variation all HP-E list data
cvf2s(float, int) - Method in class MJAutil
cvf2s() - convert float to string with precision # of digits
cvf2s(float, int) - Static method in class Util
cvf2s() - convert float to string with precision # of digits.
cvFileNameWithMod(String, String) - Static method in class MJAutil
cvFileNameWithMod() - insert modifier string before file extension
cvFileNameWithMod(String, String) - Static method in class Util
cvFileNameWithMod() - insert modifier string before file extension
cvFontS2I(String) - Static method in class Util
cvFontS2I() - convert font size "8Ppt", "10pt", "12pt", or "14pt" to int
cvGene2TabDelimStr(Gene, int, String, boolean, Table, Table) - Method in class Report
cvGene2TabDelimStr() - convert a gene to printable tab-delimited string
cvHist2RIscale(float) - Method in class MaHybridSample
cvHist2RIscale() - convert histogram scale to raw intensity data for the gid.
cvLongToHex(long) - Static method in class Util
cvLongToHex() - convert long to hex string
cvPrecision - Variable in class Draw2Dplot
fraction precision reporting data
cvPrecision - Variable in class DrawHistogram
precision in intensity data report
cvRatioToScrollValue(float) - Method in class StateScrollers
cvRatioToScrollValue() - convert state ratio to ratio-scroller value
cvRI2HistScale(int) - Method in class MaHybridSample
cvRI2HistScale() - convert raw intensity to histogram scale data for the gid.
cvRLO2string(int, String, String) - Method in class RevalBase
cvRLO2string() - create string representing the R LayOut (RLO) of the instance
cvs2Array(String, int, String) - Method in class MJAutil
cvs2Array() - convert String arg list "1,4,3,6,..." to String[] If there are more than maxExpected number of args in string, ignore them and just return what has been parsed so far.
cvs2Array(String, int, String) - Static method in class Util
cvs2Array() - cvt arg list "1,4,3,6,..." to "," - delim String[].
cvs2d(String) - Method in class MJAutil
cvs2d() - convert String to double
cvs2d(String) - Static method in class Util
cvs2d() - convert String to double
cvs2d(String, double) - Method in class MJAutil
cvs2d() - convert String to double
cvs2d(String, double) - Static method in class Util
cvs2d() - convert String to double with default value
cvs2f(String) - Method in class MJAutil
cvs2f() - convert String to float
cvs2f(String) - Static method in class Util
cvs2f() - convert String to float
cvs2f(String, float) - Method in class MJAutil
cvs2f() - convert String to float
cvs2f(String, float) - Static method in class Util
cvs2f() - convert String to float with default value
cvs2i(String) - Method in class MJAutil
cvs2i() - convert String to int
cvs2i(String) - Static method in class Util
cvs2i() - convert String to int
cvs2i(String, int) - Method in class MJAutil
cvs2i() - convert String to int
cvs2i(String, int) - Static method in class RevalBase
cvs2i() - convert String to int with default value
cvs2i(String, int) - Static method in class Util
cvs2i() - convert String to int with default value
cvs2iArray(String, int, String) - Method in class MJAutil
cvs2iArray() - convert String arg list "1,4,3,6,..." to int[] If there are more than maxExpected number of args in string, ignore them and just return what has been parsed so far.
cvs2iArray(String, int, String) - Static method in class Util
cvs2iArray() - convert String arg list "1,4,3,6,..." to int[]
cvScrollToStateValue(int, int) - Method in class StateScrollers
cvScrollToStateValue() - cvt scrollbar value to (float) STATE value
cvScrollValueToRatio(int, int) - Method in class StateScrollers
cvScrollValueToRatio() - convert ratio-scroller value to ratio STATE value
cvStateToScrollValue(int, float) - Method in class StateScrollers
cvStateToScrollValue() - convert STATE value to scrollbar current value.
cvtBackslash2Fwdslash(String) - Method in class MJAutil
cvtBackslash2Fwdslash() - convert '\\' to '/' in the string
cvtBackslash2Fwdslash(String) - Static method in class RevalBase
cvtBackslash2Fwdslash() - convert '\\' to '/' in the string
cvtBackslash2Fwdslash(String) - Static method in class Util
cvtBackslash2Fwdslash() - convert '\\' to '/' in the string
cvtBStoCL(GeneList) - Method in class GeneBitSet
cvtBStoCL() - convert GeneBitSet ml.bitSet to GeneList c1.mList[] (allocate data structures if needed).
cvtCol2Alpha(int) - Method in class SSstatusBar
cvtCol2Alpha() - set the cells values (int) to alphabet ie A,B,C ...
cvtEnvPaths2Properties() - Static method in class MJAutil
cvtEnvPaths2Properties() - get all system ENV variables and set them as separate Java properties so we can get them individually from System.getProperty(var) calls.
cvtEnvPaths2Properties() - Static method in class RevalBase
cvtEnvPaths2Properties() - get all system ENV variables and set them as separate Java properties so we can get them individually from System.getProperty(var) calls.
cvtEnvPaths2Properties() - Static method in class Util
cvtEnvPaths2Properties() - get all system ENV variables and set them as separate Java properties so we can get them individually from System.getProperty(var) calls.
cvTestMode - Variable in class MAExplorer
CV test mode: SS_MODE_xxxx
cvtFGRC2str(int, int, int, int, boolean) - Method in class GridCoords
cvtFGRC2str() - convert grid coordinate f,g,r,c to string name
cvtFloatArrayData2Table(RLO, SimpleTable, float[][], float[][], float[][], float[][], int, int, int, boolean[], String[], String[]) - Method in class Reval
cvtFloatArrayData2Table() - convert xData,yData nX,nY expression data for nGenes active genes to SimpleTable.
cvtGeneList2GeneMIDlist(GeneList) - Static method in class MJAbase
cvtGeneList2GeneMIDlist() - convert GeneList to list of gene indexes Only used by MJA classes.
cvtGID2str(int, boolean) - Method in class GridCoords
cvtGID2str() - convert grid coord GridCoords(gid) to string name
cvtHashtable2SimpleTable(Hashtable) - Static method in class MJAbase
cvtHashtable2SimpleTable() - creating table from Hashtable encoded table.
cvtImg24toImg8(int) - Method in class MedianCut
cvtImg24toImg8() - Uses Heckbert's median-cut algorithm to divide the color space defined by "hist15[]" into "maxcubes" cubes.
cvtInputType2Str(int) - Method in class RevalBase
cvtInputType2Str() - convertinput file type R_FILE_TYPE_xxxx to string
cvtNAME_GCR2FGRC(int, String) - Method in class GridCoords
cvtNAME_GCR2FGRC() - parse Molecular Dynamics "GRID- 8-R12C11" coding to FGRC coords.
cvtOutType2Str(int) - Method in class RevalBase
cvtOutType2Str() - convert output file type to string
cvtQualCheckStrToFloat(String) - Method in class MaHPquantTable
cvtQualCheckStrToFloat() - do conversion from QualCheck string to float value.
cvtR2ClientType2Str(int) - Method in class RevalBase
cvtR2ClientType2Str() - convert R2Client file type R to string
cvtRawQdataToMAEdata(boolean) - Method in class MaHybridSample
cvtRawQdataToMAEdata() - convert .quant data to MAE data using HP array data ms.(bkgrdQ,totQ)[] Note: totQ is RawIntensity, or unscaled ratio RawIntensity1/RawIntensity2.
cvtSpacesToUnderscores(String) - Method in class MJAutil
cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable.
cvtSpacesToUnderscores(String) - Method in class Rtest
cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable.
: space( ) ; " { } < > = , ? \ / % * ! @ & | ' ` \t
cvtSpacesToUnderscores(String) - Method in class RtestBase
cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable.
: space( ) ; " { } < > = , ? \ / % * ! @ & | ' ` \t
cvtSpacesToUnderscores(String) - Static method in class Util
cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable.
cvtStrArrayToStr(String[]) - Static method in class Util
cvtStrArrayToStr() - create(String) from String[] array with "\n"
cvtStrArrayToStr(String[], int) - Static method in class Util
cvtStrArrayToStr() - create(String) from String[] array with "\n" w/len Fast method creates a tmp Character [] of required size and stuffs it, then converts it to a string at one time instead of repeatedly using concat(i.e.
cvtStrArrayToStr(String[], String, String) - Static method in class Util
cvtStrArrayToDelimStr() - create delimited(String) from String[] array with terminator as last character.
cvtStringArrayData2Table(RLO, SimpleTable, String[][], int, int, String[]) - Method in class Reval
cvtStringArrayData2Table() - convert sData, nS, nRows to SimpleTable.
cvtTable2Hashtable(SimpleTable) - Static method in class MJAbase
cvtTable2Hashtable() - convert SimpleTable tbl to Hashtable object.
cvtTableToPrepData(String[][], String[], int, int) - Method in class ShowSpreadsheetPopup
cvtTableToPrepData() - cvt tFields & tData into one prepData[][] string[].
cvtTblRowDataToFGRC(int, String[]) - Method in class MaHPquantTable
cvtTblRowDataToFGRC() - convert table row data to GridCoord data by setting (f,g,r,c) in the mae.grcd object.
cvtValueToStars(float, float, int, boolean) - Method in class MJAutil
cvtValueToStars() - cvt val in[0:valMax] to "****"+" " string where the maximum # of stars for v==vMax is specified.
cvtValueToStars(float, float, int, boolean) - Static method in class Util
cvtValueToStars() - cvt val in[0:valMax] to "****"+" " string where the maximum # of stars for v==vMax is specified.
cvXdata - Variable in class HPxyData
Coefficient of variation all HP-X set data
cvYdata - Variable in class HPxyData
Coefficient of variation all HP-Y set data
cx1 - Variable in class Draw2Dplot
clipped x1 for clipping divider
cx2 - Variable in class Draw2Dplot
clipped x2 for clipping divider
cy1 - Variable in class Draw2Dplot
clipped y1 for clipping divider
cy2 - Variable in class Draw2Dplot
clipped y2for clipping divider

D

d2dp - Variable in class ExprProfileOverlay
draw 2D overlay of EP plots
data - Variable in class Gene
dynamic generic data such as ratio, etc associated with this gene
data - Variable in class PopupDialogQuery
for returning data back to MAE
DATA_F1TOT - Static variable in class MJAbase
type code: for f1 data
DATA_F1TOT - Static variable in class MaHybridSample
type code: for f1 data
DATA_F2TOT - Static variable in class MJAbase
type code: for f2 data
DATA_F2TOT - Static variable in class MaHybridSample
type code: for f2 data
DATA_MEAN_F1F2TOT - Static variable in class MJAbase
type code: for (f1+f2)/2 data
DATA_MEAN_F1F2TOT - Static variable in class MaHybridSample
type code: for (f1+f2)/2 data
DATA_RATIO_F1F2TOT - Static variable in class MJAbase
type code: for f1/f2 data
DATA_RATIO_F1F2TOT - Static variable in class MaHybridSample
type code: for f1/f2 data
data1 - Variable in class Gene
dynamic generic data for Field 1 associated with this gene
data1 - Variable in class PopupBinOprDialogQuery
for returning data back to MAE
data2 - Variable in class Gene
dynamic generic data for Field 2 associated with this gene
data2 - Variable in class PopupBinOprDialogQuery
for returning data back to MAE
data3 - Variable in class PopupBinOprDialogQuery
for returning data back to MAE
dataAvailFromQuantFileFlag - Variable in class MaHybridSample
set if can get quant data data from .quant file
database - Variable in class Config
PARAM "databaseName"
databaseFileID - Variable in class MaHybridSample
(opt) DatabaseFileID used with some databases (eg.
dataBkgrd - Variable in class PopupCondChooser
Text data report background color that may be changed
dataBkgrd - Variable in class PopupOrderedCondChooser
Text data report background color that may be changed
dataBkgrd - Variable in class RtestBase
Text data report background color that may be changed
dataCL - Variable in class GeneGeneDist
Gene list to generate geneEPvector
dataCol - Variable in class SStextCell
virtual coordinate for status bar
dataColor - Variable in class PopupCondChooser
Text data report foreground color that may be changed
dataColor - Variable in class PopupOrderedCondChooser
Text data report foreground color that may be changed
dataColor - Variable in class RtestBase
Text data report foreground color that may be changed
dataFont - Variable in class ChooserGUI
font used by data
dataFont - Variable in class PopupCondChooser
font for data used in the Chooser GUI
dataFont - Variable in class PopupCondChooserGUI
font used by data
dataFont - Variable in class PopupHPChooser
font for data of popup chooser window
dataFont - Variable in class PopupOrderedCondChooser
font for data used in the Chooser GUI
dataFont - Variable in class PopupOrderedCondChooserGUI
font used by data
dataFontSize - Variable in class SSspreadPanel
Calculated default or overidden
dataFromStateFileFlag - Variable in class MaHybridSample
flag: set if can get data from .state file
dataOK - Variable in class PopupLoginDialogQuery
flag set by OK and Cancel buttons
dataRow - Variable in class SStextCell
virtual coordinate for status bar
dataTF - Variable in class RtestBase
Text data report line
dataURL - Variable in class ShowSpreadsheetPopup
ARG: if url [0:maxRows-1][0:maxCols-1] from and not null, use this for URL
dataURL - Variable in class SpreadSheet
ARG: opt.
dataURL - Variable in class SSspreadPanel
opt.
dataV - Variable in class HierClustNode
Dynamic node: mean vector [0:nDataV-1] of left and right
dataV1 - Variable in class HierClustNode
Dynamic node: [0:nDataV-1] copy of dataV1[]
dataV2 - Variable in class HierClustNode
Dynamic node: [0:nDataV-1] copy of dataV1[]
date - Static variable in class MAExplorer
startup date
date - Variable in class RLO
RLO creation date
DATE - Static variable in class PopupCondChooser
 
DATE - Static variable in class PopupOrderedCondChooser
 
DATE - Static variable in class RtestBase
 
dateStr() - Static method in class Util
dateStr() - return a new Date string of the current day and time
dbEST3 - Variable in class Gene
NCBI dbEST database 3' id
dbEST5 - Variable in class Gene
NCBI dbEST database 5' id
dbESTid3 - Variable in class SpotFeatures
lookup dbEST id 3'
dbESTid3Idx - Variable in class GipoTable
index for "dbEst3'"
dbESTid5 - Variable in class SpotFeatures
lookup dbEST id 5'
dbESTid5Idx - Variable in class GipoTable
index for "dbEst5'"
dbEstURL - Variable in class Config
base addr PARAM "dbEstURL"
dbESTviewerFlag - Variable in class MAExplorer
dbEST popup browser Mode
dbID - Static variable in class MAExplorer
Unique Database ID ("DIDxxxxxx") - used as prefix for State/ files
dbSubset - Variable in class Config
PARAM "dbSubset" database subset
DBUG_APPEND_REPORT - Static variable in class RtestBase
 
DBUG_CV_DISPLAY_EPLIST - Static variable in class MAExplorer
if debugging display the CV of HP-EP samples as colors [0:1.0] lie for p-value display.
DBUG_FLAG - Variable in class MJAcondition
 
DBUG_FLAG - Static variable in class PopupCondChooser
 
DBUG_FLAG - Static variable in class PopupOrderedCondChooser
 
DBUG_FLAG - Variable in class RtestBase
 
DBUG_GENERIC_NORM_PLUGIN - Static variable in class MAExplorer
[DEBUGGING] If debugging a plugin extending NormalizationPlugin, you may debug it in the MAExplorer core image by temporarily including in in the code.
DBUG_GENOMIC_URLS_FLAG - Static variable in class MAExplorer
debugging Genomic Menu/URLs
DBUG_HCN - Static variable in class MAExplorer
debugging HierClustNode lists
DBUG_LOGIN - Static variable in class MAExplorer
Debugging variablen - debugging CGI login locally
DBUG_MAEP - Static variable in class MAEPlugin.MAEPlugin
 
DBUG_MAERlibr_ZIP_UPDATE - Static variable in class MAExplorer
If debugging MAERlibr.zip file update.
DBUG_MAX_MIDS - Static variable in class GenNormalizationPlugin
only report mids analysis in this range if DBUG_FLAG is on
DBUG_MEDMINER_FLAG - Static variable in class MAExplorer
debugging MedMiner Menu/URLs
DBUG_MIN_MIDS - Static variable in class GenNormalizationPlugin
only report mids analysis in this range if DBUG_FLAG is on
DBUG_NORM_PLUGIN - Static variable in class MAExplorer
if debugging NormalizationPlugins using the PluginLoader
DBUG_QUALCHK_QUANT_FLAG - Static variable in class MAExplorer
debugging QualCheck
DBUG_SET_EGL_FROM_DENDROGRAM - Static variable in class MAExplorer
if debugging setting EGL set from subtree of HCN dendrogram
DBUG_STANDALONE - Static variable in class MAExplorer
debugging Stand-Alone code
DBUG_TEST_PLUGIN_FLAG - Static variable in class MAExplorer
Enable testing MAEPlugin from the intial menu without dynamic MAEPlugin loading of the class.
DBUG_TEST_R_OR_SPLUS_CHECKBOX - Static variable in class MAExplorer
Test the code to let the user switch between R or S-Plus as the statistics evaluation engine.
dbugCheckbox - Variable in class RtestBase
dbug checkbox toggles output being appended to reportText window
dbugFlag - Variable in class RevalBase
Flag set debugging - toggled by dbugCheckbox if DBUG_FLAG is set
dbugFlag - Variable in class RtestBase
Flag set debugging - toggled by dbugbox if DBUG_FLAG is set
dcg - Variable in class ClusterGramCanvas
parent class
dcg - Variable in class StatusCanvas
 
DEBUG - Static variable in class MAExplorer
General purpose debugging flag.
DEF_BASESERVER - Static variable in class MAExplorer
Default microarray database server.
DEF_CANVAS_HSIZE - Static variable in class Config
default uArray canvas horizontal size
DEF_CANVAS_VSIZE - Static variable in class Config
default uArray canvas vertical size
DEF_CLUSTER_DIST - Static variable in class Config
Default cluster distance
DEF_COL_SIZE - Static variable in class PopupDialogQuery
default # of columns
DEF_COLS_TO_SHOW - Static variable in class ShowSpreadsheetPopup
# of cols to show in dynamic spreadsheet
DEF_DIFF_THR - Static variable in class Config
DEFAULT Diff(HP-X,HP-Y) in [minNorm:maxNorm] as fct.
DEF_GNMID_TA_COLS - Static variable in class PopupGeneGuesser
default size of text area
DEF_GNMID_TA_ROWS - Static variable in class PopupGeneGuesser
default size of text area
DEF_GUESSER_DISP_SIZE - Static variable in class Guesser
max items to display in ta area
DEF_HP_TA_COLS - Static variable in class PopupHPmenuGuesser
 
DEF_HP_TA_ROWS - Static variable in class PopupHPmenuGuesser
 
DEF_MAX_ANALSYSES - Static variable in class RtestBase
Maximum # scripts (may grow over time)
DEF_MAX_INTENSITY - Static variable in class Config
default maximum intensity.
DEF_NBR_CLUSTERS - Static variable in class Config
Default # of clusters
DEF_NBR_RESAMPLE_RUNS - Static variable in class ClusterGenes
Default number of resampling runs
DEF_P_VALUE_THR - Static variable in class Config
DEFAULT: t-test threshold
DEF_PD_TA_COLS - Static variable in class PopupProjDirGuesser
default col size of text area
DEF_PD_TA_ROWS - Static variable in class PopupProjDirGuesser
default row size of text area
DEF_RADIUS - Static variable in class Config
Default spot radius (-1)
DEF_SP_HEIGHT - Static variable in class PopupCondChooser.CondParamEditForm
default preferred size used prior to mainPanel being constructed
DEF_SP_HEIGHT - Static variable in class PopupOrderedCondChooser.CondParamEditForm
default preferred size used prior to mainPanel being constructed
DEF_SP_WIDTH - Static variable in class PopupCondChooser.CondParamEditForm
default preferred size used prior to mainPanel being constructed
DEF_SP_WIDTH - Static variable in class PopupOrderedCondChooser.CondParamEditForm
default preferred size used prior to mainPanel being constructed
DEF_SPOT_CV_THR - Static variable in class Config
DEFAULT: SPOT CV threshold
DEF_TA_COLS - Static variable in class Guesser
default # columns size of text area
DEF_TA_ROWS - Static variable in class Guesser
default # rows size of text area
default_font - Variable in class LogTextFrame
default font
DEFAULT_N_KMEANS_NODES - Static variable in class ClusterGenes
Default # of K-means nodes
DEFAULT_N_SOM_NODES1 - Static variable in class ClusterGenes
Default # of SOM map nodes
DEFAULT_N_SOM_NODES2 - Static variable in class ClusterGenes
Default # of SOM map nodes
DEFAULT_PANEL_HEIGHT - Variable in class StateScrollers
default height size of state scroller panel
DEFAULT_PANEL_WIDTH - Variable in class StateScrollers
default width size of state scroller panel
DEFAULT_R_OUTPUT_FILE - Static variable in class RevalBase
default output file for R to save any output if we do not specify an output file for the current analysis.
defaultFloat - Static variable in class Util
default float value for conversions
defaultGene - Variable in class MJAgene
 
defaultInt - Static variable in class Util
default int value for conversions
defaultMsg - Variable in class PopupLoginDialogQuery
default prompt string
defaultThreadJavaCGIBridgeTimeOut - Static variable in class JavaCGIBridge
This is the default CGI Timeout in milliseconds.
defClassName - Static variable in class GeneClass
 
defDir - Static variable in class MAExplorer
Default standalone directory (=null JWS hack)
defGifFile - Variable in class ShowPlotPopup
default output .gif file name
defSAprjName - Variable in class MAExplorer
Standalone current project DB name
defSAwebAddr - Static variable in class MAExplorer
Default standalone assoc.
defStartupFile - Static variable in class MAExplorer
Default standalone .mae startup file
defTxtFile - Variable in class ShowStringPopup
 
delButton - Variable in class ChooserGUI
mv Selected entry to Remainder
delButton - Variable in class PopupCondChooserGUI
Nove the Selected entry to Remainder
delButton - Variable in class PopupOrderedCondChooserGUI
Nove the Selected entry to Remainder
deleteColumn(int) - Method in class SpreadSheet
deleteColumn() - delete row at column k
deleteColumn(int) - Method in class SSspreadPanel
deleteColumn() - delete the k-th col
deleteLocalFile(String) - Method in class FileIO
deleteLocalFile() - delete local file.
deleteLocalFile(String) - Method in class MJAutil
deleteLocalFile() - delete local file.
deleteLocalFile(String) - Method in class Reval
deleteLocalFile() - delete local file.
deleteLocalFile(String) - Method in class RevalBase
deleteLocalFile() - delete local file.
deleteRecursive(File) - Method in class FileIO
 
deleteRLOButton - Variable in class RtestBase
"Delete RLO" window button
DelFileWalker - class DelFileWalker.
 
DelFileWalker() - Constructor for class DelFileWalker
 
delObjs(String) - Method in class ChooserGUI
delObjs() - move SELECTED obj from ta2 (RIGHT) to REMAINDER ta1 (LEFT) list if ta1 is not same prj list.
delObjs(String) - Method in class PopupCondChooserGUI
delObjs() - move SELECTED obj from selTextArea (RIGHT) to REMAINDER remTextArea (LEFT) list if remTextArea is not same prj list.
delObjs(String) - Method in class PopupOrderedCondChooserGUI
delObjs() - move SELECTED obj from selTextArea (RIGHT) to REMAINDER remTextArea (LEFT) list if remTextArea is not same prj list.
DELTA_X_SPACING - Static variable in class MaHPquantTable
(opt) Horiz.
DELTA_Y_SPACING - Static variable in class MaHPquantTable
Vert.
deltaBin - Variable in class DrawHistogram
value of hist[] bin in [minX:maxX]
deltaBin - Variable in class MaHybridSample
Filter hist: #bins/maxData-minData)
deltaBinH - Variable in class Statistics
width of the histogram bins computed as: nBinsH/(maxDataH-minDataH)
deltaHistBin - Variable in class MaHybridSample
total array: width of a logRatio histogram bin
demoWizardList - Variable in class PopupEditRscript
List of wizards for Demo Wizard of pre-constructed RLOs
DESCENDING - Static variable in class Report
flag: sort rows by desending column data
deselectAll(List) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
deselectAll() -
destroy() - Method in class MAExplorer
destroy() - destroy this class
destroy2() - Method in class MAExplorer
destroy2() - destroy this class, but clean up the mess of statics first.
destroyStaticState() - Method in class MAExplorer
destroyStaticState() - reset static state variables in MAE instance
detValueQ - Variable in class MaHybridSample
(opt) list of spot Detection Value within spot for all spots.
detValueSpotDataCL - Variable in class Filter
"Filter by Spot (Detection Value) Data"
detValueSpotTestMode - Variable in class MAExplorer
Spot (Detection Value) test mode: SS_MODE_xxxx
detValueSpotThr - Variable in class Config
Threshold PARAM: "detValueSpotThr" continuous spot Detection Value threshold
dF - Variable in class Statistics
CALC: degrees of freedom of t-test or F-test (2 conditions) set by calcTandPvalues()
dfBetween - Variable in class Statistics
CALC: degrees of freedom dfBetween, f-statistic nConditions test set by calcNCondFtestStat()
dFks - Variable in class Statistics
CALC: degrees of freedom for KS-test set by calcKStestStat()
dfWithin - Variable in class Statistics
CALC: degrees of freedom dfWithin, f-statistic nConditions test set by calcNCondFtestStat()
dGramCheckBox - Variable in class DrawClusterGram
toggle drawing the dendrogram
dGramDist - Static variable in class HierClustNode
[0:nObj-2] distance between children
dGramDistL - Variable in class ClusterGramCanvas
[0:nObj-2] log dist.
dGramDistL - Static variable in class HierClustNode
[0:nObj-2] distance between Left's children
dGramDistR - Variable in class ClusterGramCanvas
[0:nObj-2] log dist.
dGramDistR - Static variable in class HierClustNode
[0:nObj-2] distance between Right's children
dGramDistS - Variable in class ClusterGramCanvas
[0:nObj-2] log dist.
dGramEnumOrder - Variable in class ClusterGramCanvas
[0:nObj-2] enumeration order
dGramEnumOrder - Static variable in class HierClustNode
[0:nObj-2] enumeration order
dGramEOleft - Variable in class ClusterGramCanvas
[0:nObj-2] left child enum order
dGramEOleft - Static variable in class HierClustNode
[0:nObj-2] left child enum order
dGramEOright - Variable in class ClusterGramCanvas
[0:nObj-2] right child enum order
dGramEOright - Static variable in class HierClustNode
[0:nObj-2] right child enum order
dGramLeftNNbr - Variable in class ClusterGramCanvas
[0:nObj-2] Left Node Number
dGramLeftNNbr - Static variable in class HierClustNode
[0:nObj-2] Left Node Number
dGramNodeNbr - Variable in class ClusterGramCanvas
[0:nObj-2] Node Number
dGramNodeNbr - Static variable in class HierClustNode
[0:nObj-2] Node Number
dGramRightNNbr - Variable in class ClusterGramCanvas
[0:nObj-2] Right Node Number
dGramRightNNbr - Static variable in class HierClustNode
[0:nObj-2] Right Node Number
dGramX1 - Variable in class ClusterGramCanvas
left horizontal size of dendrogram region
dGramX2 - Variable in class ClusterGramCanvas
right horizontal size of dendrogram region
dGramZoomMag - Variable in class ClusterGramCanvas
zoom in on dendrogram - set by DrawClusterGram checkbox
dialogFrame - Variable in class MenuBarFrame
dialog frame created but not displayed until needed
dialogFrame - Variable in class UserState
for pLdq login dialog popup
dialogQuery(String, float) - Method in class PopupDialogQuery
dialogQuery() - query float variable
dialogQuery(String, int) - Method in class PopupDialogQuery
dialogQuery() - query int variable
dialogQuery(String, String) - Method in class PopupDialogQuery
dialogQuery() - query String variable requested
dialogQuery(String, String) - Method in class PopupLoginDialogQuery
dialogQuery() - query user name and password Note: must go in after return to get loginNameData, and passwordData.
dialogQuery(String, String, String[], int) - Method in class PopupDialogQuery
dialogQuery() - query String variable int requested
dialogQuery(String, String, String, String, String, String, String) - Method in class PopupBinOprDialogQuery
dialogQuery() - query String variables for the three operands.
dialogQuery(String, String, String, String, String, String, String, String[], int) - Method in class PopupBinOprDialogQuery
dialogQuery() - query String variables for the three operands.
didDataSetupFlag - Variable in class ClusterGramCanvas
flag: set by setupData() if successful
didDataSetupFlag - Variable in class ExprProfile
flag: set by setupData() if successful
didDataSetupFlag - Variable in class ExprProfileCanvas
set by setupData() if successful
didDataSetupFlag - Variable in class HPxyData
flag: set by setupXYdata() if successful
didGetParms - Variable in class Config
Flag: once only code for single call to getStateParamValues()
didStatisticsFlag - Variable in class HPxyData
flag: set by calcXYstatistics() and calcEPstatistics() if successful
dieFlag - Variable in class MAExplorer
Flag: call quit() if flag set to exit run().
difference(Condition, Condition, String) - Method in class Condition
difference() - compute difference of two conditions cond1 and cond2.
difference(GeneBitSet, GeneBitSet, GeneBitSet) - Method in class GeneBitSet
difference() - difference of GeneBitSets (b2 - b1)==> b3.
difference(GeneList, GeneList, GeneList) - Method in class GeneList
difference() - compute difference of gene lists (c2 - c1)==> c3.
difference(String, String, String) - Method in class MJAcondition
difference() - compute resultCond = difference (Condition 1 - Condition 2)
DiffHP_XYCL - Variable in class Filter
"Filter by Diff(HP-X,HP-Y)"
diffThr - Variable in class Config
Threshold PARAM: diff (HP-X,HP-Y) Filter threshold
dir - Variable in class MAEPlugin.FileClassLoader
String path
disableNormalizationPlugin() - Method in class MaeJavaAPI
disableNormalizationPlugin() - clear activeNormalization state.
disableNormalizationPlugin() - Method in interface MAEPlugin.MAEStub
disableNormalizationPlugin() - clear activeNormalization state.
disableNormalizationPlugin() - Static method in class MAEPlugin.analysis.NormalizationPlugin
disableNormalizationPlugin() - clear activeNormalization state.
disconnect() - Method in class JavaCGIBridge
disconnect() - implements abstract method for HttpURLconnection.
dispCL - Variable in class Draw2Dplot
associated GeneList if not null
displayCL - Variable in class Filter
"Spots in the display list"
displayPDF(String) - Method in class MJAutil
displayPDF() - popup Adobe Acrobat for PDF file.
displayPDF(String) - Method in class Rtest
displayPDF() - Display PDF file in adobe, for use in stand-alone.
displayPDF(String) - Method in class RtestBase
displayPDF() - Display PDF file in adobe, for use in stand-alone.
displayPDF(String) - Method in class Util
displayPDF() - Display PDF file in adobe, for use in stand-alone.
displayStr - Variable in class KeyEventHandler
displayed in ta
displayURL(String) - Method in class MJAutil
displayURL() - popup web browser on current URL.
displayURL(String) - Method in class Rtest
displayURL() - Display URL file in system Web browser, for use in stand-alone mode.
displayURL(String) - Method in class RtestBase
displayURL() - Display URL file in system Web browser, for use in stand-alone mode.
displayURL(String) - Method in class Util
displayURL() - Display URL file in system Web browser, for use in stand-alone mode.
dist - Variable in class HierClustNode
Dynamic node: local variables allocated once for speedup
distLR - Variable in class HierClustNode
Dynamic node: nDistV*(distance**2) between right & left nodes
distToMeanDP - Variable in class ClusterGenes.Cluster
[0:nGenes-1] distance to meanEP
dKS - Static variable in class MathMAE
RTN: K-S statistic
doAnyLoginsRequired() - Method in class MAExplorer
doAnyLoginsRequired() - do any Web server logins required for PARAM images that access a Web server database of primary MAExplorer data.
docCodeBase - Variable in class MAExplorer
codebase where the documentation Reference Manual is kept
doesPopupExist(String) - Method in class PopupRegistry
doesPopupExist() - check to see if popup exists for this key.
doesPopupExistByKey(String) - Method in class MJApopupRegistry
doesPopupExistByKey() - does instance of registered MAEPlugin exist by keyName
doesUniquePopupExist(String) - Method in class PopupRegistry
doesUniquePopupExist() - check to see if popup exists for this key
doesUniquePopupExistByKey(String) - Method in class MJApopupRegistry
doesUniquePopupExistByKey() - does unique instance of registered MAEPlugin exist by keyName
doFilterPluginPipelineInitOpr(String, int) - Method in class Filter
doFilterPluginPipelineInitOpr() - do pipeline Init operation on all active FilterPlugin's.
doFilterPluginPipelineOpr() - Method in class Filter
doFilterPluginPipelineOpr() - do pipeline operation on all active FilterPlugin's.
doGCflag - Variable in class MAExplorer
Flag: run the Garbage Collector.
doLogin(String, boolean) - Method in class UserState
doLogin() - get user login,password and do validation if requested
doMeanPlotsFlag - Variable in class ExprProfile
flag: generate mean plots (of the clusters) else individual plots
doMeanPlotsFlag - Variable in class ExprProfileCanvas
mean else individual plots
doMeanPlotsFlag - Variable in class ExprProfileOverlay
if plot means and SD
doMeanPlotsFlag - Variable in class ExprProfileScrollPane
if plot means and SD
done(String) - Method in class PopupGeneGuesser
done() - process the selected text, set current gene, and then popdown the guesser
done(String) - Method in class PopupHPmenuGuesser
done() - process the selected text and then popdown the guesser
done(String) - Method in class PopupProjDirGuesser
done() - process the selected text and then popdown the guesser
doneButton - Variable in class PopupCondChooser
done
doneButton - Variable in class PopupCondChooser.PopupTextField
done button
doneButton - Variable in class PopupCondChooser.ChoiceList
Done button
doneButton - Variable in class PopupOrderedCondChooser
done
doneButton - Variable in class PopupOrderedCondChooser.PopupTextField
done button
doneButton - Variable in class PopupOrderedCondChooser.ChoiceList
Done button
doneButton - Variable in class PopupScrollableSelector
[0:nList-1] values
doneButton - Variable in class StateScrollers
pop down (hide) the box - only in adjust all scrollers mode.
DONT_SORT - Static variable in class Report
flag: Do not sort
doRatioFlag - Variable in class MaHPquantTable
flag: if maxFIELD==1 && useRatioDataFlag
doRatioFlag - Variable in class MaHybridSample
flag: if maxFIELD==1 && useRatioDataFlag
doRepaint - Variable in class StateScrollers
 
doSpreadSheet() - Method in class SpreadSheet
doSpreadSheet() - create the spreadsheet panel, title, and control buttons
doSSspreadPanel() - Method in class SSspreadPanel
doSSspreadPanel() - actually build the spreadsheet panel
doubleListFlag - Variable in class PopupGeneGuesser
numeric/alpha or alpha only
doUnMountPlugin() - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
doUnMountPlugin() - Begin the process of unloading the plugins in question
downButton - Variable in class ChooserGUI
move SELECTED entry down if possible
downButton - Variable in class PopupCondChooserGUI
Move SELECTED entry down if possible
downButton - Variable in class PopupOrderedCondChooserGUI
Move SELECTED entry down if possible
downPoint - Variable in class MaHybridSample
[FUTURE] for dragging- could be used for defining rubber-band regions
dp - Variable in class OverlayMap
link to global instance
DRAW_BIN - Static variable in class MAExplorer
Plotting types - draw histogram bin
DRAW_BIN - Static variable in class MJAbase
Plotting types - draw histogram bin
DRAW_BOX - Static variable in class MAExplorer
Plotting types - draw box symbol in scatter plot
DRAW_BOX - Static variable in class MJAbase
Plotting types - draw box symbol in scatter plot
DRAW_CIRCLE - Static variable in class MAExplorer
Plotting types - draw circle symbol in scatter plot
DRAW_CIRCLE - Static variable in class MJAbase
Plotting types - draw circle symbol in scatter plot
DRAW_PLUS - Static variable in class MAExplorer
Plotting types - draw plus symbol in scatter plot
DRAW_PLUS - Static variable in class MJAbase
Plotting types - draw plus symbol in scatter plot
draw180lineFlag - Variable in class Draw2Dplot
flag: draw 180 degree line
Draw2Dplot - class Draw2Dplot.
This is a base class used for drawing 2D graphics plots.
draw2Dplot(Graphics) - Method in class Draw2Dplot
draw2Dplot() - draw a plot in the current graphics context.
Draw2Dplot(MAExplorer, int, ShowPlotPopup, ExprProfileOverlay, String, int, int, boolean) - Constructor for class Draw2Dplot
Draw2Dplot() - constructor
draw45lineFlag - Variable in class Draw2Dplot
flag: draw 45 degree line
drawAdditionalDataFlag - Variable in class ExprProfileCanvas
draw title & additional data if larger format.
drawCircle(Graphics, int, int, int, Color) - Method in class Draw2Dplot
drawCircle() - draw a circle as overlay graphic in specified color.
drawCircleAroundSpot(Point, Graphics, Color, int, int) - Method in class ScrollableImageCanvas
drawCircleAroundSpot() - draw a circle around spot if visible.
drawCircleAroundSpot(Point, Graphics, Color, int, int, String) - Method in class ScrollableImageCanvas
drawCircleAroundSpot() - draw circle & title around spot if visible.
DrawClusterGram - class DrawClusterGram.
This class creates and displays a ClusterGram canvas window.
DrawClusterGram(MAExplorer, ShowPlotPopup, Panel, HierClustNode, GeneList, String, int, boolean) - Constructor for class DrawClusterGram
DrawClusterGram() - Create popup grid of ClusterGram plots.
drawCountsOfGeneClusters(Graphics) - Method in class ScrollableImageCanvas
drawCountsOfGeneClusters() - draw colored circles as nGeneClusterCnt's.
drawDendrogram(Graphics, int, int) - Method in class ClusterGramCanvas
drawDendrogram() - draw dendrogram from row r1 to r2.
drawDendroGramFlag - Variable in class DrawClusterGram
set if draw dendrogram as well
drawEditedGeneList(Graphics) - Method in class ScrollableImageCanvas
drawEditedGeneList() - draw magenta squares of Filter.editedCL genes
drawFilledColoredCircle(Graphics, int, int, int, Color) - Method in class DrawPseudoImage
drawFilledColoredCircle() - draw filled circle of specified color.
drawFilledColoredCircle(Graphics, int, int, int, int, int, int) - Method in class Draw2Dplot
drawFilledColoredCircle() - draw filled circle of specified RGB color
drawFilledColoredCircle(Graphics, int, int, int, int, int, int) - Method in class DrawPseudoImage
drawFilledColoredCircle() - draw filled circle of specified color Clip colors to [0:255].
drawFilledGrayCircle(Graphics, int, int, int, int) - Method in class Draw2Dplot
drawFilledGrayCircle() - draw filled circle of specified grayvalue
drawFilledGrayCircle(Graphics, int, int, int, int) - Method in class DrawPseudoImage
drawFilledGrayCircle() - draw filled circle of specified grayvalue [0:255].
drawGeneClustersOfCurrentGene(Graphics) - Method in class ScrollableImageCanvas
drawGeneClustersOfCurrentGene() - draw genes in clusters as colored circles or squares
drawGeneList(Graphics, GeneList, int) - Method in class ScrollableImageCanvas
drawGeneList() - draw a gene list on either SaveAsGif or Pseudoarray Image.
drawGifFile(String) - Method in class ClusterGramCanvas
drawGifFile() - draw clustergram into Gif image file if in stand-alone mode.
drawGifFile(String) - Method in class DrawHistogram
drawGifFile() - draw plot into Gif image file if in stand-alone mode.
drawGifFile(String) - Method in class DrawRatioHistogram
drawGifFile() - draw plot into Gif image file if in stand-alone mode.
drawGifFile(String) - Method in class DrawScatterPlot
drawGifFile() - draw plot into Gif image file if in standalone mode.
drawGifFile(String) - Method in class ExprProfileCanvas
drawGifFile() - draw expression plot into Gif image file if in standalone mode.
drawGifFile(String) - Method in class ExprProfileOverlay
drawGifFile() - draw plot into Gif image file if in standalone mode.
drawGifFile(String) - Method in class ScrollableImageCanvas
drawGifFile() - draw pseudoimage into Gif image file if in standalone mode.
drawGridLabelsInImage(MaHybridSample, Graphics, boolean, boolean) - Method in class DrawPseudoImage
drawGridLabelsInImage() - draw ms.textQ[] in the image at (x,y)[] locations.
DrawHistogram - class DrawHistogram.
Class to draw an intensity histogram in popup frame.
drawHistogram(Graphics) - Method in class DrawHistogram
drawHistogram() - draw histogram of hist[].
DrawHistogram(MAExplorer, ShowPlotPopup, String, String, int) - Constructor for class DrawHistogram
DrawHistogram() - constructor to create an intensity histogram.
drawHistogramRatios(Graphics) - Method in class DrawRatioHistogram
drawHistogramRatios() - draw histogram of rg.ratioHist[].
drawImageTitle() - Method in class ArrayScroller
drawImageTitle() - draw title in image.
drawImageTitle() - Method in class ScrollableImageCanvas
drawImageTitle() - draw title in image.
drawIntoImageFlag - Variable in class ClusterGramCanvas
set if draw clustergram to GIF file
drawIntoImageFlag - Variable in class Draw2Dplot
flag: set if draw plot to GIF file
drawIntoImageFlag - Variable in class DrawHistogram
set if draw plot to GIF file
drawIntoImageFlag - Variable in class DrawRatioHistogram
set if draw plot to GIF file
drawIntoImageFlag - Variable in class ExprProfileCanvas
set if draw plot to GIF file
drawIntoImageFlag - Variable in class ScrollableImageCanvas
set if draw clustergram to GIF file
drawLabelsFlag - Variable in class ExprProfileCanvas
ARG: draw labels for larger version
drawNamedOverlayMaps(Graphics, float, float, double, double, int, int) - Method in class Draw2Dplot
drawNamedOverlayMaps() try to draw overlay maps if there are any and they are enabled
drawNprimaryNodesGenes(Graphics) - Method in class ScrollableImageCanvas
drawNprimaryNodesGenes() - draw magenta circles as nGeneClusterCnt's.
drawPlus(Graphics, int, int, Color) - Method in class Draw2Dplot
drawPlus() - draw plus sign as overlay graphic in specified color.
drawPlus(Graphics, int, int, Color) - Static method in class DrawHistogram
drawPlus() - draw plus sign at the specified color.
drawPlus(Graphics, int, int, Color) - Method in class DrawPseudoImage
drawPlus() - draw plus sign using specified color.
drawPlus(Graphics, int, int, Color) - Static method in class DrawRatioHistogram
drawPlus() - draw plus sign in the specified color.
drawPlustAtSpot(Point, Graphics, Color) - Method in class ScrollableImageCanvas
drawPlustAtSpot() - draw a 7x7 + around spot if visible.
DrawPseudoImage - class DrawPseudoImage.
Class to draw microarray data (ratio, intensity, p-value, etc) as a pseudoarray image.
drawPseudoImage(Graphics, int, int, int, MaHybridSample) - Method in class DrawPseudoImage
drawPseudoImage() - draw pseudoarray image of filled grayscale circles using the totC[] density values.
DrawPseudoImage(MAExplorer) - Constructor for class DrawPseudoImage
DrawPseudoImage() - constructor
DrawRatioHistogram - class DrawRatioHistogram.
This class draws a ratio histogram on an extended Canvas.
DrawRatioHistogram(MAExplorer, ShowPlotPopup, int) - Constructor for class DrawRatioHistogram
DrawRatioHistogram() - constructor to draw ratio histogram
drawRectangleBin(Graphics, int, int, int, int, Color) - Method in class Draw2Dplot
drawRectangleBin() - draw rectangle (histogram) bin as overlay graphic in specified color.
drawRectangleBin(Graphics, int, int, int, int, Color, int, boolean) - Method in class DrawHistogram
drawRectangleBin() - draw histogram bin at the specified color
drawRectangleBin(Graphics, int, int, int, int, Color, int, boolean) - Method in class DrawRatioHistogram
drawRectangleBin() - draw histogram bin
drawReportText(Graphics) - Method in class RtestBase
drawReportText() - repaint report.
drawRow(Graphics, int, float[]) - Method in class ClusterGramCanvas
drawRow() - draw row of boxes, left & right label, save the coords.
drawScaleMap(Graphics) - Method in class ClusterGramCanvas
drawScaleMap() - draw the X/Y color scale map.
drawScaleMap(Graphics, boolean, boolean, float, float) - Method in class DrawPseudoImage
drawScaleMap() - draw color scale map on the left of the canvas
drawScaleMapAndVerticalLabels(Graphics) - Method in class DrawClusterGram
drawScaleMapAndVerticalLabels() - draw scale map & vert lbls i in the title panel status area
DrawScatterPlot - class DrawScatterPlot.
Class to draw scatter plot in an extended Draw2Dplot canvas.
drawScatterPlot() - Method in class DrawScatterPlot
drawScatterPlot() - draw scatter plot (repeatedly) of Filter data
DrawScatterPlot(MAExplorer, ShowPlotPopup, int) - Constructor for class DrawScatterPlot
DrawScatterPlot() - constructor to create scatter plot
drawSelectedHP(Graphics, int, int) - Method in class ClusterGramCanvas
drawSelectedHP() - draw selected box as white circle if the selected row is within [r1:r2].
drawSquare(Graphics, int, int, int, Color) - Method in class Draw2Dplot
drawSquare() - draw a square as overlay graphic in specified color.
drawSquareAroundSpot(Point, Graphics, Color, int) - Method in class ScrollableImageCanvas
drawSquareAroundSpot() - draw a square around spot if visible.
drawVerticalLabels(Graphics) - Method in class ClusterGramCanvas
drawVerticalLabels() - Draw the vertical labels of samples
dryRotExcept - Variable in class MAExplorer
Global instance of DryRotException class
DryRotException - exception DryRotException.
Class to implement DRYROT messages for MAExplorer.
DryRotException() - Constructor for class DryRotException
DryRotException() - constructor to create new DryRotException without detail message.
DryRotException(String) - Constructor for class DryRotException
Constructs an DryRotException with the specified detail message.
dryrotLogStr - Variable in class MAExplorer
List of dryrot messages if any occur.
dualXYpseudoPlotFlag - Variable in class MAExplorer
Flag: plot mean HP-X in F1, HP-Y in F2 pseudoimg
DuplicatePluginLoadException - exception MAEPlugin.DuplicatePluginLoadException.
This exception is used to allow self registering of plugins for a max number of plugins.
DuplicatePluginLoadException() - Constructor for class MAEPlugin.DuplicatePluginLoadException
 
dwCG - Variable in class ShowPlotPopup
instance of DrawClusterGram if drawing a scatter plot
dwH - Variable in class ShowPlotPopup
instance of DrawHistogram if drawing a scatter plot
dwPI - Variable in class MAExplorer
Global instance of draw pseudo image
dwRH - Variable in class ShowPlotPopup
instance of DrawRatioHistogram if drawing a scatter plot
dwSP - Variable in class ShowPlotPopup
instance of DrawScatterPlot if drawing a scatter plot
dynFileSeparator - Variable in class MAExplorer
dynamic paths separator, "/" or "|", depends on OS and if using URL from Stand-Alone

E

EDIT_ADD - Static variable in class MAExplorer
Edited Gene List mouse click action mode: ADD gene on click
EDIT_ADD - Static variable in class MJAbase
Edited Gene List mouse click action mode: ADD gene on click
EDIT_NOP - Static variable in class MAExplorer
Edited Gene List mouse click action mode: NO-OP
EDIT_NOP - Static variable in class MJAbase
Edited Gene List mouse click action mode: NO-OP
EDIT_RMV - Static variable in class MAExplorer
Edited Gene List mouse click action mode: REMOVE gene on click
EDIT_RMV - Static variable in class MJAbase
Edited Gene List mouse click action mode: REMOVE gene on click
EDIT_WINDOW_HEIGHT - Static variable in class PopupEditRscript
 
EDIT_WINDOW_WIDTH - Static variable in class PopupEditRscript
MIN size of scrollable Canvas
editButtonsPanel - Variable in class PopupEditRscript
Control Panel to hold buttons in popup window.
editedCL - Variable in class GeneClass
"edited gene list"
EditedGeneList - class EditedGeneList.
Class to edit the Edited Gene List.
EditedGeneList(MAExplorer) - Constructor for class EditedGeneList
EditedGeneList() - constructor
editedRscriptFile - Variable in class PopupEditRscript
edited Load .R script File
editingRLOflag - Variable in class PopupEditRscript
Flag set if editing a RLO
editMenu - Variable in class MenuBarFrame
"Edit" menu
editMode - Variable in class MAExplorer
EGL mode for 'edited gene list': EDIT_xxxx
editRLO(int) - Method in class PopupEditRscript
editRLO() - edit an existing RLO database entry.
editRLOButton - Variable in class RtestBase
"Edit RLO" to edit existing RLO
editRscriptText - Variable in class PopupEditRscript
.R text or help message
editRscriptTextArea - Variable in class PopupEditRscript
Text area to draw editRscriptText in popup window.
egl - Variable in class MAExplorer
Global instance of edit editedCL gene (clone) list
Elist - Variable in class Config
HP-E list
em - Variable in class MAExplorer
Global instance of handle MenuItem and MenuItemCheckbox events
em - Static variable in class MJAbase
link to global Config instance
em - Static variable in class MaeJavaAPI
link to global Config instance
emptyWellCL - Variable in class GeneClass
special list of "EmptyWell" genes
emptyWellName - Variable in class Config
PARAM "emptyWellName" (opt) what you call "EmptyWell"
enableFIOcachingFlag - Variable in class MAExplorer
Flag: stand-alone PARAM "enableFIOcaching"
enableFlag - Variable in class OverlayMap
Enable/display the overlay to be drawn when redisplay the scatterplot
enableMenus(String) - Method in class MenuBarFrame
enableMenus() - enable/disable all menus, checkboxes, typein fields etc.
enableOverlayMapDisplay(String, boolean) - Static method in class MJAplot
enableOverlayMapDisplay() - enable/disable display of named scatterplot named overlay map.
enableOverlayMapDisplay(String, boolean) - Static method in class OverlayMap
enableOverlayMapDisplay() - enable/disable display of named scatterplot named overlay map.
enumCnt - Static variable in class HierClustNode
# enumerated so far in an enumeration
enumerateLeafNodes() - Static method in class HierClustNode
enumerateLeafNodes() - enumerate Leaf nodes (Right then left) of tree.
enumerateNodes() - Static method in class HierClustNode
enumerateNodes() - enumerate the nodes (Right then Left) of tree.
enumOrder - Variable in class HierClustNode
Dynamic node: set to enumeration order in range [0:nObj-1].
EOF - Static variable in class WriteGifEncoder
 
EOFCode - Variable in class WriteGifEncoder
 
ep - Variable in class ExprProfileCanvas
expression profile for mid
ep - Static variable in class MJAexprProfile
Expression profile used for accessing data
EP_BUTTON_HEIGHT - Static variable in class ExprProfilePopup
hight of expression profile ploit
epc - Variable in class ExprProfilePanel
expression profile canvas we put into panel
EPILOGUE_END - Static variable in class RtestBase
fixed epilogue end string
EPILOGUE_END - Static variable in class PopupEditRscript
fixed epilogue end string
EPILOGUE_START - Static variable in class RtestBase
fixed epilogue start string
EPILOGUE_START - Static variable in class PopupEditRscript
fixed epilogue start string
epov - Variable in class Draw2Dplot
if ExprProfileOverlay is the parent, else null
epov - Variable in class ShowExprProfilesPopup
Overlay EP plots
epOverlayList - Variable in class ExprProfileOverlay
list of overlay expr.
epOverlayList - Variable in class ExprProfileScrollPane
list of overlay expr.
epOvrLayCL - Variable in class ExprProfileOverlay
special [nGenes*nHP_E] CL
epOvrLayCL - Variable in class ExprProfileScrollPane
special [nGenes*nHP_E] CL
epPane - Variable in class ShowExprProfilesPopup
Scrollable panel
epPanel - Variable in class ExprProfileOverlay
holds g2D overlay plot
epPanel - Variable in class ExprProfileScrollPane
holds grid of ExprProfilePanel's
eppl - Variable in class ExprProfilePopup
panel we put into this popup window
epplList - Variable in class ExprProfileOverlay
Expr Profs [nGridElements]
epplList - Variable in class ExprProfileScrollPane
Expr Profs [nGridElements]
epsp - Variable in class ShowExprProfilesPopup
scrollable panel of ExprProfilePanel's
epspStatusLabel - Variable in class ShowExprProfilesPopup
 
ESTsCL - Variable in class GeneClass
special list of unknown ESTs
et_defaultInt() - Method in class MJAutil
get_defaultInt() - default int value for conversions
euclidDist(float[], float[], int, boolean) - Static method in class MathMAE
euclidDist() - compute Euclidean distance or (sum dist**2) The data is data1[0:n-1] and data2[0:n-1].
euclideanDistance(float[], float[], int, boolean) - Method in class MJAmath
euclideanDistance() - compute Euclidean distance of 2 vectors as either the Euclidean distance or (sum dist**2).
evalButton - Variable in class RtestBase
"Evaluate" window button
evalCommands(String, String) - Method in class MJAeval
evalCommands() - invoke and process a MAExplorer command.
eventHandlerCL - Variable in class Draw2Dplot
set to gene list being used
EventMenu - class EventMenu.
Event handler class to process menubar Menu selection and menu checkbox events.
EventMenu(MAExplorer) - Constructor for class EventMenu
EventMenu() - constructor for event menu instance
EXCELMAXLABEL - Variable in class SSstatusBar
 
execRscript() - Method in class RevalBase
execRscript() - exec R with cmd to process the .R script.
ExprProfile - class ExprProfile.
The class creates an nHP_E sample expression profile object for a gene.
ExprProfile(MAExplorer, int, boolean) - Constructor for class ExprProfile
ExprProfile() - Constructor to create expresion profile object
ExprProfileCanvas - class ExprProfileCanvas.
The ExprProfileCanvas is used to draw the expression profile.
ExprProfileCanvas(MAExplorer, int, String, Font, int, int, boolean, boolean) - Constructor for class ExprProfileCanvas
ExprProfileCanvas() - Constructor to display an expression profile in a canvas.
exprProfileCL - Variable in class ExprProfileOverlay
GeneList being used
exprProfileCL - Variable in class ExprProfileScrollPane
GeneList being used
ExprProfileOverlay - class ExprProfileOverlay.
This class displays a scrollable expression profile overlay.
ExprProfileOverlay(MAExplorer, ShowExprProfilesPopup, GeneList, String, int, boolean) - Constructor for class ExprProfileOverlay
ExprProfileOverlay() - Create popup overlay plot of ExprProfiles.
ExprProfilePanel - class ExprProfilePanel.
This class creates and displays a window containing an ExprProfileCanvas.
ExprProfilePanel(MAExplorer, int, String, Font, int, int, boolean, boolean) - Constructor for class ExprProfilePanel
ExprProfilePanel() - Constructor to display expression profile in canvas.
exprProfilePopup - Variable in class MenuBarFrame
command pops it up
ExprProfilePopup - class ExprProfilePopup.
This class creates and displays a popup window containing an ExprProfilePanel.
ExprProfilePopup(MAExplorer, int, String, Font, int, int, boolean) - Constructor for class ExprProfilePopup
ExprProfilePopup() - Constructor to popup expression profile window.
ExprProfileScrollPane - class ExprProfileScrollPane.
This creates and displays a scrollable pane list of individual expression profile graphic plots.
ExprProfileScrollPane(MAExplorer, ShowExprProfilesPopup, GeneList, String, int, boolean) - Constructor for class ExprProfileScrollPane
ExprProfileScrollPane() - Create a popup grid of ExprProfile plots.
extractUserRscript(String) - Method in class RtestBase
extractUserRscript() - extract user R script from center of complete.
extractUserRscript(String) - Method in class PopupEditRscript
extractUserRscript() - extract user R script from center of complete.
extractZipFiles(String, String) - Method in class FileIO
extractZipFiles() - extract files from zip file.
extraHeight - Variable in class ScrollableImageCanvas
status area MaHPquantTable.Y_SPOTQ_OFFSET
extraWidth - Variable in class ScrollableImageCanvas
status area MaHPquantTable.X_SPOTQ_OFFSET

F

f - Variable in class GridCoords
field #
f - Variable in class PopupCondChooser.CondDialogBox
Frame where dialog box is added
f - Variable in class PopupCondChooser.ChoiceList
pass down frame for dialog
f - Variable in class PopupHPChooser
frame to install choosers
f - Variable in class PopupOrderedCondChooser.CondDialogBox
Frame where dialog box is added
f - Variable in class PopupOrderedCondChooser.ChoiceList
pass down frame for dialog
f - Variable in class Statistics
CALC: calculated f statistic set by calcTandPvalues()
F_TestOCLFilterFlag - Variable in class MAExplorer
filter genes passing current OCL (Ordered Condition List) F-test
f1f2CV_E - Variable in class HPxyData
Coefficient of variation each HP-E f1 f2 sample in the set data
f1f2CV_X - Variable in class HPxyData
Coefficient of variation each HP-X f1 f2 sample in the set data
f1f2CV_Y - Variable in class HPxyData
Coefficient of variation each HP-Y f1 f2 sample in the set data
f1SampleName - Variable in class RgenDemo
F1 sample name if used
f2SampleName - Variable in class RgenDemo
F2 sample name if used
FATAL_MSG - Static variable in class PopupCondChooser
Error codes for reportMsg()
FATAL_MSG - Static variable in class PopupOrderedCondChooser
Error codes for reportMsg()
fc - Static variable in class ClusterGenes
link to global Filter instance
fc - Variable in class CompositeDatabase
link to global Filter instance
fc - Variable in class Draw2Dplot
link to global Filter instance
fc - Variable in class EditedGeneList
link to global Filter instance
fc - Static variable in class EventMenu
link to global Filter instance
fc - Variable in class MAExplorer
Global instance of data Filter gene operations
fc - Static variable in class MJAbase
link to global Filter instance
fc - Variable in class MaHybridSample
link to global Filter instance
fc - Static variable in class MaeJavaAPI
link to global Filter instance
fc - Variable in class Report
link to global Filter instance
fc - Variable in class ScrollableImageCanvas
link to global instance of Filter
featuresStr - Variable in class ClusterGramCanvas
current gene feature data
featuresStr - Static variable in class SpotFeatures
Strings generated by getSpotFeatures()
fgrc2gid - Variable in class Maps
map: [f][g][r][c] to gid (GridCoords index GID).
fieldIdx - Variable in class GipoTable
index for "field"
fieldSeparator - Variable in class JavaCGIBridge
The field separator.
fileBasePath - Static variable in class MAExplorer
either Applet or file I/O or standalone
FileClassLoader - class MAEPlugin.FileClassLoader.
Class to dynamic classes from local disks.
FileClassLoader(File) - Constructor for class MAEPlugin.FileClassLoader
FileClassLoader() - Constructor to load .classfile.
FileClassLoader(String) - Constructor for class MAEPlugin.FileClassLoader
FileClassLoader() - Constructor to load path.
fileDialog - Variable in class MAEPlugin.popup.PluginLoader
Reference to the Dialog that will load files
FileIO - class FileIO.
This file I/O class includes methods to do file I/O to a local disk or URL.
FileIO(MAExplorer) - Constructor for class FileIO
FileIO() - constructor to create fio instance and to close the log file.
fileMenu - Variable in class MenuBarFrame
"File" menu
fileName - Variable in class SimpleTable
Optional file name associated with table
fileOKflag - Variable in class Table
File exists and was able to be read
fileSep - Variable in class RtestBase
 
fileSeparator - Variable in class MAExplorer
paths, "/" or "|", depends on OS
fileSeparator - Static variable in class RevalBase
 
Filter - class Filter.
The class computes the intersection of selected data filter gene list.
FILTER - Static variable in class PopupRegistry
Property bit type: Notify bit if Filter changed
Filter(MAExplorer) - Constructor for class Filter
Filter() - constructor to initialize data filter but not initial gene lists
Filter(MAExplorer, int) - Constructor for class Filter
Filter() - constructor to initialize data filter and initial gene lists.
filterByBin() - Method in class DrawHistogram
filterByBin() - filter genes by current activeBin histogram bin(s).
filterByBin() - Method in class DrawRatioHistogram
filterByBin() - filter genes by current activeBin histogram bin.
filterMenu - Variable in class MenuBarFrame
"Filter" menu
FilterPlugin - class MAEPlugin.analysis.FilterPlugin.
This class is the filter MAEPlugin base class and is be used to implement a filter base class:
FilterPlugin() - Constructor for class MAEPlugin.analysis.FilterPlugin
FilterPlugin() - Constructor for new FilterPlugin called when load the plugin.
FilterPlugin(String) - Constructor for class MAEPlugin.analysis.FilterPlugin
FilterPlugin() - Constructor for new FilterPlugin
findAllGeneClusterCounts(MAExplorer, float) - Static method in class ClusterGenes
findAllGeneClusterCounts() - # genes such that geneDist LEQ geneDistThr.
findClosestNode(HierClustNode, int) - Method in class HierClustNode
findClosestNode() - find closest unvisited node hcJ to node hcI such that the distance between hcI and HcJ is a minmum.
findClustersOfGene(MAExplorer, Gene, float, boolean) - Static method in class ClusterGenes
findClustersOfGene() - find all HP-E gene clusters LT clusterDist.
findCountAndhighMID(GeneList) - Method in class GeneBitSet
findCountAndhighMID() - find count and highest MID in gene bit set BitData[].
findCountAndhighMIDinGeneBitset(String) - Method in class MJAgeneList
findCountAndhighMIDinGeneBitset() - find count and highest MID in GeneBitSet
findFileClass(String) - Method in class MAEPlugin.FileClassLoader
findFileClass() - find file of class by name.
findGeneWithLeastSumDistances(float[], int) - Static method in class GeneGeneDist
findGeneWithLeastSumDistances() - find gene with minimum cluster distance toall other genes.
findGeneWithLeastSumDistances(float[], int) - Method in class MJAcluster
findGeneWithLeastSumDistances() - find gene with minimum cluster distance to all other genes.
findIndexForKey(String[], String) - Static method in class Util
findIndexForKey() - lookup index of key in data[].
findMatch(char[], int, char[], int, char[], int, char[], int) - Method in class KeyEventHandler
findMatch() - find match of 3 strings in order (2 wild cards) of the form "*abc*".
findMenuStubByName(String) - Method in class MenuBarFrame
findMenuStubByName() - find menu stub associated with name in Menu Stub List.
findStrLoc(String[], String) - Method in class KeyEventHandler
findStrLoc() - Find location within an array of Strings of searchStr.
findSubtreeOfNodeNbrs(int) - Method in class HierClustNode
findSubtreeOfNodeNbrs() - return an int[] list of node ID numbers for nodes in the subtree defined by topNodeNbrOfSubtree.
finishPipeline(int) - Method in class GenNormalizationPlugin
finishPipeline() - overide finish filter at end of normalization of all genes (if required).
finishPipeline(int) - Method in interface MAEPlugin.Normalization
finishPipeline() - finish filter at end of normalization of all genes (if required).
finishPipeline(int) - Method in class MAEPlugin.analysis.NormalizationPlugin
finishPipeline() - finish filter at end of normalization of all genes (if required).
finishPipeline(int) - Method in class MAEPlugin.analysis.FilterPlugin
finishPipeline() - finish filter at end of test of all genes (if required).
fio - Static variable in class ClusterGenes
link to global FileIO instance
fio - Variable in class Filter
link to globalFileIO instance
fio - Static variable in class GeneGeneDist
link to global FileIO instance
fio - Static variable in class HierClustNode
link to global FileIO instance
fio - Variable in class MAExplorer
Global instance of file and URL I/O
fio - Variable in class MaHPquantTable
link to global FileIO vinstance
fio - Variable in class Table
link to global instance of FileIO
fio - Variable in class UserState
link to global instance of FileIO
fio - Static variable in class Util
link to global FileIO instance
flickerXYflag - Variable in class MAExplorer
Flicker HP-X and HP-Y in run() loop
flipRowsColsFlag - Variable in class MaHybridSample
flag: flip rows and columns
fluoresLbl1 - Variable in class Config
PARAM "fluorescentLbl1" (Cy3) or F1
fluoresLbl2 - Variable in class Config
PARAM "fluorescentLbl2" (Cy5) or F2
flush_char(FileOutputStream) - Method in class WriteGifEncoder
flush_char() - flush packet to disk, and reset the accumulator
flushPluginHashState() - Method in class MJAstate
flushPluginHashState() - flush the MAEPlugin hash state storage to the disk.
fm - Variable in class ClusterGramCanvas
font metrics for font
fName - Static variable in class Maps
list of alphabetic names of Names of fields
fntSize - Variable in class ShowStringPopup
font size
focusGained(FocusEvent) - Method in class Guesser
 
focusLost(FocusEvent) - Method in class Guesser
 
font - Variable in class ClusterGramCanvas
drawing font
font - Variable in class DrawPseudoImage
regular font
font - Static variable in class ExprProfileCanvas
 
font - Variable in class Guesser
Font for guesser list
font_textHP - Variable in class CompositeDatabase
text HP labels shared fonts
fontFamily - Variable in class Config
PARAM "fontFamily" 'SansSerif'
fontFamily - Variable in class PopupCondChooser
Font family from MAExplorer - using mjaProperty.getReportFontFamily()
fontFamily - Variable in class PopupOrderedCondChooser
Font family from MAExplorer - using mjaProperty.getReportFontFamily()
fontHdr - Variable in class DrawPseudoImage
Header font
fontHeight - Variable in class ClusterGramCanvas
 
fontHeight - Variable in class ExprProfileCanvas
height font size of current font
fontLeading - Variable in class ClusterGramCanvas
 
fontLeading - Variable in class ExprProfileCanvas
leading font size of current font
fontReg - Variable in class Draw2Dplot
regular font
fontSize - Variable in class ShowSpreadsheetPopup
integer value of fontSizeStr
fontSize - Variable in class SpreadSheet
font size number for cell entries
fontSize - Variable in class SSspreadPanel
ARG: only if no fonts specified
fontSizeStr - Variable in class ShowSpreadsheetPopup
ARG: font size
fontWidth - Variable in class ClusterGramCanvas
 
formatClassName(String) - Method in class MAEPlugin.JarClassLoader
formatClassName() - generate a name with ".class" extension
foundObjFlag - Variable in class ClusterGramCanvas
found object row when clicked on it
foundStr - Variable in class ChooserGUI.MouseEventHandler
set text field if match is found
foundStr - Variable in class PopupCondChooserGUI.MouseEventHandler
set text field if match is found
foundStr - Variable in class PopupOrderedCondChooserGUI.MouseEventHandler
set text field if match is found
frame - Variable in class Guesser
frame where guesser is built
frame - Variable in class PopupBinOprDialogQuery
popup frame instance
frame - Variable in class PopupDialogQuery
popup frame instance
frame - Variable in class PopupLoginDialogQuery
 
frame - Variable in class PopupScrollableSelector
 
frame - Variable in class ShowSpreadsheetPopup
frame which holds popup spreadsheet
frameBkGrdColor - Variable in class LogTextFrame
Background color of entire frame
frameHeight - Variable in class PopupHPChooser
default frame size - must be here!
frameHeight - Variable in class ShowExprProfilesPopup
this frame size computed
frameHeight - Variable in class ShowPlotPopup
working frame size neight
frameWidth - Variable in class PopupHPChooser
default frame size - must be here!
frameWidth - Variable in class ShowExprProfilesPopup
this frame size computed
frameWidth - Variable in class ShowPlotPopup
working frame size width
free_ent - Variable in class WriteGifEncoder
 
freeTable() - Method in class SimpleTable
freeTable() - free Table tData[][] and tFields so can garbage collect it Also zero tRows, tCols
fromPoint - Variable in class ScrollableImageCanvas
mousePressed record
fStat - Variable in class Statistics
CALC: f-statistic 2 conditions
fStatNconds - Variable in class Statistics
CALC: f-statistic nConditions test set by calcNCondFtestStat()
fullLogFilePath - Variable in class LogTextFrame
optional full path of log file if it exists.
fullRoutputFilePath - Variable in class RevalBase
full path of R output file
fullRscriptInputPath - Static variable in class RevalBase
full path of .R input script file
fullRunRfilePath - Static variable in class RevalBase
full path of batch R startup script file
fullStageText - Variable in class MaHybridSample
full Stage text name of hybridized sample used in menus, etc
fullWizardList - Variable in class PopupEditRscript
List of wizards for full Wizard of new RLOs

G

g - Variable in class GridCoords
grid #
g - Variable in class WriteGifEncoder
 
g_init_bits - Variable in class WriteGifEncoder
 
gammln_cof - Static variable in class MathMAE
 
gangSpotFlag - Variable in class MAExplorer
Flag: report f1 or f1&f2 (ganged)
gbid2LocusLinkURL - Variable in class Config
base addr PARAM "gbid2LocusLinkURL"
gcMemberCL - Variable in class Filter
"Filter by GeneClass membership"
gct - Static variable in class ClusterGenes
link to global GeneClass instance
gct - Variable in class EditedGeneList
link to global GeneClass instance
gct - Static variable in class EventMenu
link to global GeneClass instance
gct - Variable in class Filter
link to global GeneClass instance
gct - Variable in class MAExplorer
Global instance of Gene Class table
gct - Static variable in class MJAbase
link to global GeneClass instance
gct - Variable in class MaHybridSample
link to global GeneClass instance
gct - Static variable in class MaeJavaAPI
link to global GeneClass instance
gct - Variable in class ScrollableImageCanvas
link to global instance of GeneClass
GenBankAcc - Variable in class Gene
NCBI GenBankAcc id if it exists
GenBankAcc - Variable in class SpotFeatures
lookup GenBank Acc
GenBankAcc3 - Variable in class Gene
NCBI GenBankAcc 3' id if it exists
GenBankAcc3 - Variable in class SpotFeatures
lookup GenBank Acc 3'
GenBankAcc3Idx - Variable in class GipoTable
index for "GenBankAcc3'" or "GeneBankAcc3'"
GenBankAcc5 - Variable in class Gene
NCBI GenBankAcc 5' id if it exists
GenBankAcc5 - Variable in class SpotFeatures
lookup GenBank Acc 5'
GenBankAcc5Idx - Variable in class GipoTable
index for "GenBankAcc5'" or "GeneBankAcc5'"
GenBankAccIdx - Variable in class GipoTable
index for "GenBankAcc" or "GeneBankAcc"
genBankAccURL - Variable in class Config
base addr PARAM "genBankAccURL"
genBankCloneURL - Variable in class Config
base addr PARAM "genBankCloneURL"
genBankCloneURLepilogue - Variable in class Config
base addr PARAM "genBankCloneURLepilogue"
genBankViewerFlag - Variable in class MAExplorer
GenBank popup browser Mode
genClientEpilogue() - Method in class RgenDemo
genClientEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.
genClientReaderPrologue() - Method in class RgenDemo
genClientReaderPrologue() - generate client dependent Reader prologue R script to read data commands.
genCurAnnotationDataFile(RLO, SimpleTable) - Method in class Reval
genCurAnnotationDataFile() - generate exported input data file for current gene annotation data.
genCurHPdataFile(RLO, SimpleTable) - Method in class Reval
genCurHPdataFile() - generate exported input data file for current HP.
genCurHPsetDataFile(RLO, SimpleTable, int) - Method in class Reval
genCurHPsetDataFile() - generate exported input data file for current HP set data (including: HP-X set, HP-Y set, HP-E list, current condition list).
genCurHPXYdataFile(RLO, SimpleTable, boolean) - Method in class Reval
genCurHPXYdataFile() - generate exported input data file for current HP-X and HP-Y or mean (HP-X set and mean HP-Y set).
genCurHPXYsetsDataFile(RLO, SimpleTable) - Method in class Reval
genCurHPXYsetsDataFile() - generate exported input data file for current HP-X and HP-Y sets data.
genCurOCLdataFile(RLO, SimpleTable) - Method in class Reval
genCurOCLdataFile() - generate exported input data file for current Ordered Condition List data.
genCurStateThresholdsFile(RLO, SimpleTable) - Method in class Reval
genCurStateThresholdsFile() - generate exported input data file for current state thresholds data.
genCurStateValuesFile(RLO, SimpleTable) - Method in class Reval
genCurStateValuesFile() - generate exported input data file for current state flags and names values data.
genDataANOVA() - Method in class RgenDemo
genDataANOVA() - generate data ANOVA commands [TODO] debug...
genDataBoxplot() - Method in class RgenDemo
genDataBoxplot() - generate data boxplot commands
genDataCorrelation() - Method in class RgenDemo
genDataCorrelation() - generate data Correlation tables commands
genDataDensity() - Method in class RgenDemo
genDataDensity() - generate data density plots commands
genDataHistogram() - Method in class RgenDemo
genDataHistogram() - generate data histogram plot commands
genDataLoess() - Method in class RgenDemo
genDataLoess() - generate data loess commands
genDataScatterplots() - Method in class RgenDemo
genDataScatterplots() - generate data scatterplots commands
genDataSummary() - Method in class RgenDemo
genDataSummary() - generate data summary commands
genDataTtest() - Method in class RgenDemo
genDataTtest() - generate data t-test commands
genDemoPart2ClientPrologue() - Method in class RgenDemo
genDemoPart2ClientPrologue() - generate the demo part 2 client- dependent prologue to set global R vars from data frame just read in.
gene - Variable in class MAExplorer
Global instance of Gene
gene - Variable in class MJAgene
 
Gene - class Gene.
 
GENE_ATCC_ID - Static variable in class MJAbase
Gene property: Clone is an ATCC numbered clone
GENE_BAD_DATA - Static variable in class MJAbase
property: has bad data
GENE_BAD_LOCAL_SPOT_BKGRD - Static variable in class MJAbase
Gene property: bad local spot background
GENE_BAD_MID - Static variable in class MJAbase
Gene property: the gene is bad, good gene name
GENE_BAD_SPOT - Static variable in class MJAbase
Gene property: non-analyzable gene (eg.
GENE_BAD_SPOT_GEOMETRY - Static variable in class MJAbase
Gene property: bad spot geometry
Gene_Class - Variable in class Gene
opt.
Gene_ClassIdx - Variable in class GipoTable
index for "Gene Class"
GENE_DUP_SPOT - Static variable in class MJAbase
Gene property: is duplicate of another gene on array
GENE_GOOD_MID - Static variable in class MJAbase
Gene property: the gene is good, good gene name.
GENE_IMAGE_ID - Static variable in class MJAbase
Gene property: Clone is an I.M.A.G.E.
GENE_IS_CUR_GENE - Static variable in class MJAbase
Gene property: is Current Gene (not normally used)
GENE_IS_EGL_GENE - Static variable in class MJAbase
Gene property: is an E.G.
GENE_IS_FILTERED - Static variable in class MJAbase
Gene property: is a gene that did pass data Filter
GENE_IS_KMEANS - Static variable in class MJAbase
Gene property: Is a K-means node gene
GENE_IS_NOT_FILTERED - Static variable in class MJAbase
Gene property: is a gene that did not pass data Filter
GENE_LOW_SPOT_REF_SIGNAL - Static variable in class MJAbase
Gene property: low spot reference signal
GENE_MARGINAL_SPOT - Static variable in class MJAbase
Gene property: Marginal spot
Gene_Name - Variable in class Gene
opt.
GENE_USE_GBID_FOR_CLONEID - Static variable in class MJAbase
Gene property: use GenBank ID for Clone ID
Gene(int, int) - Constructor for class Gene
Gene() - constructor with gid, mid and no quantified data.
Gene(MAExplorer) - Constructor for class Gene
Gene() - constructor to set up global mae instance - MUST BE CALLED FIRST!!! Note: we only need the mae instance to setup the map instance.
geneAnnotationFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("Annotation")
GeneBitSet - class GeneBitSet.
The class manipulates lists of 64-bit bit sets for performing Boolean set operations.
GeneBitSet(MAExplorer, int, GeneList) - Constructor for class GeneBitSet
GeneBitSet() - constructor to create a GeneBitSet without a name.
GeneBitSet(MAExplorer, int, String, GeneList) - Constructor for class GeneBitSet
GeneBitSet() - constructor to create a named GeneBitSet.
geneCardURL - Variable in class Config
base addr PARAM "geneCardURL"
geneClass - Variable in class SpotFeatures
lookup "Gene_Class"
GeneClass - class GeneClass.
The GeneClass sets up GeneLists for operating on classes of genes.
GeneClass(MAExplorer) - Constructor for class GeneClass
GeneClass() - constructor to create gene class database
geneClassCLS - Variable in class GeneClass
Gene index lists for each gene class.
geneClassMbrFilterFlag - Variable in class MAExplorer
filter genes by GeneClass mbrshp
geneClassMenu - Variable in class MenuBarFrame
"GeneClass" menu
geneClassName - Static variable in class GeneClass
List of GeneClass names [0:nbrGC-1]
geneClustersPopup - Static variable in class ClusterGenes
for updateable String Cluster Report if used
geneDBnamesButton - Variable in class Guesser
toggle: "Master ID", "GeneName", "GenBank", "dbEst", "UniGene", "LocusID"
geneDist - Variable in class Gene
Opt.
geneEPvector - Variable in class ClusterGenes
normalized quantitation vector for all genes of size [0:nClist-1][0:nEPmsList-1] and also [0:nObj-1][0:nDataVect-1]
geneEPvector - Variable in class GeneGeneDist
normalized quantitation vector for all genes [0:nClist-1][0:nEP-1] also [0:nObj-1][0:nEP-1]
GeneGeneDist - class GeneGeneDist.
 
geneGeneDist(float[], float[], int) - Method in class GeneGeneDist
geneGeneDist() - compute the gene-gene distance between two gene vectors.
GeneGeneDist(MAExplorer) - Constructor for class GeneGeneDist
GeneGeneDist() - constructor
geneIDname - Variable in class Guesser
button labels
geneInWorkingGeneList - Variable in class Filter
table lookup for gene membership
GeneList - class GeneList.
The GeneList class manipulate lists of genes (clones, oligos, etc).
GeneList(MAExplorer, int) - Constructor for class GeneList
GeneList() - constructor to specify list sizes with both mList[] and bitSet.
GeneList(MAExplorer, int, String) - Constructor for class GeneList
GeneList() - constructor to make new Gene named list with both mList[] and bitSet.
GeneList(MAExplorer, int, String, boolean) - Constructor for class GeneList
GeneList() - constructor to make new Gene named list with bitSet but optional mList[].
geneName - Variable in class SpotFeatures
lookup "Gene_Name"
GeneNameIdx - Variable in class GipoTable
index for "GeneName"
geneNameList - Static variable in class PopupGeneGuesser
unsorted list of geneName, is G.C.'ed
geneNameListSize - Static variable in class PopupGeneGuesser
unsorted list of geneName size
geneOperation(int) - Method in class MAEPlugin.analysis.FilterPlugin
geneOperation() - implemented by plugin writer.
genEpilogue() - Method in class RtestBase
genEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.
genEpilogue() - Method in class PopupEditRscript
genEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.
generateTemplateButton - Variable in class PopupEditRscript
Generate R template code button
Generic_ID - Variable in class Gene
Generic Identifier - "if all else fails" the use may use some arbitrary unique ID
genericFlag - Variable in class Guesser
if true, don't put Clone opt.
geneSets - Static variable in class GeneList
list of all gene lists
genGridsFromNbrGenes - Static variable in class Config
Flag: generate grid coords from nbrGENES
GenNormalizationPlugin - class GenNormalizationPlugin.
This class implements a wrapper for a general purpose class GenericNormalizationPlugin MAExplorer plugin.
GenNormalizationPlugin(MaeJavaAPI, boolean) - Constructor for class GenNormalizationPlugin
GenNormalizationPlugin() - constructor ONLY for use with debugging using the mae.DBUG_GENERIC_NORM_PLUGIN flag to add (Analysis | Normalization | Test Generic Norm Plugin [DBUG]) to the normalization menu.
genomicDataStr - Variable in class ClusterGramCanvas
current gene genomic data
genomicDataStr - Static variable in class SpotFeatures
Strings generated by getSpotFeatures()
GenomicID - Variable in class Gene
(Optional) External Genomic IDs values if specified via the MaeConfig.txt or .mae startup files.
genomicViewerFlag - Variable in class MAExplorer
holds sGenomicMenu[cfg.nGenomicMenus] menu flags
genPrologue() - Method in class RtestBase
genPrologue() - generate prologue R script to read data commands.
genPrologue() - Method in class PopupEditRscript
genPrologue() - generate prologue R script to read data commands.
genRbits - Variable in class RLO
GenR Bits is a bit pattern of selected (R_GENR_xxxx) options used during .R script generation.
genRbits - Variable in class RgenDemo
Data R generation processing bits: RB_GENR_xxxx
genRbits - Variable in class PopupEditRscript
GenR Bits is a bit pattern of selected (R_GENR_xxxx) options used during .R script generation.
genRbits2String(int) - Method in class RgenDemo
genRbits2String() - create string representing the genRbits of the current RLayOut (RLO) of the instance
geoFullDataTableURL - Variable in class Config
Get full HTML list of a specific GEO microarray platform.
geoListOfPlatformsURL - Variable in class Config
Get HTML list of www.ncbi.nlm.nih.gov/geo Gene Express Omnibus GEO microarray platforms numbered GPL4, GPL5, ..."
geoPlatformID - Variable in class Config
GEO platform Identifier of the form "GPL"+.
get_abortFlag() - Method in class MJAstate
get_abortFlag() - get "abortFlag" flag status
get_addExprProfileFlag() - Method in class MJAreport
get_addExprProfileFlag() - get flag: add EP ratios in gene REPORTS
get_addHP_XYstatFlag() - Method in class MJAreport
get_addHP_XYstatFlag() - get flag: add HP_XY statistics in gene REPORTS
get_allowNegQuantDataFlag() - Method in class MJAstate
get_allowNegQuantDataFlag() - get "allowNegQuantData" flag status allow Negative Quantified intensity data
get_Clone_ID() - Method in class MJAgene
get_Clone_ID() - get Clone_ID for default gene, if exists
get_clusterNodeNbr() - Method in class MJAgene
get_clusterNodeNbr() - get clusterNodeNbr for default gene, if exists
get_clusterOnFilteredGenesFlag() - Method in class MJAcluster
get_clusterOnFilteredGenesFlag() - get flag to cluster on Filtered genes else All genes.
get_coeffOfVarTestMode() - Method in class MJAfilter
get_coeffOfVarTestMode() - get samples-to-use mode for testing coefficient of variation threshold.
get_conditionsData() - Method in class MJAstatistics
get_conditionsData() - data[0:nConditions-1][sampleNbrInClass] for computations of N-condition F-test
get_CV() - Method in class MJAgene
get_CV() - get Coefficient of Variation for default gene, if exists
get_data() - Method in class MJAgene
get_data() - get data for default gene, if exists
get_data1() - Method in class MJAgene
get_data1() - get data1 for default gene, if exists
get_data2() - Method in class MJAgene
get_data2() - get data2 for default gene, if exists
get_dbEST3ID() - Method in class MJAgene
get_dbEST3ID() - get dbEST3 ID for default gene, if exists
get_dbEST5ID() - Method in class MJAgene
get_dbEST5ID() - get dbEST5 ID for default gene, if exists
get_defaultFloat() - Method in class MJAutil
get_defaultFloat() - default float value for conversions
get_deltaBinH() - Method in class MJAstatistics
get_deltaBinH() - width of the histogram bins computed as: nBinsH/(maxDataH-minDataH) previously computed
get_dF() - Method in class MJAstatistics
get_dF() - CALC: degrees of freedom previously computed
get_dKS() - Method in class MJAmath
get_dKS() - K-S statistic for Kolmogorov-Smirnov stat d & prob of the null hypothesis of 2 bins of data.
get_doGCFlag() - Method in class MJAstate
get_doGCFlag() - get "doGCflag" flag status invoke the Garbage Collector when have time as determined by the main idle loop
get_duplMIDlist() - Method in class MJAgene
get_duplMIDlist() - get list of MIDs for duplicate genes for default gene, if exists
get_f() - Method in class MJAstatistics
get_f() - CALC: calculated f statistic previously computed
get_fStat() - Method in class MJAstatistics
get_fStat() - CALC: f-statistic previously computed
get_gangSpotDuplicatesFlag() - Method in class MJAstate
get_gangSpotDuplicatesFlag() - get "gangSpotDuplicates" flag status display and report ganged (F1,F2) data else just F1 data
get_GenBankAcc3ID() - Method in class MJAgene
get_GenBankAcc3ID() - get GenBank Acc 3' ID for default gene, if exists
get_GenBankAcc5ID() - Method in class MJAgene
get_GenBankAcc5ID() - get GenBank Acc 5' ID for default gene, if exists
get_GenBankAccID() - Method in class MJAgene
get_GenBankAccID() - get GenBankAcc ID for default gene, if exists
get_Gene_Name() - Method in class MJAgene
get_Gene_Name() - get Gene_Name for default gene
get_Generic_ID() - Method in class MJAgene
get_Generic_ID() - get Generic_ID for default gene, if exists
get_genomicDB_URLs() - Method in class MJAgenomicDB
get_genomicDB_URLs() - get user-defined genomic DB URLs
get_GenomicID() - Method in class MJAgene
get_GenomicID() - geta list of additional genomic IDs for the default gene, if exists.
get_goodSpotTestMode() - Method in class MJAfilter
get_goodSpotTestMode() - get samples-to-use mode for testing for good spots (as determined by QualCheck field in .quant data files.
get_hist() - Method in class MJAstatistics
get_hist() - histogram of size [0:nBinsH-1] previously computed
get_HP_EclustersMembershioFlag() - Method in class MJAfilter
get_HP_EclustersMembershioFlag() - get flag for filter by HP-E clustering membership
get_HP_SampleName(int, boolean) - Method in class MJAsampleList
get_HP_SampleName() - get HP sample name for sample number
get_isZscoreNormFlag() - Method in class MJAstate
get_isZscoreNormFlag() - get "isZscoreNorm" flag status using one of the Zscore normalizations
get_LocusID() - Method in class MJAgene
get_LocusID() - get LocusID for default gene, if exists
get_Master_ID() - Method in class MJAgene
get_Master_ID() - get Master_ID for default gene
get_MasterGeneName() - Method in class MJAgene
get_MasterGeneName() - get MasterGeneName for default gene
get_maxDataH() - Method in class MJAstatistics
get_maxDataH() - max value in data[] for histogram previously computed
get_meanAbsDevH() - Method in class MJAstatistics
get_meanAbsDevH() - mean absolute deviation for histogram previously computed
get_meanH() - Method in class MJAstatistics
get_meanH() - mean of data[] for histogram previously computed
get_meanIdx() - Method in class MJAstatistics
get_meanIdx() - index of mean in hist[] previously computed
get_meansAllConditions() - Method in class MJAstatistics
get_meansAllConditions() - means of samples in each of the nConditions used in computation of N-condition F-test
get_medianH() - Method in class MJAstatistics
get_medianH() - mode of data[] for histogram previously computed
get_medianIdx() - Method in class MJAstatistics
get_medianIdx() - index of median in hist[] previously computed
get_minDataH() - Method in class MJAstatistics
get_minDataH() - min value in data[] for histogram previously computed
get_mnX() - Method in class MJAmath
get_mnX() - get mean X previously computed
get_mnY() - Method in class MJAmath
get_mnY() - get mean Y previously computed
get_modeH() - Method in class MJAstatistics
get_modeH() - mode of data[] for histogram previously computed
get_modeIdx() - Method in class MJAstatistics
get_modeIdx() - index of mode in hist[] previously computed
get_nBinsH() - Method in class MJAstatistics
get_nBinsH() - 0 if none.
get_nCond_dfBetween() - Method in class MJAstatistics
get_nCond_dfBetween() - get dfBetween degrees of freedom used in computation of N-condition F-test
get_nCond_dfWithin() - Method in class MJAstatistics
get_nCond_dfWithin() - get dfWithin degrees of freedom used in computation of N-condition F-test
get_nCond_pValue() - Method in class MJAstatistics
get_nCond_pValue() - get p-value computed of N-condition F-test
get_nCondFstat() - Method in class MJAstatistics
get_nCondFstat() - get f-statistic computed in N-condition F-test
get_nConditions() - Method in class MJAstatistics
get_nConditions() - get nConditions used in computation of N-condition F-test
get_nCondMeanSqBetweenVariance() - Method in class MJAstatistics
get_nCondMeanSqBetweenVariance() - get mnSqBetween variance used in computation of N-condition F-test
get_nCondMeanSqWithinVariance() - Method in class MJAstatistics
get_nCondMeanSqWithinVariance() - get mnSqWithin variance used in computation of N-condition F-test
get_nDuplGenes() - Method in class MJAgene
get_nDuplGenes() - # duplicate genes in duplMIDlist[] for default gene, if exists
get_nGeneClustersCnt() - Method in class MJAgene
get_nGeneClustersCnt() - get nGeneClustersCnt for default gene, if exists
get_nGenomicID() - Method in class MJAgene
get_nGenomicID() - get # additional genomic IDs in the GenomicID[] list for the default gene, if exists.
get_normHierClusterByRatioHPFlag() - Method in class MJAcluster
get_normHierClusterByRatioHPFlag() - get flag to that normalizing each HP-E gene expression vector dataV[1:nHP] by the ratio of HP-X dataV[HP-X].
get_NratiosToReport() - Method in class MJAfilter
get_NratiosToReport() - get # of ratios to report
get_nSamplesAllConditions() - Method in class MJAstatistics
get_nSamplesAllConditions() - # of samples in each of the nConditions used in computation of N-condition F-test
get_nXY() - Method in class MJAmath
get_nXY() - # of genes used in calcXYstat computation
get_okBetaCF() - Method in class MJAmath
get_okBetaCF() - test if nr_betaCF() was ok
get_okBetaI() - Method in class MJAmath
get_okBetaI() - test if nr_betai() was ok
get_okProbKS() - Method in class MJAmath
get_okProbKS() - test if Kolmogorov-Smirnov test was ok
get_pF() - Method in class MJAstatistics
get_pF() - CALC: f-test p-value w/NULL hypoth previously computed
get_plate_col() - Method in class MJAgene
get_plate_col) - get original plate_col for default gene, if exists
get_plate_row() - Method in class MJAgene
get_plate_row() - get original plate_row for default gene, if exists
get_plate() - Method in class MJAgene
get_plate() - get original plate for default gene, if exists
get_positiveQuantTestMode() - Method in class MJAfilter
get_positiveQuantTestMode() - get samples-to-use mode for testing for positive spot quantification values.
get_presentationViewFlag() - Method in class MJAstate
get_presentationViewFlag() - get "presentationView" flag status use larger fonts and graphics for presentations
get_probKS() - Method in class MJAmath
get_probKS() - probability of null hypoth same distrib for previously computed Kolmogorov-Smirnov stat d & prob of the null hypothesis of 2 bins of data.
get_properties() - Method in class MJAgene
get_properties() - get properties for default gene, if exists
get_pT() - Method in class MJAstatistics
get_pT() - CALC: t-test p-value w/NULL hypoth previously computed
get_pValue() - Method in class MJAgene
get_pValue() - get pValue for default gene, if exists
get_pValueThr() - Method in class MJAfilter
get_pValueThr() - get Sample p-Value for t-Test Filter threshold
get_ratioCy3Cy5RangeMode() - Method in class MJAfilter
get_ratioCy3Cy5RangeMode() - get inside/outside mode for testing sample Cy3/Cy5 ratio range.
get_ratioRangeMode() - Method in class MJAfilter
get_ratioRangeMode() - get inside/outside mode for testing sample ratio range.
get_rSq() - Method in class MJAmath
get_rSq() - get correlation coefficient previously computed
get_sampleIntensityRangeMode() - Method in class MJAfilter
get_sampleIntensityRangeMode() - get inside/outside mode for testing sample intensity range.
get_sdX() - Method in class MJAmath
get_sdX() - get standard deviation X previously computed
get_sdY() - Method in class MJAmath
get_sdY() - get standard deviation Y previously computed
get_spotIntensityCompareMode() - Method in class MJAfilter
get_spotIntensityCompareMode() - get how-to compare samples mode for testing spot intensity range.
get_spotIntensityRangeMode() - Method in class MJAfilter
get_spotIntensityRangeMode() - get inside/outside mode for testing spot intensity range.
get_spotIntensityTestMode() - Method in class MJAfilter
get_spotIntensityTestMode() - get samples-to-use mode for testing spot intensity range.
get_stdDevAllConditions() - Method in class MJAstatistics
get_stdDevAllConditions() - stdDev of samples in each of the nConditions used in computation of N-condition F-test
get_stdDevH() - Method in class MJAstatistics
get_stdDevH() - standard deviation of data[] for histogram previously computed
get_SwissProtID() - Method in class MJAgene
get_SwissProtID() - get SwissProt ID for default gene, if exists
get_t() - Method in class MJAstatistics
get_t() - CALC: t or t' statistic computed previously computed
get_thrClusterDist() - Method in class MJAfilter
get_thrClusterDist() - get Sample gene-gene cluster distance threshold
get_thrCR1() - Method in class MJAfilter
get_thrCR1() - get Sample Cy3/Cy5 lower limit CR1 threshold
get_thrCR2() - Method in class MJAfilter
get_thrCR2() - get Sample Cy3/Cy5 lower limit CR2 threshold
get_thrDiff() - Method in class MJAfilter
get_thrDiff() - get Sample diff (HP-X,HP-Y) Filter threshold
get_thrI1() - Method in class MJAfilter
get_thrI1() - get Sample Intensity lower limit I1 threshold
get_thrI2() - Method in class MJAfilter
get_thrI2() - get Sample Intensity lower limit I2 threshold
get_thrNbrClusters() - Method in class MJAfilter
get_thrNbrClusters() - get # of clusters in K-means clustering
get_thrPercentOK() - Method in class MJAfilter
get_thrPercentOK() - get % of samples meeting Spot Intensity criteria threshold
get_thrQualCheck() - Method in class MJAfilter
get_thrQualCheck) - get Sample QualCheck threshold
get_thrR1() - Method in class MJAfilter
get_thrR1() - get Sample Ratio lower limit R1 threshold
get_thrR2() - Method in class MJAfilter
get_thrR2() - get Sample Ratio lower limit R2 threshold
get_thrSI1() - Method in class MJAfilter
get_thrSI1() - get Spot Intensity lower limit SI1 threshold
get_thrSI2() - Method in class MJAfilter
get_thrSI2() - get Spot Intensity lower limit SI2 threshold
get_thrSpotCV() - Method in class MJAfilter
get_thrSpotCV() - get Sample spot Coefficient Of Variation Filter threshold
get_title() - Method in class MJAstatistics
get_title() - title for data used in histogram previously computed
get_UGclusterName() - Method in class MJAgene
get_UGclusterName() - get UGclusterName for default gene, if exists
get_Unigene_ID() - Method in class MJAgene
get_Unigene_ID() - get Unigene_ID for default gene, if exists
get_updatePseudoImgFlag() - Method in class MJAstate
get_updatePseudoArrayImageFlag() - get "updatePseudoArrayImage" flag status.
get_useAbsDiffFilterFlag() - Method in class MJAfilter
get_useAbsDiffFilterFlag() - get flag for filter by absolute diff |HP-X - HP-Y|
get_useAutoStateScrollersPopupFlag() - Method in class MJAfilter
get_useAutoStateScrollersPopupFlag() - flag for Auto state-scroller popup window
get_useClusterCountsDisplayFlag() - Method in class MJAcluster
get_useClusterCountsDisplayFlag() - get flag to show if gene cluster counts cluster method is active.
get_useClusterDistanceCacheFlag() - Method in class MJAcluster
get_useClusterDistanceCacheFlag() - get flag to use cluster distance cache to speed up computations.
get_useCorrelationCoefficientFlag() - Method in class MJAcluster
get_useCorrelationCoefficientFlag() - get gene-gene distance metric flag.
get_useCVmeanElseMaxInFilterFlag() - Method in class MJAfilter
get_useCVmeanElseMaxInFilterFlag() - flag for use mean of CV else use max in Coefficient of Variation filter
get_useCy5OverCy3Flag() - Method in class MJAstate
get_useCy5OverCy3Flag() - get "useCy5OverCy3Flag" flag status Swap Cy3/Cy to Cy5/Cy3 for reporting purposes
get_useDbESTViewerFlag(boolean) - Method in class MJAgenomicDB
get_useDbESTViewerFlag() - access popup Web browser dbEST database
get_useDichromasyDisplayFlag() - Method in class MJAstate
get_useDichromasyDisplayFlag() - get "useDichromasyDisplay" flag status enable Dichromasy color-blindness display options
get_useEGLgeneListFilterFlag() - Method in class MJAfilter
get_useEGLgeneListFilterFlag() - flag for filter by genes in EGL
get_useEPrawIntensityValuesFlag() - Method in class MJAreport
get_useEPrawIntensityValuesFlag() - get flag: use Raw intensity for EP ratios in gene REPORTS
get_useExprProfileOverlayFlag() - Method in class MJAstate
get_useExprProfileOverlayFlag() - get "useExprProfileOverlay" flag status Plot EP list as overlay 2Dplot else scrollable EP list
get_useF_TestOCLFilterFlag() - Method in class MJAfilter
get_useF_TestOCLFilterFlag() - flag for filter passing ur.
get_useGenBankViewerFlag(boolean) - Method in class MJAgenomicDB
get_useGenBankViewerFlag() - access popup Web browser GenBank database
get_useGeneClassMbrFilterFlag() - Method in class MJAfilter
get_useGeneClassMbrFilterFlag() - flag for filter by GeneClass membership
get_useGeneSetFilterFlag() - Method in class MJAfilter
get_useGeneSetFilterFlag() - flag for filter by user gene set membership
get_useGoodGeneGIPOfilterFlag() - Method in class MJAfilter
get_useGoodGeneGIPOfilterFlag() - flag for filter by GIPO Good Genes List
get_useGoodSpotDataFlag() - Method in class MJAfilter
get_useGoodSpotDataFlag() - flag for filter by Good spot data
get_useHierClusterDisplayFlag() - Method in class MJAcluster
get_useHierClusterDisplayFlag() - get flag show hierarchical clusters in the pseudoarray image for All Filtered genes.
get_useHighRatiosFilterFlag() - Method in class MJAfilter
get_useHighRatiosFilterFlag() - flag for Use highest X/Y ratios filter
get_useHP_E_ListDataFlag() - Method in class MJAstate
get_useHP_E_ListDataFlag() - get "useMeanHPeListDataFlag" flag status use mean HP-E 'list' data else single current HP sample data
get_useHPxySetsDataFlag() - Method in class MJAstate
get_useHPxySetsDataFlag() - get "useHPxySetsData" flag status use mean HP-X,Y 'sets' data else HP-X,HP-Y single samples data
get_useIntensHistBinsFilterFlag() - Method in class MJAfilter
get_useIntensHistBinsFilterFlag() - flag for filter by Intensity histogram bin
get_useIntensityFilterFlag() - Method in class MJAfilter
get_useIntensityFilterFlag() - flag for filter by intensity threshold
get_useKmeansClusterCountsDispFlag() - Method in class MJAcluster
get_useKmeansClusterCountsDispFlag() - get flag show K-means cluster counts for all Filtered genes in the pseudoarray image.
get_useKStestXYsetsFilterFlag() - Method in class MJAfilter
get_useKStestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' KS-test
get_useLocksLinkViewerFlag(boolean) - Method in class MJAgenomicDB
get_useLocksLinkViewerFlag() - access popup Web browser LocusLink database
get_useLowRatiosFilterFlag() - Method in class MJAfilter
get_useLowRatiosFilterFlag() - flag for Use lowest X/Y ratios filter
get_useLSQmagnitudeNormalizationFlag() - Method in class MJAcluster
get_useLSQmagnitudeNormalizationFlag() - get flag to normalize cluster expression vector geneEPvect[] to 1.0 for clustering
get_useMadbViewerFlag(boolean) - Method in class MJAgenomicDB
get_useMadbViewerFlag() - access popup Web browser mAdb clone database
get_useMedianForKmeansClusteringFlag() - Method in class MJAcluster
get_useMedianForKmeansClusteringFlag() - get flag for K-median else K-means clustering
get_useMedMinerViewerFlag(boolean) - Method in class MJAgenomicDB
get_useMedMinerViewerFlag() - access popup Web browser MedMiner database
get_useMouseOverFlag() - Method in class MJAstate
get_useMouseOverFlag() - get "useMouseOver" flag status
get_useOmimViewerFlag(boolean) - Method in class MJAgenomicDB
get_useOmimViewerFlag() - access popup Web browser OMIM database
get_usePIRViewerFlag(boolean) - Method in class MJAgenomicDB
get_usePIRViewerFlag() - access popup Web browser PIR database
get_usePosQuantIntensDataFlag() - Method in class MJAfilter
get_usePosQuantIntensDataFlag() - get flag for filter by postive intensity data
get_useRatioCy3Cy5FilterFlag() - Method in class MJAfilter
get_useRatioCy3Cy5FilterFlag() - flag for filter by Cy3/Cy5 ratio range threshold
get_useRatioDataFlag() - Method in class MJAstate
get_useRatioDataFlag() - get "useRatioData" flag status data is Cy3/Cy5 ratio else Intensity
get_useRatioFilterFlag() - Method in class MJAfilter
get_useRatioFilterFlag() - flag for filter by ratio threshold
get_useRatioHistBinsFilterFlag() - Method in class MJAfilter
get_useRatioHistBinsFilterFlag() - flag for filter by Ratio histogram bin
get_useReplicateGenesFilterFlag() - Method in class MJAfilter
get_useReplicateGenesFilterFlag() - flag for filter by => 2 replicates/gene
get_useShortClusterDistanceCacheFlag() - Method in class MJAcluster
get_useShortClusterDistanceCacheFlag() - get flag t ouse short[] cluster distance cache to save memory
get_useSimilarGeneClusterDisplayFlag() - Method in class MJAcluster
get_useSimilarGeneClusterDisplayFlag() - get flag to show if similar genes cluster method is active.
get_useSpotCVfilterFlag() - Method in class MJAfilter
get_useSpotCVfilterFlag() - get flag for filter by Spot Coefficient of Variation
get_useSpotIntensityFilterFlag() - Method in class MJAfilter
get_useSpotIntensityFilterFlag() - flag for filter by intensity threshold
get_useSwissProtViewerFlag(boolean) - Method in class MJAgenomicDB
get_useSwissProtViewerFlag() - access popup Web browser SwissProt database
get_useTest() - Method in class MJAstatistics
get_useTest() - CALC: 'B' or 'T' - t-test to use computed using F-statistic previously computed
get_useTtestXYfilterFlag() - Method in class MJAfilter
get_useTtestXYfilterFlag() - get flag for filter genes passing HP-X,-Y t-test
get_useTtestXYsetsFilterFlag() - Method in class MJAfilter
get_useTtestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' t-test
get_useUniGeneViewerFlag(boolean) - Method in class MJAgenomicDB
get_useUniGeneViewerFlag() - access popup Web browser UniGene database
get_varianceAllConditions() - Method in class MJAstatistics
get_varianceAllConditions() - variance of samples in each of the nConditions used in computation of N-condition F-test
get_viewFilteredSpotsFlag() - Method in class MJAstate
get_viewFilteredSpotsFlag() - get "viewFilteredSpots" flag status in PseudoArray image show Filtered spots else don't show overlays
getActiveFilterPluginList() - Static method in class MAEPlugin.analysis.FilterPlugin
getActiveFilterPluginList() - Bean-style method for getting activeFilterPluginList.
getActiveNormalization() - Method in class MaeJavaAPI
getActiveNormalization() - get active normalization.
getActiveNormalization() - Static method in class MAEPlugin.analysis.NormalizationPlugin
getActiveNormalization() - Bean-style method for getting the activeNormalization.
getAdditionalParams() - Method in class Config
getAdditionalParams() - get additional params from .mae file or Applet etc.
getAllCondNames() - Method in class MJAcondition
getAllCondNames()- get a list of all condition names.
getAllF1F2dataForSample(float[], float[], int) - Method in class MJAsampleList
getAllF1F2dataForSample() - get all (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[]) for ALL gene data.
getAllGenRbits() - Method in class MJAReval
getAllGenRbits() - get GenR Bits using R_GENR_xxxx bits for current RLO.
getAllHP_XandYsamplesData(float[], float[], int, int) - Method in class MJAsampleList
getAllHP_XandYsamplesData() - get all (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[]) for ALL genes.
getAllHP_XandYsetDataForSample(float[], float[]) - Method in class MJAsampleList
getAllHP_XandYsetDataForSample() - get all HP-X, -Y 'sets' (X,Y) normalized data lists for sample in (Xdata[],Ydata[] for ALL genes.
getAllHPdataForSample(float[], int) - Method in class MJAsampleList
getAllHPdataForSample() - get all normalized (data,prop) list single sample's data for sample in (dataList[]) for ALL genes.
getAllMeanDataForCondition(float[], float[], String) - Method in class MJAsampleList
getAllMeanDataGeneListDataForCondition() - get all (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in in (meanData[], stdDevData[]) for data filtered by the specified gene list.
getAllMIDsForGene(String, int) - Method in class GipoTable
getAllMIDsForGene() - get Gene midList[] for gene name.
getAllProcessBits() - Method in class MJAReval
 
getAllProcessBits() - Method in class RevalBase
 
getAllRawF1F2DataAndBkgdForSample(float[], float[], float[], float[], int[], int[], int) - Method in class MJAsampleList
getAllawF1F2DataAndBkgdForSample() - get all spot list raw intensity and background data for genes and return it in the arrays pre-specified by the user.
getAllSampleNames() - Method in class MJAsampleList
getAllSampleNames()- get list of all active sample names used in DB
getAllSampleNamesInDB() - Method in class MJAcondition
getAllSampleNamesInDB() - get list of all sample names in the database
getArrayOfTabDelimitedTokens(String, int) - Method in class Table
getArrayOfTabDelimitedTokens() - get array of tab-delim tokens from table.
getBottomSeparator() - Method in class JavaCGIBridge
getBottomSeparator() - Returns the bottom separator for the object When getParsedData method is called, the object uses the bottom separator to determine where the rows of data inside the raw HTML output actually end.
getCalcEPdataFlag() - Method in class HPxyData
getCalcEPdataFlag() - get the also calculate EP data flag status.
getClassXname() - Method in class MJAsampleList
getClassXname() - get the current Class X name.
getClassYname() - Method in class MJAsampleList
getClassYname() - get the current Class Y name.
getClusterOfSimilarGenes(String, float, int) - Method in class MJAcluster
getClusterOfSimilarGenes() - get Hashtable list of gene cluster similar to seed gene.
getComputedMaxMeanEP() - Method in class MJAexprProfile
getComputedMaxMeanEP() - max mean of the current EP sample data
getCondIdxFromName(String) - Method in class PopupCondChooser
getCondIdxFromName() - Look up and return index of current cond.
getConditionByName(String) - Static method in class Condition
getConditionByName() - lookup Condition entry by name
getConditionIdxInOrderedCondList(Condition, String) - Method in class Condition
getConditionIdxInOrderedCondList() - get condition index in named ordered condition list.
getConditionIdxInOrderedCondList(String, String) - Method in class MJAcondition
getConditionIdxInOrderedCondList() - get condition index in named ordered condition list.
getConditionsInOrderedCondList(String) - Method in class MJAcondition
getConditionsInOrderedCondList() - get list of names conditions in OCL
getCondListLength() - Method in class Condition
getCondListLength() - get Condition list length
getCondListLength(String) - Method in class MJAcondition
getCondListLength() - get # of samples in the condition list
getCondListName() - Method in class Condition
getCondListName() - get Condition list name
getCondListsNames() - Method in class MJAcondition
getCondListsNames() - get list of active condition lists names
getCondListsSizes() - Method in class MJAcondition
getCondListsSizes() - get list of active condition lists sizes
getCondNameFromIdx(int) - Method in class PopupCondChooser
getCondNameFromIdx() - Look up and return name of current ocl.
getCondParamNames() - Method in class MJAcondition
getCondParamNames() - get list of condition parameter names for all conditions
getCondParamValues(String) - Method in class MJAcondition
getCondParamValues() - get list of parameter values for specific condition
getConfigAndPARAMvalue(String) - Method in class GetParams
getConfigAndPARAMvalue() - get Config then val for tag 1.
getConfigRowByRowIdx(int) - Method in class ConfigTable
getConfigRowByRowIdx() - get row of Config data table Row
getConfigRowFieldByName(int, String) - Method in class ConfigTable
getConfigRowFieldByName() - get row field data by array coords
getConfigRowFieldByRowFieldIdxes(int, int) - Method in class ConfigTable
getConfigRowFieldByRowFieldIdxses() - get row field by row and field indices
getConfigRowFieldByRowNameIdx(int, String) - Method in class ConfigTable
getConfigRowFieldByRowIdxName() - get row field by row index and name
getCorrCoefQuantDataList(int) - Method in class MJAsample
getCorrCoefQuantDataList() - get spot intensity correlation coefficient data for the given sample.
getCurCondition() - Method in class MJAcondition
 
getCurDateStr() - Static method in class RevalBase
getCurDateStr() - return date string in the format of YYMMDDHHMMSS.
getCurDateStr() - Static method in class Util
getCurDateStr() - return date string in the format of YYMMDDHHMMSS.
getCurGeneCol() - Method in class MJAgene
getCurGeneCol() - get the column in the grid for current gene
getCurGeneFeaturedata() - Static method in class SpotFeatures
getCurGeneFeaturedata() - get spot feature summary of current gene.
getCurGeneField() - Method in class MJAgene
getCurGeneField() - get the MID (Master Gene ID) number for current gene
getCurGeneGenomicdata() - Static method in class SpotFeatures
getCurGeneGenomicdata() - get spot feature summary of current gene.
getCurGeneGIDG() - Method in class MJAgene
getCurGeneGIDG() - get the GIDG (Ganged Grid layout ID) number for current gene
getCurGeneGrid() - Method in class MJAgene
getCurGeneGrid() - get the grid for current gene
getCurGeneMID() - Method in class MJAgene
getCurGeneMID() - get the MID (Master Gene ID) number for current gene
getCurGeneRow() - Method in class MJAgene
getCurGeneRow() - get the rowin the grid for current gene
getCurGeneXcoord() - Method in class MJAgene
getCurGeneXcoord() - get the X coordinate in the pseudoarray for current gene
getCurGeneXYGdata() - Static method in class SpotFeatures
getCurGeneXYGdata() - get spot quantitation summary of current gene.
getCurGeneYcoord() - Method in class MJAgene
getCurGeneYcoord() - get the Y coordinate in the pseudoarray for current gene
getCurOCL() - Method in class MJAcondition
 
getCurrent_HP_index() - Method in class MJAsampleList
getCurrent_HP_index() - get Current HP sample index.
getCurrent_HP_name(boolean) - Method in class MJAsampleList
getCurrent_HP_name() - get Current HP sample name
getCurrent_HP_X_index() - Method in class MJAsampleList
getCurrent_HP_X_index() - get Current HP-X sample index.
getCurrent_HP_X_name(boolean) - Method in class MJAsampleList
getCurrent_HP_X_name() - get Current HP-X sample name
getCurrent_HP_Y_index() - Method in class MJAsampleList
getCurrent_HP_Y_index() - get Current HP-Y sample index.
getCurrent_HP_Y_name(boolean) - Method in class MJAsampleList
getCurrent_HP_Y_name() - get Current HP-Y sample name
getCurrentGeneClassIndex() - Method in class MJAgeneList
getCurrentGeneClassIndex() - get index of current gene class in DB
getCurrentRLO() - Method in class RevalBase
getCurrentRLO() - get the current RLO analysis method object
getCurrentRLO() - Method in class RLO
getCurrentRLO() - return current RLO
getCurrentRLOid() - Method in class MJAReval
getCurrentRLOid() - get the current RLO analysis method id
getCurrentRLOmenuName() - Method in class MJAReval
getCurrentRLOmenuName() - get the current RLO analysis menu string name
getCurrentRLOmenuStubName() - Method in class MJAReval
getCurrentRLOmenuStubName() - get the current RLO analysis menu stub string name
getCurrentRLORscriptName() - Method in class MJAReval
getCurrentRLORscriptName() - get current RLO analysis .R script file name
getCVtestMode() - Method in class MJAproperty
getCVtestMode() - get Coefficient of Variation (CV) test mode: SS_MODE_xxxx
getData(String, String, String[], boolean) - Method in class Table
getData() - read the data and store it in the table.
getDataByGID(int, boolean, int) - Method in class MaHybridSample
getDataByGID() - get scaled intensity data specified by gid and data type.
getDbEstURL() - Method in class MJAstate
getDbEstURL() - get the current url value
getDefaultThreadJavaCGIBridgeTimeOut() - Static method in class JavaCGIBridge
getDefaultThreadJavaCGIBridgeTimeOut() - default communication time out Return default static value in milliseconds for the class.
getDoMeanPlotsFlag() - Method in class MJAexprProfile
getDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots
getEditMode() - Method in class MJAproperty
getEditMode() - get EGL mode for 'edited gene list': EDIT_xxxx
getEnumOrder() - Method in class HierClustNode
getEnumOrder() - lookup or RECURSIVELY compute enumOrder of this node.
getEPmaxMeanSampleData() - Method in class MJAexprProfile
getEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles.
getEPsamplesCV(int) - Method in class MJAexprProfile
getEPsamplesCV() - opt.
getEPsamplesData(int) - Method in class MJAexprProfile
getEPsamplesData() - list of normalized HP-E samples data for MID.
getEPsamplesMean(int) - Method in class MJAexprProfile
getEPsamplesMean() - opt.
getEPsamplesStdDev(int) - Method in class MJAexprProfile
getEPsamplesStdDev() - opt.
getF1F2Data(float[], float[], int[], GeneList, boolean, boolean, boolean) - Method in class MaHybridSample
getF1F2Data() - get list spot (F1,F2)'s intensity data for data filtered genes and return it in the xList[1:n] is the field 1 data, yList[0:n-1] is field 2 data and the property in propList[0:n-1].
getF1F2dataForSample(float[], float[], int[], int, String) - Method in class MJAsampleList
getF1F2dataForSample() - get filtered (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[], propList[]) for FILTERED data by the specified gene list.
getFGRCtoGIDmap() - Method in class MJAgeometry
getFGRCtoGIDmap() - get map of [field][grid][grid_row][grid_col] to gid (GridCoords index GID).
getField(String) - Method in class JavaCGIBridge
getField() - helper routine for parsing header key PFL - 8-7-00 See pg931, Patrick Chan etal, Java Class Libraries 2nd Ed, Vol 1.
getFieldSeparator() - Method in class JavaCGIBridge
getFieldSeparator() - Returns the field separator for the object.
getFilterState() - Static method in class MAEPlugin.analysis.FilterPlugin
getFilterState() - Static method for using getActiveFilter().
getFlag() - Method in class MAEPlugin.MAEPlugin
getFlag() - get the menu status (CheckBox) menuFlag
getFloatValFromLine(String, StringTokenizer) - Method in class UserState
getFloatValFromLine() - get next line and parse value for key 'name='.
getFlourescentLabel1Name() - Method in class MJAproperty
getFlourescentLabel1Name() - get current fluorescent label 1 name.
getFlourescentLabel2Name() - Method in class MJAproperty
getFlourescentLabel2Name() - get current fluorescent label 1 name.
getFrame() - Method in class MaeJavaAPI
getFrame() - provide the dominate Frame for other AWT components
getFrame() - Method in interface MAEPlugin.MAEStub
getFrame() - provides Frame for Dialogs and other AWT components that need frames.
getFullGEOplatformDataTableURL() - Method in class MJAproperty
getFullGEOplatformDataTableURL() - get URL for current full GEO platform data table
getFullRoutputFilePath() - Method in class MJAReval
getFullRoutputFilePath() - get full path of R output file after file setup
getFullRscriptInputPath() - Method in class MJAReval
getFullRscriptInputPath() - full path of R input script file after file setup
getFullRunRfilePath() - Method in class MJAReval
getFullRunRfilePath() - full path of batch R startup script file after file setup
getFullSampleTextBySampleNbr(int) - Method in class MJAsample
getFullSampleTextBySampleNbr() - lookup the full sample text description by sample number.
getGbid2LocusLinkURL() - Method in class MJAstate
getGbid2LocusLinkURL() - get the current url value
getGBSnames() - Method in class GeneBitSet
getGBSnames() - return String array of active Gene Bit Set names.
getGenBankCloneURL() - Method in class MJAstate
getGenBankCloneURL() - get the current url value
getGenBankCloneURLepilogue() - Method in class MJAstate
getGenBankCloneURLepilogue() - get the current url value
getGeneBankAccURL() - Method in class MJAstate
getGenBankAccURL() - get the current url value
getGeneBitsetData(String) - Method in class MJAgeneList
getGeneBitsetData() - get Hashtable list of GeneBitSet data by GeneBitSet name.
getGeneCardURL() - Method in class MJAstate
getGeneCardURL() - get the current url value
getGeneFeatureLine(int) - Static method in class MJAgene
getGeneFeatureLine() - get spot feature summary of gene.
getGeneFieldDataFromGeneList(String, String) - Method in class MJAgeneList
getGeneFieldDataFromGeneList() - get String list of Gene fields for gene list.
getGeneGenomicLine(int) - Static method in class MJAgene
getGeneGenomicLine() - get spot genomic data summary of gene.
getGeneList() - Method in class GeneList
getGeneList() - get gene mList[] data as Gene[].
getGeneListByName(String) - Method in class GeneList
getGeneListByName() - get GeneList if geneListName is a valid GeneList cName.
getGeneListData(String) - Method in class MJAgeneList
getGeneListData() - get Hashtable list of GeneList data by GeneList name.
getGeneListNames() - Method in class MJAgeneList
getGeneListNames() - get list of the names for all of the GeneLists
getGeneListOfCurrentGeneClass() - Method in class GeneClass
getGeneListOfCurrentGeneClass() - get the current GeneClass Gene List
getGeneListOfGeneClass(String) - Method in class GeneClass
getGeneListOfGeneClass() - return a Gene List for the gene class
getGeneMeasurementSummary(int, int) - Static method in class MJAgene
getGeneMeasurementSummary() - get spot quantitation summary of (gene,sample).
getGeneTabDelimFieldsStr(String, boolean, Table, Table) - Method in class Report
getGeneTabDelimFieldsStr() - create tab delimited gene fields string
getGEOplatformID() - Method in class MJAproperty
getGEOplatformID() - get current GEO platform ID for this database
getGIDtoFGRCmap() - Method in class MJAgeometry
getGIDtoFGRCmap() - get the map of GIDs to FGRC 5-tuples Each map entry is {gid, field, grid, row, column}
getGIDtoGangGIDmap() - Method in class MJAgeometry
getGIDtoGangGIDmap() - get the map from GIDs to Ganged GIDs
getGIDtoMIDmap() - Method in class MJAgeometry
getGIDtoMIDmap() - get the map from GIDs to MIDs
getGoodSpotTestMode() - Method in class MJAproperty
getGoodSpotTestMode() - get Good Spot (QualCheck) test mode: SS_MODE_xxxx
getGrandMeanCalDNA(boolean) - Method in class MJAsampleList
getGrandMeanCalDNA() - get compute grand mean of calibration DNA
getGrandMeanUseGeneSet(boolean) - Method in class MJAsampleList
getGrandMeanUseGeneSet() - get compute grand mean of 'Use Gene Set'
getGridIDnbr() - Method in class MJAgene
getGridIDnbr() - get the GID (Grid layout ID) number for current gene
getGridIndexMap() - Method in class MJAgeometry
getGridIndexMap() - get the map of mid to gene.
getHeaderField(int) - Method in class JavaCGIBridge
getHeaderField() - implements getHeaderField for HttpURLconnection.
getHeaderField(String) - Method in class JavaCGIBridge
getHeaderField() - implements HeaderField for HttpURLconnection.
getHeaders() - Method in class JavaCGIBridge
getHeaders() - help routine read header from HTTP connection.
getHelpStr() - Method in class PopupEditRscript
getHelpStr() - get popup edit help message.
getHierClusterOfGenes(String) - Method in class MJAcluster
getHierClusterOfGenes() - get Hashtable list of hierarchical gene cluster of genes.
getHierClustMode() - Method in class MJAproperty
getHierClustMode() - get hierarchical clustering linkage mode: HIER_CLUST_xxxxx
getHP_Elist_SampleIDs() - Method in class MJAsampleList
getHP_Elist_SampleIDs()- get list of HP-E 'list' sample IDs used in DB
getHP_Elist_SampleNames() - Method in class MJAsampleList
getHP_Elist_SampleNames()- get list of HP-E 'list' sample IDs used in DB
getHP_Elist_SampleNbrs() - Method in class MJAsampleList
getHP_Elist_SampleNbrs()- get list of HP-E 'list' sample numbers used in DB
getHP_XandYsamplesData(float[], float[], int[], int, int, String) - Method in class MJAsampleList
getHP_XandYsamplesData() - get filtered (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data by the specified gene list.
getHP_XandYsetData(float[], float[], int[], GeneList, boolean, boolean) - Method in class CompositeDatabase
getHP_XandYsetData() - get list spot (HP-X,HP-Y) sets data passing the data filter mae.fc.workingCL.
getHP_XandYsetDataForSample(float[], float[], int[], String) - Method in class MJAsampleList
getHP_XandYsetDataForSample() - get normalized HP-X, -Y 'sets' (X,Y,prop) data lists for sample in (Xdata[],Ydata[], propList[] for FILTERED data by the specified gene list.
getHP_Xset_SampleIDs() - Method in class MJAsampleList
getHP_Xset_SampleIDs()- get list of HP-X 'set' sample IDs used in DB
getHP_Xset_SampleNames() - Method in class MJAsampleList
getHP_Xset_SampleNames()- get list of HP-X 'set' sample names used in DB
getHP_Xset_SampleNbrs() - Method in class MJAsampleList
getHP_Xset_SampleNbrs()- get list of HP-X 'set' sample numbers used in DB
getHP_XYsetsStatistics(int) - Method in class MJAsampleList
getHP_XYsetsStatistics() - get HP-X and HP-Y 'set statistics for gene.
getHP_Yset_SampleIDs() - Method in class MJAsampleList
getHP_Yset_SampleIDs()- get list of HP-Y 'set' sample IDs used in DB
getHP_Yset_SampleNames() - Method in class MJAsampleList
getHP_Yset_SampleNames()- get list of HP-Y 'set' sample names used in DB
getHP_Yset_SampleNbrs() - Method in class MJAsampleList
getHP_Yset_SampleNbrs()- get list of HP-Y 'set' sample numbers used in DB
getHPdataForSample(float[], int[], int, String) - Method in class MJAsampleList
getHPdataForSample() - get normalized filtered (data,prop) list single sample's data for sample in (dataList[], propList[]) for FILTERED data by the specified gene list.
getHPlist() - Method in class Condition
getHPlist() - get sample list for condition [1:nMScond]
getHPnbrInImage(MouseEvent) - Method in class ScrollableImageCanvas
getHPnbrInImage() - return HP # if within threshold distance
getHttpRequestInThread(URL, Hashtable) - Method in class JavaCGIBridge
getHttpRequestInThread() - Returns HTTP Request data to the thread that was launched to GET/POST data for a URL.
getIMAGE2GenBankURL() - Method in class MJAstate
getIMAGE2GenBankURL() - get the current url value
getIMAGE2unigeneURL() - Method in class MJAstate
getIMAGE2unigeneURL() - get the current url value
getImgCursor() - Method in class ArrayScroller
getImgCursor() - get the (x,y) scrollable cursor for this image
getImgCursorMax() - Method in class ArrayScroller
getImgCursorMax() - get the (x,y) scrollable image cursor maxima.
getImgPos() - Method in class ArrayScroller
getImgPos() - get the Image position
getImgPos() - Method in class ScrollableImageCanvas
getImgPos() - get the Image position (xImg,yImg).
getInputDataFileNames() - Method in class MJAReval
getInputDataFileNames() - get current RLO list of input data file names
getInputDataFileNames() - Method in class RevalBase
getInputDataFileNames() - get current RLO list of input data file names
getInputDataTypes() - Method in class MJAReval
getInputDataTypes() - get current RLO list of input data file types
getInputDataTypes() - Method in class RevalBase
getInputDataTypes() - get current RLO list of input data file types
getInputRscriptFileName() - Method in class MJAReval
getInputRscriptFileName() - get current name of .R input script file
getInputStream() - Method in class JavaCGIBridge
getInputStream() - implements getInputStream for HttpURLconnection.
getInstance() - Method in class MAEPlugin.MAEPlugin
getInstance() - returns Registry instance of this class or new if not loaded
getIntValFromLine(String, StringTokenizer) - Method in class UserState
getIntValFromLine() - get next line and parse value for key 'name='.
getJarResources() - Method in class MAEPlugin.JarClassLoader
 
getKey(String) - Static method in class JavaCGIBridge
getKey() - helper routine for parsing header field PFL - 8-7-00 See pg931, Patrick Chan etal, Java Class Libraries 2nd Ed, Vol 1.
getKeyValuePairs(Vector) - Method in class JavaCGIBridge
getKeyValuePairs() - cvt getParsedData to hashtable.
getKmeansClusters(String, int, int) - Method in class MJAcluster
getKmeansClusters() - get Hashtable list of K-means clustering data.
getLastorderedCondListName() - Method in class MJAexprProfile
getLastorderedCondListName() - get name of last ordered condition list computation computed using calcOrderedCondListExprProfile().
getListCondListsStr() - Method in class Condition
getListCondListsStr() - get a list of the names of the Condition lists
getListCondListsStr() - Method in class MJAcondition
getListCondListsStr() - get list of Conditions pretty-print string
getListFilterNames() - Method in class MJAfilter
getListFilterNames() - getlist of active data Filter names.
getListGeneBitSetsStr() - Method in class GeneBitSet
getListGeneBitSetsStr() - convert list of active GeneBitSets userBS[] to summary print string.
getListOfAllActiveHPsampleIndices() - Method in class MJAsampleList
getListOfAllActiveHPsampleIndices() - get list of all active sample HP indices.
getListOfGeneFieldsForMID(int) - Method in class MJAgeneList
getListOfGeneFieldsForMID() - get list of Gene fields for a gene by MID DataFieldNames: "GeneName", "GenBankID", "GenBank3ID", "GenBank5ID", "CloneID", "LocusID", "UniGeneID", "SwissProtID", "RefSeqID", "Master_ID", "MasterGeneName", "Generic_ID"
getListOfGEOplatformsURL() - Method in class MJAproperty
getListOfGEOplatformsURL() - get URL for list of current GEO platforms
getListOfHPEsampleIndices() - Method in class MJAsampleList
getListOfHPEsampleIndices() - get list of sample indices in HP-E list.
getListOfHPXsampleIndices() - Method in class MJAsampleList
getListOfHPXsampleIndices() - get list of sample indices in HP-X set.
getListOfHPYsampleIndices() - Method in class MJAsampleList
getListOfHPYsampleIndices() - get list of sample indices in HP-Y set.
getListOfMenuActionCmds() - Method in class MJAeval
getListOfMenuActionCmds() - get list of current menu action short-form commands
getListOfMenuActionLabels() - Method in class MJAeval
getListOfMenuActionLabels() - get list of current menu action commands labels
getListOfMenuCheckboxLabels() - Method in class MJAeval
getListOfMenuCheckboxLabels() - get list of current menu checkbox label commands.
getListOfMenuStubNames() - Static method in class MJAutil
getListOfMenuStubNames() - get list of menu stub names
getListOfMenuStubNames() - Method in class Rtest
getListOfMenuStubNames() - get list of menu stub names
getListOfMenuStubNames() - Method in class RtestBase
getListOfMenuStubNames() - get list of menu stub names
getListofRLOids() - Method in class RLO
getListofRLOids() - get list of all IDs
getListofRLOmenuNames() - Method in class MJAReval
getListofRLOmenuNames() - get list of all menuNames
getListofRLOmenuNames() - Method in class RevalBase
getListofRLOmenuNames() - get list of all menuNames
getListofRLOmenuNames() - Method in class RLO
getListofRLOmenuNames() - get list of all menuNames
getListofRLOscriptNames() - Method in class MJAReval
getListofRLOscriptNames() - get list of all R script names
getListofRLOscriptNames() - Method in class RevalBase
getListofRLOscriptNames() - get list of all R script names
getListofRLOscriptNames() - Method in class RLO
getListofRLOscriptNames() - get list of all R script names
getListOfSampleMenuEntries() - Method in class MJAsampleList
getListOfSampleMenuEntries() - get list of sample menu names as appears in the MAExplorer Samples menu.
getListOfSampleNames() - Method in class MJAsampleList
getListOfSampleNames() - get list sample database file name (no .quant).
getListOfSampleProjectEntries() - Method in class MJAsampleList
getListOfSampleProjectEntries() - get list of sample project names.
getListOfSampleStageNames() - Method in class MJAsampleList
getListOfSampleStageNames() - get list of sample full stage text names.
getListScrollerNames() - Method in class MJAfilter
getListScrollerNames() - get list of ALL State Scrollers
getListsOfEPsamplesCV(int[]) - Method in class MJAexprProfile
getListsOfEPsamplesCV() - lists of normalized HP-E samples CoefOfVar EPs for list of MIDs.
getListsOfEPsamplesData(int[]) - Method in class MJAexprProfile
getListsOfEPsamplesData() - lists of normalized HP-E samples data EPs for list of MIDs.
getListsOfEPsamplesMean(int[]) - Method in class MJAexprProfile
getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs Compute expression profiles for all of the mid's in the midList[] that are legal (i.e.
getListsOfEPsamplesStdDev(int[]) - Method in class MJAexprProfile
getListsOfEPsamplesStdDev() - lists of normalized HP-E samples StdDev EPs for list of MIDs.
getListsOfOrderedCondListCVs() - Method in class MJAexprProfile
getListsOfOrderedCondListCVs() is last conditions Coeff of Variation[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
getListsOfOrderedCondListMeans() - Method in class MJAexprProfile
getListsOfOrderedCondListMeans() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
getListsOfOrderedCondListNames() - Method in class MJAexprProfile
getListsOfOrderedCondListNames() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
getListsOfOrderedCondListNbrs() - Method in class MJAexprProfile
getListsOfOrderedCondListNbrs() is last conditions sizes [] from ordered condition list computation computed using calcOrderedCondListExprProfile().
getListsOfOrderedCondListStdDevs() - Method in class MJAexprProfile
getListsOfOrderedCondListStdDevs() is last conditions StdDev[] from ordered condition list computation computed using calcOrderedCondListExprProfile().
getLocusLinkURL() - Method in class MJAstate
getLocusLinkURL() - get the current url value
getLongValFromLine(String, StringTokenizer) - Method in class UserState
getLongValFromLine() - get next line and parse value for key 'name='.
getMAdbURL() - Method in class MJAstate
getMAdbURL() - get the current url value
getMaeBrowserTitle() - Method in class MJAproperty
getMaeBrowserTitle() - get current browser MAExplorer title.
getMaeCurProjectPath() - Method in class MJAproperty
getMaeCurProjectPath() - get path of current project MAExplorer session.
getMaeDatabaseTitle() - Method in class MJAproperty
getMaeDatabaseTitle() - get current MAExplorer database title.
getMaeDbSubsetTitle() - Method in class MJAproperty
getMaeDbSubsetTitle() - get current MAExplorer DB subset title.
getMAEstartupValue(String) - Method in class UserState
getMAEstartupValue() - get value from MAE startup file DB
getMAEStub() - Method in class MAEPlugin.MAEPlugin
getMAEStub() - get the menu stub for this instance of plugin
getMaps() - Method in class MJAgeometry
getMaps() - get Hashtable list of a MAExplorer maps
getMasterGeneIDMap() - Method in class MJAgeometry
getMasterGeneIDMap() - get the map of mid to gene.
getMasterGeneIDname() - Method in class MJAgeneList
getMasterGeneIDname() - get the type of name used for Master Gene ID
getMasterGeneName() - Method in class MJAgeneList
getMasterGeneName() - get the type of name used for Master Gene Name
getMasterIDMode() - Method in class MJAgeneList
getMasterIDMode() - get the mode of name used for Master Gene ID It will be either MASTER_GENE_NAME or MASTER_UG_NAME
getMasterNameMode() - Method in class MJAgeneList
getMasterGeneName() - get the mode of name used for Master Gene Name It will be either MASTER_GENE_NAME or MASTER_UG_NAME
getMaxCondListSize() - Method in class MJAcondition
getMaxCondListSize() - get maximum # of samples condition list can hold
getMaxFields() - Method in class MJAgeometry
getMaxFields() - get the number of Max replicate grid Fields
getMaxGenes() - Method in class MJAgeometry
getMaxGenes() - get number of genes in the database
getMaxGridCols() - Method in class MJAgeometry
getMaxGridCols() - get the number of columns/grid in the array
getMaxGridRows() - Method in class MJAgeometry
getMaxGridRows() - get the number of rows/grid in the array
getMaxGrids() - Method in class MJAgeometry
getMaxGrids() - get the number of Max Grids in the array not counting replicate fields.
getMaxNbrCondParams() - Method in class MJAcondition
getMaxNbrCondParams() - get maximum # of condition parameters DB may hold
getMaxNbrOCLParams() - Method in class MJAcondition
getMaxNbrOCLParams() - return max number of Ordered Condition List parameters.
getMaxNbrSamplesInDB() - Method in class MJAcondition
getMaxNbrSamplesInDB() - get maximum # of samples database list can hold
getMaxOrderedCondListSize() - Method in class MJAcondition
getMaxOrderedCondListSize() - get maximum # of condition lists that an ordered condition list can hold
getMeanDataForCondition(float[], float[], int[], String, String) - Method in class MJAsampleList
getMeanDataGeneListDataForCondition() - get filtered (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in (meanData[], stdDevData[], propList[]) for data filtered by the specified gene list.
getMedMinerURL() - Method in class MJAstate
getMedMinerURL() - get the current url value
getMedMinerURLepilogue() - Method in class MJAstate
getMedMinerURLepilogue() - get the current url value
getMenuHook() - Method in class MaeJavaAPI
getMenuHook() - get the menu hook for the plugin
getMenuHook() - Method in class MAEPlugin.MAEPlugin
getMenuHook() - get menu Item hook to put our instance of plugin
getMenuHook() - Method in interface MAEPlugin.MAEStub
getMenuHook() - method to retrieve the root menu
getMenuInsertionPointName() - Method in class MAEPlugin.MAEPlugin
getMenuInsertionPointName() - get the name of menu insertion point If it is not defined, then it returns null that indicates the Plugins menu.
getMenuItem() - Method in class MAEPlugin.MAEPlugin
getMenuItem() - get menu item for this instance of the plugin
getMenuTreeFromSamplesTable(MAExplorer) - Method in class StageNames
getMenuTreeFromSamplesTable() - build tree from Samples.txt Table
getMIDfromMaster_IDhashTable(String) - Method in class GipoTable
getMIDfromMaster_IDhashTable() - get Gene index (mid) given Master_ID.
getMIDindicesForFilterGeneList() - Method in class MJAgeneList
getMIDindicesForFilterGeneList() - get list MIDs for data Filter GeneList.
getMIDindicesFromGeneList(String) - Method in class MJAgeneList
getMIDindicesFromGeneList() - get list of GeneList MIDs by GeneList name.
getMIDtoGIDmap() - Method in class MJAgeometry
getMIDtoGIDmap() - get the map from MIDs to GIDs
getMinimumSize() - Method in class ClusterGramCanvas
getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class Draw2Dplot
getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class DrawClusterGram
getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class StatusCanvas
getMinimumSize() - get the minimumpreferred size
getMinimumSize() - Method in class DrawHistogram
getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class DrawRatioHistogram
getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class ExprProfileCanvas
getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class ExprProfilePanel
getMinimumSize() - get the minimumpreferred size
getMinimumSize() - Method in class ExprProfilePopup
getMinimumSize() - get the minimum preferred window size and add on room for the buttons at the bottom.
getMinimumSize() - Method in class ScrollableImageCanvas
getMinimumSize() - get the minimum current size of the canvas size
getNamedOrderedCondListIdx(String) - Method in class MJAcondition
getNamedOrderedCondListIdx() - get named ordered condition list index
getNbrActiveFilters() - Method in class MJAfilter
getNbrActiveFilters) - get number of active data Filters
getNbrAnalyses() - Method in class MJAReval
getNbrAnalyses() - get the number of analyses in the RLO DB
getNbrAnalyses() - Method in class RevalBase
getNbrAnalyses() - get the number of analyses in the RLO DB
getNbrCondLists() - Method in class MJAcondition
getNbrCondLists() - get # of active condition lists
getNbrCondParams() - Method in class MJAcondition
getNbrCondParams() - get the number of condition parameters
getNbrGeneBitSubsets() - Method in class MJAgeneList
getNbrGeneBitSubsets() - get total # of gene list bit subsets in DB
getNbrGenesPassingFilter() - Method in class MJAfilter
getNbrGenesPassingFilter() - get boolean flags for genes passing data Filter indexed by MID.
getNbrGeneSubsets() - Method in class MJAgeneList
getNbrGeneSubsets() - get total # of gene subsets in DB
getNbrGridIDs() - Method in class MJAgeometry
getNbrGridIDs() - get the number of genes
getNbrHPsamples() - Method in class MJAsampleList
getNbrHPsamples() - get # of ALL HP samples currently loaded in DB
getNbrMasterIDs() - Method in class MJAgeometry
getNbrMasterIDs() - get the number of Master Gene IDs
getNbrOrderedCondLists() - Method in class MJAcondition
getNbrOrderedCondLists() - get # of active ordered condition lists
getNbrSpecialGeneSubsets() - Method in class MJAgeneList
getNbrSpecialGeneSubsets() - get # of special gene subsets in DB
getNbrSpots() - Method in class MJAgeometry
getNbrSpots() - get the number of Nbr Spots in entire array
getNextInt(StringTokenizer) - Method in class UserState
getNextInt() - parse next int from StringTokenizer the integers are separated by ',' or '\n'.
getNextStrNameValFromLine(StringTokenizer) - Method in class RevalBase
getNextStrNameValFromLine() - get next line and parse 'name=value\n'.
getNextStrNameValFromLine(StringTokenizer) - Method in class UserState
getNextStrNameValFromLine() - get next line and parse 'name=value\n'.
getNormalizationState() - Method in class MaeJavaAPI
getNormalizationState() - update Normalization state based on normalization method selected in plugins.
getNormalizationState() - Method in interface MAEPlugin.MAEStub
getNormalizationState() - alias to: EventMenu.getNormalizationState used by: NormalizationPlugin
getNormalizationState() - Static method in class MAEPlugin.analysis.NormalizationPlugin
getNormalizationState() - Static method for using testing getActiveNormalization().
getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean) - Method in class CompositeDatabase
getNormHP_XandYdata() - get normalized list spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
getNormMethod() - Method in class MJAnormalization
getNormMethod() - get name of current normalization method
getNormMethodDisplayName() - Method in class MJAnormalization
getNormMethodDisplayName() - get display name of current normalization method
getNormToOneFlag() - Method in class MJAexprProfile
getNormToOneFlag() - flag of normalize expression profile to 1.0 flag
getNthValueByName(String, int) - Method in class ConfigTable
getNthValueByName() - get n'th Configuration table Value by Name
getNumberedParamList(String) - Method in class GetParams
getNumberedParamList() - get a numbered parameter list The parameters are of the form: "image1", "image2", ...
getNumberPlugins() - Static method in class MAEPlugin.MAEPlugin
getNumberPlugins() - get the number of plugins (loaded).
getNumbersOfGenesInGeneSubsets() - Method in class MJAgeneList
getNumbersOfGenesInGeneSubsets() - get list of # genes in each of the gene subsets
getObjPos() - Method in class ArrayScroller
getObjPos() - get the object position
getObjPos() - Method in class ScrollableImageCanvas
getObjPos() - get the object position (xObj,yObj).
getOCLidxFromName(String) - Method in class PopupOrderedCondChooser
getOCLidxFromName() - Look up and return index of current ocl.
getOCLnameFromIdx(int) - Method in class PopupOrderedCondChooser
getOCLnameFromIdx() - Look up and return name of current ocl.
getOfileTypeDBmenus() - Method in class MJAReval
getOfileTypeDBmenus() - get the R output file type menus
getOfileTypeDBmenus() - Method in class RevalBase
getOfileTypeDBmenus() - get the R output file type menu
getOfileTypeDBnames() - Method in class MJAReval
getOfileTypeDBnames() - get the R output file type names
getOfileTypeDBnames() - Method in class RevalBase
getOfileTypeDBnames() - get the R output file type names
getOfileTypeDBtypes() - Method in class MJAReval
getOfileTypeDBtypes() - get the R output file type values
getOfileTypeDBtypes() - Method in class RevalBase
getOfileTypeDBtypes() - get the R output file names type values
getOrderedCondListsNames() - Method in class MJAcondition
getOrderedCondListsNames() - get list of active ordered condition lists names
getOrderedCondListsSizes() - Method in class MJAcondition
getOrderedCondListsSizes() - get list of active ordered condition lists sizes
getOrderedCondNamesInCondList(String) - Method in class MJAcondition
getOrderedCondNamesInCondList() - get a list of all condition names in ordered cond list
getOrderedCondParamNames() - Method in class MJAcondition
getOrderedCondParamNames() - return list of Ordered condition paramter names.
getOrderedCondParamValues(String) - Method in class MJAcondition
getOrderedCondParamValues() - return list of Ordered condition paramter values.
getOutputDataFileNames() - Method in class MJAReval
getOutputDataFileNames() - get current RLO list of output data file names.
getOutputDataFileNames() - Method in class RevalBase
getOutputDataFileNames() - get current RLO list of output data file names.
getOutputDataTypes - Variable in class RgenDemo
Output types [0:nOutputFiles-1] if any
getOutputDataTypes() - Method in class MJAReval
getOutputDataTypes() - get current RLO list of output data file types
getOutputDataTypes() - Method in class RevalBase
getOutputDataTypes() - get current RLO list of output data file types
getOutputStream() - Method in class JavaCGIBridge
getOutputStream() - implements getOutputStream for HttpURLconnection.
GetParams - class GetParams.
This class get the argument list from the Applet or .mae startup file.
GetParams(MAExplorer) - Constructor for class GetParams
GetParams() - constructor
getParamVal(String) - Method in class GetParams
getParamVal() - get parameter from Configuration database file
getParsedData(URL) - Method in class JavaCGIBridge
getParsedData() - returns parsed data in form of Vector of Vectors containing the returned fields inside of a Vector of returned rows.
getParsedData(URL, Hashtable) - Method in class JavaCGIBridge
getParsedData() - returns parsed data in form of Vector of Vectors Returns parsed data in the form of a Vector of Vectors containing the returned fields inside of a Vector of returned rows.
getPassword() - Method in class MJAproperty
getPassword() - get current user password name if exists
getPirURL() - Method in class MJAstate
getPirURL() - get the current url value
getPlate(int) - Method in class SpotFeatures
getPlate(gid) - return the Plate coords Grid[r,c] as B3,4 etc.
getPlotModeImage() - Method in class MJAproperty
getPlotModeImage() - get pseudoarray image plot mode: PLOT_xxxx_IMAGE
getPluginDescription() - Method in class MAEPlugin.MAEPlugin
getPluginDescription() - returns a human readable description of the Plugin if any is defined by the plugin writer.
getPluginDescription() - Method in interface MAEPlugin.PluginStub
getPluginDescription() - returns a human readable description of the Plugin.
getPluginDescription() - Method in class MAEPlugin.popup.PluginLoader
getPluginDescription() - This returns a human readable description of the Plugin
getPluginDescription() - Method in class MAEPlugin.popup.PluginUnLoader
getPluginDescription() - This returns a human readable description of the Plugin
getPluginFileName() - Method in class MAEPlugin.MAEPlugin
getPluginFileName() - returns the plugin file name without the ".jar"
getPluginFileName() - Method in interface MAEPlugin.PluginStub
getPluginFileName() - returns the plugin file name without the ".jar"
getPluginHashState(String, String) - Method in class MJAstate
getPluginHashState() - get state object value from MAEPlugin hash state storage.
getPluginHashState(String, String, boolean) - Method in class MJAstate
getPluginHashState() - get boolean state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.
getPluginHashState(String, String, byte) - Method in class MJAstate
getPluginHashState() - get byte state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.
getPluginHashState(String, String, double) - Method in class MJAstate
getPluginHashState() - get double state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.
getPluginHashState(String, String, float) - Method in class MJAstate
getPluginHashState() - get float state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.
getPluginHashState(String, String, int) - Method in class MJAstate
getPluginHashState() - get int state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.
getPluginHashState(String, String, long) - Method in class MJAstate
getPluginHashState() - get long state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.
getPluginHashStateFileName() - Method in class MJAstate
getPluginHashStateFileName() - get the MAEPlugin hash state disk file name.
getPluginName() - Method in class MAEPlugin.MAEPlugin
getPluginName() - This is the human readable name for use in menu labels
getPluginName() - Method in interface MAEPlugin.PluginStub
getPluginName() - returns the human readable name for use in labels.
getPlugins() - Static method in class MAEPlugin.MAEPlugin
getPlugins() - gets Registry list of MAEPlugins
getPosQuantTestMode() - Method in class MJAproperty
getPosQuantTestMode() - get positive Quant data test mode: SS_MODE_xxxx
getPreferredSize_DEPRICATED() - Method in class StateScrollers
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ArrayScroller
getPreferredSize() - get the preferred window size
getPreferredSize() - Method in class ClusterGramCanvas
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class Draw2Dplot
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class DrawClusterGram
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class StatusCanvas
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class DrawHistogram
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class DrawRatioHistogram
getPreferredSize() - get the preferred size.
getPreferredSize() - Method in class ExprProfileCanvas
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ExprProfilePanel
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ExprProfilePopup
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class PopupCondChooser.CondParamEditForm
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class PopupOrderedCondChooser.CondParamEditForm
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class RtestBase
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class PopupEditRscript
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ScrollableImageCanvas
getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ShowExprProfilesPopup
getPreferredSize() - get the preferred size
getProcessBitsDBmenus() - Method in class MJAReval
getProcessBitsDBmenus() - get Export/Import ProcessBits DB menus
getProcessBitsDBmenus() - Method in class RevalBase
getProcessBitsDBmenus() - get Export/Import ProcessBits DB menus entries
getProcessBitsDBnames() - Method in class MJAReval
getProcessBitsDBnames() - get Export/Import ProcessBits DB names
getProcessBitsDBnames() - Method in class RevalBase
getProcessBitsDBnames() - get Export/Import ProcessBits DB names
getProcessBitsDBvalues() - Method in class MJAReval
getProcessBitsDBvalues() - get Export/Import ProcessBits DB values
getProcessBitsDBvalues() - Method in class RevalBase
getProcessBitsDBvalues() - get Export/Import ProcessBits DB values
getProject() - Method in class MJAproperty
getProject() - get current project associated with database
getProjectNameBySampleNbr(int) - Method in class MJAsample
getProjectNameBySampleNbr() - lookup the sample project name by sample number.
getQualCheckList(int) - Method in class MJAsample
getQualCheckList() - get list of QualCheck data for sample number.
getQualCheckQuantDataList(int) - Method in class MJAsample
getQualCheckQuantDataList() - get spot QualCheck good spot data list for the given sample.
getR2ClientActionDBmenus() - Method in class MJAReval
getR2ClientActionDBmenus() - get R to client Actions DB menus
getR2ClientActionDBmenus() - Method in class RevalBase
getR2ClientActionDBmenus() - get R to client Actions DB menus
getR2ClientActionDBnames() - Method in class MJAReval
getR2ClientActionDBnames() - get R to client Actions DB names
getR2ClientActionDBnames() - Method in class RevalBase
getR2ClientActionDBnames() - get R to client Actions DB names
getR2ClientActionDBtypes() - Method in class MJAReval
getR2ClientActionDBtypes() - get R to client Actions DB type values
getR2ClientActionDBtypes() - Method in class RevalBase
getR2ClientActionDBtypes() - get R to client Actions DB type values
getRatioCy3Cy5RangeMode() - Method in class MJAproperty
getRatioCy3Cy5RangeMode() - get Cy3/Cy5 range restriction mode for threshold filter: RANGE_xxxx
getRatioRangeMode() - Method in class MJAproperty
getRatioRangeMode() - get Ratio range restriction for threshold mode: RANGE_xxxx
getRatioStr() - Method in class MJAutil
getRatioStr() - get "F1/F2", "Cy3/Cy5" or "Cy5/Cy3", etc.
getRatioStr() - Static method in class Util
getRatioStr() - get "F1/F2", "Cy3/Cy5" or "Cy5/Cy3", etc.
getRatioString() - Method in class MJAproperty
getRatioString() - get "F1/F2", "Cy3/Cy5" or "Cy5/Cy3", or user-defined channels "channel1/channel2" etc.
getRawBackgroundDataByGID(int, int) - Method in class MJAgene
getRawBackgroundDataByGID() - return spot raw background intensity data specified by gid (Grid Index ID) and data type.
getRawBkgrd(int) - Method in class MaHybridSample
getRawBkgrd() - get raw background intensity specified by the gid.
getRawBkgrdQuantDataList(int) - Method in class MJAsample
getRawBkgrdQuantDataList() - get raw spot background quant data for the given sample.
getRawCGIData(URL) - Method in class JavaCGIBridge
getRawCGIData() - returns raw HTML data as a String from the passed URL.
getRawCGIData(URL, Hashtable) - Method in class JavaCGIBridge
getRawCGIData() - returns raw HTML data as a String from URL & hashtable.
getRawCGIDataByte(URL, Hashtable) - Method in class JavaCGIBridge
getRawCGIDataByte() - returns raw HTML data as byte[] from URL&hashtable.
getRawDataByGID(int, boolean, int) - Method in class MaHybridSample
getRawDataByGID() - get raw data specified by gid and data type.
getRawDataByGID(int, int) - Method in class MJAgene
getRawDataByGID() - return spot intensity data specified by gid (Grid Index ID) and data type.
getRawF1F2DataAndBkgdForSample(float[], float[], float[], float[], int[], int[], int, String) - Method in class MJAsampleList
getRawF1F2DataAndBkgdForSample() - get filtered spot list raw intensity and background data for genes and return it in the arrays pre-specified by the user.
getRawHP_XandYdata(float[], float[], float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean) - Method in class CompositeDatabase
getRawHP_XandYdata() - get list raw spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
getRawHP_XandYsamplesData(float[], float[], float[], float[], int[], int, int, String) - Method in class MJAsampleList
getAllRawHPdataForSample() - get all raw (data,prop) list single sample's intensity data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data by the specified gene list.
getRawIntens(int, boolean) - Method in class MaHybridSample
getRawIntens() - get spot (rawIntensity - rawBackground) data by gid and data type
getRawIntensData(int, boolean) - Method in class MJAgene
getRawIntensData() - get spot raw (Intensity - Background) data specified by gid (Grid Index ID) and data type.
getRawIntensityQuantDataList(int) - Method in class MJAsample
getRawIntensityQuantDataList() - get raw spot intensity quant data list for the given sample.
getRawSampleData(int) - Method in class MJAsample
getRawSampleData() - get list of a sample's total histogram statistics.
getRdataTypeDBmenus() - Method in class MJAReval
getRdataTypeDBmenus() - get the R input file type menus
getRdataTypeDBmenus() - Method in class RevalBase
getRdataTypeDBmenus() - get the R input file type menus
getRdataTypeDBnames() - Method in class MJAReval
getRdataTypeDBnames() - get the R input file type names
getRdataTypeDBnames() - Method in class RevalBase
getRdataTypeDBnames() - get the R input file type names
getRdataTypeDBtypes() - Method in class MJAReval
getRdataTypeDBtypes() - get the R input file type values
getRdataTypeDBtypes() - Method in class RevalBase
getRdataTypeDBtypes() - get the R input file type values
getRemCondData(int) - Method in class PopupOrderedCondChooser
getRemCondData() - get remainder data, locally.
getRemCondDataFromChooserGUI(int) - Method in class PopupOrderedCondChooser
getRemCondDataFromChooserGUI() - get remainder data from chooserGUI
getRemSamplesData(int) - Method in class PopupCondChooser
getRemSamplesData() - get remainder data, locally.
getRemSamplesDataFromChooserGUI(int) - Method in class PopupCondChooser
getRemSamplesDataFromChooserGUI() - get remainder data from chooserGUI
getReportBasePath() - Method in class MJAReval
getReportBasePath() - get current path of client /Report/
getReportFontFamily() - Method in class MJAproperty
getReportFontFamily() - get current Report font family
getReportFontSize() - Method in class MJAproperty
getReportFontSize() - get current Report font size
getReportTestMode() - Method in class MJAproperty
getReportTestMode() - get Report type mode: 'RPT_xxxx'
getResource(String) - Method in class MAEPlugin.FileClassLoader
getResource() - Returns a URL containing the location of the named resource.
getResource(String) - Method in class MAEPlugin.JarResources
getResource() - Extracts a jar resource as a blob.
getResourceAsStream(String) - Method in class MAEPlugin.FileClassLoader
getResourceAsStream() - returns an input stream to the named source.
getRLObasePath() - Method in class MJAReval
getRLObasePath() - get current path of /RLO/
getRLObyID(int) - Method in class RLO
getRLObyID() - get the RLO by id
getRLObyMenuName(String) - Method in class RLO
getRLObyMenuName() - get the RLO by menuName
getRLObyRscriptName(String) - Method in class RLO
getRLObyRscriptName() - get the RLO by RscriptName
getRLOidByRscriptName(String) - Method in class MJAReval
getRLOidByRscriptName() - get the current RLO analysis method id by RscriptName
getRLOidByRscriptName(String) - Method in class RevalBase
getRLOidByRscriptName() - get the current RLO analysis method id by RscriptName
getRLOidByRscriptName(String) - Method in class RLO
getRLOidByRscriptName() - get the current RLO analysis method id by RscriptName
getRLOinputFile(int, int) - Method in class MJAReval
getRLOinputFile() get the nth Input Data file by input file type.
getRLOinputFile(int, int) - Method in class RLO
getRLOinputFile() get the nth Input Data file by input file type.
getRLOoutFile(int, int) - Method in class MJAReval
getRLOoutFile() get the nth Output Data file by out file type.
getRLOoutFile(int, int) - Method in class RLO
getRLOoutFile() get the nth Output Data file by out file type.
getRLORlibrBasePath() - Method in class MJAReval
getRLORlibrBasePath() - get current base path of client RLORibr/ directory lives in "{installation directory}/".
getRLOstring(String) - Method in class MJAReval
getRLOstring() - get prettyprint string for the current RLO
getRmList() - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
 
getRowSeparator() - Method in class JavaCGIBridge
getRowSeparator() - Returns the row separator for the object.
getRreportStr() - Method in class MJAReval
getRreportStr() - get R report after doing eval of .R script after file setup
getRscriptBasePath() - Method in class MJAReval
getRscriptBasePath() - get current path of /R/
getRscriptByRLOid(int) - Method in class PopupEditRscript
getRscriptByRLOid() - generate or read the current Rscript into RscriptText.
getRstartupOptions() - Method in class MJAReval
getRstartupOptions() - get R command line startup options
getRstartupOptions(String) - Method in class MJAReval
setRstartupOptions() - set R command line startup options
getSample() - Method in interface MAEPlugin.Normalization
getSample() - get the sample object
getSample() - Method in class MAEPlugin.analysis.NormalizationPlugin
getSample() - used to Get the primary sample, to get the variables
getSampleCalibDNAdata(int, boolean) - Method in class MJAsample
getSampleCalibDNAdata() - get list of a Sample calibration DNA data this sample.
getSampleF1F2Extrema(int) - Method in class MJAsample
getSampleF1F2Extrema() - get list of sample's normalized F1F2 intensity extrema and 1st order histogram statistics.
getSampleHistStats(int, boolean) - Method in class MJAhistogram
getSampleHistStats() - compute Filtered sample intensity histogram and get list of statistics and return list of statistics
getSampleIDbySampleNbr(int) - Method in class MJAsample
getSampleIDbySampleNbr() - lookup the sample ID name by sample number.
getSampleIntensRangeMode() - Method in class MJAproperty
getSampleIntensRangeMode() - get Sample intensity range restriction mode for filter: RANGE_xxxx
getSampleNamesInCondList(String) - Method in class MJAcondition
getSampleNamesInCondList() - get list of sample names in named condition.
getSampleNbrByCondNameAndSampleName(String, String) - Method in class MJAcondition
getSampleNbrByCondNameAndSampleName() - get sample number by sample name and condition name.
getSampleNbrBySampleName(String) - Method in class PopupCondChooser
getSampleNbrBySampleName() - lookup the sample # by its name
getSamplesDataVector(float[], int[], int) - Method in class MJAsample
getSamplesDataVector() - get sample data for sample indexes for gene mid.
getSamplesInCondList(String) - Method in class MJAcondition
getSamplesInCondList() - get list of sample numbers in named condition.
getSampleStatisticsTable() - Method in class MJAsampleList
getSampleStatisticsTable() - get list of all Sample statistics table.
getSampleTotHistStats(int) - Method in class MJAsample
getSampleTotHistStats() - get list of a sample's total histogram statistics.
getSampleTotHistStats(Object) - Method in class MaeJavaAPI
getSampleTotHistStats() - get Hashtable list of a sample's total histogram statistics.
getSampleTotHistStats(Object) - Method in interface MAEPlugin.MAEStub
getSampleTotHistStats() - get Hashtable list of a sample's total histogram statistics.
getSampleTypeFlags(int) - Method in class MJAsample
 
getSampleVsSampleCorrelationsTable() - Method in class MJAsampleList
getSampleVsSampleCorrelationsTable() - get list of Sample Vs Sample correlations table.
getSAParam(String) - Method in class GetParams
getSAParam() - get parameter from applet or standalone application startup database Table previously read from file.
getScaledSpotData(int, boolean) - Method in class MJAgene
getScaledSpotData() - get scaled spot (Intensity - Background) data specified by gid (Grid Index ID) and data type.
getScaledSpotData1(int, boolean) - Method in class MJAgene
getScaledSpotData1() - get scaled spot (Intensity - Background) data1 specified by gid (Grid Index ID) and data type.
getScaledSpotData2(int, boolean) - Method in class MJAgene
getScaledSpotData2() - get scaled spot (Intensity - Background) data2 specified by gid (Grid Index ID) and data type.
getScaleFactors(int) - Method in class MJAsample
getSampleScaleFactors() - get list of a sample's scale factors.
getSelCondData(int) - Method in class PopupOrderedCondChooser
getSelCondData() - get Select data, locally.
getSelCondDataFromChooserGUI(int) - Method in class PopupOrderedCondChooser
getSelCondDataFromChooserGUI() - get selected data from chooserGUI
getSelSamplesData(int) - Method in class PopupCondChooser
getSelSamplesData() - get Select data, locally.
getSelSamplesDataFromChooserGUI(int) - Method in class PopupCondChooser
getSelSamplesDataFromChooserGUI() - get selected data from chooserGUI
getSetR2ClientFileNames() - Method in class MJAReval
getSetR2ClientFileNames() - get current RLO list of R2Client data file names.
getSetR2ClientFileNames() - Method in class RevalBase
getSetR2ClientFileNames() - get current RLO list of R2Client data file names.
getSetR2ClientObjNames() - Method in class MJAReval
getSetR2ClientObjNames() - get current RLO list of R2Client object names
getSetR2ClientObjNames() - Method in class RevalBase
getSetR2ClientObjNames() - get current RLO list of R2Client object names
getSetR2ClientObjTypes() - Method in class MJAReval
getSetR2ClientObjTypes() - get current RLO list of R2Client object types
getSetR2ClientObjTypes() - Method in class RevalBase
getSetR2ClientObjTypes() - get current RLO list of R2Client object types
getSizeOf_HP_E_set() - Method in class MJAsampleList
getSizeOf_HP_E_set() - get # of HP-E 'set' samples.
getSizeOf_HP_X_set() - Method in class MJAsampleList
getSizeOf_HP_X_set() - get # of HP-X 'set' samples
getSizeOf_HP_Y_set() - Method in class MJAsampleList
getSizeOf_HP_Y_set() - get # of HP-Y 'set' samples
getSortedListOfNearestGenesIdx(int) - Method in class ClusterGenes
getSortedListOfNearestGenesIdx()- get sorted list of nearest genes[] of cIdx.
getSpotData12Static(int, int, boolean) - Method in class MaHybridSample
getSpotData12Static() - get STATIC scaled spot data object for gid1, gid2.
getSpotDataStatic(int, boolean) - Method in class MaHybridSample
getSpotDataStatic() - get a STATIC scaled spot data object for this gid.
getSpotFeatures(Point, MaHybridSample) - Method in class SpotFeatures
getSpotFeatures() - get spot coords and features associated with spot at (x,y)
getSpotFeaturesLine(int) - Method in class SpotFeatures
getSpotFeaturesLine() - get spot coords and features associated with spot gid.
getSpotGenomicData(Point, MaHybridSample) - Method in class SpotFeatures
getSpotGenomicData() - get additional genomic name features by (x,y) coordindate of current spot for sample if the features exist.
getSpotGenomicLine(int) - Method in class SpotFeatures
getSpotGenomicLine() - get additional Genomic name features by GID if they exist.
getSpotIntensCompareMode() - Method in class MJAproperty
getSpotIntensCompareMode() - get Spot Intensity compare restriction mode for filter: COMPARE_xxxx
getSpotIntensRangeMode() - Method in class MJAproperty
getSpotIntensRangeMode() - get Spot intensity range restriction mode for filter: RANGE_xxxx
getSpotIntensTestMode() - Method in class MJAproperty
getSpotIntensTestMode() - get spot intensity test mode: SS_MODE_xxxx
getSpotMeasurementStr(int, MaHybridSample) - Method in class SpotFeatures
getSpotMeasurementStr() - return pretty-print spot measurement string.
getStartupRscriptFileName() - Method in class MJAReval
getStartupRscriptFileName() - get name of batch R startup script file to exec() by the OS after file setup
getState() - Method in class MAEPlugin.CheckBoxMenuPlugin
getState() - utility to get the checkbox state
getState() - Method in interface MAEPlugin.Normalization
getState() - get the state of the checkbox
getStateParamValues() - Method in class Config
getStateParamValues() - get non-file state PARAMs
getStateScrollersStatus() - Method in class MJAfilter
getStateScrollersStatus() - get list of active status of ALL State Scrollers
getStrValFromLine(String) - Method in class UserState
getStrValFromLine() - parse value for key 'name=value\n'.
getStrValFromLine(String, StringTokenizer) - Method in class RevalBase
getStrValFromLine() - get line and parse value for key 'name=value\n'.
getStrValFromLine(String, StringTokenizer) - Method in class UserState
getStrValFromLine() - get line and parse value for key 'name=value\n'.
getSwissProtURL() - Method in class MJAstate
getSwissProtURL() - get the current url value
getTableFieldDataByHPname(String, String) - Method in class SamplesTable
getTableFieldDataByHPname() - get data of fieldName of particular HP sample
getTableRowByMaInfoId(String) - Method in class MaInfoTable
getTableRowByMaInfoId() - get row of MaInfos data by MaInfo_Id
getTableRowByParameter(String) - Method in class ConfigTable
getTableRowByParameter() - get row of Configuration table data by Parameter
getTableRowFieldByRowIdx(int, String) - Method in class SimpleTable
getTableRowFieldByRowIdx() - get field in row by Table row index
getTableRowFieldIdxByRowIdx(int, int) - Method in class SimpleTable
getTableRowFieldIdxByRowIdx() - get data by field idx with row index
getTableRowsSubset(SimpleTable, String, String, String) - Method in class Table
getTableRowsSubset() - make new table subset of table by (field,key)
getTableRowsSubset(Table, String[], String[], String[], String[], int, String) - Method in class Table
getTableRowsSubset() - make new table of specified fields by fieldList[] and in the order in which they appear in the fieldList[].
getTblFmtMode() - Method in class MJAproperty
getTblFmtMode() - get Report table format mode: RPT_FMT_xxxx
getTempBasePath() - Method in class MJAReval
getTempBasePath() - get current path of client /Temp/
getTextField(int, int) - Method in class SStextArray
getTextField() - returns the (row,col) SStextCell
getThreadJavaCGIBridgeTimeOut() - Method in class JavaCGIBridge
getThreadJavaCGIBridgeTimeOut() - actual communication time out in msec.
getTopSeparator() - Method in class JavaCGIBridge
getTopSeparator() - Returns the top separator for the object.
getUniGeneClusterIdURL() - Method in class MJAstate
getUniGeneClusterIdURL() - get the current url value
getUniGeneURL() - Method in class MJAstate
getUniGeneURL() - get the current url value
getUniqueTableFieldData(int) - Method in class SamplesTable
getUniqueTableFieldData() - get list from SamplesDB.txt database Sort the array in ASCENDING order.
getURLEncodedHashTable(Hashtable) - Method in class JavaCGIBridge
getURLEncodedHashTable() - form variables inside hashtable as URLencoded string of parameters for a CGI based program to process.
getUseGenRbit(int) - Method in class RtestBase
getUseGenRbit() - lookup the use R_GENR_xxxx bit specified by method
getUserName() - Method in class MJAproperty
getUserName() - get current user login name if exists
getValue(int, int) - Method in class SpreadSheet
getValue() - get the String from the cell at grid position (i,j)
getValue(int, int) - Method in class SSspreadPanel
getValue() - get a single value from prepDataEdit cell(i,j)
getValueByName(String) - Method in class ConfigTable
getValueByName() - get Configuration table Value by Name
getValues() - Method in class SpreadSheet
getValues() - gets the whole grid as String[][] incl.
getValues() - Method in class SSspreadPanel
getValues() - get all values in a String[][] array
getXYdataList(int) - Method in class MJAsample
getXYdataList() - get list of XY coordinates data for sample.
getXYG(Point, MaHybridSample) - Method in class SpotFeatures
getXYG() - return pretty-print string for status of x,y,grayvalue string.
gGif - Variable in class DrawClusterGram
draw status at top of Gif image
gid - Variable in class Gene
a Grid Identifier (GID) index index corresponding to MasterID.
gid - Variable in class GridCoords
index cooresponding to ...[f][g][r][c]
gid1 - Variable in class ExprProfile
GID derived from mid
gid1 - Variable in class HPxyData
GID derived from mid
gid1S - Static variable in class SpotData
GridCoords gid of spot 1
gid2 - Variable in class ExprProfile
(opt) ganged GID derived from mid
gid2 - Variable in class HPxyData
Ggang ID derived from mid
gid2fgrc - Variable in class Maps
map: gid (GridCoords index) to [f][g][r][c] values in GridCoords object.
gid2GipoTableRow - Variable in class GipoTable
contains index of row in tData[], lookup by grid index (gid), of size maxGTmapSize
gid2mid - Variable in class Maps
map: gid (gridCoords index) to mid (Master Gene index).
gid2S - Static variable in class SpotData
GridCoords gid of spot 2
gidMapQ - Variable in class MaHybridSample
map GridCoord id for [f][g][r][c] for each row of this sample's tData[].
gidMaxF1 - Variable in class MaHybridSample
gid for max intens values F1 in getF1F2list
gidMaxF2 - Variable in class MaHybridSample
gid for max intens values F2 in getF1F2list
gidMinF1 - Variable in class MaHybridSample
gid for min intens values F1 in getF1F2list
gidMinF2 - Variable in class MaHybridSample
gid for min intens values F2 in getF1F2list
gidS - Static variable in class SpotData
GridCoords gid of a spot
gidStaticCL - Variable in class Maps
map: GridCoords gid index to list of genes.
gidToGangGid - Variable in class Maps
map: gid (GridCoords index) to the Gang gid.
GIFEncode(FileOutputStream, int, int, boolean, byte, int, int, byte[], byte[], byte[]) - Method in class WriteGifEncoder
GIFEncode() - encode the image Adapted from ppmtogif, which is based on GIFENCOD by David Rowley .
GIFNextPixel() - Method in class WriteGifEncoder
GIFNextPixel() - Return the next pixel from the image
gincDB - Variable in class GeneClass
(opt.) Table of gene classes if it exists
gipo - Variable in class Guesser
link to global GipoTable instance
gipo - Variable in class MAExplorer
Global instance of GIPO table mapping genes to other data
gipo - Static variable in class MJAbase
link to global GipoTable instance
gipo - Variable in class Report
link to global GipoTable instance
gipoFile - Variable in class Config
PARAM "gipoFile" or URL
GipoTable - class GipoTable.
The GipoTable class read sthe tab-delimited GipoTable file.
GipoTable(MAExplorer, String) - Constructor for class GipoTable
GipoTable() - constructor to read the GIPO table.
gLUT - Variable in class MedianCut
[0:255] Green Color map look up table
gmax - Variable in class MC_Cube
 
gmin - Variable in class MC_Cube
 
gName - Static variable in class Maps
list of alphabetic names of Names of grids
gName - Static variable in class SSstatusBar
 
gnMidGuesser - Variable in class MenuBarFrame
create when needed
gnp - Variable in class MAExplorer
Only while debugging: if DBUG_GENERIC_NORM_PLUGIN is set for use with TestPlugin.
goodGenesCL - Variable in class GeneClass
special list of good genes
goodSpotQualChkCL - Variable in class Filter
"Filter by Good Spot(QualChk) Data"
goodSpotTestMode - Variable in class MAExplorer
Good Spot (QualChk) test mode: SS_MODE_xxxx
gotHdrFlag - Variable in class JavaCGIBridge
 
gp - Variable in class Config
link to global instance of GetParams
gp - Variable in class MAExplorer
Global instance of contains set of applet/configuration PARAM parsers
gp - Variable in class ShowExprProfilesPopup
Grid panel
grandMeanCalDNA - Variable in class CompositeDatabase
grand mean HP Calib.DNA means for normalization.
grandMeanUseGeneSet - Variable in class CompositeDatabase
grand mean HP 'User Filter Gene Set' means for normalization.
grcd - Variable in class MAExplorer
Global instance of share grid coordinate mapper
greenBits(int) - Method in class MedianCut
greenBits() - Get 8-bit green component of a 15-bit color 8-bit pixel with low 3 bits zero.
grid_colIdx - Variable in class GipoTable
index for "grid col"
grid_rowIdx - Variable in class GipoTable
index for "grid row"
gridCharOffset - Variable in class MaHPquantTable
Grid alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters
gridCol - Variable in class StateScrollers
size of grid for panel
GRIDCOL - Variable in class StateScrollers
size of grid for panel
gridColCharOffset - Variable in class MaHPquantTable
Grid Column alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters
GridCoords - class GridCoords.
The class contains data structures to map a spot on the array to a GRC coodinate.
GridCoords() - Constructor for class GridCoords
GridCoords() - constructor to build empty instance.
GridCoords(int, int, int, int, int) - Constructor for class GridCoords
GridCoords() - constructor of individual grid coordinates for a gid spot.
GridCoords(MAExplorer) - Constructor for class GridCoords
GridCoords() - constructor which builds (f,g,r,c) - (gid or cid) mapping tables.
gridIdx - Variable in class GipoTable
index for "grid"
gridRow - Variable in class StateScrollers
size of grid for panel
gridRowCharOffset - Variable in class MaHPquantTable
Grid Row alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters
gScatterPlot - Variable in class Draw2Dplot
Graphics context used with displayPlot
gsr - Variable in class KeyEventHandler
instance of Guesser
gsr - Variable in class MouseEventHandler
instance of Guesser
GT_BAD_MID - Static variable in class GipoTable
analyzable bad clone id, good gene name
GT_BAD_SPOT - Static variable in class GipoTable
non-analyzable gene,, e.g.
GT_DUP_SPOT - Static variable in class GipoTable
analyzable genes, duplicated gene.
GT_GOOD - Static variable in class GipoTable
analyzable, good gene/clone id.
GUARD_REGION - Static variable in class MaHPquantTable
# pixels in target image on each edge
guardRegion - Variable in class DrawPseudoImage
# pixels in target image on each edge
guardRows - Variable in class ClusterGramCanvas
# of extra rows so cover the viewport
Guesser - class Guesser.
The Guesser class to used to create popup string guessers from list of strings.
Guesser(MAExplorer, boolean, boolean) - Constructor for class Guesser
Guesser() - constructor for Guesser.
guesserTitle - Static variable in class PopupGeneGuesser
title for window
guesserTitle - Static variable in class PopupHPmenuGuesser
title of guesser
guesserTitle - Static variable in class PopupProjDirGuesser
fixed prompt
guiReadyFlag - Variable in class RtestBase
set if GUI is ready for action!

H

handleActions(ActionEvent) - Static method in class EventMenu
handleActions() - handle menu item events (stateless command).
handleCheckboxStateChanged(ItemEvent) - Static method in class EventMenu
handleCheckboxStateChanged() - handle check box item state changed events.
handleEvent(Event) - Method in class PopupCondChooser
handleEvent() - process special events
handleEvent(Event) - Method in class PopupOrderedCondChooser
handleEvent() - process special events
handleEvent(Event) - Method in class RtestBase
handleEvent() - process special events
handleEvent(Event) - Method in class PopupEditRscript
handleEvent() - process special events
handleItemStateChanged(ItemEvent) - Static method in class EventMenu
handleItemStateChanged() - handle checkbox menu item state changed events.
handleKeyTyped(char) - Method in class Guesser
handleKeyTyped() - handle key Typed/Released in textfield of guesser
handleKeyTyped(char) - Method in class KeyEventHandler
handleKeyTyped() - handle key Typed/Released in textfield of guesser
hasActualXYcoordsFlag - Variable in class MaHybridSample
flag: set if have actual XY coords - not pseudoCoords
hasBkgrdPerSpotFlag - Variable in class MaHybridSample
flag: set if have bkgrd intens/spot
hasDetValueSpotDataFlag - Variable in class MaHybridSample
flag: if using spot data "CorrCoef" or "DetValue" field
hasMeanPlotsFlag - Variable in class ExprProfileOverlay
if hpDataXXX[] exists
hasMeanPlotsFlag - Variable in class ExprProfileScrollPane
if hpDataXXX[] exists
hasMeanPlotsFlag - Variable in class ShowExprProfilesPopup
Flag indicating that mean values should be plotted
hasPluginHashTableInMemoryFlag - Static variable in class MJAstate
flag indicating that hash table is active
hasQualChkFlag - Variable in class MaHybridSample
flag: if using "QualCheck" field
hasStopButtonFlag - Variable in class MenuBarFrame
set if stopButton has "STOP!" label
hasValidData - Variable in class ConfigTable
flag: set if data was read ok
hasValidDataFlag - Variable in class MaHybridSample
flag: set if .quant array data is set up ok
hasValidDataFlag - Variable in class MaInfoTable
flag: set if data was read ok
hasValidDataFlag - Variable in class SamplesTable
set if data was read ok
hasXYimageCQflag - Variable in class MaHybridSample
flag: has xyImgCQ_X/Y[] data for Montage image
hcLeft - Variable in class HierClustNode
Dynamic node: if not null, then left cluster
hcn - Static variable in class ClusterGenes
hierarchical clustering tree
hcParent - Variable in class HierClustNode
Dynamic node: if not null, then the parent of this node
hcRight - Variable in class HierClustNode
Dynamic node: if not null, then right cluster
headerClicked - Variable in class ShowSpreadsheetPopup
color for header when click on cell
headerClickedCol - Variable in class SSspreadPanel
 
HeaderFieldKey(int) - Method in class JavaCGIBridge
HeaderFieldKey() - implements HeaderFieldKey for HttpURLconnection.
headerFontSize - Variable in class SSspreadPanel
Calculated default or overidden
headerName - Variable in class ShowSpreadsheetPopup
header name for col clicked on in virData
headers - Variable in class JavaCGIBridge
 
height - Variable in class PopupBinOprDialogQuery
size of frame
height - Variable in class PopupDialogQuery
size of frame
height - Variable in class PopupLoginDialogQuery
size of frame
height - Variable in class WriteGifEncoder
 
height - Variable in class MedianCut
width size of image
Height - Variable in class WriteGifEncoder
 
helpButton - Variable in class RtestBase
"Help Msg" window button
helpMenu - Variable in class MenuBarFrame
"Help" menu
helpMsg - Variable in class RtestBase
Help text
helpStr - Variable in class PopupEditRscript
The help message
hideButton - Variable in class LogTextFrame
hide button to hide the Log window.
hideWindow() - Method in class LogTextFrame
hideWindow() - flush the buffer and hide the log window
HIER_CLUST_NEXT_MIN_LNKG - Static variable in class MAExplorer
Hierarchical clustering mode: next-minimum cluster linkage
HIER_CLUST_NEXT_MIN_LNKG - Static variable in class MJAbase
Hierarchical clustering mode: next-minimum cluster linkage
HIER_CLUST_PGMA_LNKG - Static variable in class MAExplorer
Hierarchical clustering mode: Average-arithmetic linkage
HIER_CLUST_PGMA_LNKG - Static variable in class MJAbase
Hierarchical clustering mode: Average-arithmetic linkage
HIER_CLUST_PGMC_LNKG - Static variable in class MAExplorer
Hierarchical clustering mode: Average-centroid linkage
HIER_CLUST_PGMC_LNKG - Static variable in class MJAbase
Hierarchical clustering mode: Average-centroid linkage
hierClusterGramPopup - Static variable in class ClusterGenes
plot popup for ClusterGram display for hierarchical clustering
hierClusters - Static variable in class HierClustNode
hierarchical clusters [0:2*nObj-1] nHierClusters is the current one.
hierClustersExprProfPopup - Variable in class DrawClusterGram
exists if create EP plot subset popup
hierClustMode - Static variable in class HierClustNode
linkage mode
hierClustMode - Variable in class MAExplorer
Hier.Clustering linkage mode: HIER_CLUST_xxxxx
HierClustNode - class HierClustNode.
The HierClustNode class computes a general purpose hierarchical clustering tree.
HierClustNode(HierClustNode, HierClustNode) - Constructor for class HierClustNode
HierClustNode() - construct top level hierarchical cluster node
HierClustNode(int, float[], String, int) - Constructor for class HierClustNode
HierClustNode() - construct bottom level hierarchical cluster nodes which will provide data for both a Clustergram and Dendrogram...
HierClustNode(MAExplorer, int, int, GeneList, float[][]) - Constructor for class HierClustNode
HierClustNode() - setup static variables for ONLY ClusterGram for use with K-means clustering data.
HierClustNode(MAExplorer, int, int, int, boolean, boolean, boolean, boolean, int) - Constructor for class HierClustNode
HierClustNode() - setup static variables for full hier clustering which will provide data for both a Clustergram and Dendrogram...
hierClustUnWtAvgFlag - Variable in class MAExplorer
use UPGMA or WPGMA for computing the average node vector when hierarchical clustering.
highestRatiosCL - Variable in class Filter
"Highest ratios"
highMID - Variable in class GeneBitSet
highest MID in this GeneBitSet
hist - Variable in class DrawHistogram
freq hist[0:nHist-1].
hist - Variable in class MaHybridSample
normalized intensity histogram [0:nBins]
hist - Variable in class Statistics
histogram of size [0:nBinsH-1] set by calcHistStats()
hist15 - Variable in class MedianCut
[0:32K] 15-bit RGB hist.
histBinMode - Variable in class ShowPlotPopup
Histogram Bind Mode using TH_xx: "= " is 1, "< " is 2, "> " is 3, "<>" is 4, "><" is 5
histBinRange - Variable in class ShowPlotPopup
Histogram (intens/ratio) bin range button.
histBinRangeButton - Variable in class ShowPlotPopup
histogram (intens/ratio) bin range button
histologyURL - Variable in class Config
base addr PARAM "histologyURL"
historyFileName - Static variable in class Util
Full path name of history file if enabled.
historyIsVisibleFlag - Static variable in class Util
History window visibility flag
historyTextFrame - Static variable in class Util
Log History text frame.
histPtr - Variable in class MedianCut
[0:colorMax-1] points to colors in "hist15[]"
histRatio - Variable in class DrawRatioHistogram
freq bin hist[0:nHist-1].
histRatioBin - Static variable in class MAExplorer
preloaded set of legal ratios in [1/100 : 100]
histValue - Variable in class DrawRatioHistogram
value bin hist[0:nHist-1].
hLB - Variable in class ExprProfileOverlay
lower HP sample # to display
horizCaption - Variable in class Draw2Dplot
ARGS: horizontal caption
horizCaption - Variable in class DrawHistogram
horizontal caption
horizCaption - Variable in class DrawRatioHistogram
horizontal caption
horizLBscr - Variable in class ShowPlotPopup
horizontal LowerBound scrollbar for canvas
horizUBscr - Variable in class ShowPlotPopup
horizontal UpperBound scrollbar for canvas
horizVariableCaption - Variable in class DrawHistogram
horizontal variable caption
horizVariableCaption - Variable in class DrawRatioHistogram
horizontal variable caption
housekeepingGenesCL - Variable in class GeneClass
special list of all housekeeping genes
howManyWildCards(String) - Method in class KeyEventHandler
howManyWildCards() - return number of wildcards present 0 if none found.
HP_EclustersCL - Variable in class Filter
"Filter by HP-E clusters"
HP_Xlabel - Variable in class MenuBarFrame
GUI label for current HP-X
HP_XY_t_TestCL - Variable in class Filter
"Filter genes by HP-X,HP-Y t-Test" i.e.
HP_XYsets_KS_TestCL - Variable in class Filter
"Filter genes by HP-X,HP-Y sets Kolmagorove-Smirnov -Test" i.e.
HP_XYsets_t_TestCL - Variable in class Filter
"Filter genes by HP-X,HP-Y sets t-Test" i.e.
HP_Ylabel - Variable in class MenuBarFrame
GUI label for current HP-Y
hpCmdItemList - Static variable in class PopupHPmenuGuesser
unsorted HP cmd list, is G.C.'ed
hpData - Variable in class ExprProfile
normalized quantified data for all HP-E samples
hpDataE - Variable in class HPxyData
quant data for all HP-E (list) members
hpDataMn - Variable in class ExprProfile
opt.
hpDataMnA - Variable in class ClusterGenes
opt Mean HP-E quant data [nKmeansNodes][nEPmsList]
hpDataMnA - Variable in class ExprProfileOverlay
mean[0:nMnGenes-1][0:nHP_E-1]
hpDataMnA - Variable in class ExprProfileScrollPane
mean[0:nMnGenes-1][0:nHP_E-1]
hpDataMnA - Variable in class ShowExprProfilesPopup
opt.
hpDataNbr - Variable in class ExprProfile
opt.
hpDataNbrA - Variable in class ClusterGenes
opt # genes/K-means-cluster for nEPmsList HP-Es [nKmeansNodes]
hpDataNbrA - Variable in class ExprProfileOverlay
# of samples for hpDataXXX[n][]
hpDataNbrA - Variable in class ExprProfileScrollPane
# of samples for hpDataXXX[n][]
hpDataNbrA - Variable in class ShowExprProfilesPopup
opt.
hpDataSD - Variable in class ExprProfile
opt.
hpDataSDA - Variable in class ClusterGenes
opt S.D.
hpDataSDA - Variable in class ExprProfileOverlay
S.D.[0:nMnGenes-1][0:nHP_E-1]
hpDataSDA - Variable in class ExprProfileScrollPane
S.D.[0:nMnGenes-1][0:nHP_E-1]
hpDataSDA - Variable in class ShowExprProfilesPopup
opt.S.D.
hpDataX - Variable in class HPxyData
quant data for all HP-X (set) members
hpDataY - Variable in class HPxyData
quant data for all HP-Y (set) members
HPdistances - Variable in class ClusterSamples
Euclidean distance or correlation coefficient of sample HP pattern vector from another gene.
hpEPlistDataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("HP-E-list")
hpLabel - Variable in class ExprProfile
(hpName,hpData,cvData) HP-E samples
HPlabelPanel - Variable in class MenuBarFrame
holds HP-X & -Y labels, STOP button
hpLabelX - Variable in class HPxyData
plot label: (className,mnData,sdData,cvData) HP-X (set)
hpLabelY - Variable in class HPxyData
plot label: (className,mnData,stdData,cvData) HP-Y (set)
hpMenuChooserIsPoppedUp - Variable in class MenuBarFrame
if chooser was popped up
hpMenuGuesser - Variable in class MenuBarFrame
HP menu guesser: create when needed
hpMenuGuesserIsPoppedUp - Variable in class MenuBarFrame
if guesser was popped up
hpMenuItemList - Static variable in class PopupHPmenuGuesser
unsorted HP names list, is G.C.'ed
hpMenuItemListSize - Variable in class PopupHPChooser
sorted list of HP menu size
hpMenuItemListSize - Static variable in class PopupHPmenuGuesser
unsorted list of HP menu size
hpMenuToUpdateFromChooser - Variable in class MenuBarFrame
Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"
hpMenuToUpdateFromGuesser - Variable in class MenuBarFrame
Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"
HPmnuEntry - Variable in class StageNames
list of menus that the entry belongs to
hpName - Variable in class ExprProfile
names for all HP-E samples
hpName - Variable in class MaHybridSample
basename hybridized sample DB file name without file extension
hpNameE - Variable in class HPxyData
names for all HP-Y (set) members
hpNameX - Variable in class HPxyData
name for all HP-X (set) members
hpNameY - Variable in class HPxyData
names for all HP-Y (set) members
hpNbr - Variable in class StageNames
idx of mae.snHPNames[]
hps - Variable in class CompositeDatabase
link to global SamplesSets instance
hps - Variable in class Filter
link to global SampleSets instance
hps - Variable in class GeneGeneDist
link to global SampleSets instance
hps - Variable in class HPxyData
Global instance of HP-X, HP-Y and HP-E sets and lists
hps - Variable in class MAExplorer
Global instance of HP-X, HP-Y and HP-E sets and lists
hps - Static variable in class MJAbase
link to global SampleSets instance
hps - Static variable in class MaeJavaAPI
link to global SampleSets instance
hps - Variable in class PopupHPChooser
link to global SampleSets instance
HPvector - Variable in class ClusterSamples
normalized quantitation gene vector for all HPs
hpXsetDataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("HP-X-set")
hpXYdata - Static variable in class CompositeDatabase
generic HP-X/Y set object
hpXYdata - Static variable in class MJAbase
link to global HPxyData instance
hpXYdata - Static variable in class MaeJavaAPI
link to global HPxyData instance
HPxyData - class HPxyData.
The HPxyData class creates HP-X and HP-Y data 'sets' for a given gene mid.
HPxyData(MAExplorer, int, boolean) - Constructor for class HPxyData
HPxyData() - Constructor to create HP XY data object.
hpXYdataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("Cur-HP-XY")
hpXYpseudoImgList - Variable in class DrawPseudoImage
list of HP names [mae.hps.nHP+1]
hpXYsetDataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("HP-XY-sets")
hpYsetDataFile - Variable in class RgenDemo
Input file for current RLO, if lookupRdataTypeDBvalue("HP-Y-set")
hs - Variable in class ArrayScroller
opt.
hsize - Variable in class WriteGifEncoder
 
HSIZE - Static variable in class WriteGifEncoder
 
HSIZE - Static variable in class MedianCut
max size of image histogram
hsL - Variable in class ExprProfileOverlay
lower bound horizontal scroll bar
hsU - Variable in class ExprProfileOverlay
upper bound horizontal scroll bar
htab - Variable in class WriteGifEncoder
 
hUB - Variable in class ExprProfileOverlay
upper HP sample # to display

I

i - Variable in class SStextCell
grid index
id - Variable in class ChooserGUI
id # for this instance
id - Variable in class ClusterGenes.Cluster
id # of this cluster
id - Variable in class PopupCondChooserGUI
id # for this instance
id - Variable in class PopupHPChooser
id # for this instance
id - Variable in class PopupOrderedCondChooserGUI
id # for this instance
id - Variable in class RLO
sequence # of description
id - Variable in class MC_Cube
 
iDataV - Variable in class ClusterGramCanvas
col to norm by in [0:nDataV-1]
iDataV - Static variable in class HierClustNode
col to norm by in [0:nDataV-1]
idxAllGenes - Variable in class GeneClass
index for special class in the list
idxAllGenesAndESTs - Variable in class GeneClass
index for special class in the list
idxAllNamedGenes - Variable in class GeneClass
index for special class in the list
idxBGAvg - Variable in class MaInfoTable
lookup field index.
idxBGAvg - Variable in class SamplesTable
 
idxBGLow - Variable in class MaInfoTable
lookup field index.
idxBGLow - Variable in class SamplesTable
 
idxBGRms - Variable in class MaInfoTable
lookup field index.
idxBGRms - Variable in class SamplesTable
 
idxBkgrd - Variable in class MaHPquantTable
background raw intensity spot data
idxBkgrd1 - Variable in class MaHPquantTable
background raw intensity channel 1, if code mult fields in each row
idxBkgrd2 - Variable in class MaHPquantTable
background raw intensity channel 2, if code mult fields in each row
idxCalDNA - Variable in class GeneClass
index for special class in the list
idxClusterDist - Static variable in class StateScrollers
index for clusterDist threshold for cluster distance clustering
idxComments - Variable in class ConfigTable
optional comments
idxComments - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxContrib_Institute - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxContributor - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxCR1 - Static variable in class StateScrollers
index for CR1 Cy(3/5) ratio value lower bound
idxCR2 - Static variable in class StateScrollers
index for CR2 Cy(3/5) ratio value upper bound
idxCurGeneClass - Static variable in class GeneClass
index of current GeneClass
idxCZ1 - Static variable in class StateScrollers
index for CZ1 Cy(3/5) zscore value lower bound
idxCZ2 - Static variable in class StateScrollers
index for CZ2 Cy(3/5) zscore value upper bound
idxDatabase_File - Variable in class MaInfoTable
lookup field index.
idxDatabase_File - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxDatabaseFileID - Variable in class MaInfoTable
lookup field index.
idxDatabaseFileID - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxDataType - Variable in class ConfigTable
i.e "int", "boolean" or "float"
idxDate - Variable in class MaInfoTable
lookup field index.
idxDetValue - Variable in class MaHPquantTable
Opt.
idxdetValueSpotThr - Static variable in class StateScrollers
index for continuous threshold of Spot Detection values
idxDiffXY - Static variable in class StateScrollers
index for Diff(HP-X,HP-Y) intensity differerence threshold
idxEGL - Variable in class GeneClass
index for special class in the list
idxEmptyWell - Variable in class GeneClass
index for special class in the list
idxESTs - Variable in class GeneClass
index for special class in the list
idxExposure - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxfield - Variable in class MaHPquantTable
opt.
idxFilterType - Variable in class SamplesTable
 
idxFilterType_Descr - Variable in class MaInfoTable
lookup field index.
idxFilterType_Descr - Variable in class SamplesTable
 
idxGeneCard_URL - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxGoodGenes - Variable in class GeneClass
index for special class in the list
idxgrid - Variable in class MaHPquantTable
separate GRC spec.
idxgrid_col - Variable in class MaHPquantTable
separate GRC spec.
idxgrid_row - Variable in class MaHPquantTable
separate GRC spec.
idxHeader_Descr - Variable in class MaInfoTable
lookup field index.
idxHistology_URL - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxHousekeepingGenes - Variable in class GeneClass
index for special class in the list
idxHP - Variable in class MaHybridSample
index in list of all samples (mae.hps.msList[]) for this HP sample
idxLocation - Variable in class MaHPquantTable
opt.
idxLogin - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxMAEP - Variable in class PopupRegistry
MAEPlugin Object current index
idxMenu_Stage_Name - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxModel_URL - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxName - Variable in class UserState
indices for values in startup DB table
idxNameGridIdx - Variable in class MaHPquantTable
MolDyn GRC coding for (grid,grid-row,grid-column) as "NAME_GRC" e.g.
idxNbrClusters - Static variable in class StateScrollers
index for # of clusters threshold for K-means clustering
idxNormGeneSet - Variable in class GeneClass
index for special class in the list
idxParameter - Variable in class ConfigTable
parameter string name
idxPctOK - Static variable in class StateScrollers
index for Percent SI OK (SI AT_LEAST/AT_MOST) QualCheck threshold
idxPrjDir - Variable in class PopupProjDirGuesser
Table field: "Project-Directory"
idxPrjName - Variable in class PopupProjDirGuesser
Table field: "Project-Name"
idxProbe - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxProject - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxPvalue - Static variable in class StateScrollers
index for p-value threshold value
idxQualCheck - Variable in class MaHPquantTable
Opt.
idxQualThr - Static variable in class StateScrollers
index for qualType continuous threshold of QualCheck values
idxR1 - Static variable in class StateScrollers
index for R1 ratio HP-X/HP-Y value lower bound
idxR2 - Static variable in class StateScrollers
index for R2 ratio HP-X/HP-Y value upper bound
idxRadius - Static variable in class StateScrollers
index for Radius for drawing spots in the pseudo array
idxRatioHP - Variable in class SampleSets
1/msRatioHP for ratio EP calcs.
idxRawIntens - Variable in class MaHPquantTable
raw intensity spot data
idxRawIntens1 - Variable in class MaHPquantTable
raw intensity spot data for channel 1, if code mult fields in each row
idxRawIntens2 - Variable in class MaHPquantTable
raw intensity spot data for channel 2, if code mult fields in each row
idxReplicateGenes - Variable in class GeneClass
index for special class in the list
idxResearcher - Variable in class MaInfoTable
lookup field index.
idxSample_ID - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxSample_Nbr - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxSEPP - Variable in class PopupRegistry
ShowExprProfilesPopup current index
idxShortName - Variable in class MaInfoTable
lookup field index.
idxSI1 - Static variable in class StateScrollers
index for Spot SI1 intensity value lower bound
idxSI2 - Static variable in class StateScrollers
index for Spot SI2 intensity value upper bound
idxSimilarESTs - Variable in class GeneClass
index for special class in the list
idxSource - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxSpot_CV - Static variable in class StateScrollers
index for spot Coefficient of Variation threshold value
idxSPP - Variable in class PopupRegistry
ShowPlotPopup popups currrent index
idxSSP - Variable in class PopupRegistry
ShowStringPopup popups current index
idxSSSP - Variable in class PopupRegistry
ShowSpreadsheetPopup popups current index
idxStage - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxStrain - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxSubmission_Date - Variable in class SamplesTable
The following fields were from the original Membranes.txt file.
idxT1 - Static variable in class StateScrollers
index for I1 (T1) HP intensity value lower bound
idxT2 - Static variable in class StateScrollers
index for I2 (T2) HP intensity value upper bound
idxTableName - Variable in class MaInfoTable
lookup field index.
idxUserFilterGeneSet - Variable in class GeneClass
index for special class in the list
idxValue - Variable in class ConfigTable
value of parameter
idxValue - Variable in class UserState
indices for values in startup DB table
idxX - Variable in class MaHPquantTable
opt.
idxY - Variable in class MaHPquantTable
opt.
idxYourPlates - Variable in class GeneClass
index for special class in the list
idxZ1 - Static variable in class StateScrollers
index for Z1 zscore value of (HP-X - HP-Y) lower bound
idxZ2 - Static variable in class StateScrollers
index for Z2 zscore value of (HP-X - HP-Y) upper bound
iFontHdrSize - Variable in class Draw2Dplot
 
iFontHdrSize - Variable in class DrawPseudoImage
integer header font size is 2+ regular size unless the latter is 12pt in which case the header font size is also 12 pt.
iFontSize - Variable in class Draw2Dplot
integer regular font size
iFontSize - Variable in class DrawPseudoImage
integer regular font size
ignoreExtraFIELDS - Static variable in class Config
Flag: ignore extra fields > maxFIELDS.
iHeight - Variable in class Draw2Dplot
working canvas height
iHeight - Variable in class DrawHistogram
working canvas height
iHeight - Variable in class DrawRatioHistogram
 
iHeight - Variable in class ScrollableImageCanvas
size of array area within canvas
iHPnbr - Variable in class MAExplorer
# of entries in "image#" PARAM list.
iImageFile - Variable in class MAExplorer
image files to read allocated [MAX_HYB_SAMPLES+1]
IMAGE2GenBankURL - Variable in class Config
base addr PARAM "IMAGE2GenBankURL"
IMAGE2unigeneURL - Variable in class Config
base addr PARAM "IMAGE2unigeneURL"
img - Variable in class WriteGifEncoder
Image if specified
img_selectedFlag - Variable in class ArrayScroller
flag: set if xObj,yObj is set
iMode - Variable in class Guesser
one of the above MODE_xxxx values
implicitFieldsFlag - Variable in class MaHybridSample
flag: set true if no "field" field
importRfileButton - Variable in class PopupEditRscript
"Import .R file"
index - Variable in class ChooserGUI.MouseEventHandler
index of entry in the alphaList
index - Variable in class PopupCondChooserGUI.MouseEventHandler
index of entry in the alphaList
index - Variable in class PopupOrderedCondChooserGUI.MouseEventHandler
index of entry in the alphaList
index - Variable in class SSspreadPanel
for sorting
index - Variable in class WriteGifEncoderHashitem
 
info1 - Variable in class Draw2Dplot
ARGS:
info2 - Variable in class Draw2Dplot
ARGS:
info3 - Variable in class Draw2Dplot
ARGS:
info4 - Variable in class Draw2Dplot
ARGS:
infoDB - Variable in class MAExplorer
Global instance of depricated "MaExplorerInfo.txt" DB list of .info data for entire DB.
infoTA1 - Variable in class PopupHPChooser
first line of info about selected HP
infoTA2 - Variable in class PopupHPChooser
second line of info about selected HP
infoTA3 - Variable in class PopupHPChooser
third line of info about selected HP
init() - Method in class MAExplorer
init() - allocate,clear state, read PARAMs, build GUI and start things off.
initClientStateFromRLO(int) - Method in class RgenDemo
initClientStateFromRLO() - init create script state prior to generating R scripts.
initCondition(String) - Method in class Condition
initCondition() - initialize Condition list to empty - i.e.
initData() - Method in class ClusterGenes
initData() - init data
initData() - Method in class PopupCondChooser
initData() - initialize the database.
initData() - Method in class PopupOrderedCondChooser
initData() - initialize the database.
initFGRCtoGTidxMap() - Method in class MaHPquantTable
initFGRCtoGTidxMap() - create FGRC to quant table row index lookup table.
initializeDataAndGUI() - Method in class RtestBase
initializeDataAndGUI() - build the GUI, then repaint to build the initial display.
initialMsg - Variable in class PopupCondChooser.ChoiceList
in the list at position 0, first thing the user will see
initialMsg - Variable in class PopupOrderedCondChooser.ChoiceList
in the list at position 0, first thing the user will see
initialSeedGene - Variable in class ClusterGenes
initial seed gene - either 1st or current Obj gene
initPreloads() - Method in class StateScrollers
initPreloads() - setup the preloaded arrays of filter names, values and range gang-scroll option.
initRtest(Rtest) - Method in class RtestBase
initRtest() - initialize the Rtest popup and create the GUI
initStateAndMJAchildren(MAExplorer) - Method in class MaeJavaAPI
initStateAndMJAchildren() - init the children classes.
initUserFilterScrollerCounters() - Method in class StateScrollers
initUserFilterScrollerCounters() - initialize scroller use counters based on the State flags.
initValues() - Method in class SSspreadPanel
initValues() - show prepDataEdit inside the grid in U.L.H.C.
initValues(String[][]) - Method in class SpreadSheet
initValues() - initialize data values for spreadsheet data structures
initValues(String[][]) - Method in class SSspreadPanel
initValues() - show prepDataEdit inside grid in U.L.H.C.
inputDataFileNames - Variable in class RLO
Name of input file if any (if not null)
inputDataFileNames - Variable in class PopupEditRscript
Name of input file if any (if not null)
inputDataTypes - Variable in class RLO
R_DATA_TYPE_xxxx type of input file if any
inputDataTypes - Variable in class RgenDemo
R_DATA_TYPE_xxxx type of input file if any
inputDataTypes - Variable in class PopupEditRscript
R_DATA_TYPE_xxxx type of input file if any
inputPanel - Variable in class RtestBase
input panel to hold scriptChoice
inputRscriptFileName - Static variable in class RevalBase
 
inputTF - Variable in class RtestBase
Text input data line
inputTypesChoice - Variable in class PopupEditRscript
Input data type Choices [0:MAX_WIZ_CHOICES-1]
inputTypesChoiceNames - Variable in class PopupEditRscript
Input data types Choice names [0:nInputTypes-1]
inputTypesChoiceValues - Variable in class PopupEditRscript
data types Choice values [0:nInputTypes-1].
insertColumn(int) - Method in class SpreadSheet
insertColumn() - insert a column at column k
insertColumn(int) - Method in class SSspreadPanel
insertColumn() - insert a row at k'th row
insertPluginMenu(MenuItem) - Method in class MaeJavaAPI
insertPluginMenu() - insert plugin into menu using (menuName:menuSubtreeName) [TODO]
insertPluginMenu(MenuItem) - Method in interface MAEPlugin.MAEStub
insertPluginMenu() - method to insert plugin into menu
insertPluginMenuEntries() - Method in class MenuBarFrame
insertPluginMenuEntries() - insert Plugin menus if any at proper stubs.
insertTblInULHCtable(int, int, String) - Method in class Table
insertTblInULHCtable() - insert table into U.L.H.C.
intensFilterFlag - Variable in class MAExplorer
filter genes by intensity threshold
intensHistCL - Variable in class Filter
"Intensity histogram selected genes"
intensityThrCL - Variable in class Filter
"Threshold: intensity [I1:I2]"
intensL - Variable in class DrawHistogram
idx lower intensity range binDataValue[] space
intensU - Variable in class DrawHistogram
idx upper intensity range binDataValue[] space
interlace - Variable in class WriteGifEncoder
80% occupancy
Interlace - Variable in class WriteGifEncoder
80% occupancy
intersection(Condition, Condition, String) - Method in class Condition
intersection() - compute intersection of two conditions cond1 and cond2.
intersection(GeneBitSet, GeneBitSet, GeneBitSet) - Method in class GeneBitSet
intersection() - intersection of GeneBitSets (b1 | b2) ==> b3.
intersection(GeneList, GeneList, GeneList) - Method in class GeneList
intersection() - compute intersection of GeneLists (c1 & c2) ==> c3.
intersection(String, String, String) - Method in class MJAcondition
intersection() - compute resultCond= Intersection (Condition 1, Condition 2)
invokeMenuEntryByName(String, int) - Static method in class EventMenu
invokeMenuEntryByName() - process the menu command by name.
invokeMenuEntryByName(String, int) - Method in class MJAeval
invokeMenuEntryByName() - invoke and process a menu command by name.
invokeMenuEntryByName(String, int, String[]) - Static method in class EventMenu
invokeMenuEntryByName() - process the menu command by name with extra argList.
invokeUpdateCurGene(Object, int, int) - Method in class MJApopupRegistry
invokeUpdateCurGene() - invoke updates for registered popups and plugins for current gene.
invokeUpdateFilter() - Method in class MJApopupRegistry
invokeUpdateFilter() - invoke registered plugins updates for data filter changed
invokeUpdateLabels() - Method in class MJApopupRegistry
invokeUnvokeUpdateLabels() - invoke registered plugins updates for sample labels, etc data changed
invokeUpdateSlider() - Method in class MJApopupRegistry
invokeUpdateSlider() - invoke registered plugins updates for slider state data changed
is - Variable in class MAExplorer
Global instance of ArrayScroller obj to hold pseudoarray image scrollable canvas
is - Variable in class ScrollableImageCanvas
Parent class
is1DdataFlag - Variable in class RgenDemo
 
is1DsetDataFlag - Variable in class RgenDemo
 
is2DdataFlag - Variable in class RgenDemo
 
is2DsetDataFlag - Variable in class RgenDemo
 
iSampleName - Variable in class MAExplorer
HP name from "image*" [1:iHPnbr] allocated [MAX_HYB_SAMPLES+1]
isAppletFlag - Variable in class MAExplorer
Flag: cleared if enter through standalone main()
isBoxSelectedFlag - Variable in class ClusterGramCanvas
set by event handler mouse on click
isClientGenRmethodLegal(int) - Method in class RgenDemo
isClientGenRmethodLegal() - test if specified Gen R method is legal for this data types for the current RLO.
isConditionInOrderedCondList(Condition, String) - Method in class Condition
isConditionInOrderedCondList() - test if condition is in named ordered condition list.
isConditionInOrderedCondList(String, String) - Method in class MJAcondition
isConditionInOrderedCondList() - test if condition is in named ordered condition list.
isCondList(String) - Method in class MJAcondition
isCondList() - tests if this is a name of a condition list
isCurGeneValid() - Method in class MJAgene
isCurGeneValid() - test if mid is a valid gene for the current gene.
isGeneInGeneBitset(String, int) - Method in class MJAgeneList
isGeneInGeneBitset() - add gene MID to Gene bitset, ignore if already there
isGeneInGeneList(Gene) - Method in class GeneList
isGeneInGeneList() - test if gene is in GeneList.
isGeneInGeneList(String, int, String[]) - Method in class MJAgeneList
isGeneInGeneList() - test if gene MID is GeneList
isGeneProperty(int) - Method in class Gene
isGeneProperty() - test if C_xxxx gene property is set.
isGenRbit(int) - Method in class MJAReval
isGenRbit() - test GenR Bits for current RLO.
isGIDinGeneList(int) - Method in class GeneList
isGIDinGeneList() - test if GridCoords gid in GeneList.
isGIDinWorkingCL(int) - Method in class Filter
isGIDinWorkingCL() - return true if GridCoords gid is in the workingCL of genes
isGIDinWorkingGeneList(int) - Method in class MJAfilter
isGIDinWorkingGeneList() - test if Grid Index (gid) is in filtered genes
isGridColDigitFlag - Variable in class MaHPquantTable
flag: Grid-Col value is coded as digit else alpha
isGridDigitFlag - Variable in class MaHPquantTable
flag: Grid value is coded as digit else alpha
isGridRowDigitFlag - Variable in class MaHPquantTable
flag: Grid-Row value is coded as digit else alpha
isHPinCondList(MaHybridSample) - Method in class Condition
isHPinCondList() - is Sample in condition list
isHPnameIsAccessible(String) - Method in class SamplesTable
isHPnameIsAccessible() - test if HP database name is accessible.
isInCondList(String) - Static method in class Condition
isInCondList() - tests if this is the name of a condition list
isInputDataType(int) - Method in class RgenDemo
isInputDataType() - test if specified input data type is used in this RLO.
isItemInGeneBitSet(int) - Method in class GeneBitSet
isItemInGeneBitSet() - is an item (i.e.
isLoggedInFlag - Variable in class MAExplorer
set if valid login has been performed
isMIDinGeneList(int) - Method in class GeneList
isMIDinGeneList() - test if Gene id (mid) is in GeneList.
isMIDinWorkingCL(int) - Method in class Filter
isMIDinWorkingCL() - return true if Master Gene Id (mid) is in workingCL
isMIDinWorkingGeneList(int) - Method in class MJAfilter
isMIDinWorkingGeneList() - test if Master Gene Id (mid) is in filtered genes
isName - Variable in class ScrollableImageCanvas
name of ArrayScroller parent
isNewRLOflag - Variable in class PopupEditRscript
Flag that indicates we are editing a new RLO or editing an old one
isOCLdataFlag - Variable in class RgenDemo
Data category flag: OCL data - cur Ordered Condition Lists of samples.
isOrderedCondList(String) - Method in class Condition
isOrderedCondList() - test if is named ordered condition list.
isOrderedCondList(String) - Method in class MJAcondition
isOrderedCondList() - tests if this is a name of an ordered condition list
isOverlayMap(String) - Static method in class MJAplot
isOverlayMap() - test if a scatterplot named overlay map exists
[TODO] does not exist yet
isOverlayMap(String) - Static method in class OverlayMap
isOverlayMap() - test if a scatterplot named overlay map exists
isProcessBit(int) - Method in class MJAReval
isProcessBit() - test Process Bits for current RLO.
isPseudoDataFlag - Variable in class RgenDemo
 
isResource(String) - Method in class MAEPlugin.JarResources
isResource() - checks to see if resource exists
isSampleInCondList(int, String) - Method in class MJAcondition
isSampleInCondList() - is sample in named condition list?
isTransparent - Variable in class WriteGifEncoderHashitem
 
isValidObjFlag - Static variable in class CompositeDatabase
Flag to indicate that the current gene (i.e.
isVisible - Variable in class StateScrollers
Flag: if StateScroller GUI is visible
isVisibleFlag - Variable in class LogTextFrame
Visibility flag
isWindowsFlag - Static variable in class RevalBase
Flag set if running on a Windows computer
isWindowsFlag - Variable in class RtestBase
Flag set if running on a Windows computer
isWinPCflag - Variable in class MAExplorer
Flag: set to TRUE if any Windows PC
isWinPCflag - Variable in class PopupCondChooserGUI
The system is a windows PC
isWinPCflag - Variable in class PopupOrderedCondChooserGUI
The system is a windows PC
isWorkingMAE - Variable in class MAExplorer
Flag indicating whether using the Working server (mae/) or not
isZip - Variable in class MAEPlugin.FileClassLoader
zip path flag
isZscoreFlag - Variable in class MAExplorer
Flag: is using one of the Zscore normalizations
ITEMS - Static variable in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
 
itemStateChanged(ItemEvent) - Method in class DrawClusterGram
 
itemStateChanged(ItemEvent) - Method in class ExprProfilePopup
 
itemStateChanged(ItemEvent) - Method in class MenuBarFrame
itemStateChanged() - handle item state changed events.
itemStateChanged(ItemEvent) - Method in class PopupBinOprDialogQuery
itemStateChanged() - event handler for pull-down selector Choices for selecting an operand
itemStateChanged(ItemEvent) - Method in class PopupCondChooser
itemStateChanged() - user clicked on condtion in the condition list, must change CondParamEditForm data, remainder and selected data, save condForm data.
itemStateChanged(ItemEvent) - Method in class PopupCondChooser.ChoiceList
 
itemStateChanged(ItemEvent) - Method in class PopupDialogQuery
itemStateChanged() - event handler for Choices
itemStateChanged(ItemEvent) - Method in class PopupOrderedCondChooser
itemStateChanged() - user clicked on condtion in the ocl list, must change CondParamEditForm data, remainder and selected data, save condForm data.
itemStateChanged(ItemEvent) - Method in class PopupOrderedCondChooser.ChoiceList
 
itemStateChanged(ItemEvent) - Method in class RtestBase
itemStateChanged() - handle item state changed eventsms.
itemStateChanged(ItemEvent) - Method in class PopupEditRscript
itemStateChanged() - handle item state changed eventsms.
itemStateChanged(ItemEvent) - Method in class PopupScrollableSelector
itemStateChanged() - handle item state checkbox selectors.
itemStateChanged(ItemEvent) - Method in class ShowExprProfilesPopup
 
itemStateChanged(ItemEvent) - Method in class ShowPlotPopup
itemStateChanged() - handle check box item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and not for Checkbox MenuItems.
itemStateChanged(ItemEvent) - Method in class ShowSpreadsheetPopup
 
itemStateChanged(ItemEvent) - Method in class MAEPlugin.CheckBoxMenuPlugin
itemStateChanged() - implements ItemListener for checkbox change
itemStateChanged(ItemEvent) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
itemStateChanged() -
iWidth - Variable in class Draw2Dplot
working canvas width
iWidth - Variable in class DrawHistogram
working canvas width
iWidth - Variable in class DrawRatioHistogram
 
iWidth - Variable in class ScrollableImageCanvas
size of array area within canvas

J

j - Variable in class SStextCell
grid index
JarClassLoader - class MAEPlugin.JarClassLoader.
JarClassLoader provides a minimalistic ClassLoader which shows how to instantiate a class which resides in a .jar file.
JarClassLoader(File) - Constructor for class MAEPlugin.JarClassLoader
JarClassLoader() - constructor2 that loads jar from the path that is derived from the jarFile.
JarClassLoader(String) - Constructor for class MAEPlugin.JarClassLoader
JarClassLoader() - default constructor that loads jar from the jarPath.
jarContents - Variable in class MAEPlugin.JarResources
 
jarFileName - Variable in class MAEPlugin.JarResources
 
jarResources - Variable in class MAEPlugin.MAEPlugin
access to the jar file for loading support files
jarResources - Variable in class MAEPlugin.JarClassLoader
utility object that loads resources from a Jar
JarResources - class MAEPlugin.JarResources.
JarResources: JarResources maps all resources included in a Zip or Jar file.
JarResources(String) - Constructor for class MAEPlugin.JarResources
JarResources() - constructor for createing a JarResources.
JavaCGIBridge - class JavaCGIBridge.
The JavaCGIBridge class POSTS and GETS data from URLs using various helper methods.
JavaCGIBridge() - Constructor for class JavaCGIBridge
JavaCGIBridge() - Constructs the object with no initialization.
JavaCGIBridge(URL) - Constructor for class JavaCGIBridge
JavaCGIBridge() - Constructs the object with no initialization.
JavaCGIBridge(URL, String, String) - Constructor for class JavaCGIBridge
JavaCGIBridge() - Constructs the object with userName, password.
JavaCGIBridgeSep(String, String, String, String) - Method in class JavaCGIBridge
JavaCGIBridgeSep() - constructs the object with new separator values
JavaCGIBridgeTimeOutException - exception JavaCGIBridgeTimeOutException.
This class Signals that the JavaCGIBridge Timed out while attempting to POST or GET data from a URL connection.
JavaCGIBridgeTimeOutException() - Constructor for class JavaCGIBridgeTimeOutException
JavaCGIBridgeTimeOutException() - constructor with no detail msg Constructs a JavaCGIBridgeTimeOutException with no detail message.
JavaCGIBridgeTimeOutException(String) - Constructor for class JavaCGIBridgeTimeOutException
JavaCGIBridgeTimeOutException() - constructor with detail msg Constructs a JavaCGIBridgeTimeOutException with the specified detail message.
javaHome - Static variable in class MAExplorer
Standalone getProperties("java.home")
javaHome - Static variable in class RevalBase
 
javaHome - Variable in class RtestBase
 
jaxURL - Variable in class Config
base addr PARAM "jaxURL"
jGrpList - Variable in class Draw2Dplot
group # for EP [0:maxGenes-1]
jpgFile - Variable in class RgenDemo
Current JPEG file for current RLO, if specified
junk_BAD_DATA - Static variable in class Filter
property: has bad data
junk_IS_FILTERED - Static variable in class Filter
property: is filtered
junk_NOT_FILTERED - Static variable in class Filter
property: is not filtered

K

keepFlagsOnClosing - Variable in class DrawClusterGram
mode of operation used in creating thiswindow for use in closing the window
kev - Variable in class Guesser
handle events for text field
KeyEventHandler - class KeyEventHandler.
 
KeyEventHandler(MAExplorer, Guesser, TextField, TextArea, String[], int, MouseEventHandler) - Constructor for class KeyEventHandler
KeyEventHandler() - constructor for key events.
keyPressed(KeyEvent) - Method in class ChooserGUI
keyPressed() - get key Pressed event
keyPressed(KeyEvent) - Method in class MenuBarFrame
keyPressed() - get key Pressed event - look for ESCAPE key to set STOP flag
keyPressed(KeyEvent) - Method in class PopupCondChooserGUI
keyPressed() - get key Pressed event
keyPressed(KeyEvent) - Method in class PopupHPChooser
keyPressed() - get key Pressed event - look for ESCAPE key to set STOP flag
keyPressed(KeyEvent) - Method in class PopupOrderedCondChooserGUI
keyPressed() - get key Pressed event
keyPressed(KeyEvent) - Method in class PopupEditRscript
keyPressed() - key pressed in TextField
keyReleased(KeyEvent) - Method in class ChooserGUI
keyReleased() - get key Released event
keyReleased(KeyEvent) - Method in class KeyEventHandler
keyReleased() - handle keyboard inputs from TextField tf.
keyReleased(KeyEvent) - Method in class MenuBarFrame
keyReleased() - get key Released event
keyReleased(KeyEvent) - Method in class PopupCondChooserGUI
keyReleased() - get key Released event
keyReleased(KeyEvent) - Method in class PopupHPChooser
keyReleased() - get key Released event
keyReleased(KeyEvent) - Method in class PopupOrderedCondChooserGUI
keyReleased() - get key Released event
keyReleased(KeyEvent) - Method in class PopupEditRscript
keyReleased() - key released in TextField
keys - Variable in class JavaCGIBridge
 
keySeparator - Static variable in class JavaCGIBridge
 
keyTyped(KeyEvent) - Method in class ChooserGUI
keyTyped() - get key typed event
keyTyped(KeyEvent) - Method in class MenuBarFrame
keyTyped() - get key typed event - look for ESCAPE key to set STOP flag
keyTyped(KeyEvent) - Method in class PopupCondChooserGUI
keyTyped() - get key typed event
keyTyped(KeyEvent) - Method in class PopupHPChooser
keyTyped() - get key typed event - look for ESCAPE key to set STOP flag
keyTyped(KeyEvent) - Method in class PopupOrderedCondChooserGUI
keyTyped() - get key typed event
keyTyped(KeyEvent) - Method in class PopupEditRscript
keyTyped() - key typed in TextField
killAppletFlag - Variable in class MAExplorer
Flag: set if do "Quit".
KmeansClustersExprProfPopup - Static variable in class ClusterGenes
 
KmeansClustersPopup - Static variable in class ClusterGenes
string report exists if not null
kMeansDist - Variable in class ClusterGenes
[1:maxKmeansNodes] distance between K-means primary clusters
kMeansList - Variable in class ClusterGenes
[1:maxKmeansNodes] index of gene as K-means cluster node
kMeansMaxDist - Variable in class ClusterGenes
[1:maxKmeansNodes] max distance within each K-means primary clusters
KmeansNodesCL - Variable in class Filter
"Genes in primary K-means nodes"
KS_TestXYsetsFilterFlag - Variable in class MAExplorer
filter genes passing HP-X/-Y sets KS-test
ksD - Variable in class Statistics
CALC: KS-test Kolmogorov-Smirnov D statistic set by calcKStestStat()

L

label - Variable in class PopupDialogQuery
for data label
LABEL - Static variable in class PopupRegistry
Property bit type: Notify bit if Labels changed
label1 - Variable in class PopupBinOprDialogQuery
for data label
label2 - Variable in class PopupBinOprDialogQuery
for data label
label3 - Variable in class PopupBinOprDialogQuery
for data label
labelFont - Variable in class ChooserGUI
font used by label
labelFont - Variable in class PopupCondChooser
font for labels
labelFont - Variable in class PopupCondChooserGUI
font used by label
labelFont - Variable in class PopupHPChooser
font for labels of popup chooser window
labelFont - Variable in class PopupOrderedCondChooser
font for labels
labelFont - Variable in class PopupOrderedCondChooserGUI
font used by label
labelGL - Variable in class PopupCondChooser.CondParamEditForm
labels GridLayout to create condition form
labelGL - Variable in class PopupOrderedCondChooser.CondParamEditForm
labels GridLayout to create condition form
labelPanel - Variable in class PopupCondChooser.CondParamEditForm
labels go here
labelPanel - Variable in class PopupOrderedCondChooser.CondParamEditForm
labels go here
labelWizard - Variable in class PopupEditRscript
Wizard title labels [0:MAX_WIZ_ROWS-1]
lastBG1 - Variable in class ArrayScroller
last background colors cached for showMsg1
lastBG2 - Variable in class ArrayScroller
last background colors cached for showMsg2
lastBG3 - Variable in class ArrayScroller
last background colors cached for showMsg3
lastFG1 - Variable in class ArrayScroller
last foreground colors cached for showMsg1
lastFG2 - Variable in class ArrayScroller
last foreground colors cached for showMsg2
lastFG3 - Variable in class ArrayScroller
last foreground colors cached for showMsg3
lastRow - Variable in class ShowSpreadsheetPopup
ARG: end of table data to use, counts from 0?
lastWizardNbr - Variable in class PopupEditRscript
 
lay - Variable in class SSspreadPanel
 
layout - Variable in class LogTextFrame
GUI layout
learnGRCcodingFlag - Variable in class MaHPquantTable
flag: once only code when analyze for MolDyn "NAME_GRC" coding
LECBdebug - Variable in class MAExplorer
Developer debug flag.
leftEdge - Variable in class ClusterGramCanvas
left edge of box array
leftLabel - Variable in class ClusterGramCanvas
left edge of Left label
legalMenuStubNames - Variable in class PopupEditRscript
 
length - Variable in class GeneList
# of genes used in this gene list
listAllButton - Variable in class PopupOrderedCondChooser
list all ordered cond lists
listAllCondButton - Variable in class PopupCondChooser
list all condition
listAllOrderedConditions() - Method in class Condition
listAllOrderedConditions() - popup a report showing list of all OCLs
listCondButton - Variable in class PopupCondChooser
list condition
listCondition(String) - Method in class Condition
listCondition() - popup a window listing of all samples in the named Condition lists
listCondLists() - Method in class Condition
listCondLists() - popup a window listing of all Condition lists in database
listener - Variable in class PopupBinOprDialogQuery
Tried this instead of "this"
listener - Variable in class PopupDialogQuery
Tried this instead of "this"
listener - Variable in class PopupLoginDialogQuery
 
listGeneBitSets(String) - Method in class GeneBitSet
listGeneBitSets() - popup a text window to list the user's gene sets.
listOCLButton - Variable in class PopupOrderedCondChooser
list order cond
listOrderedCondition(String) - Method in class Condition
listOrderedCondition() - popup a window listing of all Conditions in the Ordered Condition list
ln10 - Static variable in class MathMAE
log(10 base e
ln2 - Static variable in class MathMAE
log(2) base e
loadClass(File) - Method in class MAEPlugin.FileClassLoader
loadClass() - Implementation of ClassLoader.loadClass() by name of File pointer.
loadClass(File, boolean) - Method in class MAEPlugin.FileClassLoader
* loadClass() - Implementation of ClassLoader.loadClass() by name of File pointer and user option to resolve.
loadClass(String) - Method in class MAEPlugin.FileClassLoader
loadClass() - Implementation of ClassLoader.loadClass() by name of class.
loadClass(String) - Method in class MAEPlugin.JarClassLoader
loadClass() - load specified class and let it resolve the class if necessary.
loadClass(String, boolean) - Method in class MAEPlugin.FileClassLoader
loadClass() - Implementation of ClassLoader.loadClass() From javadoc v.
loadClass(String, boolean) - Method in class MAEPlugin.JarClassLoader
loadClass() - load specified class
loadClassBytes(String) - Method in class MAEPlugin.JarClassLoader
loadClassBytes() loads bytes for class files.
loadClassFromZip(String, String) - Method in class MAEPlugin.FileClassLoader
loadClassFromZip() - loads classes and resources of a zip or jar file and loads the one class that has the same name as the archive.
loadJarContents() - Method in class MAEPlugin.JarResources
loadJarContents() - initializes internal hash tables with jar file resources.
loadPlugin(String) - Method in class MAEPlugin.popup.PluginLoader
loadPlugin() - tests and loads good MAPlugin from the path.
loadPlugin(String, String) - Method in class MAEPlugin.popup.PluginLoader
loadPlugin() - tests and loads good MAEplugin.
loadPluginsAtStartup() - Method in class MaeJavaAPI
loadPluginsAtStartup() - load plugins from file via startup.
loadPluginSilently(String) - Method in class MAEPlugin.popup.PluginLoader
loadPluginSilently() - silently tests and loads good MAPlugin from the path.
loadPluginsStartup() - Method in class MaeJavaAPI
loadPluginsStartup() - load plugins from file via startup
loadPluginsStartup() - Method in interface MAEPlugin.MAEStub
loadPluginsStartup() - method to load plugins from file via startup
locationIdx - Variable in class GipoTable
index for "Location"
locCol - Variable in class SSspreadPanel
 
locRow - Variable in class SSspreadPanel
 
LocusID - Variable in class Gene
NCBI LocusLink LocusID if it exists
LocusID - Variable in class SpotFeatures
lookup LocusLink LocusID
LocusLinkIdIdx - Variable in class GipoTable
index for "LocusID"
locusLinkURL - Variable in class Config
base addr PARAM "locusLinkURL"
locusLinkViewerFlag - Variable in class MAExplorer
LocusLink LocusID page popup browser Mode
LOG_MSG - Static variable in class PopupCondChooser
Error codes for reportMsg()
LOG_MSG - Static variable in class PopupOrderedCondChooser
Error codes for reportMsg()
log10(double) - Method in class MJAmath
log10() - compute log(x) base 10.
log10(double) - Static method in class MathMAE
log10() - compute log(x) base 10.
log10e - Static variable in class MathMAE
log(e) base 10
log2(double) - Method in class MJAmath
log2() - compute log(x) base 2.
log2(double) - Static method in class MathMAE
log2() - compute log(x) base 2.
log2e - Static variable in class MathMAE
log(e) base 2
log2Zero(double) - Method in class MJAmath
log2Zero() - compute log2((x==0.0 ? 0.0 : x) - avoids log2(0.0)! This defaults log2(0.0) to log2(1.0).
log2Zero(double) - Static method in class MathMAE
log2Zero() - compute log2((x==0.0 ? 0.0 : x) - avoid log2(0.0)! This defaults log2(0.0) to log2(1.0).
logDataBuf - Variable in class FileIO
standalone log file data buff
logDataBuf - Variable in class LogTextFrame
standalone log file data buff
logDataBufSize - Variable in class FileIO
size of standalone log file data buff
logDataBufSize - Variable in class LogTextFrame
size of standalone log file data buff
logDeltaBin - Variable in class MaHybridSample
total array: (mae.MAX_INTENSITY/logRange)
logDRYROTerr(String) - Method in class MAExplorer
logDRYROTerr() - add the dryrot error to the dryrotLogStr and log it by printing it to the system log.
logDRYROTerr(String) - Method in class MJAutil
logDRYROTerr() - notify MAExplorer of a fatal dryrot message
logFile - Variable in class FileIO
standalone log file descriptor
logFile - Variable in class LogTextFrame
optional log file if logging
logFileName - Variable in class FileIO
standalone log file name
logFileName - Variable in class LogTextFrame
optional log file "maeHistory.log"
logFileWriter - Variable in class FileIO
standalone log file writer
logFileWriter - Variable in class LogTextFrame
standalone log file writer
loginLabel - Variable in class PopupLoginDialogQuery
for login label
loginNameData - Variable in class PopupLoginDialogQuery
login name to pass back to MAE
loginTextField - Variable in class PopupLoginDialogQuery
place login text to be edited here
logMaxRatioRI - Variable in class MaHybridSample
total array: log maxRatioRI
logMaxRI - Variable in class MaHybridSample
total array: log of maxRI
logMean - Variable in class MaHybridSample
Filter hist: log of mean raw intensity
logMeanAbsDev - Variable in class MaHybridSample
Filter hist: log of mean absolute deviation raw intensity
logMeanAbsDevRI - Variable in class MaHybridSample
total array: Filter hist: log of mean absolute deviation raw intensity
logMeanRI - Variable in class MaHybridSample
total array: mean of log of rawIntensity
logMiddle - Variable in class MaHybridSample
total array: -logMinRatioRI for finding RI==1.0
logMinRatioRI - Variable in class MaHybridSample
total array: log minRatioRI
logMinRI - Variable in class MaHybridSample
total array: log of minRI
logMsg(String) - Method in class FileIO
logMsg() - write msg to opened log file if stand-alone else print to Java console.
logMsg(String, String, boolean, boolean) - Method in class FileIO
logMsg() - write msg to log file.
logMsgln(String) - Method in class FileIO
logMsgln() - write msg+"\n" to opened log file if stand-alone else if applet, just do System.out.println() call to java console.
logRange - Variable in class MaHybridSample
total array: log ratio range [Rmin:Rmax]
logScalingFlag - Variable in class Draw2Dplot
flag: Linear(false)/Log(true)
logScalingFlag - Variable in class DrawHistogram
Linear(false)/Log(true)
logScalingFlag - Variable in class DrawRatioHistogram
Linear(false)/Log(true)
logScalingFlag - Variable in class ShowPlotPopup
flag: toggle with Linear/Log button
logStdDev - Variable in class MaHybridSample
Filter hist: log of stdDev raw intensity
logStdDevRI - Variable in class MaHybridSample
total array: std dev of log of means
LogTextFrame - class LogTextFrame.
LogTextFrame() - simple text area frame with control buttons Derived from TextFrame.java written by Bob Stephens, ABCC,FCRDC
LogTextFrame(String, String, String, boolean, boolean, int) - Constructor for class LogTextFrame
LogTextFrame() - constructor to create popup logging text window
logTextStr - Variable in class LogTextFrame
text to be written to text area
logZero(double) - Method in class MJAmath
logZero() - compute log10((x==0.0 ? 0.0 : x) - avoids log(0.0)! This defaults log10(0.0) to log(1.0).
logZero(double) - Method in class MaeJavaAPI
logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
logZero(double) - Static method in class MathMAE
logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
logZero(double) - Method in interface MAEPlugin.MAEStub
logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
lookUp(String) - Method in class MAEPlugin.popup.PluginUnLoader
lookUp() - finds plugin in the loaded list from MAExplorer
lookupCompareModeName(int) - Method in class MJAproperty
lookupCompareModeName() - lookup the compare-criteria Mode Name for values COMPARE-xxxx.
lookupCondListIdxByName(String, boolean) - Static method in class Condition
lookupCondListIdxByName() - lookup a Condition by name and return the index.
lookupFieldIdx(String) - Method in class SimpleTable
lookupFieldIdx() - lookup column index of field if exists.
lookupFieldIdxAndRemapFieldName(String, String) - Method in class Table
lookupFieldIdxAndRemapFieldName() - lookup field idx and remap name if need to.
lookupFilterSampleSubsetModeName(int) - Method in class MJAproperty
lookupFilterSampleSubsetModeName() - lookup the sample-subset Mode Name for values SS_MODE-xxxx.
lookupGeneClassIdx(String) - Method in class GeneClass
lookupGeneClassIdx() - lookup index of gene class if exists.
lookupGeneFromXY(Point) - Method in class MaHybridSample
lookupGeneFromXY() - lookup mid if find Point xy in sample HP pseudoarray image
lookupGeneListByName(String) - Static method in class MJAbase
lookupGeneListByName() - lookup GeneList by name Only used by MJA classes.
lookupGeneSetByName(String, boolean) - Static method in class GeneBitSet
lookupGeneSetByName() - lookup index of GeneBitSet in userBS[] database.
lookupGeneSetObjByName(String, boolean) - Static method in class GeneBitSet
lookupGeneSetObjByName() - lookup GeneBitSet object by name in userBS[] DB.
lookupGIDtoGangGID(int) - Method in class MJAgeometry
lookupGIDtoGangGID() - lookup ganged GID given the GID
lookupGIDtoMID(int) - Method in class MJAgeometry
lookupGIDtoMID() - lookup GID given the MID
lookupHPcoords(int, int, int, boolean, MaHybridSample) - Method in class CompositeDatabase
lookupHPcoords() - lookup closest gene name by (x,y) in sample pseudoarray and set current gene if < distThreshold away, else return "".
lookupHPsampleNbr(MaHybridSample) - Static method in class MJAbase
lookupHPsampleNbr() - lookup MaHybidSample's sampleNbr.
lookupHPsampleNbr(MaHybridSample) - Static method in class SampleSets
lookupHPsampleNbr() - lookup MaHybidSample's sampleNbr.
lookupHPsampleNbrByObject(Object) - Static method in class MJAbase
lookupHPsampleNbrByObject() - lookup MaHybidSample's sampleNbr.
lookupIDbyName(String) - Method in class Gene
lookupIDbyName() - lookup the genomic gene id value given the ID name.
lookupMAEPluginInstanceObjectInstance(String) - Method in class PopupRegistry
lookupMAEPluginInstanceObjectInstance() - lookup MAEPlugin Object for unique key instance
lookupMIDfrom_dbEST(String) - Method in class MJAgene
lookupMIDfrom_dbEST() - lookup mid from dbEST 3' or 5' ID.
lookupMIDfrom_dbEST(String) - Method in class Maps
lookupMIDfrom_dbEST() - lookup mid from dbEST 3' or 5' ID.
lookupMIDfromCloneID(String) - Method in class MJAgene
lookupMIDfromCloneID() - lookup mid from CloneID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromCloneID(String) - Method in class Maps
lookupMIDfromCloneID() - lookup mid from CloneID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromGenBankACC(String) - Method in class MJAgene
lookupMIDfromGenBankACC() - lookup mid from GenBank ACC ID.
lookupMIDfromGenBankACC(String) - Method in class Maps
lookupMIDfromGenBankACC() - lookup mid from GenBank ACC ID.
lookupMIDfromGeneName(String) - Method in class MJAgene
lookupMIDfromGeneName() - lookup mid from Gene Name.
lookupMIDfromGeneName(String) - Method in class Maps
lookupMIDfromGeneName() - lookup mid from Gene Name.
lookupMIDfromLocusID(String) - Method in class MJAgene
lookupMIDfromLocusID() - lookup mid from Locus ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromLocusID(String) - Method in class Maps
lookupMIDfromLocusID() - lookup mid from Locus ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromRefSeqID(String) - Method in class MJAgene
lookupMIDfromRefSeqID() - lookup mid from RefSeq ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromRefSeqID(String) - Method in class Maps
lookupMIDfromRefSeqID() - lookup mid from RefSeq ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromSwissProtID(String) - Method in class MJAgene
lookupMIDfromSwissProtID() - lookup mid from SwissProt ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromSwissProtID(String) - Method in class Maps
lookupMIDfromSwissProtID() - lookup mid from SwissProt ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromUniGeneID(String) - Method in class MJAgene
lookupMIDfromUniGeneID() - lookup mid from UniGene ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDfromUniGeneID(String) - Method in class Maps
lookupMIDfromUniGeneID() - lookup mid from UniGene ID Note this returns the first instance of the gene found if there are duplicates.
lookupMIDlistFrom_dbEST(String) - Method in class MJAgene
lookupMIDlistFrom_dbEST() - lookup mid list from dbEST 3' or 5' ID.
lookupMIDlistFrom_dbEST(String) - Method in class Maps
lookupMIDlistFrom_dbEST() - lookup mid list from dbEST 3' or 5' ID.
lookupMIDListFromCloneID(String) - Method in class MJAgene
lookupMIDlistFromCloneID() - lookup mid list from CloneID.
lookupMIDListFromCloneID(String) - Method in class Maps
lookupMIDlistFromCloneID() - lookup mid list from CloneID.
lookupMIDlistFromGenBankACC(String) - Method in class MJAgene
lookupMIDlistFromGenBankACC() - lookup mid list from GenBank ID.
lookupMIDlistFromGenBankACC(String) - Method in class Maps
lookupMIDlistFromGenBankACC() - lookup mid list from GenBank ID.
lookupMIDListFromGeneName(String) - Method in class MJAgene
lookupMIDlistFromGeneName() - lookup mid list from Gene Name.
lookupMIDListFromGeneName(String) - Method in class Maps
lookupMIDlistFromGeneName() - lookup mid list from Gene Name.
lookupMIDListFromLocusID(String) - Method in class MJAgene
lookupMIDlistFromLocusID() - lookup mid list from Locus ID.
lookupMIDListFromLocusID(String) - Method in class Maps
lookupMIDlistFromLocusID() - lookup mid list from Locus ID.
lookupMIDListFromRefSeqID(String) - Method in class MJAgene
lookupMIDlistFromRefSeqID() - lookup mid list from RefSeq ID.
lookupMIDListFromRefSeqID(String) - Method in class Maps
lookupMIDlistFromRefSeqID() - lookup mid list from RefSeq ID.
lookupMIDListFromSwissProtID(String) - Method in class MJAgene
lookupMIDlistFromSwissProtID() - lookup mid list from SwissProt ID.
lookupMIDListFromSwissProtID(String) - Method in class Maps
lookupMIDlistFromSwissProtID() - lookup mid list from SwissProt ID.
lookupMIDListFromUniGeneID(String) - Method in class MJAgene
lookupMIDlistFromUniGeneID() - lookup mid list from UniGene ID.
lookupMIDListFromUniGeneID(String) - Method in class Maps
lookupMIDlistFromUniGeneID() - lookup mid list from UniGene ID.
lookupMIDtoGID(int) - Method in class MJAgeometry
lookupMIDtoGID() - lookup MID given the GID
lookupNamedOrderedCondList(String) - Method in class Condition
lookupNamedOrderedCondList() - lookup named ordered condition list
lookupNamedOrderedCondListIdx(String) - Method in class Condition
lookupNamedOrderedCondListIdx() - lookup named ordered condition list index
lookupOfileTypeDBmenu(int) - Method in class MJAReval
lookupOfileTypeDBmenu() - lookup R output file type menu entry by value.
lookupOfileTypeDBmenu(int) - Method in class RevalBase
lookupOfileTypeDBmenu() - lookup R output file type menu entry by value.
lookupOfileTypeDBmenu(String) - Method in class MJAReval
lookupOfileTypeDBmenu() - lookup R output file type menu entry by name.
lookupOfileTypeDBmenu(String) - Method in class RevalBase
lookupOfileTypeDBmenu() - lookup R output file type menu entry by name.
lookupOfileTypeDBvalue(String) - Method in class MJAReval
lookupOfileTypeDBvalue() - lookup R output file type value by name.
lookupOfileTypeDBvalue(String) - Method in class RevalBase
lookupOfileTypeDBvalue() - lookup R output file type value by name.
lookupOrMakeNewGeneBitSet(String, GeneBitSet) - Static method in class GeneBitSet
lookupOrMakeNewGeneBitSet() - lookup or create new GeneBitSet in userBS[].
lookupOverlayMapIdx(String) - Static method in class MJAplot
lookupOverlayMapIdx() - lookup named scatterplot overlay map index
[TODO] does not exist yet
lookupOverlayMapIdx(String) - Static method in class OverlayMap
lookupOverlayMapIdx() - lookup named scatterplot overlay map index
lookupProcessBitsDBmenu(int, int) - Method in class MJAReval
lookupProcessBitsDBmenu() - lookup Export/Import ProcessBits menu by value
lookupProcessBitsDBmenu(int, int) - Method in class RevalBase
lookupProcessBitsDBmenu() - lookup Export/Import ProcessBits menu by value
lookupProcessBitsDBvalue(String) - Method in class MJAReval
lookupProcessBitsDBvalue() - lookup Export/Import ProcessBits value by name
lookupProcessBitsDBvalue(String) - Method in class RevalBase
lookupProcessBitsDBvalue() - lookup the Export/Import ProcessBits value by name
lookupR2ClientActionDBMenu(int) - Method in class MJAReval
lookupR2ClientActionDBMenu() - lookup R to client Action menu by value
lookupR2ClientActionDBMenu(int) - Method in class RevalBase
lookupR2ClientActionDBMenu() - lookup R to client Action menu by value
lookupR2ClientActionDBMenu(String) - Method in class MJAReval
lookupR2ClientActionDBMenu() - lookup R to client Action menu by name
lookupR2ClientActionDBMenu(String) - Method in class RevalBase
lookupR2ClientActionDBMenu() - lookup R to client Action menu by name
lookupR2ClientActionDBtype(String) - Method in class RevalBase
lookupR2ClientActionDBtype() - lookup R to client Action type value by name
lookupR2ClientActionDBvalue(String) - Method in class MJAReval
lookupR2ClientActionDBvalue() - lookup R to client Action value by name
lookupR2ClientActionDBvalue(String) - Method in class RevalBase
lookupR2ClientActionDBvalue() - lookup R to client Action value by name
lookupRangeModeName(int) - Method in class MJAproperty
lookupRangeModeName() - lookup the inside/outside range Mode Name for values RANGE-xxxx.
lookupRdataTypeDBmenu(int) - Method in class MJAReval
lookupRdataTypeDBmenu() - lookup export-types menu entry by value.
lookupRdataTypeDBmenu(int) - Method in class RevalBase
lookupRdataTypeDBmenu() - lookup the export-types menu entry by value.
lookupRdataTypeDBmenu(String) - Method in class MJAReval
lookupRdataTypeDBmenu() - lookup export-types menu entry by name.
lookupRdataTypeDBmenu(String) - Method in class RevalBase
lookupRdataTypeDBmenu() - lookup the export-types menu entry by name.
lookupRdataTypeDBvalue(String) - Method in class MJAReval
lookupRdataTypeDBvalue() - lookup export-types value by name.
lookupRdataTypeDBvalue(String) - Method in class RevalBase
lookupRdataTypeDBvalue() - lookup the export-types value by name.
lookupSampleByFreeTextName(String, String) - Method in class MJAsample
lookupSampleByFreeTextName() - lookup sample number by SampleID (free-text) name.
lookupSampleName(String, String) - Method in class MJAsample
lookupSampleName() - lookup sample number by sample databaseFileID.
lookupSampleNameByDBfileID(String, String) - Method in class MJAsample
lookupSampleNameByDBfileID() - lookup sample number by sample databaseFileID.
lookupSampleNameByDBfileName(String, String) - Method in class MJAsample
lookupSampleNameByDBfileName() - lookup sample number by sample DB file name.
lookupScrollerIdx(String) - Method in class StateScrollers
lookupScrollerIdx() - lookup a particular scroller index
lookupShowExprProfilesPopupInstance(String) - Method in class PopupRegistry
lookupShowExprProfilesPopupInstance() - lookup ShowExprProfilesPopup for unique key instance
lookupShowPlotPopupInstance(String) - Method in class PopupRegistry
lookupShowPlotPopupInstance() - lookup ShowPlotPopup for unique key instance
lookupShowSpreadsheetPopupInstance(String) - Method in class PopupRegistry
lookupShowSpreadsheetPopupInstance() - lookup ShowSpreadsheetPopup for unique key instance
lookupShowStringPopupInstance(String) - Method in class PopupRegistry
lookupShowStringPopupInstance() - lookup ShowStringPopup for unique key instance
low - Variable in class MC_Cube
 
lowerControlPanel - Variable in class StateScrollers
holds buttons, textAreas, etc for state scroller GUI
lowestRatiosCL - Variable in class Filter
"Lowest ratios"
lowRangeScaleFactor - Variable in class Config
Scale factor for pseudoarray image.
lowRangeZoomFlag - Variable in class MAExplorer
Scale pseudoarray image by 1/100 to zoom low-range values
lTitle - Variable in class ChooserGUI
label for title for entire GUI window
lTitle - Variable in class PopupCondChooserGUI
label for title for entire GUI window
lTitle - Variable in class PopupOrderedCondChooserGUI
label for title for entire GUI window
ltList - Variable in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
 
lvl - Variable in class MC_Cube
 

M

maAnalysisProg - Variable in class Config
PARAM default M.A.
mAdbURL - Variable in class Config
base addr PARAM "mAdbURL"
mAdbViewerFlag - Variable in class MAExplorer
mAdb Clone page popup browser Mode
madeChanges() - Method in class MJAnormalization
madeChanges() - set the madeChangesFlag since state changed.
madeChangesFlag - Variable in class MAExplorer
made changes to DB so may want to SAVE DB
madHPri - Variable in class MaHybridSample
total array: rawIntens meanAbsDev, all genes in HP w/o bkgrd
mae - Variable in class ArrayScroller
link to global MAExplorer instance
mae - Static variable in class ChooserGUI
link to global MAExplorer instance
mae - Variable in class ChooserGUI.MouseEventHandler
 
mae - Static variable in class ClusterGenes
link to global MAExplorer instance
mae - Static variable in class ClusterGramCanvas
link to global MAExplorer instance
mae - Variable in class ClusterSamples
link to global MAExplorer instance
mae - Variable in class CompositeDatabase
link to global MAExplorer instance
mae - Static variable in class Condition
link to global MAExplorer instance
mae - Variable in class Config
link to global instance of MAExplorer
mae - Variable in class Draw2Dplot
link to global instance
mae - Variable in class DrawClusterGram
link to global instance
mae - Variable in class DrawHistogram
link to global MAExplorer instance
mae - Variable in class DrawPseudoImage
link to global MAExplorer instance
mae - Variable in class DrawRatioHistogram
link to global instance
mae - Variable in class DrawScatterPlot
link to global instance
mae - Variable in class EditedGeneList
link to global MAExplorer instance
mae - Static variable in class EventMenu
link to global MAExplorer instance
mae - Variable in class ExprProfile
link to global MAExplorer instance
mae - Variable in class ExprProfileCanvas
instance of MAExplorer so we can clear flags indicating the user did a manual quit()
mae - Variable in class ExprProfileOverlay
links to global MAExplorer instance
mae - Variable in class ExprProfilePanel
link to global MAExplorer instance
mae - Variable in class ExprProfilePopup
link to global MAExplorer instance
mae - Variable in class ExprProfileScrollPane
link to global MAExplorer instance
mae - Variable in class FileIO
link to global MAExplorer instance
mae - Variable in class Filter
link to global MAExplorer instance
mae - Static variable in class Gene
link to global MAExplorer instance
mae - Static variable in class GeneBitSet
link to global MAExplorer instance
mae - Variable in class GeneClass
link to global instance
mae - Static variable in class GeneGeneDist
link to global MAExplorer instance
mae - Variable in class GeneList
link to global MAExplorer instance
mae - Static variable in class GetParams
link to global MAExplorer instance
mae - Variable in class GipoTable
link to global MAExplorer instance
mae - Static variable in class GridCoords
link to global MAExplorer instance
mae - Variable in class Guesser
link to global instance
mae - Variable in class KeyEventHandler
instance of MAExplorer
mae - Variable in class MouseEventHandler
instance of MAExplorer
mae - Variable in class HPxyData
link to global MAExplorer instance
mae - Static variable in class HierClustNode
link to global MAExplorer instance
mae - Static variable in class MJAbase
link to global MAExplorer instance
mae - Variable in class MaHPquantTable
link to global MAExplorer instance
mae - Variable in class MaHybridSample
link to global MAExplorer instance
mae - Variable in class MaInfoTable
link to global MAExplorer instance
mae - Static variable in class MaeJavaAPI
link to global MAExplorer instance
mae - Variable in class Maps
link to global MAExplorer instance
mae - Variable in class MenuBarFrame
link to global instance
mae - Variable in class OverlayMap
link to global instance
mae - Variable in class PopupBinOprDialogQuery
link to MAExplorer instance
mae - Variable in class PopupDialogQuery
link to global instance to MAExplorer
mae - Variable in class PopupHPChooser
link to global MAExplorer instance
mae - Variable in class PopupLoginDialogQuery
link to global instance of MAExplorer
mae - Variable in class PopupRegistry
link to global MAExplorer instance
mae - Variable in class Report
link to global MAExplorer instance
mae - Static variable in class Reval
Global link
mae - Variable in class SampleSets
link to global MAExplorer instance
mae - Variable in class PopupScrollableSelector
 
mae - Variable in class SamplesTable
link to global instance of MAExplorer
mae - Variable in class ScrollableImageCanvas
link to global instance of MAExplorer
mae - Variable in class ShowExprProfilesPopup
 
mae - Variable in class ShowPlotPopup
link to global MAExplorer instance
mae - Variable in class ShowSpreadsheetPopup
link to global MAExplorer instance
mae - Variable in class ShowStringPopup
link to global MAExplorer nstance
mae - Static variable in class SpotData
link to global MAExplorer instance
mae - Static variable in class SpotFeatures
link to global MAExplorer instance
mae - Variable in class SpreadSheet
link to global MAExplorer instance
mae - Variable in class SSspreadPanel
 
mae - Variable in class SSstatusBar
max number col with alphabet
mae - Variable in class StateScrollers
link to global MAExplorer instance
mae - Variable in class Statistics
link to global instance of MAExplorer
mae - Variable in class Table
link to global instance of MAExplorer
mae - Variable in class UserState
link to global instance of MAExplorer
mae - Static variable in class Util
link to global MAExplorer instance
MAE_STARTUP_FILE - Static variable in class MAExplorer
Default empty .mae startup database
MaeJavaAPI - class MaeJavaAPI.
This class implements MAEPlugin.MAEStub and is the Open Java API.
MaeJavaAPI(MAExplorer) - Constructor for class MaeJavaAPI
MaeJavaAPI() - constructor for Gather Scatter API for MAExplorer to access MAExplorer data in a uniform interface.
maepKey - Variable in class PopupRegistry
[0:nMAEP-1] MAEPlugin Object key names
maepList - Variable in class PopupRegistry
[0:nMAEP-1] list of active MAEPlugin Objects
MAEPlugin - package MAEPlugin
 
MAEPlugin - class MAEPlugin.MAEPlugin.
This abstract class defines the base MAEPlugin base class.
MAEPlugin.analysis - package MAEPlugin.analysis
 
MAEPlugin.connection - package MAEPlugin.connection
 
MAEPlugin.popup - package MAEPlugin.popup
 
MAEPlugin() - Constructor for class MAEPlugin.MAEPlugin
MAEPlugin() - This private constructor prevents non-labeled and registered plugins
MAEPlugin(String) - Constructor for class MAEPlugin.MAEPlugin
MAEPlugin() - Constructor registers the plugin and sets up menu item.
MAEPlugin(String, String) - Constructor for class MAEPlugin.MAEPlugin
MAEPlugin() - Constructor registers the plugin and sets up menu item.
maepPropBits - Variable in class PopupRegistry
[0:nMAEP-1] bits requesting notification of MAEPlugin Object list of changes
maeRepaint() - Method in class MJAutil
maeRepaint() - repaint MAExplorer main window.
maeServerBase - Variable in class MAExplorer
top level codebase for MAE server
maestub - Variable in class MAEPlugin.MAEPlugin
This interface must be implemented in the user's plugin code
maestub - Variable in class MAEPlugin.popup.PluginUnLoader
Reference to MAE Stub
MAEStub - interface MAEPlugin.MAEStub.
This interface Enforces MAE compliance with Plugin requirements.
maeTbl - Variable in class GipoTable
name of remapped table name
maeTbl - Variable in class MaHPquantTable
name of remap Table
maeTbl - Variable in class MaInfoTable
name of the remap Table
maeTbl - Variable in class SamplesTable
remap table name
maeTitleVer - Static variable in class MAExplorer
Compiled MAExplorer title with version number
MAEUpdateListener - interface MAEUpdateListener.
The MAEUpdateListener class interface is used with MAEPlugins to specify the update interface for the PopupRegistry event handlers.
MAExplorer - class MAExplorer.
MicroArray Explorer main() class.
MAExplorer() - Constructor for class MAExplorer
 
magnification - Variable in class ArrayScroller
magnification
MaHPquantTable - class MaHPquantTable.
The class is only used to read a .quant file (File or URL) into an mae.ms instance.
MaHPquantTable(MAExplorer, MaHybridSample, String, String, boolean) - Constructor for class MaHPquantTable
MaHPquantTable() - constructor to read the .quant file table and setup MaHybridSample
MaHybridSample - class MaHybridSample.
The MaHybridSample class is the primary instance of hybridized sample array data.
MaHybridSample(MAExplorer, String, String, String, String, String, String, String, boolean, boolean, int) - Constructor for class MaHybridSample
MaHybridSample() - constuctor for an instance of a Microarray hybridized sample data
main(String[]) - Static method in class MAExplorer
main() - for MAExplorer started by standalone application.
maInfoFile - Variable in class Config
PARAM "maInfoFile" or URL (opt)
MaInfoTable - class MaInfoTable.
This class reads optional extra sample specific information from the MaInfoTable.txt file.
MaInfoTable(MAExplorer, String) - Constructor for class MaInfoTable
MaInfoTable() - constructor
mainPanel - Variable in class PopupCondChooser.CondParamEditForm
place both labelPanel & tfPanel to create form
mainPanel - Variable in class PopupOrderedCondChooser.CondParamEditForm
place both labelPanel & tfPanel to create form
mainWizardPanel - Variable in class PopupEditRscript
main wizard panel, separates top label from grid of TF and labels
mainWizardPanelLabel - Variable in class PopupEditRscript
main label for wizard panel
make8BitImage() - Method in class MedianCut
make8BitImage() - Generate 8-bit image from interla 15-bit image.
makeChkBoxMenuItem(Menu, String, String, int, boolean) - Method in class MenuBarFrame
makeChkBoxMenuItem() - make CheckboxMenuItem entry in popup menu list.
makeHPrestrictedTable(Table) - Method in class SamplesTable
makeHPrestrictedTable() - make a Table of HPs restricted by login required.
makeInverseMap(int[], int) - Method in class MedianCut
makeInverseMap() - for all cubes, compute centroid of colors in cube.
makeMenuItem(Menu, String, String, int) - Method in class MenuBarFrame
makeMenuItem() - make menuItem entry in menu list.
makeNewGeneList(String, boolean) - Method in class MJAgeneList
makeNewGeneList() - create a new empty named gene list and gene bit set
makeReport() - Method in class Report
makeReport() - make gene-report instance using reportMode to determine report
makeSearchList(int, String[], int, String, int) - Method in class KeyEventHandler
makeSearchList() - Find all strings and make a list, handle wild cards.
makeSearchList(String[], int, String, int) - Method in class KeyEventHandler
makeSearchList() - Find all strings in list that have the same begining.
makeSubMenu(Menu, String, String, int) - Method in class MenuBarFrame
makeSubMenu() - make submenu entry in menu list.
makeTabDelimReport(String) - Method in class Table
makeTabDelimReport() - make tab-delimited string report string from this Table
makeTmpVectors(int) - Method in class GeneGeneDist
makeTmpVectors() - create temp vectors if needed.
map - Variable in class CompositeDatabase
link to global Maps instance
map - Variable in class DrawScatterPlot
link to global instance
map - Variable in class EditedGeneList
link to global Maps instance
map - Variable in class ExprProfile
link to global Maps instance
map - Static variable in class Gene
link to global Maps instance
map - Variable in class GeneClass
link to global instance
map - Variable in class GipoTable
link to global Maps instance
map - Variable in class Guesser
link to global Maps instance
map - Variable in class HPxyData
Global instance of lookup table maps populated elsewhere
map - Static variable in class MJAbase
link to global Maps instance
map - Variable in class MaHPquantTable
link to global Maps instance
map - Variable in class MaHybridSample
link to global Maps instance
map - Static variable in class MaeJavaAPI
link to global Maps instance
map - Variable in class PopupRegistry
link to global Maps instance
map - Variable in class ScrollableImageCanvas
link to global instance of Maps
map - Static variable in class SpotFeatures
link to global Maps instance
mapHPtoMenuName - Variable in class MAExplorer
index of snHPName[] corresponding to iSampleName[] entry allocated [MAX_HYB_SAMPLES+1].
mapMFname - Variable in class ConfigTable
[map 0:nMUmap-1] names of MAE Field
mapMTname - Variable in class ConfigTable
map [0:nMUmap-1] names of MAE Table
mapPntToMid - Variable in class Draw2Dplot
map point # in [0:nGroup*maxGenes] to [0:maxGenes]
mapPointToMid - Variable in class ExprProfileOverlay
[nGenes*nHP_E] mid mapping
mapRelXYtoImage(MouseEvent, int, int) - Method in class ScrollableImageCanvas
mapRelXYtoImage() - map (x,y) Mouse in current canvas to (xImg,yImg) as well as updating the parent (xImg,yImg) values.
Maps - class Maps.
The Maps class holds various gene maps for mapping: GID, MID, GCRF, gene names.
Maps(MAExplorer) - Constructor for class Maps
Maps() - constructor that allocates mapping tables calc size from F*G*R*C These is populated @GipoTable.setupMapLookupTables().
mapUFname - Variable in class ConfigTable
map 0:nMUmap-1] names of User Field
mapUsrFieldToMaeField(String, String) - Method in class ConfigTable
mapUsrFieldToMaeField() - map user (Tbl,Field) name to MAE Field name
mapUTname - Variable in class ConfigTable
map [0:nMUmap-1] names of User Table
MARKER_CIRCLE - Static variable in class MAExplorer
pseudoarray canvas - draw circle of size radius
MARKER_CIRCLE - Static variable in class MJAbase
pseudoarray canvas - draw circle of size radius
MARKER_CURRENT - Static variable in class MAExplorer
pseudoarray canvas - draw Current object
MARKER_CURRENT - Static variable in class MJAbase
pseudoarray canvas - draw Current object
MARKER_GENES - Static variable in class MAExplorer
pseudoarray canvas - draw all spots in gene list
MARKER_GENES - Static variable in class MJAbase
pseudoarray canvas - draw all spots in gene list
MARKER_KMEANS_CLUSTER - Static variable in class MAExplorer
pseudoarray canvas - draw K-means cluster #
MARKER_KMEANS_CLUSTER - Static variable in class MJAbase
pseudoarray canvas - draw K-means cluster #
MARKER_NONE - Static variable in class MAExplorer
pseudoarray canvas - No overlay
MARKER_NONE - Static variable in class MJAbase
pseudoarray canvas - No overlay
MARKER_PLUS - Static variable in class MAExplorer
pseudoarray canvas - draw 5x5 plus
MARKER_PLUS - Static variable in class MJAbase
pseudoarray canvas - draw 5x5 plus
MARKER_SQUARE - Static variable in class MAExplorer
pseudoarray canvas - draw square of size radius
MARKER_SQUARE - Static variable in class MJAbase
pseudoarray canvas - draw square of size radius
markerShape - Variable in class ScrollableImageCanvas
either MARKER_PLUS or MARKER_CIRCLE
masks - Variable in class WriteGifEncoder
 
MASTER_CLONE_ID - Static variable in class MAExplorer
Master masterIDmode Mode - clone ID
MASTER_CLONE_ID - Static variable in class MJAbase
Master masterIDmode Mode - clone ID
MASTER_DBEST3 - Static variable in class MAExplorer
Master masterIDmode Mode - dbEST 3' ID
MASTER_DBEST3 - Static variable in class MJAbase
Master masterIDmode Mode - dbEST 3' ID
MASTER_DBEST5 - Static variable in class MAExplorer
Master masterIDmode Mode - dbEST 5' ID
MASTER_DBEST5 - Static variable in class MJAbase
Master masterIDmode Mode - dbEST 5' ID
MASTER_GENBANK - Static variable in class MAExplorer
Master masterIDmode Mode - GenBank ID
MASTER_GENBANK - Static variable in class MJAbase
Master masterIDmode Mode - GenBank ID
MASTER_GENBANK3 - Static variable in class MAExplorer
Master masterIDmode Mode - GenBank 3' ID
MASTER_GENBANK3 - Static variable in class MJAbase
Master masterIDmode Mode - GenBank 3' ID
MASTER_GENBANK5 - Static variable in class MAExplorer
Master masterIDmode Mode - GenBank 5' ID
MASTER_GENBANK5 - Static variable in class MJAbase
Master masterIDmode Mode - GenBank 5' ID
MASTER_GENE_NAME - Static variable in class MAExplorer
Master masterNameMode Mode - gene name
MASTER_GENE_NAME - Static variable in class MJAbase
Master masterNameMode Mode - gene name
MASTER_GENERIC_ID - Static variable in class MAExplorer
Master masterIDmode Mode - generic ID
MASTER_GENERIC_ID - Static variable in class MJAbase
Master masterIDmode Mode - generic ID
Master_ID - Variable in class Gene
Master Gene Identifier (i.e.
MASTER_LOCUSLINK - Static variable in class MAExplorer
Master masterIDmode Mode - LocusLink ID
MASTER_LOCUSLINK - Static variable in class MJAbase
Master masterIDmode Mode - LocusLink ID
MASTER_OMIM - Static variable in class MAExplorer
Master masterIDmode Mode - OMIM ID
MASTER_SWISS_PROT - Static variable in class MAExplorer
Master masterIDmode Mode - SwissProt ID
MASTER_SWISS_PROT - Static variable in class MJAbase
Master masterIDmode Mode - SwissProt ID
MASTER_UG_ID - Static variable in class MAExplorer
Master masterIDmode Mode - UniGene ID
MASTER_UG_ID - Static variable in class MJAbase
Master masterIDmode Mode - UniGene ID
MASTER_UG_NAME - Static variable in class MAExplorer
Master masterNameMode Mode - UniGene name
MASTER_UG_NAME - Static variable in class MJAbase
Master masterNameMode Mode - UniGene name
masterGeneName - Variable in class MAExplorer
either "GeneName", "UGclusterName, etc"
MasterGeneName - Variable in class Gene
Master Gene Name will be one of the gene names below ([NOTE] as of V.0.90.01)
masterID - Static variable in class ChooserGUI
increments for each instance
masterID - Static variable in class PopupCondChooserGUI
Total number of instances of this class.
masterID - Static variable in class PopupHPChooser
 
masterID - Static variable in class PopupOrderedCondChooserGUI
Total number of instances of this class.
masterID - Variable in class SpotFeatures
lookup master Gene identifier
masterIDguesserIsPoppedUp - Variable in class MenuBarFrame
if guesser was popped up
masterIdIdx - Variable in class GipoTable
generic Master_ID index
masterIDList - Static variable in class PopupGeneGuesser
unsorted list of clone_id, is G.C.'ed
masterIDListSize - Static variable in class PopupGeneGuesser
unsorted list of clone_id size
masterIDmode - Variable in class MAExplorer
either MASTER_CLONE_ID or MASTER_GENBANK or MASTER_GENBANK5 or MASTER_GENBANK3 or MASTER_UG_ID, MASTER_SWISS_PROT, MASTER_GENERIC_ID
masterIDname - Variable in class MAExplorer
either "CloneID", "UniGeneID, GenBank, etc"
masterNameIdx - Variable in class GipoTable
generic Master_Gene_Name index
masterNameMode - Variable in class MAExplorer
either MASTER_GENE_NAME or MASTER_UG_NAME
MathMAE - class MathMAE.
This class contains math functions used for computing statistics in MAExplorer.
MathMAE() - Constructor for class MathMAE
 
MAX_ANALYSES - Static variable in class RevalBase
default # of analyses allowed
MAX_CHKBOX_CMDS - Static variable in class MenuBarFrame
max number of menu checkbox items allowed
MAX_CLUSTER_DIST - Static variable in class Config
Maximum cluster distance
MAX_CMDS - Static variable in class MenuBarFrame
max number of menu items allowed
MAX_COLORS - Static variable in class ClusterGramCanvas
maximum colors used - Dark green to dark red
MAX_COLORS - Static variable in class DrawPseudoImage
[Dark green:dark red] - MUST BE ODD #!!!
MAX_COLORS - Static variable in class MJAbase
Max number of PseudoArray image color range for Spectrum and Ratio Map
MAX_COND_LISTS - Static variable in class Condition
maximum number of # of condition lists slots available.
MAX_COND_PARAM - Static variable in class MAExplorer
maximum number of Condition parameters
MAX_CONDITION_LISTS - Static variable in class MAExplorer
Max # of named sample condition lists.
MAX_GENE_LISTS - Variable in class GeneList
max # of gene lists(or sets) to allow
MAX_HYB_SAMPLES - Static variable in class MAExplorer
Max # of hybridized array samples to load at one time
MAX_INTENSITY - Variable in class MAExplorer
maximum # intensity values of .quant data
MAX_MENU_STUBS - Static variable in class MenuBarFrame
 
MAX_MU_MAP - Static variable in class ConfigTable
max # of (maeTable, maeField) to (userTable, userField) map entries
MAX_NBR_CLUSTERS - Static variable in class Config
Maximum # of clusters
MAX_ORDERED_COND_LISTS - Static variable in class Condition
maximum number of # of ordered condition lists slots available.
MAX_ORDERED_COND_LISTS - Static variable in class MAExplorer
maximum number of # of ordered condition lists slots available.
MAX_OVERLAY_MAPS - Static variable in class OverlayMap
max # of overlays
MAX_PLUGINS - Static variable in class MAEPlugin.popup.PluginLoader
Maximum number of MAEPlugins that may be loaded at one time
MAX_POPUPS - Static variable in class PopupRegistry
maximum # of popups for each type of popup
MAX_POSSIBLE_PARAMS - Static variable in class PopupCondChooser.CondParamEditForm
max width of textfields
MAX_POSSIBLE_PARAMS - Static variable in class PopupOrderedCondChooser.CondParamEditForm
max width of textfields
MAX_PROJECTS - Static variable in class MAExplorer
Maximum # of projects for project lists
MAX_RADIUS - Static variable in class Config
MAximum spot radius allowed
MAX_RATIO - Static variable in class MAExplorer
maximum ratio for histogram of ratios histRatioBin[]
MAX_RATIO_HIST - Static variable in class MAExplorer
# of bins in histRatioBin[]
MAX_ROWS_TO_SHOW - Static variable in class ShowSpreadsheetPopup
# of rows to show in dynamic spreadsheet
MAX_TEXT - Static variable in class ScrollableImageCanvas
max # of text items
MAX_USER_BS - Static variable in class GeneBitSet
max # user assignable gene bit setst hat can be created
MAX_WIZ_INPUT_CHOICES - Static variable in class PopupEditRscript
Maximum # rows of Input Choices in the wizard grid
MAX_WIZ_OUTPUT_CHOICES - Static variable in class PopupEditRscript
Maximum # rows of Input Choices in the wizard grid
MAX_WIZ_R2M - Static variable in class PopupEditRscript
Maximum # rows of R2Client Choices in the wizard grid
MAX_WIZ_ROWS - Static variable in class PopupEditRscript
Maximum # rows in the wizard grid ([#rows,2]
MAXBINS - Static variable in class DrawHistogram
Break histogram into bins
maxBinX - Variable in class DrawHistogram
ARG: maximum possible value range set by scrollers
maxbits - Variable in class WriteGifEncoder
 
maxCalcPseudoArraySize - Variable in class Config
Computed maximum pseudoarray canvas size, null if not using pseudoarrays as (width,height) required given the array geometry.
maxcode - Variable in class WriteGifEncoder
 
MAXCODE(int) - Method in class WriteGifEncoder
MAXCODE() - return n bits
MAXCOLORS - Static variable in class MedianCut
maximum # of output colors
maxConditions - Variable in class PopupOrderedCondChooserGUI
the MAX # of conditions specified by MAExplorer
maxDataF1 - Variable in class MaHybridSample
max intens values F1 in getF1F2list
maxDataF2 - Variable in class MaHybridSample
max intens values F2 in getF1F2list
maxDataH - Variable in class Statistics
histogram data max value set by calcHistStats()
maxDataHP_X - Variable in class CompositeDatabase
max intensity HP_X in getNormHP_XandYdata
maxDataHP_Y - Variable in class CompositeDatabase
max intensity HP_Y in getNormHP_XandYdata
maxDataS - Variable in class MaHybridSample
current norm: scaled max data
maxDgramDist - Variable in class ClusterGramCanvas
max of dGramDistS[]
maxDgramDist - Static variable in class HierClustNode
max dGramDistXXX[] (distance not dist**2)
maxDistLR - Static variable in class HierClustNode
max distLR (dist**2) found between all nodes
maxFIELDS - Variable in class Config
PARAM fields left and right
maxFIELDS - Variable in class MaHPquantTable
maximum number of fields allowed
maxFreq - Variable in class DrawHistogram
maximum range of values found in binFreq[]
maxFV - Variable in class MaHybridSample
maximum and fractions of dynamic range
maxGCOLS - Variable in class Config
PARAM grid rows
maxGCOLS - Variable in class MaHPquantTable
maximum number of grid cols allowed
maxGeneHashTableSize - Variable in class Maps
size of gene hash table estimated as 1.5*maxGenes - only to 1st instance
maxGeneListSize - Static variable in class GeneList
& number of geneSets
maxGenes - Variable in class EditedGeneList
max # genes/gene list
maxGenes - Variable in class Filter
max # genes/genelist
maxGenes - Variable in class Guesser
local map.maxGenes
maxGenes - Variable in class Maps
maximum number of genes (estimated as maxGRIDS*maxGROWS*maxGCOLS)
maxGenes - Static variable in class Reval
current active genes lists for generating export data
maxGeneSets - Static variable in class GeneList
# of gene sets - keep title in gene set
maxGenesForKmeansClustering - Static variable in class ClusterGenes
max # filtered genes to do K-means clustering
maxGenesInCurCluster - Static variable in class ClusterGenes
max # filtered genes to do curClusterCL clustering
maxGenesToRpt - Variable in class Config
PARAM Max # of genes to report in highest or lowest # genes
maxGlobalDist - Variable in class ClusterGenes
maximum global distance seen for all distances
maxGRIDS - Variable in class Config
PARAM grids labeled A, B, ..., H
maxGRIDS - Variable in class MaHPquantTable
maximum number of grids allowed
maxGROWS - Variable in class Config
PARAM grid cols
maxGROWS - Variable in class MaHPquantTable
maximum number of grid rows allowed
maxGTmapSize - Variable in class GipoTable
Sizeof gid2GipoTableRow[1:map.maxSpots]
maxHistData - Variable in class MaHybridSample
total array: mode hist data value
maxHPdataMn - Variable in class ExprProfile
opt.
maxHPdataMn - Variable in class ExprProfileOverlay
max of hpDataMnA[][] data
maxHPdataMn - Variable in class ExprProfileScrollPane
max of hpDataMnA[][] data
maxHsize - Static variable in class MaHPquantTable
 
maxHsteps - Variable in class ExprProfileOverlay
# of steps for hsL hsU
maxHybSamples - Variable in class PopupCondChooserGUI
the MAX # of samples is specified by MAExplorer
maxIntens - Variable in class MaHybridSample
max intensity of histogram data
maxItems - Variable in class GeneBitSet
maximum # ITEMS in bit space allocated
maxKmeansNodes - Variable in class ClusterGenes
max # of K-means primary nodes will be set by thresholding slider
maxLeftLabelPixelsWidth - Variable in class DrawPseudoImage
max # pixels in left labels
maxLineList - Variable in class Draw2Dplot
max allowed # of EGL genes
maxmaxcode - Variable in class WriteGifEncoder
 
maxMean - Variable in class ExprProfile
maximum of the hpDataMn[] values
maxMIDs - Variable in class Maps
maximum # of Master Gene IDs = size of gene (i.e clone,oligo, etc) list
maxNbrCond - Variable in class PopupOrderedCondChooser
Maximum # of Conditions currently in the database.
maxNbrSamples - Variable in class PopupCondChooser
Maximum # of samples currently in the database.
maxNgeneClusterCnt - Static variable in class ClusterGenes
max # of clusters found
MaxNumberPluginsException - exception MAEPlugin.MaxNumberPluginsException.
This exception is used to allow self registering of plugins for a max number of plugins.
MaxNumberPluginsException() - Constructor for class MAEPlugin.MaxNumberPluginsException
 
maxOCLmean - Static variable in class MJAexprProfile
Ordered Condition List maximum mean seen in any condition
maxOrderedCondLists - Static variable in class Condition
max # of ordered condition lists that have been created.
maxOverlayMaps - Static variable in class OverlayMap
max # of named overlay maps
maxPossibleCond - Static variable in class PopupCondChooser
maximum possible number of conditions
maxPossibleConditions - Static variable in class PopupOrderedCondChooser
max possible conditions
maxPossibleCondParam - Static variable in class PopupCondChooser
maximum possible number of Condition parameters
maxPossibleOcl - Static variable in class PopupOrderedCondChooser
maximum possible number of Ordered Lists of Conditions
maxPossibleOCLParam - Static variable in class PopupOrderedCondChooser
maximum possible number of OCL parameters
maxPossibleSamples - Static variable in class PopupCondChooser
maximum possible number of hybridized saaples expected
maxPreloadImgs - Variable in class MAExplorer
PARAM max # images to preload set from "maxPreloadImages"
maxQualCheck - Variable in class Config
Set from .quant file data: Maximum QualCheck Value
maxRatioHistIdx - Variable in class CompositeDatabase
max value found in ratioHist[]
maxRatioRI - Variable in class MaHybridSample
total array: max(f1RI/f2RI) for all spots
maxRaw - Variable in class MaHybridSample
total array: if Ratio, maximum of range of F1 or F2 RawIntens
maxRawS - Variable in class MaHybridSample
current norm: scaled maxRaw data
maxRI - Variable in class MaHybridSample
total array: range of RI or ratio
maxRI1 - Variable in class MaHybridSample
total array: range of RawIntensity1
maxRI2 - Variable in class MaHybridSample
total array: range of RawIntensity2
maxRLO - Static variable in class RevalBase
max # of Rscript analysis procedures
MAXRLO - Static variable in class PopupEditRscript
Maximum # of array slots for editing
maxSize - Variable in class GeneList
maximum allocation size
maxSpots - Variable in class Maps
maximum # of spots estimated as maxFIELDS*maxGRIDS*maxGROWS*maxGCOL
maxSpotsFound - Variable in class Maps
max # spots found.
maxStepsScr - Variable in class ShowPlotPopup
number of prewired scroller steps
maxTextItems - Variable in class CompositeDatabase
Common Grid labels for drawing onto the canvas.
maxUserBS - Static variable in class GeneBitSet
max # user assignable gene bit sets
maxVsize - Static variable in class MaHPquantTable
 
maxVsteps - Variable in class ExprProfileOverlay
# of steps for vsL vsU
maxWords - Variable in class GeneBitSet
max # 64-bit WORDS alloc'ed in bitData[]
maxX - Variable in class Draw2Dplot
max X range set in initial call
maxX - Variable in class DrawHistogram
ARG: maximum possible value range set by scrollers
maxX - Variable in class DrawRatioHistogram
ARG: maximum possible value range set by scrollers
maxXfound - Variable in class DrawRatioHistogram
min value of range of values found
maxXscroll - Variable in class Draw2Dplot
max X range set by ShowPlotPopup scrollers
maxY - Variable in class Draw2Dplot
max X range set in initial call
maxYscroll - Variable in class Draw2Dplot
max Y range set by ShowPlotPopup scrollers
mbar - Static variable in class MenuBarFrame
menu bar
mbf - Static variable in class EventMenu
link to global MenuBarFrame instance
mbf - Variable in class Guesser
link to global MenuBarFrame instance
mbf - Variable in class MAExplorer
Global instance of Frame based MenuBar
mbf - Variable in class PopupRegistry
link to global MenuBarFrame instance
mbf - Variable in class ShowStringPopup
link to global instance
MC_Cube - class MC_Cube.
 
MC_Cube() - Constructor for class MC_Cube
MC_Cube() - constructor
mean - Variable in class MaHybridSample
Filter hist: mean raw intensity
mean - Variable in class Statistics
means[0:nConditions-1] of data for computations, set by calcMeanAndVariance()
meanAbsDev - Variable in class MaHybridSample
Filter hist: mean absolute deviation raw intensity
meanAbsDevH - Variable in class Statistics
histogram data mean absolute deviation set by calcHistStats()
meanBin - Variable in class DrawHistogram
mean bin intensity value for medianFreq
meanCalDNA - Variable in class MaHybridSample
mean 'calibration DNA' intensity
meanClusterVector - Variable in class ClusterGenes
mean normalized quantitation vector for K-means nodes [1:nKmeansNodes][0:nMSList-1]
meanDist - Variable in class ClusterGenes.Cluster
mean distance to meanEP
meanEP - Variable in class ClusterGenes.Cluster
mean expr profile of this cluster
meanFreq - Variable in class DrawHistogram
mean binFreq[]
meanH - Variable in class Statistics
histogram data median set by calcHistStats()
meanIdx - Variable in class MaHybridSample
Filter hist: index of mean raw intensity
meanIdx - Variable in class Statistics
index of mean in hist[] set by calcHistStats()
meanIntens - Variable in class MaHybridSample
mean of histogram data
meanUseGeneSet - Variable in class MaHybridSample
mean 'User Filter Gene set' intensity
meanValue - Variable in class DrawHistogram
mean binFreq of weighted binFreq[]
median - Variable in class MaHybridSample
Filter hist: median raw intensity
medianBin - Variable in class DrawHistogram
median bin intensity value for medianFreq
MedianCut - class MedianCut.
MedianCut converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.
MedianCut(int[], int, int) - Constructor for class MedianCut
MedianCut() - Constructor Then call cvtImg24toImg8() to get the 8-bit image.
medianDist - Variable in class ClusterGenes.Cluster
median distance to medianEP
medianEP - Variable in class ClusterGenes.Cluster
median expr profile of this cluster
medianF1 - Variable in class MaHybridSample
median of F1 channel
medianF1Bkgd - Variable in class MaHybridSample
median background of F1 channel
medianF2 - Variable in class MaHybridSample
median of F2 channel if present
medianF2Bkgd - Variable in class MaHybridSample
median background of F2 channel if present
medianFreq - Variable in class DrawHistogram
median binFreq[]
medianH - Variable in class DrawHistogram
set from ms hist[] statistics
medianH - Variable in class Statistics
histogram data median set by calcHistStats()
medianIdx - Variable in class MaHybridSample
Filter hist: index of median raw intensity
medianIdx - Variable in class Statistics
index of median in hist[] set by calcHistStats()
medianIntens - Variable in class MaHybridSample
median of histogram data
medianRI - Variable in class MaHybridSample
total array: median value of rawIntensity
medianValue - Variable in class DrawHistogram
median binFreq of binDataValue[]
mediumFont - Variable in class ScrollableImageCanvas
small char font - 12pt
mediumFontLbl - Variable in class MenuBarFrame
current global medium font
medMinerURL - Variable in class Config
base addr PARAM "medMinerURL"
medMinerURLepilogue - Variable in class Config
base addr PARAM "medMinerURLepilogue"
medMinerViewerFlag - Variable in class MAExplorer
MedMiner gene page popup browser Mode
meh - Variable in class Guesser
handle events for text area
meh - Variable in class KeyEventHandler
for passing flag
meh1 - Variable in class ChooserGUI
handle mouse events for text areas for ta1 LEFT
meh2 - Variable in class ChooserGUI
handle mouse events for text areas for ta2 RIGHT
memAllocFailedFlag - Variable in class HierClustNode
 
menuActionCmdList - Static variable in class MenuBarFrame
[MAX_CMDS] list of menuItem (short-form) commands for event handler
menuActionLabelList - Static variable in class MenuBarFrame
[MAX_CMDS] list of menuItem commands labels
menuActivated() - Method in class MAEPlugin.MAEPlugin
menuActivated() - this method calls the pluginMain() method in GUI contexts.
menuActivated() - Method in interface MAEPlugin.PluginStub
menuActivated() - method called when menu is clicked for menu driven plugins.
MenuBarFrame - class MenuBarFrame.
The class builds the MAExplorer GUI including a menu bar in a new Frame.
MenuBarFrame(MAExplorer) - Constructor for class MenuBarFrame
MnuBarFrame() - constructor used with the Applet.
MenuBarFrame(MAExplorer, String, int, int) - Constructor for class MenuBarFrame
MenuBarFrame() - constructor for main GUI window and menubar.
menuFlag - Variable in class MAEPlugin.MAEPlugin
Menu flag, activated from menuItem.
menuHook - Variable in class MJAbase
Hook for Plugins into Menubar
menuHook - Variable in class MaeJavaAPI
Hook for Plugins into Menubar
menuHook - Variable in class MAEPlugin.MAEPlugin
Provides a hook into the mae Menubar
menuHook - Static variable in interface MAEPlugin.MAEStub
menu where plugins should hook themselves.
menuInsertionPointName - Variable in class MAEPlugin.MAEPlugin
menu insertion point name if not null.If null, then put into PluginMenu hook
menuItem - Variable in class MAEPlugin.MAEPlugin
GUI Elements
menuJ - Variable in class StageNames
index for menuNames[]
menuName - Variable in class RLO
Analysis menu name
menuName - Variable in class PopupEditRscript
Analysis menu name
menuNames - Variable in class StageNames
List unique menu name entries for various entities in Samples tbl
MenuPlugin - class MAEPlugin.MenuPlugin.
This abstract class defines MenuPlugin class.
MenuPlugin() - Constructor for class MAEPlugin.MenuPlugin
MenuPlugin() - constructor to override to implement the plugin
MenuPlugin(String) - Constructor for class MAEPlugin.MenuPlugin
MenuPlugin() - constructor for menu.
menuStubChoice - Variable in class PopupEditRscript
menu stub choice widget
menuStubName - Variable in class RLO
Desired client menu stub.
menuStubName - Variable in class PopupEditRscript
Desired Client menu stub.
menuTitle - Variable in class MaHybridSample
string to use in Sample menu entry
merkRow - Variable in class SStextArray
 
method - Variable in class ClusterGenes
Current clustering method.
METHOD_CLUSTER_KMEANS - Static variable in class ClusterGenes
Method: find most orthogonal clusters and then subset rest of genes to those.
METHOD_HIERARCHICAL_CLUSTERING - Static variable in class ClusterGenes
Method: Numerical Taxonomy, Sneath&Sokol, 1973, W.H.
METHOD_SIMILAR_GENE_COUNTS_CLUSTERING - Static variable in class ClusterGenes
Method: Numerical Taxonomy, Sneath&Sokol, 1973, W.H.
METHOD_SIMILAR_GENES_CLUSTERING - Static variable in class ClusterGenes
Method: Numerical Taxonomy, Sneath&Sokol, 1973, W.H.
METHOD_SOM_CLUSTERING - Static variable in class ClusterGenes
Method: SOM - Self-Organizing-Maps, Tamayo (1999) PNAS USA 96:2907-2912
miCLHCMavgPGMALnk - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | Hierarchical) use average-arithmetic linkage for hier.clustering
miCLHCMavgPGMCLnk - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | Hierarchical) average-centroid linkage for hier.clustering
miCLHCMnextMinLnk - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | Hierarchical) next-min for linkage hier.clustering
miCLHCMunWtAvg - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | Hierarchical) unweighted/weighted average for hier.clustering
miCLHCMuseClusterDistCache - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | Hierarchical) use Cluster dist-dist cache matrix for hier.clustering
miCLHCMuseShortClusterDistCache - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | Hierarchical) use 16-bit short vs 32-bit float for hier.clustering
miCLMdispKmeansNodes - Variable in class MenuBarFrame
Menu: (Analysis | Cluster) cluster by K-means
miCLMfindSimGenesDisp - Variable in class MenuBarFrame
Menu: (Analysis | Cluster) cluster by finding similar genes
miCLMhierClusterDisp - Variable in class MenuBarFrame
Menu: (Analysis | Cluster) cluster by hierarchical clustering
miCLMnormHP - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | Hierarchical) normalize EP by HP sample for hier.clustering
miCLMsimGeneCountsDisp - Variable in class MenuBarFrame
Menu: (Analysis | Cluster) cluster by finding similar gene counts
miCLMuseCorrCoeffDist - Variable in class MenuBarFrame
Menu: (Analysis | Cluster) cluster using correlation coefficient else Euclidean distance
miCLMuseLSQmagNorm - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | hierarchical ) cluster using LSQ magnitude normalization else ...
miCLMuseMedianKmeans - Variable in class MenuBarFrame
Menu: (Analysis | Cluster | cluster by K-means) cluster using K-medians else use K-means
mid - Variable in class ExprProfile
ARG: Master Gene ID (MID) for gene we are creating if != -1
mid - Variable in class Gene
Master gene ID index # (MID).
mid - Variable in class HPxyData
ARG: gene MID idx we are creating if != -1
mid2gid - Variable in class Maps
map: mid (Master Gene index) to gid (gridCoords index) This is created by: GeneTable.setupMIDlist() It is used for lookup by: GeneTable.getGeneListOfGeneClass()
mid2MasterIdHashtable - Variable in class Maps
hash table of Master Gene IDs (MID) of size maxGeneHashTableSize.
midList - Variable in class Filter
list of Mids used in passing data back and forth to FilterPlugins
midList - Variable in class Gene
list of all mids for duplicats of this Gene [0:nMid-1] that occurs more than 2X in the in GIPO
midList - Static variable in class Reval
current active genes lists for generating export data
midStaticCL - Variable in class Maps
map: mid index to list of genes i.e.
miEMautoScrollerPopup - Variable in class MenuBarFrame
Menu: (Edit | User Edited Gene List') [DEPRICATED]
miEMclusterWorkingCL - Variable in class MenuBarFrame
Menu: (Edit | Preferences) Cluster Filtered Genes, else all genes
miEMeditAdd - Variable in class MenuBarFrame
Menu: (Edit | User Edited Gene List') add gene to 'Edited Gene List'
miEMeditNop - Variable in class MenuBarFrame
Menu: (Edit | User Edited Gene List') don't edit 'Edited Gene List'
miEMeditRmv - Variable in class MenuBarFrame
Menu: (Edit | User Edited Gene List') delete gene to 'Edited Gene List'
miEMshowEditedGenes - Variable in class MenuBarFrame
Menu: (Edit | User Edited Gene List') Show 'Edited Gene List'
miFEMenableFIOcache - Variable in class MenuBarFrame
Menu: (Edit | Preferences) enable using cache for Web database
miFEMuseWebDB - Variable in class MenuBarFrame
Menu: (Edit | Preferences) access data from Web database
miFRM_EGLfilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by EGL gene membership
miFRMclusterHP_Efilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by Cluster test
miFRMcvModeE - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample
miFRMcvModeMS - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample
miFRMcvModeXANDYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X and HP-Y 'sets' samples
miFRMcvModeXORYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X or HP-Y 'sets' samples
miFRMcvModeXset - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X 'set' samples
miFRMcvModeXY - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample
miFRMcvModeYset - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) test current HP-Y 'set' samples
miFRMCy3Cy5RatioRngIn - Variable in class MenuBarFrame
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) in range
miFRMCy3Cy5RatioRngOut - Variable in class MenuBarFrame
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) outside of range
miFRMdetValueSpotModeE - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-E 'list' samples
miFRMdetValueSpotModeMS - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Spot Detection Valuedata) test current HP sample
miFRMdetValueSpotModeXANDYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y 'set' samples
miFRMdetValueSpotModeXY - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y samples
miFRMfTestOCLFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by cur.
miFRMgeneClassMbrFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by GeneClass membership
miFRMgoodGeneListFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by good genes membership
miFRMgoodSpotModeE - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Good Spot data) test current HP-E 'list' samples
miFRMgoodSpotModeMS - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Good Spot data) test current HP sample
miFRMgoodSpotModeXANDYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y 'set' samples
miFRMgoodSpotModeXORYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Good Spot data)
miFRMgoodSpotModeXY - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y samples
miFRMgrayRngIn - Variable in class MenuBarFrame
Menu: (Analysis | Filter | by intensity range test) within range
miFRMgrayRngOut - Variable in class MenuBarFrame
Menu: (Analysis | Filter | by intensity range test) outside range
miFRMhighXYratioFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by high ratio range test
miFRMhistIntensRngFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by intensity histogram bin
miFRMhistRatioRngFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by ratio histogram bin
miFRMksTestXYsetsFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' KS-Test
miFRMlowXYratioFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by low ratio range test
miFRMOnlyGenesWithNonZeroDensityFlag - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use only genes with non-zero intensity)
miFRMposQuantModeE - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use positive quantified data) test current HP-E 'list' samples
miFRMposQuantModeMS - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use positive quantified data) test current HP sample
miFRMposQuantModeXY - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y samples
miFRMposQuantModeXYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y 'set' samples
miFRMratioRngIn - Variable in class MenuBarFrame
Menu: (Analysis | Filter | by ratio range test) in range
miFRMratioRngOut - Variable in class MenuBarFrame
Menu: (Analysis | Filter | Filter by ratio range test) outside of range
miFRMreplicateGenesFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by replicate genes membership
miFRMspotCVfilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by spot CV test
miFRMspotIntensCompareModeALL - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ALL selected samples
miFRMspotIntensCompareModeANY - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ANY selected samples
miFRMspotIntensCompareModeAT_LEAST - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT LEAST (n) selected samples
miFRMspotIntensCompareModeAT_MOST - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT MOST (n) selected samples
miFRMspotIntensCompareModePRODUCT - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have PRODUCT selected samples less than threshold
miFRMspotIntensCompareModeSUM - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have SUM selected samples less than threshold
miFRMspotIntensModeE - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-E 'list' samples
miFRMspotIntensModeMS - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP sample
miFRMspotIntensModeXANDYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y 'sets' samples
miFRMspotIntensModeXORYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X or HP-Y 'sets' samples
miFRMspotIntensModeXsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X 'sets' samples
miFRMspotIntensModeXY - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y samples
miFRMspotIntensModeYsets - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-Y 'sets' samples
miFRMspotIntensRngIn - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) within range test
miFRMspotIntensRngOut - Variable in class MenuBarFrame
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) outside range test
miFRMthrCy3Cy5Ratio - Variable in class MenuBarFrame
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) enabled
miFRMthrGray - Variable in class MenuBarFrame
Menu: (Analysis | Filter | by intensity range test) enabled
miFRMthrRatio - Variable in class MenuBarFrame
Menu: (Analysis | Filter | by ratio range test) enabled
miFRMthrSpotIntens - Variable in class MenuBarFrame
Menu: (Analysis | Filter | Filter by spot intensity [SI1:SI2] sliders) Filter by spot intensity range test
miFRMtTestXYfilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by HP-X and HP-Y F1+F2 t-Test
miFRMtTestXYsetsFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' t-Test
miFRMuseCVmeanElseMax - Variable in class MenuBarFrame
Menu: (Analysis | Filter | CV threshold sliders) use the CV mean else the CV max in computation
miFRMuseDetValueSpotDataFlag - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Spot Detection Value data)
miFRMuseDiffFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by difference test
miFRMuseGeneSetFilter - Variable in class MenuBarFrame
Menu: (Analysis | Filter) Filter by user gene set membership
miFRMuseGoodSpotDataFlag - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use Good Spot data)
miFRMusePosQuantDataFlag - Variable in class MenuBarFrame
Menu: (Analysis | Filter | use positive quantified data)
miHPMuseHPxySets - Variable in class MenuBarFrame
Menu: (Samples) use HP-X and HP-Y 'sets' of multiple samples else use individual HP-X and HP-Y samples.
MIN_CANVAS_HEIGHT - Static variable in class ClusterGramCanvas
default canvas height
MIN_CANVAS_HEIGHT - Static variable in class Draw2Dplot
default canvas height
MIN_CANVAS_HEIGHT - Static variable in class DrawHistogram
default canvas height
MIN_CANVAS_HEIGHT - Static variable in class DrawRatioHistogram
 
MIN_CANVAS_HEIGHT - Static variable in class ExprProfileCanvas
default canvas height size
MIN_CANVAS_WIDTH - Static variable in class ClusterGramCanvas
default canvas width
MIN_CANVAS_WIDTH - Static variable in class Draw2Dplot
default canvas width
MIN_CANVAS_WIDTH - Static variable in class DrawHistogram
default canvas width
MIN_CANVAS_WIDTH - Static variable in class DrawRatioHistogram
 
MIN_CANVAS_WIDTH - Static variable in class ExprProfileCanvas
default canvas width size
MIN_CLUSTER_DIST - Static variable in class Config
Minimum cluster distance
MIN_COLS - Static variable in class ExprProfileScrollPane
minimum # of columns for the grid
MIN_NBR_CLUSTERS - Static variable in class Config
Minimum # of clusters
MIN_RADIUS - Static variable in class Config
Minimum spot radius allowed
MIN_RATIO - Static variable in class MAExplorer
Minimum ratio for histogram of ratios histRatioBin[]
MIN_ROWS - Static variable in class ExprProfileScrollPane
minimum # of rows for the grid
MIN_WINDOW_HEIGHT - Static variable in class PopupCondChooser
 
MIN_WINDOW_HEIGHT - Static variable in class PopupOrderedCondChooser
 
MIN_WINDOW_HEIGHT - Static variable in class RtestBase
 
MIN_WINDOW_WIDTH - Static variable in class PopupCondChooser
MIN size of scrollable Canvas
MIN_WINDOW_WIDTH - Static variable in class PopupOrderedCondChooser
MIN size of scrollable Canvas
MIN_WINDOW_WIDTH - Static variable in class RtestBase
MIN size of scrollable Canvas
minBinX - Variable in class DrawHistogram
ARG: minimum possible value range set by scrollers
minDataF1 - Variable in class MaHybridSample
min intens values F1 in getF1F2list
minDataF2 - Variable in class MaHybridSample
min intens values F2 in getF1F2list
minDataH - Variable in class Statistics
histogram data min value set by calcHistStats()
minDataHP_X - Variable in class CompositeDatabase
min intensity HP_X in getNormHP_XandYdata
minDataHP_Y - Variable in class CompositeDatabase
min intensity HP_Y in getNormHP_XandYdata
minDataS - Variable in class MaHybridSample
current norm: scaled min data
minFreq - Variable in class DrawHistogram
minimum range of values found in binFreq[]
minHistData - Variable in class MaHybridSample
total array: min hist data value
minIntens - Variable in class MaHybridSample
min intensity of histogram data
minQualCheck - Variable in class Config
Set from .quant file data: Minimum QualCheck Value
minRatioHistIdx - Variable in class CompositeDatabase
min value found in ratioHist[]
minRatioRI - Variable in class MaHybridSample
total array: min(f1RI/f2RI) for all spots
minRaw - Variable in class MaHybridSample
total array: if Ratio, minimum of range of F1 or F2 RawIntens
minRawS - Variable in class MaHybridSample
current norm: scaled minRaw data
minRI - Variable in class MaHybridSample
total array: range of RI or ratio
minRI1 - Variable in class MaHybridSample
total array: range of RawIntensity1
minRI2 - Variable in class MaHybridSample
total array: range of RawIntensity2
miNRMbkgrdCorr - Variable in class MenuBarFrame
(Analysis | Normalization) use background correction
miNRMCalDNAnorm - Variable in class MenuBarFrame
(Analysis | Normalization | Calibration DNA genes)
miNRMgeneSetNorm - Variable in class MenuBarFrame
(Analysis | Normalization | User defined gene set genes)
miNRMgoodSpotsStats - Variable in class MenuBarFrame
(Analysis | Normalization) use per-sample Good Spots data for global array statistics
miNRMhousekeepNorm - Variable in class MenuBarFrame
(Analysis | Normalization | Housekeeping genes)
miNRMlogMedianNorm - Variable in class MenuBarFrame
(Analysis | Normalization | Normalize by logMedian )
miNRMmedianNorm - Variable in class MenuBarFrame
(Analysis | Normalization | Median)
miNRMnoNorm - Variable in class MenuBarFrame
(Analysis | Normalization } No normalization)
miNRMratioMedianCorrection - Variable in class MenuBarFrame
(Analysis | Normalization) use ratio median correction for the Cy3 and Cy5 channels
miNRMscaleToMaxIntens - Variable in class MenuBarFrame
(Analysis | Normalization | Normalize to maximum intensity (65K)
miNRMtestGenericNormPlugin - Variable in class MenuBarFrame
only if mae.DBUG_GENERIC_NORM_PLUGIN is set, then (Analysis | Normalization | Test Generic Norm Plugin)
miNRMZscoreMeanAbsDevLogNorm - Variable in class MenuBarFrame
(Analysis | Normalization | Normalize by Zscore of log (AbsDev) )
miNRMZscoreMeanStdDevLogNorm - Variable in class MenuBarFrame
(Analysis | Normalization | Normalize by Zscore of log (StdDev) )
miNRMZscoreNorm - Variable in class MenuBarFrame
(Analysis | Normalization | Zscore )
minX - Variable in class Draw2Dplot
min X range set in initial call
minX - Variable in class DrawHistogram
ARG: minimum possible value range set by scrollers
minX - Variable in class DrawRatioHistogram
ARG: minimum possible value range set by scrollers
minXfound - Variable in class DrawRatioHistogram
min value of range of values found
minXscroll - Variable in class Draw2Dplot
min X range set by ShowPlotPopup scrollers
minY - Variable in class Draw2Dplot
min Y range set in initial call
minYscroll - Variable in class Draw2Dplot
min Y range set by ShowPlotPopup scrollers
miPEPlistType - Variable in class MenuBarFrame
(Analysis | Plot | Expression Profile) Menu Expression Profile list type (overlay or grid).
miPLGMuseSPLUSasComputingEngine - Variable in class MenuBarFrame
Menu: (Plugins | Use S-PLUS, else R, as computing engine [CB])
miPLGMuseTimeStampReports - Variable in class MenuBarFrame
Menu: (Plugins | Save SRLO reports in time-stampled folder [CB])
miPMdualXYpseudoImg - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor dual HP-X and HP-Y as Field 1 and Field 2 grids
miPMflickerXY - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Flicker of HP-X and HP-Y samples in intensity mode
miPMlowRangeZoom - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor low range zoom
miPMplotPseudoF1F2Img - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Cy3/Cy5 ratio or Zdiff
miPMplotPseudoHP_EP_CV_valueImg - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-EP 'list' CV-value
miPMplotPseudoHP_F1F2_RYGImg - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(Cy5)-Yellow-Green(Cy3) Cy3/Cy5 ratio or Zdiff
miPMplotPseudoHP_XY_pValueImg - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor (HP-X,HP-Y) 'sets' p-value
miPMplotPseudoHP_XY_RYGImg - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(X)-Yellow-Green(Y) HP-X/Y ratio or Zdiff
miPMplotPseudoHP_XYImg - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-X/Y ratio or Zdiff
miPMplotPseudoImg - Variable in class MenuBarFrame
Menu:(Analysis | Plot | Show Microarray) use Pseudograyscale intensity
miPRtblFontSize10pt - Variable in class MenuBarFrame
Menu: (Analysis | Report) font size is 10 pt
miPRtblFontSize12pt - Variable in class MenuBarFrame
Menu: (Analysis | Report) font size is 12 pt
miPRtblFontSize8pt - Variable in class MenuBarFrame
Menu: (Analysis | Report) font size is 8 pt
miTMtblFmtAddEPdata - Variable in class MenuBarFrame
Menu: (Analysis | Report) add Expr-Profile data to Table
miTMtblFmtAddHP_XYsetStat - Variable in class MenuBarFrame
Menu: (Analysis | Report) add HP-XY set statistics data to Table
miTMtblFmtAddOCLstatistics - Variable in class MenuBarFrame
Menu: (Analysis | Report) add OCL statistics data to Table
miTMtblFmtClickable - Variable in class MenuBarFrame
Menu: (Analysis | Report) use Dynamic clickable table format
miTMtblFmtTabDelim - Variable in class MenuBarFrame
Menu: (Analysis | Report) use Tab-Delimited table format
miTMtblFmtUseRawEPdata - Variable in class MenuBarFrame
Menu: (Analysis | Report) use raw Expr-Profile data in Table
miTMtblFontSize10pt - Variable in class MenuBarFrame
Menu: (Analysis | Report) font size is 10 pt
miTMtblFontSize12pt - Variable in class MenuBarFrame
Menu: (Analysis | Report) font size is 12 pt
miTMtblFontSize8pt - Variable in class MenuBarFrame
Menu: (Analysis | Report) font size is 8 pt
miVMdbESTviewer - Variable in class MenuBarFrame
Menu:(View) enable popup GenBank browser for new current gene
miVMGang - Variable in class MenuBarFrame
Menu:(View) show gang scrolling for duplicated grids of spots
miVMgenBankViewer - Variable in class MenuBarFrame
Menu:(View) enable popup GenBank browser for new current gene
miVMgenomicViewer - Variable in class MenuBarFrame
sGenomicMenu[cfg.nGenomicMenus] menu items as determined from Config DB
miVMlocusLinkViewer - Variable in class MenuBarFrame
Menu:(View) enable popup LocusLink gene browser for new current gene
miVMmAdbViewer - Variable in class MenuBarFrame
Menu:(View) enable popup mAdb gene browser for new current gene
miVMmedMinerViewer - Variable in class MenuBarFrame
Menu:(View) enable popup MedMiner browser for new current gene
miVMomimViewer - Variable in class MenuBarFrame
Menu:(View) enable popup OMIM browser for new current gene
miVMpirViewer - Variable in class MenuBarFrame
Menu:(View) enable popup PIRs browser for new current gene
miVMPresentView - Variable in class MenuBarFrame
Menu:(View) enable Presentation view that increases font sizes
miVMshowEditedGenes - Variable in class MenuBarFrame
Menu:(View) show EGL genes
miVMshowFilteredSpots - Variable in class MenuBarFrame
Menu:(View) show Filtered genes and spots
miVMshowHistoryLog - Variable in class MenuBarFrame
Menu:(View) enable popup command history log
miVMshowMsgLog - Variable in class MenuBarFrame
Menu:(View) enable popup message history log
miVMswissProtViewer - Variable in class MenuBarFrame
Menu:(View) enable popup SwissProt browser for new current gene
miVMuniGeneViewer - Variable in class MenuBarFrame
Menu:(View) enable popup UniGene browser for new current gene
miVMuseDichromasy - Variable in class MenuBarFrame
Menu:(View) enable Dichromasy colors that may be useful for some colorblind researchers instead of default color schemes.
miVMuseMouseOver - Variable in class MenuBarFrame
Menu:(View) enable mouse-over information for mouse over selected genes
mja - Static variable in class MAExplorer
Global instance of MaeJavaAPI Gather/Scatter API for MAEPlugins
mja - Static variable in class MJAReval
 
mja - Static variable in class Reval
MaeJavaAPI classes
mja - Variable in class RgenDemo
 
mja - Variable in class Rtest
 
mjaBase - Static variable in class MaeJavaAPI
constants and methods used by other MJA classes
MJAbase - class MJAbase.
This is base class for the Application Programming Interface (API) for accessing MAExplorer data structures This allows accessing the data structures in a uniform way that hides the actual complexity of the internal data structures.
MJAbase() - Constructor for class MJAbase
MJAbase() - constructor for methods extending this class.
MJAbase(MAExplorer) - Constructor for class MJAbase
MJAbase() - constructor for Gather Scatter API for MAExplorer to access MAExplorer data in a uniform interface.
mjaCluster - Static variable in class MaeJavaAPI
cluster data structures and methods
mjaCluster - Variable in class Reval
 
MJAcluster - class MJAcluster.
MAExplorer Open Java API class to access MJAcluster methods and data structures.
MJAcluster() - Constructor for class MJAcluster
MJAcluster() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaCondition - Variable in class MaeJavaAPI
condition lists of samples, and ordered lists of condition lists
mjaCondition - Variable in class PopupCondChooser
MaeJavaAPI classes
mjaCondition - Variable in class PopupOrderedCondChooser
MaeJavaAPI classes
mjaCondition - Variable in class Reval
 
mjaCondition - Variable in class RgenDemo
 
MJAcondition - class MJAcondition.
MAExplorer Open Java API class to access MJAcondition methods and data structures.
MJAcondition() - Constructor for class MJAcondition
MJAcondition() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaEval - Variable in class MaeJavaAPI
command interpreter
mjaEval - Variable in class RgenDemo
 
MJAeval - class MJAeval.
MAExplorer Open Java API class to access MJAeval command interpreter methods and data structures.
MJAeval() - Constructor for class MJAeval
MJAeval() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaExprProfile - Variable in class MaeJavaAPI
expression profile data and methods
MJAexprProfile - class MJAexprProfile.
MAExplorer Open Java API class to access expression profiles methods and data structures.
MJAexprProfile() - Constructor for class MJAexprProfile
MJAexprProfile() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaFilter - Static variable in class MaeJavaAPI
data filter flags and methods
mjaFilter - Variable in class PopupCondChooser
 
mjaFilter - Variable in class PopupOrderedCondChooser
 
mjaFilter - Variable in class Reval
 
mjaFilter - Variable in class RgenDemo
 
MJAfilter - class MJAfilter.
MAExplorer GatherScatter API class to access MJAfilter methods and data structures.
MJAfilter() - Constructor for class MJAfilter
MJAfilter() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaGene - Static variable in class MaeJavaAPI
single gene data
MJAgene - class MJAgene.
MAExplorer Open Java API class to access MJAgene methods and data structures.
MJAgene() - Constructor for class MJAgene
MJAgene() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaGeneList - Static variable in class MaeJavaAPI
lists of genes and gene sets methods
mjaGeneList - Variable in class Reval
 
MJAgeneList - class MJAgeneList.
MAExplorer Open Java API class to access MJAgeneList methods and data structures.
MJAgeneList() - Constructor for class MJAgeneList
MJAgeneList() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaGenomicDB - Static variable in class MaeJavaAPI
genomic databases on the Internet
MJAgenomicDB - class MJAgenomicDB.
MAExplorer Open Java API class to access MJAgenomicDB methods and data structures.
MJAgenomicDB() - Constructor for class MJAgenomicDB
MJAgenomicDB() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaGeometry - Static variable in class MaeJavaAPI
array geometry, spot to gene maps, etc.
mjaGeometry - Variable in class Reval
 
MJAgeometry - class MJAgeometry.
MAExplorer Open Java API class to access MJAgeometry methods and data structures.
MJAgeometry() - Constructor for class MJAgeometry
MJAgeometry() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaHelp - Static variable in class MaeJavaAPI
popup browser help methods
MJAhelp - class MJAhelp.
MAExplorer Open Java class to access MJAhelp methods and data structures.
MJAhelp() - Constructor for class MJAhelp
MJAhelp() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaHistogram - Static variable in class MaeJavaAPI
histogram plots
MJAhistogram - class MJAhistogram.
MAExplorer Open Java API class to access MJAhistogram methods and data structures.
MJAhistogram() - Constructor for class MJAhistogram
MJAhistogram() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaMath - Static variable in class MaeJavaAPI
built-in math methods
MJAmath - class MJAmath.
MAExplorer Open Java class to access MJAmath methods and data structures.
MJAmath() - Constructor for class MJAmath
MJAmath() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaNormalization - Static variable in class MaeJavaAPI
Access normalization data and methods
MJAnormalization - class MJAnormalization.
MAExplorer Open Java API class to access MJAnormalization methods and data structures.
MJAnormalization() - Constructor for class MJAnormalization
MJAnormalization() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaPlot - Static variable in class MaeJavaAPI
2D plot popup window base class [Future]
mjaPlot - Variable in class Reval
 
MJAplot - class MJAplot.
MAExplorer Open Java API class to access MJAplot methods and data structures.
MJAplot() - Constructor for class MJAplot
MJAplot() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaPopupRegistry - Static variable in class MaeJavaAPI
popup registry of active windows
MJApopupRegistry - class MJApopupRegistry.
MAExplorer Open Java API class to access MJApopupRegistry methods and data structures.
MJApopupRegistry() - Constructor for class MJApopupRegistry
MJApopupRegistry() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaProperty - Static variable in class MaeJavaAPI
individual MAExplorer properties methods
mjaProperty - Variable in class PopupCondChooser
 
mjaProperty - Variable in class PopupOrderedCondChooser
 
mjaProperty - Variable in class Reval
 
mjaProperty - Variable in class RgenDemo
 
mjaProperty - Variable in class Rtest
 
MJAproperty - class MJAproperty.
MAExplorer Open Java API class to access MJAproperty methods and data structures.
MJAproperty() - Constructor for class MJAproperty
MJAproperty() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaPropList - Static variable in class MaeJavaAPI
lists of MAExplorer properties methods
MJApropList - class MJApropList.
MAExplorer Open Java API class to access MJApropList methods and data structures.
MJApropList() - Constructor for class MJApropList
MJApropList() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaReport - Static variable in class MaeJavaAPI
report methods
mjaReport - Variable in class PopupCondChooser
 
mjaReport - Variable in class PopupOrderedCondChooser
 
mjaReport - Variable in class Reval
 
mjaReport - Variable in class RgenDemo
 
mjaReport - Variable in class Rtest
 
MJAreport - class MJAreport.
MAExplorer Open Java API class to access MJAreport methods and data structures.
MJAreport() - Constructor for class MJAreport
MJAreport() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaReval - Static variable in class MaeJavaAPI
Execute R program .R scripts using MAExplorer data
mjaReval - Variable in class RgenDemo
instance of Reval
mjaReval - Variable in class Rtest
instance of Reval
mjaReval - Variable in class RtestBase
instance of Reval
MJAReval - class MJAReval.
MAExplorer Open Java API class to access the MJAReval R package.
MJAReval() - Constructor for class MJAReval
MJAReval() - constructor for client interface to the R program to access client data in a uniform interface.
mjaSample - Static variable in class MaeJavaAPI
single sample top-level data methods
mjaSample - Variable in class PopupCondChooser
 
MJAsample - class MJAsample.
MAExplorer Open Java API class to access MJAsample methods and data structures.
MJAsample() - Constructor for class MJAsample
MJAsample() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaSampleList - Static variable in class MaeJavaAPI
get lists of samples top-level data methods
mjaSampleList - Variable in class Reval
 
mjaSampleList - Variable in class RgenDemo
 
MJAsampleList - class MJAsampleList.
MAExplorer GatherScatter API class to access MJAsampleList methods and data structures.
MJAsampleList() - Constructor for class MJAsampleList
MJAsampleList() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaScrollablePlot - Static variable in class MaeJavaAPI
Scrollable 2D plot base class [Future]
MJAscrollablePlot - class MJAscrollablePlot.
MAExplorer Open Java API class to access MJAscrollablePlot methods and data structures.
MJAscrollablePlot() - Constructor for class MJAscrollablePlot
MJAscrollablePlot() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaSL - Variable in class Reval
 
mjaSort - Static variable in class MaeJavaAPI
built-in sorting methods
MJAsort - class MJAsort.
MAExplorer Open Java API class to access MJAsort methods and data structures.
MJAsort() - Constructor for class MJAsort
MJAsort() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaState - Static variable in class MaeJavaAPI
MAExplorer state saving, additional state info, methods
mjaState - Variable in class Reval
 
mjaState - Variable in class RgenDemo
 
MJAstate - class MJAstate.
MAExplorer Open Java API class to access MJAstate methods and data structures.
MJAstate() - Constructor for class MJAstate
MJAstate() - constructor for Open Java API for MAExplorer to access MAExplorer data in a uniform interface.
mjaStatistics - Static variable in class MaeJavaAPI
built-in statistics methods
MJAstatistics - class MJAstatistics.
MAExplorer Gather Scatter API class to access MJAstatistics methods and data structures.
MJAstatistics() - Constructor for class MJAstatistics
MJAstatistics() - constructor for Gather Scatter API for MAExplorer to access MAExplorer data in a uniform interface.
mjaUtil - Static variable in class MaeJavaAPI
built-in general utility methods
mjaUtil - Variable in class PopupCondChooser
 
mjaUtil - Variable in class PopupOrderedCondChooser
 
mjaUtil - Variable in class Reval
 
mjaUtil - Variable in class RgenDemo
 
mjaUtil - Variable in class Rtest
 
mjaUtil - Variable in class PopupEditRscript
 
MJAutil - class MJAutil.
MAExplorer Open Java API class to access MJAutil methods and data structures.
MJAutil() - Constructor for class MJAutil
MJAutil() - constructor for OpenJava API for MAExplorer to access MAExplorer data in a uniform interface.
ml - Variable in class GeneBitSet
Associated Master GeneList if any, else null
mList - Variable in class ClusterGenes.Cluster
ordered list of genes in this cluster
mList - Variable in class ClusterSamples
list of genes used in pattern vector
mList - Variable in class GeneList
instance: (opt) sorted list of Gene objects.
mlLst - Static variable in class MJAbase
link to global GeneClass instance
mlLst - Static variable in class MaeJavaAPI
link to global GeneClass instance
mlToUse - Variable in class ShowExprProfilesPopup
Master GeneList being used
mNbr - Variable in class ExprProfileOverlay
.mList[mNbr] in database to display
mNbr - Variable in class ExprProfileScrollPane
.mList[mNbr] in database to display
mnClustersCL - Variable in class ClusterGenes
artificial mean K-means gene list
mnDataV - Static variable in class HierClustNode
Dynamic node: [0:nDataV-1] Global mean of data for samples h
mnDataVSq - Static variable in class HierClustNode
Dynamic node: [0:nDataV-1] global mean Sq data for samples h
mnEdata - Variable in class HPxyData
mean intensity HP-EP list data
mnHPri - Variable in class MaHybridSample
total array: rawIntens mean, all genes in HP w/o bkgrd
mnHPri1 - Variable in class MaHybridSample
total array: rawIntens f1 mean, all genes in HP w/o bkgrd
mnHPri2 - Variable in class MaHybridSample
total array: rawIntens f2 mean, all genes in HP w/o bkgrd
mnSqBetween - Variable in class Statistics
CALC: mean square between variance, f-statistic nConditions test set by calcNCondFtestStat()
mnSqWithin - Variable in class Statistics
CALC: mean square within variance, f-statistic nConditions test set by calcNCondFtestStat()
mnWithinClusterDist - Variable in class ClusterGenes
[1:maxKmeansNodes] mean within-cluster distance between K-means clusters
mnX - Static variable in class MathMAE
RTN: mean X
mnXdata - Variable in class HPxyData
mean intensity HP-X set data
mnY - Static variable in class MathMAE
RTN: mean Y
mnYdata - Variable in class HPxyData
mean intensity HP-Y set data
mode - Variable in class MaHybridSample
Filter hist: mode raw intensity
mode - Variable in class ShowStringPopup
mode of operation used in creating this window.
MODE_CIRCLE - Static variable in class ExprProfileCanvas
draw circles for each entry
MODE_CURVE - Static variable in class ExprProfileCanvas
draw continuous curve
MODE_DB_EST3 - Static variable in class Guesser
used to set iMode
MODE_DB_EST5 - Static variable in class Guesser
used to set iMode
MODE_GENBANK - Static variable in class Guesser
used to set iMode
MODE_GENBANK3 - Static variable in class Guesser
used to set iMode
MODE_GENBANK5 - Static variable in class Guesser
used to set iMode
MODE_LINE - Static variable in class ExprProfileCanvas
draw vertical bars
MODE_LOCUSLINK - Static variable in class Guesser
used to set iMode
MODE_MASTER_GENE_NAME - Static variable in class Guesser
used to set iMode
MODE_MASTER_ID - Static variable in class Guesser
used to set iMode
MODE_SWISSPROT - Static variable in class Guesser
used to set iMode
MODE_UNIGENE - Static variable in class Guesser
used to set iMode
modeH - Variable in class DrawHistogram
set from ms hist[] statistics
modeH - Variable in class Statistics
histogram data mode set by calcHistStats()
modeIdx - Variable in class MaHybridSample
Filter hist: index of mode raw intensity
modeIdx - Variable in class Statistics
index of mode in hist[] set by calcHistStats()
modeIntens - Variable in class MaHybridSample
mode of histogram data
modelsURL - Variable in class Config
base addr PARAM "modelsURL"
modeRI - Variable in class MaHybridSample
total array: mode value of rawIntensity
mountPlugin() - Method in class MAEPlugin.popup.PluginLoader
mountPlugin() - loads the plugin into the MAE application.
mouseClicked(MouseEvent) - Method in class ArrayScroller
mouseClicked() - handle mouse Click event by passing it to ScrollableImageCanvas to handle.
mouseClicked(MouseEvent) - Method in class Draw2Dplot
 
mouseClicked(MouseEvent) - Method in class DrawClusterGram
 
mouseClicked(MouseEvent) - Method in class DrawHistogram
 
mouseClicked(MouseEvent) - Method in class DrawRatioHistogram
 
mouseClicked(MouseEvent) - Method in class ExprProfilePanel
 
mouseClicked(MouseEvent) - Method in class ScrollableImageCanvas
mouseClicked() - handle mouse Click events
mouseClicked(MouseEvent) - Method in class ShowPlotPopup
mouseClicked() - handle mouse Click events
mouseClicked(MouseEvent) - Method in class SSspreadPanel
 
mouseClicked(MouseEvent) - Method in class StateScrollers
 
mouseDragged(MouseEvent) - Method in class ArrayScroller
mouseDragged() - handle mouse Drag event by passing it to ScrollableImageCanvas to handle.
mouseDragged(MouseEvent) - Method in class Draw2Dplot
 
mouseDragged(MouseEvent) - Method in class DrawClusterGram
 
mouseDragged(MouseEvent) - Method in class DrawHistogram
 
mouseDragged(MouseEvent) - Method in class DrawRatioHistogram
 
mouseDragged(MouseEvent) - Method in class ExprProfilePanel
mouseDragged() - just report (HP, Quant) of nearest HP sample near where mouse is
mouseDragged(MouseEvent) - Method in class ScrollableImageCanvas
mouseDragged() - handle mouse dragged.
mouseDragged(MouseEvent) - Method in class ShowPlotPopup
mouseDragged() - handle mouse Drag events
mouseDragged(MouseEvent) - Method in class SSspreadPanel
 
mouseEntered(MouseEvent) - Method in class ArrayScroller
mouseEntered() - handle mouse Enter events by passing it to ScrollableImageCanvas to handle.
mouseEntered(MouseEvent) - Method in class Draw2Dplot
 
mouseEntered(MouseEvent) - Method in class DrawClusterGram
 
mouseEntered(MouseEvent) - Method in class DrawHistogram
 
mouseEntered(MouseEvent) - Method in class DrawRatioHistogram
 
mouseEntered(MouseEvent) - Method in class ExprProfilePanel
 
mouseEntered(MouseEvent) - Method in class ScrollableImageCanvas
mouseEntered() - handle mouse Enter events
mouseEntered(MouseEvent) - Method in class ShowPlotPopup
mouseEntered() - handle mouse Enter events
mouseEntered(MouseEvent) - Method in class SSspreadPanel
 
mouseEntered(MouseEvent) - Method in class StateScrollers
mouseEntered() - put mouse over data in MouseOver text area
MouseEventHandler - class MouseEventHandler.
 
MouseEventHandler(MAExplorer, Guesser, TextField, TextArea, String[]) - Constructor for class MouseEventHandler
MouseEventHandler() - constructor
mouseExited(MouseEvent) - Method in class ArrayScroller
mouseExited() - handle mouse Exit events by passing it to ScrollableImageCanvas to handle.
mouseExited(MouseEvent) - Method in class Draw2Dplot
 
mouseExited(MouseEvent) - Method in class DrawClusterGram
 
mouseExited(MouseEvent) - Method in class DrawHistogram
 
mouseExited(MouseEvent) - Method in class DrawRatioHistogram
 
mouseExited(MouseEvent) - Method in class ExprProfilePanel
 
mouseExited(MouseEvent) - Method in class ScrollableImageCanvas
mouseExited() - handle mouse Exit events
mouseExited(MouseEvent) - Method in class ShowPlotPopup
mouseExited() - handle mouse Exit events
mouseExited(MouseEvent) - Method in class SSspreadPanel
 
mouseExited(MouseEvent) - Method in class StateScrollers
mouseExited() - clear mouseover text area.
mouseHandler(int, int) - Method in class DrawHistogram
mouseHandler() - interact with current plot if a graphic plot.
mouseHandler(int, int) - Method in class DrawRatioHistogram
mouseHandler() - interact with current plot if a graphic plot.
mouseHandler(int, int, int, boolean) - Method in class DrawScatterPlot
mouseHandler() - interact with current plot if a graphic plot.
mouseHandler(int, int, int, boolean) - Method in class ExprProfileOverlay
mouseHandler() - interact with current 2D plot if a graphic plot.
mouseModifiers - Variable in class ClusterGramCanvas
set by event handler mouse coords on click
mouseMoved(MouseEvent) - Method in class ArrayScroller
mouseMoved() - handle mouse Move event by passing it to ScrollableImageCanvas to handle.
mouseMoved(MouseEvent) - Method in class Draw2Dplot
mouseMoved() - process mouse event - update MouseOver
mouseMoved(MouseEvent) - Method in class DrawClusterGram
mouseMoved() - process mouse event
mouseMoved(MouseEvent) - Method in class DrawHistogram
 
mouseMoved(MouseEvent) - Method in class DrawRatioHistogram
 
mouseMoved(MouseEvent) - Method in class ExprProfilePanel
 
mouseMoved(MouseEvent) - Method in class ScrollableImageCanvas
mouseMoved() - handle mouse Move events to update the mouseover display of the gene that is near the mouse.
mouseMoved(MouseEvent) - Method in class ShowPlotPopup
mouseMoved() - handle mouse Move events
mouseMoved(MouseEvent) - Method in class SSspreadPanel
 
mouseMoved(MouseEvent) - Method in class StateScrollers
 
mouseOverCheckBox - Variable in class MenuBarFrame
Show Mouse-over info
mouseOverCheckBox - Variable in class ShowExprProfilesPopup
 
mouseOverCheckBox - Variable in class ShowPlotPopup
Checkbox to toggle Show "Mouse-over info"
mouseoverTA - Variable in class StateScrollers
mouseover TextArea
mousePressed(MouseEvent) - Method in class ArrayScroller
mousePressed() - handle mouse pressed event by passing it to ScrollableImageCanvas to handle.
mousePressed(MouseEvent) - Method in class Draw2Dplot
mousePressed() - process mouse event, change current gene.
mousePressed(MouseEvent) - Method in class DrawClusterGram
Pass all mouse events down to the Canvas.
mousePressed(MouseEvent) - Method in class DrawHistogram
mousePressed() - process mouse event
mousePressed(MouseEvent) - Method in class DrawRatioHistogram
mousePressed() - process mouse event
mousePressed(MouseEvent) - Method in class ExprProfilePanel
mousePressed() - handle mouse Pressed events
mousePressed(MouseEvent) - Method in class ScrollableImageCanvas
mousePressed() - handle mouse dragged.
mousePressed(MouseEvent) - Method in class ShowPlotPopup
mousePressed() - handle mouse Press events
mousePressed(MouseEvent) - Method in class SSspreadPanel
mousePressed() - handle mouse Press events
mousePressed(MouseEvent) - Method in class StateScrollers
 
mouseReleased(MouseEvent) - Method in class ArrayScroller
mouseReleased() - handle mouse released event by passing it to ScrollableImageCanvas to handle.
mouseReleased(MouseEvent) - Method in class ChooserGUI.MouseEventHandler
MouseReleased() - handle mouse clicks for ta
mouseReleased(MouseEvent) - Method in class Draw2Dplot
 
mouseReleased(MouseEvent) - Method in class DrawClusterGram
mouseReleased() - Pass all mouse events down to the Canvas.
mouseReleased(MouseEvent) - Method in class DrawHistogram
 
mouseReleased(MouseEvent) - Method in class DrawRatioHistogram
 
mouseReleased(MouseEvent) - Method in class ExprProfilePanel
mouseReleased() - handle mouse Released events
mouseReleased(MouseEvent) - Method in class MouseEventHandler
MouseReleased() - handle mouse clicks for ta text area
mouseReleased(MouseEvent) - Method in class PopupCondChooserGUI.MouseEventHandler
MouseReleased() - handle mouse clicks for ta
mouseReleased(MouseEvent) - Method in class PopupOrderedCondChooserGUI.MouseEventHandler
MouseReleased() - handle mouse clicks for ta
mouseReleased(MouseEvent) - Method in class ScrollableImageCanvas
mouseReleased() - process mouse events for pseudoarray image.
mouseReleased(MouseEvent) - Method in class ShowPlotPopup
mouseReleased() - handle mouse Release events
mouseReleased(MouseEvent) - Method in class SSspreadPanel
 
mouseReleased(MouseEvent) - Method in class StateScrollers
 
move(List, List, boolean) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
move() -
moveColHeader(int) - Method in class SSspreadPanel
moveColHeader() - move the head of cols use negative ints for moving left.
moveDown(int) - Method in class SSspreadPanel
moveDown() - move diff cells down
moveLeft(int) - Method in class SSspreadPanel
moveLeft() - move diff cells to the left
moveObjDown(String) - Method in class ChooserGUI
moveObjDown() - move SELECTED obj ta2 (RIGHT) Down one position unless it is at the bottom of list.
moveObjDown(String) - Method in class PopupCondChooserGUI
moveObjDown() - move SELECTED obj selTextArea (RIGHT) Down one position unless it is at the bottom of list.
moveObjDown(String) - Method in class PopupOrderedCondChooserGUI
moveObjDown() - move SELECTED obj selTextArea (RIGHT) Down one position unless it is at the bottom of list.
moveObjUp(String) - Method in class ChooserGUI
moveObjUp() - move SELECTED obj ta2 (RIGHT) UP one position unless it is at the top of list.
moveObjUp(String) - Method in class PopupCondChooserGUI
moveObjUp() - move SELECTED obj selTextArea (RIGHT) UP one position unless it is at the top of list.
moveObjUp(String) - Method in class PopupOrderedCondChooserGUI
moveObjUp() - move SELECTED obj selTextArea (RIGHT) UP one position unless it is at the top of list.
moveRight(int) - Method in class SSspreadPanel
moveRight() - move diff cells to the right
moveRowHeader(int) - Method in class SSspreadPanel
moveRowHeader() - move first cell of rows use negative ints for moving down.
moveUp(int) - Method in class SSspreadPanel
moveUp() - move diff cells up
mp - Variable in class MAExplorer
Global instance of lookup table maps populated elsewhere
mr - Variable in class RgenDemo
 
mr - Variable in class Rtest
 
mr - Variable in class RtestBase
 
mr - Variable in class PopupEditRscript
short form instance of mjaReval
mReady - Variable in class MAExplorer
Flag set when done initialization and ready to analyze
ms - Variable in class Draw2Dplot
link to global MaHybridSample instance
ms - Variable in class DrawHistogram
link to global MaHybridSample instance
ms - Variable in class DrawScatterPlot
link to global instance
ms - Static variable in class MAExplorer
Current hybridized sample
ms - Variable in class MaHPquantTable
HP sample that owns this table instance
ms - Static variable in class SpotData
HP where this data came from
msCond - Variable in class Condition
[0:nMScond-1] elements of the list
msEPlist - Variable in class ClusterGenes
list of expression profile samples [1:nEPmsList] where genes are to be checked normally this is mae.msListE[1:mae.nHP_E].
msg - Variable in class PopupCondChooser.CondDialogBox
Message for dialog box
msg - Variable in class PopupOrderedCondChooser.CondDialogBox
Message for dialog box
msg - Variable in class SimpleTable
Optional message associated with table
msgBkgrd - Variable in class PopupCondChooser
Text message background color that may be changed
msgBkgrd - Variable in class PopupOrderedCondChooser
Text message background color that may be changed
msgBkgrd - Variable in class RtestBase
Text message background color that may be changed
msgColor - Variable in class PopupCondChooser
Text message foreground color that may be changed
msgColor - Variable in class PopupOrderedCondChooser
Text message foreground color that may be changed
msgColor - Variable in class RtestBase
Text message foreground color that may be changed
msgFileName - Static variable in class Util
Full path name of msg file if enabled.
msgFont - Variable in class PopupCondChooser
font for title at the top of the main window
msgFont - Variable in class PopupOrderedCondChooser
font for title at the top of the main window
msgFont - Variable in class RtestBase
fonts for labeling subtitle for each panel in image
msgIsVisibleFlag - Static variable in class Util
Message window visibility flag
msgTextField - Variable in class PopupEditRscript
Text field to hold popup edit messages.
msgTextFrame - Static variable in class Util
Log msg text frames.
msgTF - Variable in class PopupCondChooser
Text message report line
msgTF - Variable in class PopupOrderedCondChooser
Text message report line
msgTF - Variable in class RtestBase
Text message report line
msList - Variable in class ClusterSamples
list of samples H.P.s to cluster
msList - Variable in class PopupHPChooser
List of ALL initial samples in DB
msList - Static variable in class SampleSets
total HP list [1:nHP] for all active samples
msListE - Static variable in class SampleSets
Expression Profile [1:nHP_E]
msListEo - Variable in class PopupHPChooser
initial HP-E sample list on starting chooser
msListrE - Variable in class PopupHPChooser
rem(E) = mxListo - msListEo
msListrXY - Variable in class PopupHPChooser
rem(X+Y) = mxListo - msListXo - msListYo
msListX - Static variable in class SampleSets
X-axis [1:nHP_X]
msListXo - Variable in class PopupHPChooser
initial HP-X sample list on starting chooser
msListY - Static variable in class SampleSets
Y-axis [1:nHP_Y]
msListYo - Variable in class PopupHPChooser
initial HP-Y sample list on starting chooser
msMaxDataS - Static variable in class HierClustNode
cache mae.hps.msListE[].maQ.maxRI, for normalizng data
msPrev - Static variable in class MAExplorer
Previous (last current) hybridized sample for garbage collection
msR - Variable in class ArrayScroller
link to global MaHybridSample instance
msR - Variable in class ScrollableImageCanvas
link to current sample
mStatus - Static variable in class Util
Copy of last ShowMsg() printed
msuTbl - Variable in class UserState
application startup database table
msW - Variable in class MJAgene
 
msX - Static variable in class MAExplorer
Current HP-X hybridized sample
msY - Static variable in class MAExplorer
Current HP-Y hybridized sample
mTitle - Variable in class DrawHistogram
ARG: opt.
MULTIPLE_GENE - Static variable in class Guesser
flag for multiple gene finish

N

n_bits - Variable in class WriteGifEncoder
 
N_CONST_FILES - Static variable in class MAExplorer
# of files always read: MaExplorerConfig.txt GIPO-xxx.txt Samples.txt MaExplorerInfo.txt [DEPRICATED]
N_EP_GENES - Variable in class DrawClusterGram
default # of genes to display in EP list
N_EP_GENES - Variable in class ExprProfileScrollPane
 
N_EST_QUANT_FILES - Static variable in class MAExplorer
default est # .quant files to load
nActiveFilters - Variable in class Filter
# of active filters
name - Variable in class ArrayScroller
HP sample name
name - Variable in class HierClustNode
Dynamic node: name of node if it is not null
name - Variable in class PopupCondChooser.CondData
list of condition names
name - Variable in class PopupOrderedCondChooser.OclListData
list of condition names
NAME_METHOD_DB_FILE_ID - Static variable in class MJAsample
Lookup method to use when finding sample by DB file ID.
NAME_METHOD_DB_FILE_NAME - Static variable in class MJAsample
Lookup method to use when finding sample by DB file Name
NAME_METHOD_DB_SAMPLE_ID - Static variable in class MJAsample
Lookup method to use when finding sample by free-text Sample_ID.
nameGRCIdx - Variable in class GipoTable
index for "NAME_GRC" - NIA
nameList - Variable in class SampleSets
Names of samples for Cy5/Cy3 swap
nameList - Variable in class PopupScrollableSelector
[0:nList-1] checkboxes
nameListCB - Variable in class PopupScrollableSelector
holds "Done" and "Cancel" buttons
nameMethod - Static variable in class MJAsample
nameMethod defines the type of name to use in looking up a sample.
nameTF - Variable in class PopupCondChooser.CondParamEditForm
parameter names fields
nameTF - Variable in class PopupOrderedCondChooser.CondParamEditForm
parameter names fields
nAnalyses - Static variable in class RevalBase
# of Rscript analysis procedures
nAnalyses - Variable in class RtestBase
The total number of analyses in the RLO database
nBins - Variable in class MaHybridSample
number of bins in histogram.
nBinsH - Variable in class Statistics
0 if none.
nbrActiveScrollers() - Method in class StateScrollers
nbrActiveScrollers() - return the number of active scrollers and copy scaled scroller data to the state variables.
nbrActiveScrollersUseCounters() - Method in class StateScrollers
nbrActiveScrollersUseCounters() - return the number of active scrollers and copy scaled scroller data to the state variables.
nbrChildren - Variable in class HierClustNode
Dynamic node: # of terminal children of this node.
nbrCondLists - Variable in class PopupCondChooser
number of condition lists
nbrGC - Static variable in class GeneClass
# of all gene classes
nbrGENES - Variable in class Config
PARAM specified # of genes
nbrGenesInGC - Static variable in class GeneClass
size of the corresponding GeneClass.
nbrOclLists - Variable in class PopupOrderedCondChooser
number of condition lists
nbrOfClustersThr - Variable in class Config
Threshold PARAM: # of clusters threshold
nbrParams - Variable in class PopupCondChooser
# of condition parameters
nbrParams - Variable in class PopupOrderedCondChooser
# of condition parameters
nbrSPOTS - Variable in class Config
PARAM specified # of spots
nCBcmds - Static variable in class MenuBarFrame
# of menu CheckBoxMenuItem item cmds [0:nCBcmds-1]
nChooser - Variable in class PopupHPChooser
number of ChooseGUI instances
nClist - Variable in class ClusterGenes
i.e size of complexClusterCL.length
nCmds - Static variable in class MenuBarFrame
# of menu item commands [0:nCmds-1]
nCols - Variable in class ClusterGramCanvas
# of columns i.e.
nCols - Variable in class DrawClusterGram
# of columns in clustergram
nCols - Variable in class ExprProfileScrollPane
# of columns in the Grid
nCols - Variable in class RtestBase
# of columns size of text area for reporting
nCols - Variable in class ShowStringPopup
# of character cols to show
nCondAlloc - Variable in class Statistics
size of in mean,variance,stdDev,condData,nCondData stats arrays set by calcNCondFtestStat()
nCondData - Variable in class Statistics
data[0:nConditions-1][sampleNbrInClass] for computations, set by calcMeanAndVariance()
nConditions - Variable in class Statistics
# of conditions in mean,var stats set by calcNCondFtestStat()
nCondLists - Static variable in class Condition
# of condition lists
nCondsInOCL - Static variable in class Reval
current active genes lists for generating export data
ncStr - Variable in class DrawHistogram
Info on genes in the current bin
ncStr - Variable in class DrawRatioHistogram
Info on genes in the current bin
ncubes - Variable in class MedianCut
# of color cubes
nDataV - Static variable in class HierClustNode
size of dataV[] vector
NDEF_CLASS_NAMES - Static variable in class GeneClass
 
nDemoAnalyses - Variable in class RtestBase
The number of "Demo" analyses in the RLO database.
nE - Variable in class HPxyData
# of HP-EP list members after setup
nearestClusterDist - Variable in class ClusterGenes.Cluster
distance to nearest cluster
nearestClusterID - Variable in class ClusterGenes.Cluster
id # of nearest cluster
nearestGenesIdx - Variable in class ClusterGenes
[0:nClist-1] [0:nClist-1] sorted index of nearest genes
nearestHP - Variable in class ClusterSamples
index of nearest HP
needLoginFlag - Variable in class MaHybridSample
flag: set if requires login for this HP for it's projectName
nEP - Variable in class ClusterGenes.Cluster
# of objects (eg.
nEP - Variable in class GeneGeneDist
size of EP vector
nEPgenes - Variable in class DrawClusterGram
# of genes to display in popup EP plot
nEPgenes - Variable in class ExprProfileScrollPane
# genes to display in popup EP plot
nEPmsList - Variable in class ClusterGenes
size of geneEPvector[][0:nMSList-1]
NEVER - Static variable in class MAExplorer
Debugging flag - Always FALSE
NEVER - Static variable in class PopupCondChooser
 
NEVER - Static variable in class PopupOrderedCondChooser
 
NEVER - Static variable in class RtestBase
Debug flags
newDir - Static variable in class EventMenu
new project directory if any if not null
newFontLbl - Variable in class StateScrollers
font type for labels
newNameTF - Variable in class PopupCondChooser.PopupTextField
textfield for typing in new name
newNameTF - Variable in class PopupOrderedCondChooser.PopupTextField
textfield for typing in new name
newRLO() - Method in class MJAReval
newRLO() - create new empty R LayOut (RLO) instance to the RLO database
newRLO() - Method in class RevalBase
newRLO() - create new empty R LayOut (RLO) instance to the RLO database.
newRLO() - Method in class RLO
newRLO() - create new empty R LayOut (RLO) instance to RLO database.
newRLO() - Method in class PopupEditRscript
newRLO() - create a new local RLO instance.
newRLOButton - Variable in class RtestBase
"New RLO" to create new RLO
newString - Variable in class PopupCondChooser.PopupTextField
used to return the string the user types in
newString - Variable in class PopupOrderedCondChooser.PopupTextField
used to return the string the user types in
nextButton - Variable in class PopupEditRscript
"Next" wizard button
nextCol - Variable in class SStextCell
 
nextID - Static variable in class MC_Cube
 
nextMID() - Method in class GeneBitSet
nextMID() - get next mid in enumeration in [0:highMID] of this gene bit set
nextNode - Static variable in class HierClustNode
next node in traversal
nextRow - Variable in class SStextCell
 
nextZoomMag(int, int) - Static method in class Util
nextZoomMag() - modulo 1X, 2X, 5X, 10X, 20X, 50X, 100X, 200X, 500X, 1000X
nFilesRead - Variable in class MAExplorer
# of files read so far
nFilesTotal - Variable in class MAExplorer
# files always read + # .quant files.
nFiltered - Static variable in class Reval
current active genes lists for generating export data
nFixedGC - Static variable in class GeneClass
# of fixed special built-in gene
nGeneClustersCnt - Variable in class ExprProfile
# clustered genes to this mid
nGeneClustersCnt - Variable in class Gene
# of genes in cluster at cluster distance threshold.
nGenes - Variable in class ClusterGenes.Cluster
# of genes in this cluster
nGenes - Variable in class DrawClusterGram
# genes in orderedCL
nGenes - Variable in class ExprProfileOverlay
# genes in exprProfileCL
nGenes - Variable in class ExprProfileScrollPane
# genes in exprProfileCL
nGenes - Variable in class MaHPquantTable
# of genes
nGenes - Static variable in class Reval
current active genes lists for generating export data
nGenes - Variable in class ShowExprProfilesPopup
# of genes in expression profile
nGenesUpdated - Variable in class GipoTable
when copy data to static gene list
nGenomicID - Variable in class Gene
(Optional) If generic IDs are used this will contain the INDEX of the cfg.sGenomicMenu[] entry.
nGenomicMenus - Variable in class Config
size of sGenomicMenu[]
nGridElements - Variable in class ExprProfileScrollPane
i.e.
nHelpMenus - Variable in class Config
size of sHelpMenu[]
nHierClusters - Static variable in class HierClustNode
# of nodes clustered 2*nObj-1
nHist - Variable in class DrawHistogram
hist[0:nHist-1] of raw data.
nHist - Variable in class DrawRatioHistogram
hist[0:npoints-1]
nHP - Variable in class PopupHPChooser
# all probes in the database
nHP - Static variable in class SampleSets
number of Samples in msList[]
nHP_E - Variable in class ExprProfile
# of HP's to draw after setup
nHP_E - Variable in class ExprProfileOverlay
# of HPS in an Expr Profile
nHP_E - Variable in class ExprProfileScrollPane
# of HPS in an Expr Profile
nHP_E - Static variable in class SampleSets
list H.P.
nHP_X - Static variable in class SampleSets
list (set) Samples for X-axis msListX[]
nHP_Y - Static variable in class SampleSets
list (set) Samples for Y-Axis msListY[]
nHPEf - Variable in class PopupHPChooser
# of final selected HP-E samples
nHPEo - Variable in class PopupHPChooser
# of original HP-E selected samples
nHPmnuEntries - Variable in class StageNames
# of menu entries
nHPrE - Variable in class PopupHPChooser
# rem(E) = mxListo - msListEo
nHPrXY - Variable in class PopupHPChooser
# rem(X+Y) = mxListo - msListXo - msListYo
nHPXf - Variable in class PopupHPChooser
# of final selected HP-X samples
nHPXo - Variable in class PopupHPChooser
# of original HP-X selected samples
nHPYf - Variable in class PopupHPChooser
# of final selected HP-Y samples
nHPYo - Variable in class PopupHPChooser
# of original HP-Y selected samples
nInputFiles - Variable in class RLO
# of input files if any, 0 if none
nInputFiles - Variable in class RgenDemo
# of input files if any, 0 if none
nInputFiles - Variable in class PopupEditRscript
# of input files if any, 0 if none
nInputTypesValues - Variable in class PopupEditRscript
# of input data type values
nKmeansNodes - Variable in class ClusterGenes
# of unique K-means nodes found
nLineGroup - Variable in class Draw2Dplot
# sequential points to connect group with line for use with EP 2D plot # of lines/line-group
nList - Variable in class Draw2Dplot
# elements in x(y)(p)List[0:nList-1]
nList - Variable in class PopupScrollableSelector
holds title at top
nMAEP - Variable in class PopupRegistry
MAEPlugin Instance Object counter
nmenuNames - Variable in class StageNames
# unique menu name entries in Samples tbl
nMenuStubNames - Variable in class PopupEditRscript
# of menu stub names
nMenuStubs - Variable in class MenuBarFrame
# of menu stubs in the list
nMid - Variable in class Gene
# of genes in midList[] for this gene
nMlist - Variable in class ClusterSamples
# of genes in mList
nMlist - Variable in class GeneGeneDist
# of genes
nMnGenes - Variable in class ExprProfileOverlay
# of averaged genes ~ nGenes
nMnGenes - Variable in class ExprProfileScrollPane
# of averaged genes ~ nGenes
nMnGenes - Variable in class ShowExprProfilesPopup
# of mean nodes
nMScond - Variable in class Condition
# of entries in the list
nMSlist - Variable in class ClusterSamples
size of msList[]
nMUmap - Variable in class ConfigTable
# of map entries
NO_R_INSTALLED - Static variable in class RevalBase
This is the name of the path for the saved R base path in the Temp/.RbasePath file it it ever tried to prompt for the R base path and there was no response to the\ prompt.
nObj - Static variable in class HierClustNode
# of objects to cluster
nodeID - Variable in class HierClustNode
Dynamic node: unique cluster node #
nodeNodeDistSQ(HierClustNode, HierClustNode) - Method in class HierClustNode
nodeNodeDistSQ() - compute node-node nDistV*(Euclidian distance squared).
nOfileTypes - Static variable in class RevalBase
Number of R output file types
noMsg - Variable in class PopupCondChooser.CondDialogBox
No label for dialog box
noMsg - Variable in class PopupOrderedCondChooser.CondDialogBox
No label for dialog box
noMsgReportFlag - Variable in class MAExplorer
PARAM "noMsgReporting"
nonFilteredGenesButton - Variable in class ShowPlotPopup
non-Filtered genes button
nonTermEnumCnt - Static variable in class HierClustNode
# non-terminal nodes enumerated in order
nonZeroSpotDataCL - Variable in class Filter
"Filter by non-zero Spot Data"
nOptions - Variable in class PopupBinOprDialogQuery
optionValues[0:nOptions]
nOptions - Variable in class PopupDialogQuery
optionValues[0:nOptions]
nOrderedCondList - Static variable in class Condition
# of conditions in each of the ordered condition lists [0:maxOrderedCondLists-1]
Normalization - interface MAEPlugin.Normalization.
 
NormalizationPlugin - class MAEPlugin.analysis.NormalizationPlugin.
This class extends the analysis MAEPlugin base class to implement the Normalization base class.
NormalizationPlugin() - Constructor for class MAEPlugin.analysis.NormalizationPlugin
NormalizationPlugin() - Default Constructor puts default menu name in menu.
NormalizationPlugin(String) - Constructor for class MAEPlugin.analysis.NormalizationPlugin
NormalizationPlugin() - Default Constructor puts menu name in menu.
NormalizationPlugin(String, String) - Constructor for class MAEPlugin.analysis.NormalizationPlugin
NormalizationPlugin() - Default Constructor puts menu name in menu and file name.
normalizeDataVector(float[]) - Method in class HierClustNode
normalizeDataVector() - compute normalized terminal dataV[] using selected ratio-normalization method.
normByCalDNAflag - Variable in class MAExplorer
normalize by Calibration DNA set
normByGeneSetFlag - Variable in class MAExplorer
normalize by 'user gene set'
normByHousekeepGenesFlag - Variable in class MAExplorer
normalize by housekeeping genes
normByHPXflag - Static variable in class HierClustNode
flag: normalize data for gene in HP-X else HP[RatioHP]
normByLogMedianFlag - Variable in class MAExplorer
normalize by HP log of median
normByMedianFlag - Variable in class MAExplorer
normalize by HP median
normByZscoreFlag - Variable in class MAExplorer
normalize by HP Zscore
normByZscoreMeanAbsDevLogFlag - Variable in class MAExplorer
norm.
normByZscoreMeanStdDevLogFlag - Variable in class MAExplorer
norm by Zscore log intens,stdDev.
normCL - Variable in class GeneClass
"Normalization genes"
normCLbitSet - Static variable in class EventMenu
link to global instanceof normalization GeneBitSet
normFactor - Variable in class MaHybridSample
normalization factor for all intensity data so we can compare intensity between HP samples.
normHCbyRatioHPflag - Static variable in class HierClustNode
flag: set to true if norm dataV[h] by dataV[iDataV] else norm by HP[h] msListE[h].maQ.maxRI
normHCbyRatioHPflag - Variable in class MAExplorer
set true if normalize Hier-Clustering dataV[h] by dataV[iDataV] else norm by HP[h] msListE[h].maQ.maxRI
normMenu - Variable in class MenuBarFrame
"Normalization" menu
normName - Variable in class MAExplorer
name of normalization method
normNameDisp - Variable in class MAExplorer
name of norm.
normToOneFlag - Variable in class ExprProfile
flag: normalize hpData[] & cvData[] to 1.0
notAvailableYet() - Static method in class EventMenu
notAvailableYet() - print "Not available yet".
nOutputFiles - Variable in class RLO
# of output files if any, 0 if none
nOutputFiles - Variable in class RgenDemo
Number of output files if any
nOutputFiles - Variable in class PopupEditRscript
# of output files if any, 0 if none
nOutputTypeValues - Variable in class PopupEditRscript
# of input data types
nOverlayMaps - Static variable in class OverlayMap
# of entries in the named overlay map
nParams - Variable in class PopupCondChooser.CondData
number of rows of (name,value) parameter pairs
nParams - Variable in class PopupCondChooser.CondParamEditForm
 
nParams - Variable in class PopupOrderedCondChooser.OclListData
number of rows of (name,value) parameter pairs
nParams - Variable in class PopupOrderedCondChooser.CondParamEditForm
 
nPluginMenus - Variable in class Config
size of sPluginMenus[]
nPluginPathsList - Static variable in class MAEPlugin.popup.PluginLoader
Size of list of unique loaded plugins full path for ensuring uniqueness
nPoints - Variable in class ExprProfileOverlay
nGenes*nHP_E
nPoints - Variable in class ExprProfileScrollPane
nGenes*nHP_E
nPoints - Variable in class OverlayMap
# of (x,y) pairs in the map instance
nPointsPlotted - Variable in class Draw2Dplot
# points plotted.
nprobeNames - Variable in class StageNames
# unique probe name entries in Samples tbl
nProcessBits - Static variable in class RevalBase
Number of R2Client actions
nProcessCB - Variable in class PopupEditRscript
# of Process checkbox entries
nr_betacf(double, double, double) - Method in class MJAmath
nr_betacf() - evaluation fct for the incomplete Beta function 'x(a,b).
nr_betacf(double, double, double) - Static method in class MathMAE
nr_betacf() - evaluation fct for the incomplete Beta function 'x(a,b).
nr_betai(double, double, double) - Method in class MJAmath
nr_betai() - return the incomplete Beta function 'x(a,b).
nr_betai(double, double, double) - Static method in class MathMAE
nr_betai() - return the incomplete Beta function 'x(a,b).
nr_gammln(double) - Method in class MJAmath
nr_gammln() - Return ln(gamma()) of x by polynomial evaluation.
nr_gammln(double) - Static method in class MathMAE
nr_gammln() - Return ln(gamma()) of x by polynomial evaluation.
nr_kstwo(double[], int, double[], int) - Method in class MJAmath
nr_kstwo() - Kolmogorov-Smirnov statistic d and the probability of the null hypothesis of 2 bins of data.
nr_kstwo(double[], int, double[], int) - Static method in class MathMAE
nr_kstwo() - Kolmogorov-Smirnov statistic d and the probability of the null hypothesis of 2 bins of data.
nr_probks(double) - Method in class MJAmath
nr_probks() - Calc Kolmogorov-Smirnov probability Qks.
nr_probks(double) - Static method in class MathMAE
nr_probks() - Calc Kolmogorov-Smirnov probability qKS.
nr_sort(int, double[]) - Method in class MJAmath
nr_sort() - quick-sort of bin of data[1:n] in assend.
nr_sort(int, double[]) - Static method in class MathMAE
nr_sort() - quick-sort of bin of data[0:n-1] in assend.
nR2Client - Variable in class RgenDemo
Number of output Action files if any
nR2ClientActions - Static variable in class RevalBase
Number of R2Client actions
nr2ClientActionValues - Variable in class PopupEditRscript
# of R2Client action Choice values
nRatioHistBins - Variable in class CompositeDatabase
# of bins in ratioHist[]
nRdataTypes - Static variable in class RevalBase
Number of client export data file types for import to R
nRemCond - Variable in class PopupOrderedCondChooser.OclListData
number of remainder conditions
nRemSamples - Variable in class PopupCondChooser.CondData
number of remainder samples
nRLOs - Variable in class MenuBarFrame
# of RLO entries in the menu
nRows - Variable in class ClusterGramCanvas
# of rows i.e.
nRows - Variable in class DrawClusterGram
# of rows in clustergram
nRows - Variable in class ExprProfileScrollPane
# of rows in the Grid
nRows - Variable in class PopupProjDirGuesser
# of non-null Table rows
nRows - Variable in class RtestBase
# of rows size of text area for reporting
nRows - Variable in class ShowStringPopup
# of character rows to show
nSB - Static variable in class StateScrollers
# of entries in sbName[] tables
nSelCond - Variable in class PopupOrderedCondChooser.OclListData
number of selected conditions
nSelSamples - Variable in class PopupCondChooser.CondData
number of selected samples
nSEPP - Variable in class PopupRegistry
ShowExprProfilesPopup counter
nSetR2ClientFiles - Variable in class RLO
# of output files used to set R to Client data if any, 0 if none
nSetR2ClientFiles - Variable in class PopupEditRscript
# of output files used to set R to client data if any, 0 if none
nsourceNames - Variable in class StageNames
# unique source name entries in Samples tbl
nSpecialGC - Static variable in class GeneClass
# of all special built-in gene classes including variable
nSpots - Variable in class MaHPquantTable
number of spots read.
nSPP - Variable in class PopupRegistry
Plot popups counter
nSSP - Variable in class PopupRegistry
String popups counter
nSSSP - Variable in class PopupRegistry
ShowSpreadsheetPopup popups counter
nstageNames - Variable in class StageNames
# unique stage name entries in Samples tbl
nstrainNames - Variable in class StageNames
# unique strain name entries in Samples tbl
nTextItems - Variable in class CompositeDatabase
 
nTopSubMenus - Variable in class SampleSets
number of top level menus
numPixels - Variable in class WriteGifEncoder
 
nUseGenRCB - Static variable in class RgenDemo
Rscript generation GUI for DEMO only: # of entries
nUseGenRCB - Variable in class PopupEditRscript
Rscript generation GUI for DEMO only: # of entries
nUserBS - Static variable in class GeneBitSet
# user assignable gene bit sets in use
nValidPrj - Variable in class MAExplorer
# of login verified projects
nWizards - Variable in class PopupEditRscript
# of wizards
nX - Variable in class HPxyData
# of HP-X set members after setup
nXY - Static variable in class MathMAE
RTN: if calcXYstat
nY - Variable in class HPxyData
# of HP-Y set members after setup

O

objAction - Variable in class RgenDemo
 
objButtonPanel - Variable in class ChooserGUI
set prj button
objButtonPanel - Variable in class PopupCondChooserGUI
set prj button
objButtonPanel - Variable in class PopupOrderedCondChooserGUI
set prj button
objCidx - Static variable in class HierClustNode
sorted cluster cIdx data [0:nObj-1]
objCol - Variable in class CompositeDatabase
object Grid-Column that best matches xy coords if isValidObj is TRUE
objColor - Variable in class ScrollableImageCanvas
object color
objDataV - Variable in class ClusterGramCanvas
[0:maxGenes-1][0:nCols-1] normalized data for each object
objDataV - Static variable in class HierClustNode
sorted norm.
objField - Variable in class CompositeDatabase
object Field that best matches xy coords if isValidObj is TRUE
objGID - Static variable in class CompositeDatabase
GridCoords gid of object if isValidObj is TRUE
objGIDG - Variable in class CompositeDatabase
Gang f' GridCoords gid of object if isValidObj is TRUE
objGrid - Variable in class CompositeDatabase
object Grid that best matches xy coords if isValidObj is TRUE
objListTApanel - Variable in class ChooserGUI
obj list ta1
objListTApanel - Variable in class PopupCondChooserGUI
obj list remTextArea
objListTApanel - Variable in class PopupOrderedCondChooserGUI
obj list remTextArea
objMID - Static variable in class CompositeDatabase
Gene index mid of object if isValidObj is TRUE
objName - Variable in class RgenDemo
 
objRow - Variable in class CompositeDatabase
object Grid-Row that best matches xy coords if isValidObj is TRUE
objX - Variable in class CompositeDatabase
optimal spot X position if isValidObj is TRUE
objY - Variable in class CompositeDatabase
optimal spot Y position if isValidObj is TRUE
OCL_F_TestCL - Variable in class Filter
"Filter genes by current Ordered Condition List F-Test" i.e.
oclCondNames - Static variable in class MJAexprProfile
Ordered Condition List names for each condition
oclCV - Static variable in class MJAexprProfile
Ordered Condition List Coefficient of Variation of each condition
oclLd - Variable in class PopupOrderedCondChooser
List [0:maxPossibleCond-1] of working condition data: name, selected and remainder cond, param form (name,value).
oclLd - Variable in class PopupOrderedCondChooser.CondParamEditForm
instance of OclListData
oclList - Variable in class PopupOrderedCondChooser
The working list of conditions for GUI
oclMeans - Static variable in class MJAexprProfile
Ordered Condition List Means of each condition
oclName - Static variable in class MJAexprProfile
Ordered Condition List name
oclNbr - Static variable in class MJAexprProfile
Ordered Condition List # samples/condition
oclNbrConds - Static variable in class MJAexprProfile
Ordered Condition List # conditions in list
oclNparams - Static variable in class Condition
# of ordered condition list parameters
oclPanel - Variable in class PopupOrderedCondChooser
Panel to hold conditions list (LEFT) and Param Editor (RIGHT)
oclParamNames - Static variable in class Condition
[0:oclNparams-1] list of OCL parameter names for CondForm
oclParamValues - Static variable in class Condition
[0:maxOrderedCondLists-1][0:oclNparams-1] list of OCL parameter values for CondForm
oclStdDev - Static variable in class MJAexprProfile
Ordered Condition List StdDevs of each condition
oFeature - Variable in class HierClustNode
optional feature if not equal to -1
offSet - Variable in class SSspreadPanel
 
oGifFileName - Variable in class ClusterGramCanvas
GIF output file if used
oGifFileName - Variable in class Draw2Dplot
full Gif file path name
oGifFileName - Variable in class DrawHistogram
full Gif file path name
oGifFileName - Variable in class DrawRatioHistogram
full Gif file path name
oGifFileName - Variable in class ExprProfileCanvas
full Gif file path name
oGifFileName - Variable in class ScrollableImageCanvas
GIF output file if used
oImageName - Variable in class MaHybridSample
(opt) original image filename
ok - Variable in class WriteGifEncoder
80% occupancy
okBetaCF - Static variable in class MathMAE
RTN: if nr_betacf() was ok
okBetaI - Static variable in class MathMAE
RTN: if nr_betai() was ok
okFlag - Variable in class PopupCondChooser.CondDialogBox
flag from OK button
okFlag - Variable in class PopupOrderedCondChooser.CondDialogBox
flag from OK button
okProbKS - Static variable in class MathMAE
RTN: if nr_probks() was ok
oldContent - Variable in class SSstatusBar
 
oldCurRLOid - Variable in class RgenDemo
OLD RLO prior to creating R script
oldHorzValue - Variable in class SSscrollHorizontal
upper bounds on scroller
oldItem - Static variable in class EventMenu
previous array display mode
oldMS - Static variable in class EventMenu
save old value of MaHybridSample mae.ms
oldOCC - Static variable in class PopupOrderedCondChooser
previous instance if not null so can close it before starting new instance.
oldPCC - Static variable in class EventMenu
old PopupCondChooser to be closed if open up a new one without closing the first.
oldPCC - Static variable in class PopupCondChooser
previous instance if not null so can close it before starting new instance.
oldPccg - Variable in class PopupOrderedCondChooser
previous chooser GUI for cond data
oldPccgSample - Variable in class PopupCondChooser
previous chooser GUI for sample data
oldPlotMode - Static variable in class EventMenu
save old value of mae.plotModeImage
oldPOCC - Static variable in class EventMenu
old PopupOrderedCondChooser to be closed if open up a new one without closing the first.
oldPosition - Variable in class SSspreadPanel
keep track of col last clicked
oldTagCol - Variable in class ShowSpreadsheetPopup
old tag col for clicked cell color (before)
oldTagRow - Variable in class ShowSpreadsheetPopup
 
oldValueList - Variable in class SampleSets
originbal list for Cy5/Cy3 swap if cancel
oldVertValue - Variable in class SSscrollVertical
keep track of oldvalue
oldWorkingCLlength - Variable in class PopupRegistry
last value of fc.workingCL.length to see if update clusters - if filter changed.
olmap - Variable in class Draw2Dplot
link to scatterplot named overlay maps instance
olmap - Variable in class MAExplorer
Global instance of scatterplot named overlay maps
olmap - Static variable in class MJAbase
link to scatterplot named overlay maps instance
OmimID - Variable in class Gene
NCBI OMIM ID if it exists
OmimIdIdx - Variable in class GipoTable
index for "OMIM" ID
omimURL - Variable in class Config
base addr PARAM "omimURL"
omimViewerFlag - Variable in class MAExplorer
OMIM popup browser Mode
onceOnlyFlag - Variable in class Guesser
global setup flag
onceOnlyFlag - Variable in class MAExplorer
flag to prevent multiple instances
onlyOnePrologueEpilogueTag(String) - Method in class PopupEditRscript
onlyOnePrologueEpilogueTag() - Omit extra prologue/epilogue tags, save only the first one encountered.
openNewFileDB(String, String, boolean) - Method in class MJAstate
openNewFileDB() - open a new .mae database file.
openNewMaeDB(String, String) - Static method in class EventMenu
openNewMaeDB() - open new .mae file DB browser & select file.
openNewWebDB(String) - Static method in class EventMenu
openNewWebDB() - open new Web database after closing the old one
openOtherUserState(String, String) - Method in class UserState
openOtherUserState() - open other user's named user state [FUTURE]
openState(String) - Method in class UserState
openState() - open named user state
OPTIMIZE_WINDOW_WIDTH - Static variable in class ShowStringPopup
if optimized window with by shrinking # of buttons/row in controlPanel to OPTIMUM_BUTTONS_PER_ROW
OPTIMUM_BUTTONS_PER_ROW - Static variable in class ShowStringPopup
if optimize # buttons/row
optionChoice - Variable in class PopupDialogQuery
opt.
optionChoice1 - Variable in class PopupBinOprDialogQuery
opt.
optionChoice2 - Variable in class PopupBinOprDialogQuery
opt.
optionChoice3 - Variable in class PopupBinOprDialogQuery
opt.
optionPanel - Variable in class PopupDialogQuery
for options
optionPanel1 - Variable in class PopupBinOprDialogQuery
panel that holds choice list
optionPanel2 - Variable in class PopupBinOprDialogQuery
panel that holds choice list
optionPanel3 - Variable in class PopupBinOprDialogQuery
panel that holds choice list
optionValues - Variable in class PopupBinOprDialogQuery
list of option values if present
optionValues - Variable in class PopupDialogQuery
list of option values if present
optLabel - Variable in class PopupLoginDialogQuery
for optional message label
optMsg - Variable in class PopupLoginDialogQuery
for optional message label
optReportMode - Variable in class ShowStringPopup
Optional Report mode if > 0
orderedCL - Variable in class ClusterGramCanvas
gene list for rows
orderedCL - Variable in class DrawClusterGram
GeneList being used
orderedCondList - Static variable in class Condition
Database orderedCondList (OCL) list of all order sample condition lists [0:maxOrderedCondLists][1:nConditions] for all active samples.
orderedCondListName - Static variable in class Condition
Names of ordered condition lists [0:maxOrderedCondLists-1]
orderedCondListNames - Variable in class PopupOrderedCondChooser
list of condition names
origRemObjs - Variable in class ChooserGUI
original REMAINDER list
origRemObjs - Variable in class PopupCondChooserGUI
original REMAINDER list
origRemObjs - Variable in class PopupOrderedCondChooserGUI
original REMAINDER list
origRemObjsSize - Variable in class ChooserGUI
REMAINDER list size
origRemObjsSize - Variable in class PopupCondChooserGUI
REMAINDER list size
origRemObjsSize - Variable in class PopupOrderedCondChooserGUI
REMAINDER list size
origSelObjs - Variable in class ChooserGUI
original SELECTED list
origSelObjs - Variable in class PopupCondChooserGUI
original SELECTED list
origSelObjs - Variable in class PopupOrderedCondChooserGUI
original SELECTED list
origSelObjsSize - Variable in class ChooserGUI
SELECTED list size
origSelObjsSize - Variable in class PopupCondChooserGUI
SELECTED list size
origSelObjsSize - Variable in class PopupOrderedCondChooserGUI
SELECTED list size
osName - Static variable in class MAExplorer
operating system Windows, SUNOS, etc
osName - Static variable in class RevalBase
 
osName - Variable in class RtestBase
 
otherUserName - Variable in class MAExplorer
access other user name from Dialog
output(int, FileOutputStream) - Method in class WriteGifEncoder
output() - Output the given code.
outputDataFileNames - Variable in class RLO
List of output files if any, null if none
outputDataFileNames - Variable in class RgenDemo
Output files [0:nOutputFiles-1] if any
outputDataFileNames - Variable in class PopupEditRscript
List of output files if any, null if none
outputDataTypes - Variable in class RLO
List of R_FILE_TYPE_xxxx types of output files if any, null if none.
outputDataTypes - Variable in class PopupEditRscript
List of R_FILE_TYPE_xxxx types of output files if any, null if none.
outputTypesChoice - Variable in class PopupEditRscript
Output data type Choices [0:MAX_WIZ_CHOICES-1]
outputTypesChoiceNames - Variable in class PopupEditRscript
Output data types Choice names [0:nOutputTypes-1]
outputTypesChoiceValues - Variable in class PopupEditRscript
Output data types Choice values [0:nOutputTypes-1].
outsideLoadRscriptFile - Variable in class PopupEditRscript
outside Load .R script File
outsideRangeFlag - Variable in class DrawHistogram
for testing range
outsideRangeFlag - Variable in class DrawRatioHistogram
for testing range
outsideRangeFlag - Variable in class ShowPlotPopup
flag: toggle if "><" hist range
overlayChars - Variable in class OverlayMap
optional overlay characters [0:nPoints-1] used for overlayType 3
overlayColor - Variable in class OverlayMap
Color to draw the points
OverlayMap - class OverlayMap.
Class OverlayMap creates an database of named (x,y) scatterplot overlay maps for overlaying on the scatterplot.
OverlayMap(MAExplorer, int) - Constructor for class OverlayMap
OverlayMap() - constructor named overlay map
OverlayMap(String, float[], int, Color, int) - Constructor for class OverlayMap
OverlayMap() - constructor named overlay map
overlayMapDB - Static variable in class OverlayMap
Named scatterplot overlay map database [0:maxOverlayMaps-1]
overlayMapName - Variable in class OverlayMap
Name of a map instance
overlayType - Variable in class OverlayMap
Overlay drawing type is 0 for 'o', 1 for continuous line between points, 2 for square, 3 for overlay characters (must setOverlayMapChars() )

P

pagestep - Variable in class ArrayScroller
scrollbar thickness
paint() - Method in class DrawClusterGram
paint() - redraw clustergram
paint(Graphics) - Method in class ClusterGramCanvas
paint() - draw ClusterGram [r1:r2] from scroller percentage and canvas height.
paint(Graphics) - Method in class Draw2Dplot
paint() - draw the 2D plot.
paint(Graphics) - Method in class StatusCanvas
paint() - draw the ClusterGram status area.
paint(Graphics) - Method in class DrawHistogram
paint() - draw the histogram
paint(Graphics) - Method in class DrawRatioHistogram
paint() - draw the histogram
paint(Graphics) - Method in class ExprProfileCanvas
paint() - draw the expression profile in the canvas if a legal gene MID.
paint(Graphics) - Method in class ExprProfileOverlay
paint() - redraw plots near selected row.
paint(Graphics) - Method in class ExprProfilePanel
paint() - draw the expression profile plot only repaint if a legal gene MID.
paint(Graphics) - Method in class ExprProfilePopup
paint() - repaint buttons and canvas
paint(Graphics) - Method in class ExprProfileScrollPane
paint() - redraw plots near selected Row.
paint(Graphics) - Method in class MAExplorer
paint() - generate viewable scrollable pseudoarray image with overlays.
paint(Graphics) - Method in class PopupCondChooser
paint() - repaint full scrolled text area.
paint(Graphics) - Method in class PopupOrderedCondChooser
paint() - repaint full scrolled text area.
paint(Graphics) - Method in class RtestBase
paint() - repaint full scrolled text area.
paint(Graphics) - Method in class PopupEditRscript
paint() - update window
paint(Graphics) - Method in class ScrollableImageCanvas
paint() - repaint scrollable canvas in region defined by the scroll bars.
paint(Graphics) - Method in class ShowExprProfilesPopup
paint() - repaint by causes the ExprProfileScrollPane to repaint.
paramFont - Variable in class PopupCondChooser
font for parameter Name and Value
paramFont - Variable in class PopupOrderedCondChooser
font for parameter Name and Value
paramNames - Variable in class PopupCondChooser
list [0:nbrCondLists-1] of condition parameter names for CondParamEditForm.
paramNames - Variable in class PopupOrderedCondChooser
list [0:nbrOclLists-1] of condition parameter names for CondParamEditForm.
parentWindow - Variable in class ChooserGUI
parent window
parentWindow - Variable in class PopupCondChooserGUI
parent window
parentWindow - Variable in class PopupOrderedCondChooserGUI
parent window
parseDelimChar - Variable in class RevalBase
current delim of "name(delim)value" pair for StringTokenizer
parseDelimChar - Variable in class UserState
current delim of "name(delim)value" pair
parseGidQmapLookupTable() - Method in class MaHPquantTable
parseGidQmapLookupTable()- parse FGRC tData[][] to ms.gidMapQ[].
parseName - Variable in class RevalBase
current name of "name=value" pair for StringTokenizer
parseName - Variable in class UserState
current name of "name=value" pair
parseQuantTableToQarrays() - Method in class MaHPquantTable
parseQuantTableToQarrays() - cvt Table data to quant xxxC[] arrays data.
parseValue - Variable in class RevalBase
current value of "name=value" pair for StringTokenizer
parseValue - Variable in class UserState
current value of "name=value" pair
passwd - Variable in class JavaCGIBridge
possibly used for Authentication
passwordData - Variable in class PopupLoginDialogQuery
password data for returning back to MAE
passwordLabel - Variable in class PopupLoginDialogQuery
for password label
passwordTextField - Variable in class PopupLoginDialogQuery
place password text to be edited here
pBOdq - Variable in class MenuBarFrame
holds popup BinOpr dialog query
pCanvas - Variable in class DrawRatioHistogram
canvas used to draw ratio histogram
pcc - Variable in class PopupCondChooser.CondParamEditForm
parent class
pcc - Variable in class PopupCondChooser.PopupTextField
instance of PopupCondChooser
pcc - Variable in class PopupCondChooser.ChoiceList
instance of PopupCondChooser
pcc - Variable in class PopupOrderedCondChooser.CondParamEditForm
parent class
pcc - Variable in class PopupOrderedCondChooser.PopupTextField
instance of PopupOrderedCondChooser
pcc - Variable in class PopupOrderedCondChooser.ChoiceList
instance of PopupOrderedCondChooser
pccg - Variable in class PopupOrderedCondChooser
Ordered chooser GUI for cond data
pccgHeight - Variable in class PopupCondChooser
size for PopupCondChooserGUI
pccgHeight - Variable in class PopupOrderedCondChooser
size for PopupOrderedCondChooserGUI
pccgSample - Variable in class PopupCondChooser
chooser GUI for sample data
pccgWidth - Variable in class PopupCondChooser
size for PopupCondChooserGUI
pccgWidth - Variable in class PopupOrderedCondChooser
size for PopupOrderedCondChooserGUI
pccMsgTxtField1 - Variable in class PopupCondChooser
msg display 1
pccMsgTxtField1 - Variable in class PopupOrderedCondChooser
msg display 1
pccMsgTxtField2 - Variable in class PopupCondChooser
msg display 2
pccMsgTxtField2 - Variable in class PopupOrderedCondChooser
msg display 2
pccMsgTxtField3 - Variable in class PopupCondChooser
msg display 3
pccMsgTxtField3 - Variable in class PopupOrderedCondChooser
msg display 3
pctOKthr - Variable in class Config
Threshold PARAM: "pctOKthr" % spot intensity OK threshold
pdfFile - Variable in class RgenDemo
Current PDF file for current RLO, if specified
pdq - Variable in class MenuBarFrame
holds popup dialog query
pe - Variable in class RtestBase
 
percentDone() - Method in class MAExplorer
percentDone() - estimate percent of files done loading
pF - Variable in class Statistics
CALC: f-test p-value w/NULL hypoth set by calcTandPvalues()
PFL_NEW_READ_BUF_CODE - Static variable in class JavaCGIBridge
 
pFnConds - Variable in class Statistics
CALC: f-test p-value w/NULL hypoth for nConditions set by calcNCondFtestStat()
pgcg - Variable in class Guesser
parent class instance if it is not null
pgrid - Variable in class StateScrollers
holds the Scrollbar (SB) panels
pHashtable - Variable in class MAEPlugin.popup.PluginUnLoader
Hashtable used to remove plugs
pHeight - Variable in class MAExplorer
working size of pseudoarray image
phpmg - Variable in class Guesser
parent class instance if it is not null
piHT - Static variable in class MJAstate
Hashtable used for the MAExplorer MAEPlugins (pluginName+varName) hash storage.
piHTsize - Static variable in class MJAstate
Hashtable size of piHT.
pImage - Variable in class MAExplorer
pseudo grayscale microarray image based on .quantspot intensity data.
pirURL - Variable in class Config
base addr PARAM "pirURL"
pirViewerFlag - Variable in class MAExplorer
PIR page popup browser Mode
pixelIndex - Variable in class WriteGifEncoder
 
pixels - Variable in class WriteGifEncoder
 
pixels32 - Variable in class MedianCut
32-bit image[width*height] (Alpha,Red,Green,Blue) pixels
pixels8 - Variable in class MedianCut
8-bit image[width*height] using LUTs
pKS - Variable in class Statistics
CALC: KS-test p-value w/NULL hypoth set by calcKStestStat()
plate - Variable in class Gene
plate where clone was from
plate - Variable in class SpotFeatures
lookup corresponding plate
plate_col - Variable in class Gene
plate where clone was from
plate_col - Variable in class SpotFeatures
lookup corresponding plate_col
plate_colIdx - Variable in class GipoTable
index for "plate col"
plate_row - Variable in class Gene
plate where clone was from
plate_row - Variable in class SpotFeatures
lookup corresponding plate_row
plate_rowIdx - Variable in class GipoTable
index for "plate row"
plateIdx - Variable in class GipoTable
index for "plate name"
pLdq - Variable in class UserState
holds popup Login dialog query
pList - Variable in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
 
PLOT_CLUSTER_GENES - Static variable in class MAExplorer
Popup plot mode: cluster similar genes plot
PLOT_CLUSTER_GENES - Static variable in class MJAbase
Popup plot mode: cluster genes plot
PLOT_CLUSTER_HIER - Static variable in class MAExplorer
Popup plot mode: hierarchical cluster genes plot
PLOT_CLUSTER_HIER - Static variable in class MJAbase
Popup plot mode: hierarchical cluster genes plot
PLOT_CLUSTER_HYBSAMPLES - Static variable in class MAExplorer
Popup plot mode: cluster HP-samples plot
PLOT_CLUSTER_HYBSAMPLES - Static variable in class MJAbase
Popup plot mode: cluster HP-samples plot
PLOT_CLUSTERGRAM - Static variable in class MAExplorer
Popup plot mode: clustergram genes plot
PLOT_CLUSTERGRAM - Static variable in class MJAbase
Popup plot mode: clustergram genes plot
PLOT_EXPR_PROFILE - Static variable in class MAExplorer
Popup plot mode: expression profile plot
PLOT_EXPR_PROFILE - Static variable in class MJAbase
Popup plot mode: expression profile plot
PLOT_F1_F2_INTENS - Static variable in class MAExplorer
Popup plot mode: current F1 vs F2, or Cy3 vs Cy5 scatter plot
PLOT_F1_F2_INTENS - Static variable in class MJAbase
Popup plot mode: current F1 vs F2, or Cy3 vs Cy5 scatter plot
PLOT_F1_F2_MVSA - Static variable in class MAExplorer
Popup plot mode: M vs A scatter plot of current sample
PLOT_F1_F2_MVSA - Static variable in class MJAbase
Popup plot mode: M vs A scatter plot of current sample
PLOT_HIST_F1F2_RATIO - Static variable in class MAExplorer
Popup plot mode: current HP F1/F2 ratio histogram plot
PLOT_HIST_F1F2_RATIO - Static variable in class MJAbase
Popup plot mode: current HP F1/F2 ratio histogram plot
PLOT_HIST_HP_XY_RATIO - Static variable in class MAExplorer
Popup plot mode: HP-X/HP-Y ratio histogram plot
PLOT_HIST_HP_XY_RATIO - Static variable in class MJAbase
Popup plot mode: HP-X/HP-Y ratio histogram plot
PLOT_HIST_HP_XY_SETS_RATIO - Static variable in class MAExplorer
Popup plot mode: HP-X 'set' / HP-Y 'set' ratio histogram plot
PLOT_HIST_HP_XY_SETS_RATIO - Static variable in class MJAbase
Popup plot mode: HP-X 'set' / HP-Y 'set' ratio histogram plot
PLOT_HP_XY_INTENS - Static variable in class MAExplorer
Popup plot mode: HP-X vs HP-Y, or HP-X 'set' vs HP-Y 'set' scatter plot
PLOT_HP_XY_INTENS - Static variable in class MJAbase
Popup plot mode: HP-X vs HP-Y, or HP-X 'set' vs HP-Y 'set' scatter plot
PLOT_INTENS_HIST - Static variable in class MAExplorer
Popup plot mode: current HP intensity histogram plot
PLOT_INTENS_HIST - Static variable in class MJAbase
Popup plot mode: current HP intensity histogram plot
PLOT_KMEANS_CLUSTERGRAM - Static variable in class MAExplorer
Popup plot mode: k-means cluster genes plot
PLOT_KMEANS_CLUSTERGRAM - Static variable in class MJAbase
Popup plot mode: k-means cluster genes plot
PLOT_PSEUDO_F1F2_IMG - Static variable in class MAExplorer
Pseudoarray image plot mode: display current F1/F2 (Cy3/Cy5) ratios as [green:black:red]
PLOT_PSEUDO_F1F2_IMG - Static variable in class MJAbase
Pseudoarray image plot mode: display current F1/F2 (Cy3/Cy5) ratios as [green:black:red]
PLOT_PSEUDO_F1F2_RYG_IMG - Static variable in class MAExplorer
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]
PLOT_PSEUDO_F1F2_RYG_IMG - Static variable in class MJAbase
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]
PLOT_PSEUDO_HP_EP_CV_VALUE_IMG - Static variable in class MAExplorer
Pseudoarray image plot mode: display HP_EP 'list' CV coefficient of variation [0.0:1.0] as [black:white]
PLOT_PSEUDO_HP_XY_IMG - Static variable in class MAExplorer
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:black:red]
PLOT_PSEUDO_HP_XY_IMG - Static variable in class MJAbase
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:black:red]
PLOT_PSEUDO_HP_XY_P_VALUE_IMG - Static variable in class MAExplorer
Pseudoarray image plot mode: display X,Y 'sets' p-Value [0.0:1.0] as [black:white]
PLOT_PSEUDO_HP_XY_RYG_IMG - Static variable in class MAExplorer
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]
PLOT_PSEUDO_HP_XY_RYG_IMG - Static variable in class MJAbase
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]
PLOT_PSEUDOIMG - Static variable in class MAExplorer
Pseudoarray image plot mode: Grayscale display current HP intensity
PLOT_PSEUDOIMG - Static variable in class MJAbase
Pseudoarray image plot mode: Grayscale display current HP sample intensity
plotImageMode - Variable in class MAExplorer
Pseudo array image plot mode: PLOT_xxxx_IMAGE
plotMenu - Variable in class MenuBarFrame
"Plot" menu
plotMode - Variable in class DrawClusterGram
plot mode
plotMode - Variable in class DrawHistogram
ARG: plot mode
plotMode - Variable in class DrawRatioHistogram
plot mode
plotMode - Variable in class DrawScatterPlot
plot mode of scatter plot
plotMode - Variable in class ShowPlotPopup
Plot mode: one of the mae.PLOT_xxxx values
plotMode2D - Variable in class Draw2Dplot
plot mode for spp
plotStyleButton - Variable in class ExprProfilePopup
plot style (line, circle, curve) button
plotStyleButton - Variable in class ShowExprProfilesPopup
 
plotStyleMode - Variable in class ExprProfileCanvas
plot mode style: 0=line, 1=circle, 2=curve
plotStyleMode - Variable in class ExprProfileOverlay
plot style mode: 0=line, 1=circle, 2=curve
plotStyleMode - Variable in class ExprProfileScrollPane
plot style mode: 0=line, 1=circle, 2=curve
plotStyleMode - Variable in class ShowExprProfilesPopup
Mode for plotting points in the expr profile where: 0=(bar) line, 1=circle, 2=curve
PLUGIN_VERSION - Static variable in interface MAEPlugin.PluginStub
MAEPlugin version # for tracking
pluginClassName - Variable in class MAEPlugin.popup.PluginLoader
Reference to the plain name of the class to load
pluginClassName - Variable in class MAEPlugin.popup.PluginUnLoader
Reference to the plain name of the class to load
PluginException - exception MAEPlugin.PluginException.
This exception is used to allow self registering of plugins for a max number of plugins.
PluginException() - Constructor for class MAEPlugin.PluginException
 
plugInFileName - Variable in class MAEPlugin.MAEPlugin
File name of the plugin without the ".jar"
PluginFilenameFilter - class MAEPlugin.PluginFilenameFilter.
Class Filename filter for class files.
PluginFilenameFilter() - Constructor for class MAEPlugin.PluginFilenameFilter
PluginFilenameFilter() - Filter for class files, may be modified by regedit style wild cards.
pluginHalt() - Method in class MAEPlugin.MAEPlugin
pluginHalt() - Plugin halt method.
pluginHalt() - Method in interface MAEPlugin.PluginStub
pluginHalt() - Plugin halt method.
pluginHalt() - Method in class MAEPlugin.analysis.NormalizationPlugin
pluginHalt() - stop the plugin
pluginHalt() - Method in class MAEPlugin.analysis.FilterPlugin
pluginHalt() - stop the plugin
pluginInit() - Method in class MAEPlugin.MAEPlugin
pluginInit() - Plugin init method.
pluginInit() - Method in interface MAEPlugin.PluginStub
pluginInit() - Plugin init method.
pluginInit() - Method in class MAEPlugin.analysis.FilterPlugin
pluginInit() - Plugin init method.
PluginLoader - class MAEPlugin.popup.PluginLoader.
This class contains the dynamic MAEplugin loader.
PluginLoader(MAEStub) - Constructor for class MAEPlugin.popup.PluginLoader
PluginLoader() - Creates new LoadPlugins.
PluginLoader(MAEStub, String) - Constructor for class MAEPlugin.popup.PluginLoader
PluginLoader() - Creates new LoadPlugin but do it siliently.
pluginMain() - Method in class MAEPlugin.MAEPlugin
pluginMain() - abstract method end-users must implement to use the API.
pluginMain() - Method in class MAEPlugin.CheckBoxMenuPlugin
pluginMain() - abstract the method end-users implement to use the API
pluginMain() - Method in interface MAEPlugin.PluginStub
pluginMain() - this is the method end-users implement to use the API.
pluginMain() - Method in class MAEPlugin.MenuPlugin
pluginMain() - abstract the method end-users implement to use the API
pluginMain() - Method in class MAEPlugin.analysis.NormalizationPlugin
pluginMain() is the method activated when end-users check a checkbox API.
pluginMain() - Method in class MAEPlugin.analysis.FilterPlugin
pluginMain() is the method activated when end-users check a checkbox API.
pluginMain() - Method in class MAEPlugin.popup.PluginLoader
pluginMain() - Is the method end-users implement to use the API.
pluginMain() - Method in class MAEPlugin.popup.PluginUnLoader
pluginMain() - Is the method end-users implement to use the API.
plugInName - Variable in class MAEPlugin.MAEPlugin
The human readable name for labels and such, the class names need to be unique to identify the plugins
pluginObject - Variable in class MAEPlugin.popup.PluginLoader
Reference to the Object itself
pluginObject - Variable in class MAEPlugin.popup.PluginUnLoader
Reference to the Object itself
pluginPathsList - Static variable in class MAEPlugin.popup.PluginLoader
List of unique loaded plugins full path for ensuring uniqueness
pluginsDir - Static variable in class MAExplorer
Standalone /Plugins directory where optional MAEPlugins may be found
pluginsMenu - Variable in class MenuBarFrame
"Plugins" menu
PluginStub - interface MAEPlugin.PluginStub.
Enforces method implementations in suport of MAEPlugin.
PluginUnLoader - class MAEPlugin.popup.PluginUnLoader.
This class contains the dynamic MAEplugin unloader for .jar files
PluginUnLoader.UnloaderDialog - class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.
Class UnloaderDialog is used to select loaded plugins to unload
PluginUnLoader.UnloaderDialog.PluginList - class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList.
class PluginList was modified from Chan P.
PluginUnLoader.UnloaderDialog.PluginList(PluginUnLoader.UnloaderDialog) - Constructor for class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
PluginList() - constructor
PluginUnLoader.UnloaderDialog(PluginUnLoader, Frame) - Constructor for class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
UnloaderDialog() - constructor
PluginUnLoader.UnloaderDialog(PluginUnLoader, Frame, String) - Constructor for class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
UnloaderDialog() - constructor
PluginUnLoader.UnloaderDialog(PluginUnLoader, Frame, String, boolean) - Constructor for class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
UnloaderDialog() - constructor
PluginUnLoader(MAEStub) - Constructor for class MAEPlugin.popup.PluginUnLoader
PluginLoader() - Creates new LoadPlugins.
pngFile - Variable in class RgenDemo
Current PNG file for current RLO, if specified
pnlHeight - Variable in class StateScrollers
panel size height
pnlWidth - Variable in class StateScrollers
panel size Width
pointType - Variable in class DrawHistogram
point type: DRAW _PLUS, _CIRCLE, _BOX
pointType - Variable in class DrawRatioHistogram
point type: DRAW _PLUS, _CIRCLE, _BOX
popdownScrollers() - Method in class StateScrollers
popdownScrollers() - close down the window using dispose
POPUP_HEIGHT - Static variable in class PopupHPChooser
Height of frame holding popup HP chooser.
POPUP_HEIGHT - Static variable in class ShowPlotPopup
default frame size height of popup
POPUP_HEIGHT - Static variable in class ShowSpreadsheetPopup
size (height) of popup report window
POPUP_WIDTH - Static variable in class PopupHPChooser
Width of of frame holding popup HP chooser.
POPUP_WIDTH - Static variable in class ShowPlotPopup
default frame size width of popup
POPUP_WIDTH - Static variable in class ShowSpreadsheetPopup
size (width) of popup report window
popupAlertMsg(String, String, int, int) - Method in class MJAutil
popupAlertMsg() - popup alert message in a scrollable text area.
popupAlertMsg(String, String, int, int) - Method in class Rtest
popupAlertMsg() - popup alert message in a scrollable text area.
popupAlertMsg(String, String, int, int) - Method in class RtestBase
popupAlertMsg() - popup alert message in a scrollable text area.
popupAlertMsg(String, String, int, int) - Static method in class Util
popupAlertMsg() - popup alert message in a scrollable text area.
popupAlertMsgLine(String) - Method in class MJAutil
popupAlertMsgLine() - popup alert message line window.
popupAlertMsgLine(String) - Static method in class Util
popupAlertMsgLine) - popup ALERT message line and then timeout.
popupAllConditionsReport() - Method in class MJAcondition
popupAllConditionsReport() - popup a report showing list of all conditions
popupAllOCLsReport() - Method in class MJAcondition
popupAllOCLsReport() - popup a report showing list of all OCLs
PopupBinOprDialogQuery - class PopupBinOprDialogQuery.
The class creates apopup binary operation query dialog window.
PopupBinOprDialogQuery(MAExplorer, Frame) - Constructor for class PopupBinOprDialogQuery
PopupBinOprDialogQuery() - Constructor
PopupCondChooser - class PopupCondChooser.
Class PopupCondChooser - GUI to allow users to associate conditions with samples, define parameters of conditions and save within MAExplorer to be used in reports/plots etc.
PopupCondChooser.ChoiceList - class PopupCondChooser.ChoiceList.
Class ChoiceList Allows user to pick an item in a list of items
PopupCondChooser.ChoiceList(PopupCondChooser, Frame, String, String[], int, String, PopupCondChooser) - Constructor for class PopupCondChooser.ChoiceList
ChoiceList() - Constructor
PopupCondChooser.CondData - class PopupCondChooser.CondData.
Class CondData contains the active remainder and selected samples data for a condition instance.
PopupCondChooser.CondData(PopupCondChooser, String, int, int, String[], String[]) - Constructor for class PopupCondChooser.CondData
CondData() - Constructor
PopupCondChooser.CondDialogBox - class PopupCondChooser.CondDialogBox.
Class CondDialogBox is a dialog box with with two buttons yesMsg and noMsg that will return true or false when pressed.
PopupCondChooser.CondDialogBox(PopupCondChooser, Frame, String, String, String) - Constructor for class PopupCondChooser.CondDialogBox
CondDialogBox() - Constructor
PopupCondChooser.CondParamEditForm - class PopupCondChooser.CondParamEditForm.
Class CondParamEditForm creates a ScrollPane of the (name,value) parameters for the current condition instance.
PopupCondChooser.CondParamEditForm(PopupCondChooser, PopupCondChooser, PopupCondChooser.CondData, PopupCondChooser.CondParamEditForm) - Constructor for class PopupCondChooser.CondParamEditForm
CondParamEditForm() - Constructor for parameter (name[],value[]) data.
PopupCondChooser.PopupTextField - class PopupCondChooser.PopupTextField.
Class PopupTextField is a simple "editor" for entering a string value.
PopupCondChooser.PopupTextField(PopupCondChooser, Frame, String, PopupCondChooser, String) - Constructor for class PopupCondChooser.PopupTextField
PopupTextField() - Constructor
PopupCondChooser(MaeJavaAPI, PopupCondChooser) - Constructor for class PopupCondChooser
PopupCondChooser() - Constructor
PopupCondChooserGUI - class PopupCondChooserGUI.
The PopupCondChooserGUI class is a popup class for creating condition chooser GUIs.
PopupCondChooserGUI.MouseEventHandler - class PopupCondChooserGUI.MouseEventHandler.
 
PopupCondChooserGUI.MouseEventHandler(PopupCondChooserGUI, PopupCondChooserGUI, TextArea, String[], int) - Constructor for class PopupCondChooserGUI.MouseEventHandler
MouseEventHandler() - constructor
PopupCondChooserGUI.MouseEventHandler(PopupCondChooserGUI, TextArea) - Constructor for class PopupCondChooserGUI.MouseEventHandler
MouseEventHandler() - constructor
PopupCondChooserGUI(PopupCondChooser, PopupCondChooserGUI, int, int, int, Font, Font, Font, Font, Object, boolean) - Constructor for class PopupCondChooserGUI
PopupCondChooserGUI() - constructor for base class of Chooser GUI
popupDialog(String, String) - Method in class Reval
popupDialog() prompt with message and return response.
popupDialog(String, String) - Method in class RevalBase
popupDialog() prompt with message and return response.
PopupDialogQuery - class PopupDialogQuery.
The class is a generic popup query dialog window used throughout MAExplorer.
PopupDialogQuery(MAExplorer, Frame, int) - Constructor for class PopupDialogQuery
PopupDialogQuery() - Constructor
popupDryrotMsgsAAndQuit() - Method in class MJAutil
popupDryrotMsgsAndQuit() - test if fatal dryrot messages, then generate Dryrot exit sequence.
popupDryrotMsgsAndQuit() - Static method in class Util
popupDryrotMsgsAndQuit() - if any dryrot, tell us and die...
PopupEditRscript - class PopupEditRscript.
The PopupEditRscript class creates a popup window for editing the current RLO by invoking editRLO(), or creating a new RLO by the newRLO() method.
PopupEditRscript(RtestBase) - Constructor for class PopupEditRscript
PopupEditRscript() - build the popup window to edit R scripts
PopupGeneGuesser - class PopupGeneGuesser.
The PopupGeneGuesser class is a popup gene name/genomic ID gene guesser.
PopupGeneGuesser(MAExplorer, char, Font) - Constructor for class PopupGeneGuesser
PopupGeneGuesser() - constructor
PopupHPChooser - class PopupHPChooser.
The class creates a GUI for selecting HP-X and HP-Y 'sets', HP-E 'list'.
PopupHPChooser(MAExplorer, Font, Font, Font, int, int) - Constructor for class PopupHPChooser
PopupHPChooser() - Constructor.
PopupHPmenuGuesser - class PopupHPmenuGuesser.
The PopupHPmenuGuesser class popups up a sample name guesser.
PopupHPmenuGuesser(MAExplorer, char, Font) - Constructor for class PopupHPmenuGuesser
PopupHPmenuGuesser() - constructor assumes the HP menu item list is already sorted when it is created during MAExplorer initialization.
popupImageOfHPsample(MaHybridSample) - Method in class Util
popupImageOfHPsample() - popup image of current gene in Web browser.
popupListConditionReport(String) - Method in class MJAcondition
popupListConditionReport() - popup a report showing list of samples for condition
popupListOCLReport(String) - Method in class MJAcondition
 
PopupLoginDialogQuery - class PopupLoginDialogQuery.
The class creates apopup query dialog for requesting user login (username,password) data.
PopupLoginDialogQuery(MAExplorer, Frame) - Constructor for class PopupLoginDialogQuery
PopupLoginDialogQuery() - Constructor
popupName - Variable in class Report
ARG: name for for PopupRegistry
popupName - Variable in class ShowExprProfilesPopup
link to global instance
popupName - Variable in class ShowPlotPopup
ARG: popup name for PopupRegistry
popupName - Variable in class ShowSpreadsheetPopup
ARG: for PopupRegistry
popupName - Variable in class ShowStringPopup
ARG: name for PopupRegistry
PopupOrderedCondChooser - class PopupOrderedCondChooser.
Class PopupOrderedCondChooser - GUI to allow users to create Ordered Condition Lists (OCL), assign conditions, define parameters for OCLs and save within MAExplorer to be used in reports/plots etc.
PopupOrderedCondChooser.ChoiceList - class PopupOrderedCondChooser.ChoiceList.
Class ChoiceList Allows user to pick an item in a list of items
PopupOrderedCondChooser.ChoiceList(PopupOrderedCondChooser, Frame, String, String[], int, String, PopupOrderedCondChooser) - Constructor for class PopupOrderedCondChooser.ChoiceList
ChoiceList() - Constructor
PopupOrderedCondChooser.CondDialogBox - class PopupOrderedCondChooser.CondDialogBox.
Class CondDialogBox is a dialog box with with two buttons yesMsg and noMsg that will return true or false when pressed.
PopupOrderedCondChooser.CondDialogBox(PopupOrderedCondChooser, Frame, String, String, String) - Constructor for class PopupOrderedCondChooser.CondDialogBox
CondDialogBox() - Constructor
PopupOrderedCondChooser.CondParamEditForm - class PopupOrderedCondChooser.CondParamEditForm.
Class CondParamEditForm creates a ScrollPane of the (name,value) parameters for the current condition instance.
PopupOrderedCondChooser.CondParamEditForm(PopupOrderedCondChooser, PopupOrderedCondChooser, PopupOrderedCondChooser.OclListData, PopupOrderedCondChooser.CondParamEditForm) - Constructor for class PopupOrderedCondChooser.CondParamEditForm
CondParamEditForm() - Constructor for parameter (name[],value[]) data.
PopupOrderedCondChooser.OclListData - class PopupOrderedCondChooser.OclListData.
Class OclListData contains the active remainder and selected cond data for a ordered condition instance.
PopupOrderedCondChooser.OclListData(PopupOrderedCondChooser, String, int, int, String[], String[]) - Constructor for class PopupOrderedCondChooser.OclListData
OclListData() - Constructor
PopupOrderedCondChooser.PopupTextField - class PopupOrderedCondChooser.PopupTextField.
Class PopupTextField is a simple "editor" for entering a string value.
PopupOrderedCondChooser.PopupTextField(PopupOrderedCondChooser, Frame, String, PopupOrderedCondChooser, String) - Constructor for class PopupOrderedCondChooser.PopupTextField
PopupTextField() - Constructor
PopupOrderedCondChooser(MaeJavaAPI, PopupOrderedCondChooser) - Constructor for class PopupOrderedCondChooser
PopupOrderedCondChooser() - Constructor
PopupOrderedCondChooserGUI - class PopupOrderedCondChooserGUI.
The PopupOrderedCondChooserGUI class is a popup class for creating ordered condition chooser GUIs.
PopupOrderedCondChooserGUI.MouseEventHandler - class PopupOrderedCondChooserGUI.MouseEventHandler.
 
PopupOrderedCondChooserGUI.MouseEventHandler(PopupOrderedCondChooserGUI, PopupOrderedCondChooserGUI, TextArea, String[], int) - Constructor for class PopupOrderedCondChooserGUI.MouseEventHandler
MouseEventHandler() - constructor
PopupOrderedCondChooserGUI.MouseEventHandler(PopupOrderedCondChooserGUI, TextArea) - Constructor for class PopupOrderedCondChooserGUI.MouseEventHandler
MouseEventHandler() - constructor
PopupOrderedCondChooserGUI(PopupOrderedCondChooser, PopupOrderedCondChooserGUI, int, int, int, Font, Font, Font, Font, Object, boolean) - Constructor for class PopupOrderedCondChooserGUI
PopupOrderedCondChooserGUI() - constructor for base class of Chooser GUI
PopupPlugin - class MAEPlugin.popup.PopupPlugin.
This class is used for creating popup plugins.
PopupPlugin() - Constructor for class MAEPlugin.popup.PopupPlugin
PopupPlugin() - Constructor to create new PopupPlugin.
PopupPlugin(String) - Constructor for class MAEPlugin.popup.PopupPlugin
PopupPlugin() - Constructor to create new PopupPlugin.
PopupProjDirGuesser - class PopupProjDirGuesser.
The PopupProjDirGuesser class creates a popup project directory entry guesser.
PopupProjDirGuesser(MAExplorer, char, Font, Table) - Constructor for class PopupProjDirGuesser
PopupProjDirGuesser() - constructor for project director guesser which assumes the HP menu item list is already sorted when it is created during MAExplorer initialization.
popupPropertyBits - Variable in class Report
ARG: property bits for PopupRegistry
popupPropertyBits - Variable in class ShowExprProfilesPopup
ARG: for PopupRegistry
popupPropertyBits - Variable in class ShowPlotPopup
ARG: property bius for PopupRegistry
popupPropertyBits - Variable in class ShowSpreadsheetPopup
ARG: for PopupRegistry
popupPropertyBits - Variable in class ShowStringPopup
ARG: property bits of window for PopupRegistry
PopupRegistry - class PopupRegistry.
The PopupRegistry class implements a call-back mechanism for active popup windows It is also usable for any other objects that impelement MaeEventListeners that are dynamicaly created and need to be notified of state changes.
PopupRegistry(MAExplorer) - Constructor for class PopupRegistry
PopupRegistry() - constructor to popup registry
PopupScrollableSelector - class PopupScrollableSelector.
 
PopupScrollableSelector(MAExplorer, Frame, String, String[], boolean[], int) - Constructor for class PopupScrollableSelector
PopupScrollableSelector() - popup selector to select boolean values.
popupTextReport(String, int, int, String, String, int, int, String, int, String) - Method in class MJAreport
popupTextReport() - popup a report window with a scrollable text area
popupViewer(URL, String, String) - Method in class MJAutil
popupViewer() - popup web browser on current URL.
popupViewer(URL, String, String) - Method in class Util
popupViewer() - popup a web browser for the help HTML file.
positionX - Variable in class SSspreadPanel
ULHC base address starting at (1,1)
positionX - Variable in class SSstatusBar
 
positionY - Variable in class SSspreadPanel
ULHC base address starting at (1,1)
positionY - Variable in class SSstatusBar
 
posQuantDataCL - Variable in class Filter
"Filter by Positive Quant Data"
posQuantTestMode - Variable in class MAExplorer
positive Quant data test mode: SS_MODE_xxxx
pPDg - Variable in class Guesser
parent class instance if it is not null
PREFERRED_PANEL_HEIGHT - Variable in class StateScrollers
max width size of state scroller panel
PREFERRED_PANEL_WIDTH - Variable in class StateScrollers
max height size of state scroller panel
preferredHeight - Variable in class ArrayScroller
height of panel
preferredHeight - Variable in class ClusterGramCanvas
preferred height size of entire canvas
preferredHeight - Variable in class Draw2Dplot
preferred canvas height
preferredHeight - Variable in class StatusCanvas
 
preferredHeight - Variable in class DrawHistogram
preferred canvas height
preferredHeight - Variable in class DrawRatioHistogram
 
preferredHeight - Variable in class ExprProfileCanvas
preferred canvas height size
preferredHeight - Variable in class ExprProfilePopup
prefered height canvas size, 0 to use defaults
preferredHeight - Variable in class PopupCondChooser
preferred height size of frame
preferredHeight - Variable in class PopupOrderedCondChooser
preferred height size of frame
preferredHeight - Variable in class RtestBase
preferred height size of frame
preferredHeight - Variable in class PopupEditRscript
preferred height size of frame
preferredHeight - Variable in class ScrollableImageCanvas
 
preferredWidth - Variable in class ArrayScroller
width of panel
preferredWidth - Variable in class ClusterGramCanvas
preferred width size of entire canvas
preferredWidth - Variable in class Draw2Dplot
preferred canvas width
preferredWidth - Variable in class StatusCanvas
 
preferredWidth - Variable in class DrawHistogram
preferred canvas width
preferredWidth - Variable in class DrawRatioHistogram
 
preferredWidth - Variable in class ExprProfileCanvas
preferred canvas width size
preferredWidth - Variable in class ExprProfilePopup
prefered width canvas size, 0 to use defaults
preferredWidth - Variable in class PopupCondChooser
preferred width size of frame
preferredWidth - Variable in class PopupOrderedCondChooser
preferred width size of frame
preferredWidth - Variable in class RtestBase
preferred width size of frame
preferredWidth - Variable in class PopupEditRscript
preferred width size of frame
preferredWidth - Variable in class ScrollableImageCanvas
 
prepCols - Variable in class ShowSpreadsheetPopup
# cols in prepData table
prepCols - Variable in class SpreadSheet
original # prep columns for prepDataOrig[0:prepRows-1][0:prepCols-1] sizes w/ 2 extra col & 2 extra rows.
prepCols - Variable in class SSspreadPanel
ARG: user data size
prepData - Variable in class ShowSpreadsheetPopup
displayed data [0:prepRows-1][0:prepCols-1]
prepDataEdit - Variable in class SSspreadPanel
"virt.
prepDataEdit - Variable in class SSstatusBar
 
prepDataOrig - Variable in class SpreadSheet
ARG:orig.
prepDataOrig - Variable in class SSspreadPanel
ARG orig.
prepForFileURL(String) - Static method in class Util
prepForFileURL() - map "\" to "/" chars in string to use for URL
prepHdrPos - Variable in class ShowSpreadsheetPopup
location of col clicked in prepData
prepRows - Variable in class ShowSpreadsheetPopup
# rows in prepData table
prepRows - Variable in class SpreadSheet
original # prep rows for prepDataOrig[0:prepRows-1][0:prepCols-1] sizes w/ 2 extra col & 2 extra rows.
prepRows - Variable in class SSspreadPanel
ARG: user data size
presentViewFlag - Variable in class MAExplorer
Flag: use larger fonts, thicker lines, circles, plus, etc.
preSortLists(MAExplorer) - Static method in class PopupGeneGuesser
preSortLists() - presort lists of Gene_Name and Master_ID for Guesser It copies the Gene data into the working geneNameList[] and the masterIDList[] with sizes geneNameListSize, masterIDListSize .
prevBestMID - Variable in class DrawScatterPlot
MID closest to point click on
prevBestMID - Variable in class ExprProfileOverlay
save previous MID found with mouse
prevButton - Variable in class PopupEditRscript
"Prev" wizard button
prevCPEFidx - Variable in class PopupCondChooser
previous CondParamEditForm index
prevCPEFidx - Variable in class PopupOrderedCondChooser
previous CondParamEditForm index
previousOldContent - Variable in class SSstatusBar
 
previousSearchIndex - Variable in class KeyEventHandler
 
previousStartupState - Variable in class MAExplorer
Flag that indicates if the startup .mae file exists in PREVIOUS database
prevMethod - Static variable in class ClusterGenes
previous clustering method.
prevObjMID - Variable in class PopupRegistry
previous MID object used to see if switched current gene object
PRINT_MEM_TIMES - Static variable in class MAExplorer
print memory times at key places
printChooserState(String) - Method in class PopupHPChooser
printChooserState() - print chooser state data.
printCurrentMemoryUsage(String) - Static method in class Util
printCurrentMemoryUsage() - print: %free, total memory usage and timeOfday
printDistanceMatrix() - Method in class HierClustNode
printDistanceMatrix() - pretty print the distance matrix for debugging
prjListFile - Static variable in class MAExplorer
Standalone Sample DB project list DB file
prjListPanel - Variable in class ChooserGUI
project prj ta
prjListPanel - Variable in class PopupCondChooserGUI
project prj ta
prjListPanel - Variable in class PopupOrderedCondChooserGUI
project prj ta
prjName - Variable in class MaHybridSample
project this HP sample belongs to
prjTbl - Variable in class PopupProjDirGuesser
"Project-Name Project-Dir" table
probeJ - Variable in class StageNames
index for probeNames[]
probeNames - Variable in class StageNames
List unique probe name entries for various entities in Samples tbl
probKS - Static variable in class MathMAE
RTN: probability of null hypoth same distrib
processActionEventByName(String, String[]) - Static method in class EventMenu
processActionEventByName() - process Menu item events only...
processBits - Variable in class RLO
Process Bits is a bit pattern of selected (R_PB_xxxx) options used during processing
processBits - Variable in class RgenDemo
Data processing bits: RB_PB_xxxx
processBits - Variable in class PopupEditRscript
Process Bits is a bit pattern of selected (R_PB_xxxx) options used during processing
processCBbits - Variable in class PopupEditRscript
Process checkbox processBits [0:nProcessCB-1] from R_PB_xxxx.
processCBname - Variable in class PopupEditRscript
Process checkbox names [0:nProcessCB-1]
processCheckbox - Variable in class PopupEditRscript
Process bits checkboxes [0:nProcessCB-1]
processCheckboxMenuItemStateChangedByitem(CheckboxMenuItem, String) - Static method in class EventMenu
processCheckboxMenuItemStateChangedByitem() - process CheckboxMenuItem state changed events by item.
processCheckboxStateChangedByItem(Checkbox, String) - Static method in class EventMenu
processCheckboxStateChangedByItem() - handle checkbox menu item state changed events.
processEditCommand(int) - Method in class EditedGeneList
processEditCommand() - do an 'edited gene list' add/remove command:
processRLO(String) - Static method in class EventMenu
processRLO() - process the "RLO:RscriptName" actions to invoke the R script
processSetHP(String) - Static method in class EventMenu
processSetHP() - process the "HP_xxx:sample" actions to modify the HP-X, HP-Y, and HP-E lists and current sample.
projDirGuesser - Variable in class MenuBarFrame
Project Guesser: create when needed
projDirGuesserIsPoppedUp - Variable in class MenuBarFrame
if guesser was popped up
projDirItemList - Static variable in class PopupProjDirGuesser
unsorted projDir names list, is G.C.'ed
projDirListSize - Static variable in class PopupProjDirGuesser
size of unsorted list of proj Dir entries
projDirPathItemList - Static variable in class PopupProjDirGuesser
unsorted projDir cmd list, is G.C.'ed
projDirToUpdateFromGuesser - Variable in class MenuBarFrame
prj dir result set in event handler
PROLOGUE_END - Static variable in class RtestBase
fixed prologue end string
PROLOGUE_END - Static variable in class PopupEditRscript
fixed prologue end string
PROLOGUE_START - Static variable in class RtestBase
fixed prologue start string
PROLOGUE_START - Static variable in class PopupEditRscript
fixed prologue start string
promptDir - Static variable in class EventMenu
last prompted directory for popup dialog
promptDir - Variable in class RevalBase
directory used with popup file browser
promptExt - Static variable in class EventMenu
for FilenameFilter file extension for popup dialog
promptExt - Variable in class RevalBase
file extension used with popup file browser
promptFile - Static variable in class EventMenu
last prompted file for popup dialog
promptFile - Variable in class RevalBase
file name used with popup file browser
promptFileName(String, String, String, String, String, boolean, boolean) - Static method in class EventMenu
promptFileName() - dialog prompt for file name.
promptFileName(String, String, String, String, String, boolean, boolean) - Method in class RevalBase
promptFileName() - dialog prompt for file name.
promptProject - Static variable in class EventMenu
last prompted project for popup dialog
promptSaveAsMaeDB(boolean, boolean) - Static method in class EventMenu
promptSaveAsMaeDB() - prompt SaveAs current .mae DB Optionally:
properties - Variable in class Gene
properties of the gene defined by one or more C_xxxx bits
propertySupport - Variable in class MAEPlugin.MAEPlugin
bean property for future use
propList - Variable in class Draw2Dplot
property of data to draw
propList - Variable in class ExprProfileOverlay
[nGenes*nHP_E] EP overlay props
propList - Variable in class ExprProfileScrollPane
[nGenes*nHP_E] EP overlay props
proxyServer - Variable in class MAExplorer
base addr PARAM "proxyServer"
PRPROP_CUR_GENE - Static variable in class MJAbase
Property bit type: Notify bit if CurGene changed
PRPROP_FILTER - Static variable in class MJAbase
Property bit type: Notify bit if Filter changed
PRPROP_LABEL - Static variable in class MJAbase
Property bit type: Notify bit if Labels changed
PRPROP_SLIDER - Static variable in class MJAbase
Property bit type: Notify bit if Slider changed
PRPROP_TIMEOUT - Static variable in class MJAbase
Property bit type: set if timeout and kill itself after TIMEOUT_DELAY milliseconds
PRPROP_UNIQUE - Static variable in class MJAbase
Property bit type: set if this is a unique popup
ps - Variable in class MenuBarFrame
holds above chkboxes & scrollbar panels
PSEUDOIMG_HEIGHT - Static variable in class MAExplorer
(600x900) size of pseudoarray image canvas
PSEUDOIMG_WIDTH - Static variable in class MAExplorer
(600x900) size of pseudoarray image canvas
psFile - Variable in class RgenDemo
Current Postscript file for current RLO, if specified
pT - Variable in class Statistics
CALC: t-test p-value w/NULL hypoth set by calcTandPvalues()
pur - Static variable in class EventMenu
link to global PopupRegistry instance
pur - Variable in class MAExplorer
Global instance of holds popup registry of all active popup windows and update handlers.
pur - Static variable in class MJAbase
link to global PopupRegistry instance
pur - Static variable in class MaeJavaAPI
link to global PopupRegistry instance
Putbyte(byte, FileOutputStream) - Method in class WriteGifEncoder
Putbyte() - Write out a byte to the GIF file
Putword(int, FileOutputStream) - Method in class WriteGifEncoder
Putword() - Write out a word to the GIF file
pValue - Variable in class Gene
optional computed p-value if doing statistical test
pValueThr - Variable in class Config
Threshold PARAM: p-value threshold for t-test Filter
pValueThreshold - Variable in class RgenDemo
 
pWidth - Variable in class MAExplorer
working size of pseudoarray image

Q

qualCheckIdx - Variable in class GipoTable
index for "QualCheck" - NIA
qualChkQ - Variable in class MaHybridSample
(opt) list of spot specific quality check using Gene.XXX properties for all spots
qualThr - Variable in class Config
Threshold PARAM: "qualThr" continuous QualCheck threshold
QUALTYPE_ALPHA - Static variable in class MAExplorer
QualCheck type: Alphabetic codes
QUALTYPE_ALPHA - Static variable in class MJAbase
QualCheck type: Alphabetic codes
QUALTYPE_PROP_CODE - Static variable in class MAExplorer
QualCheck type: uses MAE Gene.xxxx prop QualCheck codes
QUALTYPE_PROP_CODE - Static variable in class MJAbase
QualCheck type: uses MAE Gene.xxxx prop QualCheck codes
QUALTYPE_THR - Static variable in class MAExplorer
QualCheck type: Uses [qualThr] QualCheck continuous data
QUALTYPE_THR - Static variable in class MJAbase
QualCheck type: Uses [qualThr] QualCheck continuous data
qualTypeMode - Variable in class MAExplorer
spot quality type mode: QUALTYPE_xxxx
quantFileExt - Variable in class Config
PARAM "quantFileExt" i.e.
quickSort(int[], int, int) - Method in class MJAsort
quickSort() - sort the int list data[].
quickSort(int[], int, int) - Static method in class SortMAE
quickSort() - sort the int[] array.
quickSort(int[], int, int) - Method in class MedianCut
quickSort() - sort the map Based on the QuickSort method by James Gosling from Sun's SortDemo applet
quickSort(String[], int, int) - Method in class MJAsort
quickSort() - sort the String list data[].
quickSort(String[], int, int) - Static method in class SortMAE
quickSort() - sort the String[] array.
quickSortMultLists(String[], String[], int, int) - Method in class MJAsort
quickSortMultLists() - sort parallel lists (data[], data[UC[]) by dataUC[].
quickSortMultLists(String[], String[], int, int) - Static method in class SortMAE
quickSortMultLists() - sort String lists (a[], a[UC[]) by aUC[].
quickSortMultLists(String[], String[], String[], int, int) - Method in class MJAsort
quickSortMultLists() - sort parallel lists (a[], b[], aUC[]) by aUC[].
quickSortMultLists(String[], String[], String[], int, int) - Static method in class SortMAE
quickSortMultLists() - sort String lists (a[], b[], aUC[]) by aUC[].
quit() - Method in class ChooserGUI
quit() - kill this window
quit() - Method in class ExprProfilePopup
quit() - dispose of this object
quit() - Method in class MAExplorer
quit() - kill this application or Applet
quit() - Method in class PopupCondChooserGUI
quit() - kill this window
quit() - Method in class PopupOrderedCondChooserGUI
quit() - kill this window
quit() - Method in class PopupScrollableSelector
quit() - kill this frame
quoteRunPathFlag - Static variable in class RevalBase
If the flag is set then add "\ ...\" around exec program "\"" + RbinBasePath + ("Rterm" or "splus") + "\"" BEFORE exec

R

r - Variable in class GridCoords
row #
r - Variable in class WriteGifEncoder
 
R_GENR_ANOVA - Static variable in class RgenDemo
Generate R script bit: add anova() to generated R script
R_GENR_BOXPLOT - Static variable in class RgenDemo
Generate R script bit: add boxplot() plot to generated R script
R_GENR_COR - Static variable in class RgenDemo
Generate R script bit: add cor() to generated R script
R_GENR_DEMO - Static variable in class RgenDemo
Generate R script bit: This defines the RLO as a Demonstration script
R_GENR_DENSITY - Static variable in class RgenDemo
Generate R script bit: add density() plot to generated R script
R_GENR_HIST - Static variable in class RgenDemo
Generate R script bit: add hist() plot to generated R script
R_GENR_LOESS - Static variable in class RgenDemo
Generate R script bit: add loess(x,y) to generated R script
R_GENR_PLOT - Static variable in class RgenDemo
Generate R script bit: add plot(samples table) plot to generated R script
R_GENR_PSEUDO_DATA - Static variable in class RgenDemo
Generate R script bit: Generate pseudo data
R_GENR_SUMMARY - Static variable in class RgenDemo
Generate R script bit: add summary() to generated R script
R_GENR_TTEST - Static variable in class RgenDemo
Generate R script bit: add ttest() to generated R script
r1 - Variable in class MAExplorer
PARAM "R1" MIN_RATIO range (HP-X/HP-Y)
r2 - Variable in class MAExplorer
PARAM "R2" MAX_RATIO range
r2ClientActionChoice - Variable in class PopupEditRscript
R2Client action Choices [0:MAX_WIZ_CHOICES-1]
r2ClientActionChoiceNames - Variable in class PopupEditRscript
R2Client action Choice names [0:nr2ClientActions-1]
r2ClientActionMenu - Static variable in class RevalBase
R2Client actions menu entries
r2ClientActionName - Static variable in class RevalBase
R2Client actions names
r2ClientActionVal - Static variable in class RevalBase
 
r2ClientFileNames - Variable in class RgenDemo
Output Action file names [0:nR2Client-1] if any
r2ClientObjNames - Variable in class RgenDemo
Output Action Object names [0:nR2Client-1] if any
r2ClientObjTypes - Variable in class RgenDemo
Output Action Object type [0:nR2Client-1] if any
r2ClientPrefix - Variable in class RevalBase
Name of the R2Client prefix
R2ClientTypesChoiceValues - Variable in class PopupEditRscript
R2Client action Choice values [0:nr2ClientActions-1]
RANGE_INSIDE - Static variable in class MAExplorer
rangeMode: Inside [v1:v2] for testing
RANGE_INSIDE - Static variable in class MJAbase
rangeMode: Inside [v1:v2] for testing
RANGE_OUTSIDE - Static variable in class MAExplorer
rangeMode: Outsiide [v1:v2] for testing
RANGE_OUTSIDE - Static variable in class MJAbase
rangeMode: Outsiide [v1:v2] for testing
rangeInc - Variable in class DrawPseudoImage
PseudoArray image color range increment
ratioColor - Variable in class ClusterGramCanvas
used for color mapping
ratioColor - Variable in class DrawPseudoImage
color table used for PseudoArray image color mapping
ratioCy3Cy5FilterFlag - Variable in class MAExplorer
filter genes by Cy3/Cy5 ratio threshold
ratioCy3Cy5RangeMode - Variable in class MAExplorer
Cy3/Cy5 range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE
ratioCy3Cy5ThrCL - Variable in class Filter
"Threshold: ratio [CR1:CR2]"
ratioFilterFlag - Variable in class MAExplorer
filter genes by ratio threshold
ratioHist - Variable in class CompositeDatabase
histogram of g1/g2 ratios [0:nRatioHistBins] in range 0.01:100.0
ratioHistCL - Variable in class Filter
"Ratio histogram selected genes"
RatioHP - Variable in class Config
HP to use for normalization
ratioLower - Variable in class DrawRatioHistogram
lower range of histogram values
ratioMedianBkgdScale - Variable in class MaHybridSample
may be set if Cy3/Cy5 median bkgrd scale correction
ratioMedianCorrectionFlag - Variable in class MAExplorer
enable cy3/cy5 ratio median correction
ratioMedianScale - Variable in class MaHybridSample
may be set if Cy3/Cy5 median scale correction.
ratioRange - Variable in class ClusterGramCanvas
used for color mapping
ratioRange - Variable in class DrawPseudoImage
ratio range for values used in PseudoArray image color mapping
ratioRangeMode - Variable in class MAExplorer
Ratio range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE
ratioThrCL - Variable in class Filter
"Threshold: ratio [R1:R2]"
ratioUpper - Variable in class DrawRatioHistogram
upper range of histogram values
ratioValue - Variable in class CompositeDatabase
scale of ratio histogram of g1/g2 ratios
RbasePath - Static variable in class RevalBase
base Path to R executable e.g.
RbinBasePath - Static variable in class RevalBase
base bin Path to R executable if it exists.
rDataTypeMenu - Static variable in class RevalBase
client export data file types menu entries for import to R
rDataTypeName - Static variable in class RevalBase
client export data file types names for import to R
rDataTypeVal - Static variable in class RevalBase
client export data file types values for import to R
readBytesFromURL(String, String) - Method in class FileIO
readBytesFromURL() - read binary data from URL
readData(String, String) - Method in class FileIO
readData() - read data from URL or local file depending on prefix.
readFileFromDisk(String) - Method in class FileIO
readFileFromDisk() - read file from disk and return entire file as String
readFileFromUrl(String, boolean) - Method in class FileIO
readFileFromUrl() - read data from http:// URL, using JavaCGIBridge.
readGeneClassCloneIDGeneNameGeneClassFile() - Method in class GeneClass
readGeneClassCloneIDGeneNameGeneClassFile() - build table data Read data from mae.geneIdNameClassFile.
readGeneClassTableFile() - Method in class GeneClass
readGeneClassTableFile() - read mae.geneClassNamesFile into database If the file is not available, then use the default data in this Class.
readHPquantFile(int) - Method in class MaHybridSample
readHPquantFile() - read the hybridized sample Quant File.
readListOfSampleDataFiles() - Method in class MAExplorer
readListOfSampleDataFiles() - populate msList[1:nHP] data structures by reading the data files up to maxPreloadImgs.
readListOfSampleNames() - Method in class SamplesTable
readListOfSampleNames() - get list of Sample (i.e.
readMAEstartupFile(String, String) - Method in class UserState
readMAEstartupFile() - read the .mae startup database File.
readPARAMvalues(String) - Method in class Config
readPARAMvalues() - read applet PARAM values overiding configuration file.
readPermanentRLOdatabase(boolean) - Method in class MJAReval
readPermanentRLOdatabase() - read RLO entries from the permanent /RLO/ database.
readPermanentRLOdatabase(boolean) - Method in class RevalBase
readPermanentRLOdatabase() - read RLO entries from the permanent /RLO/*.rlo file database.
readPluginHashState() - Method in class MJAstate
readPluginHashState() - read the MAEPlugin hash state storage from the disk.
readRLOfile(String, boolean) - Method in class MJAReval
readRLOfile() - read RLO by .rlo file name into a new RLO (rloID).
readRLOfile(String, boolean) - Method in class RevalBase
readRLOfile() - read RLO by .rlo file name into a new RLO (rloID).
readStateFile(String, String, String) - Method in class UserState
readStateFile() - read the protected user State File [FUTURE] see writeStateFile() to see what have to read.
readTable(String, String) - Method in class Table
readTable() - read a tab-delimited table from FILE/URL.
readTextFromFile(String) - Method in class MJAreport
readTextFromFile() - read text from text file.
readTextFromFile(String, String) - Method in class Reval
readTextFromFile() - read text from text file.
readTextFromFile(String, String) - Method in class RevalBase
readTextFromFile() - read text from text file.
readTextFromFile(String, String) - Method in class Rtest
readTextFromFile() - read text from text file.
readTextFromFile(String, String) - Method in class RtestBase
readTextFromFile() - read text from text file.
readUserGeneSet(String, String) - Method in class UserState
readUserGeneSet() - read user gene bit set by file name and save it as a named gene set.
readUserGeneSetUPW(String, String, int) - Static method in class UserState
readUserGeneSetUPW() - read user gene bit set by set number [FUTURE]
readUserHPlist(String, String) - Method in class UserState
readUserHPlist() - read user sample HP list by file name and save it as a named HP list.
readUserOCLlist(String, String) - Method in class UserState
readUserOCLlist() - read user OCL list by file name and save it as a named OCL list.
readZipFileFromDisk(String, String) - Method in class FileIO
readZipFileFromDisk() - [TODO] read Zip file from disk and return it as a String.
reassignKmeansNodes() - Method in class ClusterGenes
reassignKmeansNodes() - reassign nodes based on closest to new mean clusters.
REB_DBUG - Static variable in class RevalBase
DEBUG flag for RevalBase
rebuildScriptChoices() - Method in class RtestBase
rebuildScriptChoices() - rebuild the R script choices pull-down menu from the menuNames[] data.
rebuildWizardPanel(int) - Method in class PopupEditRscript
rebuildWizardPanel() - rebuild Wizard elements and the new wizardLabel in the wizardPanel.
recalcGlobalStats(boolean) - Method in class CompositeDatabase
recalcGlobalStats() - recompute global array statistics with all or just good spots.
recalcGlobalStats(boolean) - Method in class MaHybridSample
recalcGlobalStats() - recalculate global array statistics for all or just Good Spots.
recalcNormalizationExtrema() - Method in class GenNormalizationPlugin
recalcNormalizationExtrema() - set the extrema for all samples for this plugin.
recalcNormalizationExtrema() - Method in interface MAEPlugin.Normalization
recalcNormalizationExtrema() - set the extreama for all samples for this plugin
recalcNormalizationExtrema() - Method in class MAEPlugin.analysis.NormalizationPlugin
recalcNormalizationExtrema() - set the extreama for all samples for this plugin
recalcNorms(String, boolean) - Method in class CompositeDatabase
recalcNorms() - recompute normalizations for all samples in the hps.msList[].
recalcNorms(String, boolean) - Method in class MJAnormalization
recalcNorms() - recalculate normalizations of all samples
recalcNorms(String, boolean) - Method in class MaeJavaAPI
recalcNorms() - recalculate normalizations of all samples
recalcNorms(String, boolean) - Method in interface MAEPlugin.MAEStub
recalcNorms() - alias to: mae.cdb.recalcNorms(String, boolean); used by: NormalizationPlugin
recreateScollableCanvas(int, int) - Method in class ArrayScroller
recreateScollableCanvas() - Resize canvas with new size by making a new ScrollableImageCanvas.
recursionFlag - Variable in class CompositeDatabase
flag: track last updated object to avoid recursion problems
recv(InputStream) - Static method in class JavaCGIBridge
recv() - helper routine to read a \n-terminated string from input stream.
redBits(int) - Method in class MedianCut
redBits() - Get 8-bit red component of a 15-bit color 8-bit pixel with low 3 bits zero.
redoMenuBar() - Method in class MenuBarFrame
redoMenuBar() - redo the menubar if restarted a new database with different entries.
reFilterHistButton - Variable in class ShowPlotPopup
reFilterHist/NoreFilterHist button
reFilterHistFlag - Variable in class ShowPlotPopup
flag: toggle with reFilterHist/NoreFilterHist button
refreshDataFilter() - Method in class MJAfilter
refreshDataFilter() - regenerate scrollers, refresh the data filter and repaint
refreshDataFilter() - Method in class MaeJavaAPI
refreshDataFilter() - regenerate scrollers, refresh the data filter and repaint
refreshDataFilter() - Method in interface MAEPlugin.MAEStub
refreshDataFilter() - refresh the datsa filter
refreshLists() - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
refreshLists() - called whenever the state of laded plugins needs to be refreshed.
RefSeqID - Variable in class Gene
NCBI RefSeq ID if it exists
RefSeqIdIdx - Variable in class GipoTable
index for "RefSeq" ID
regenerateScrollers(boolean) - Method in class MJAfilter
regenerateScrollers() - regenerate the state scroller window
regenerateScrollers(boolean) - Method in class StateScrollers
regenerateScrollers() - regenerate scroller window
registry - Static variable in class MAEPlugin.MAEPlugin
Instance registry for all sub classes of MAEPLugin Works with constructors() and dispose() to maintain a database of all plugins
registryMaxSize - Static variable in class MAEPlugin.MAEPlugin
Set the initial and max size for the number of resgistry entries
regrowRLOdbIfNeeded() - Method in class RLO
regrowRLOdbIfNeeded() - grow RLO database if need more space
relWizardNbr - Variable in class PopupEditRscript
relative index through either fullWizardList[] or demoWizardList[] to then access wizardNames[].
remainderMeh - Variable in class PopupCondChooserGUI
handle mouse events for text areas for remTextArea LEFT
remainderMeh - Variable in class PopupOrderedCondChooserGUI
handle mouse events for text areas for remTextArea LEFT
remCond - Variable in class PopupOrderedCondChooser.OclListData
list of remainder conditions
remCondTmp - Variable in class PopupOrderedCondChooser
remaining conditions before edit
remLabelName - Variable in class PopupCondChooserGUI
label for SELECTED LEFT text area
remLabelName - Variable in class PopupOrderedCondChooserGUI
label for SELECTED LEFT text area
remObjList - Variable in class ChooserGUI
REMAINDER list, returned if needed
remObjList - Variable in class PopupCondChooserGUI
REMAINDER list of sample objects, returned if needed
remObjList - Variable in class PopupOrderedCondChooserGUI
REMAINDER list of cond objects, returned if needed
remObjListSize - Variable in class ChooserGUI
REMAINDER list size
remObjListSize - Variable in class PopupCondChooserGUI
REMAINDER list size
remObjListSize - Variable in class PopupOrderedCondChooserGUI
REMAINDER list size
remoteFlag - Variable in class ChooserGUI
true if using other prj data/ta
remoteFlag - Variable in class PopupCondChooserGUI
true if using other prj data/ta
remoteFlag - Variable in class PopupOrderedCondChooserGUI
true if using other prj data/ta
remove(String) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
 
removeActiveFilter(FilterPlugin) - Method in class MAEPlugin.analysis.FilterPlugin
removeActiveFilter() - Bean-style method for removing from activeFilterPluginList.
removeAllCondsFromOrderedCondList(String) - Method in class MJAcondition
removeAllCondsFromOrderedCondList() - Remove all conditions from condList
removeAllSamplesFromCondList(String) - Method in class MJAcondition
removeAllSamplesFromCondList() - Remove all samples from cond list.
removeButton - Variable in class PopupCondChooser.ChoiceList
remove
removeButton - Variable in class PopupOrderedCondChooser.ChoiceList
remove
removeCondButton - Variable in class PopupCondChooser
remove condition
removeConditionLocally() - Method in class PopupCondChooser
removeConditionLocally() - remove user specified condition locally.
removeCondList(String) - Method in class MJAcondition
removeCondList() - remove named condition list if it exists and also remove it from any ordered condition lists it may appear in.
removeFlag - Variable in class PopupCondChooser.ChoiceList
if selection went ok
removeFlag - Variable in class PopupOrderedCondChooser.ChoiceList
if selection went ok
removeGeneFromEditedCL(Gene) - Method in class EditedGeneList
removeGeneFromEditedCL() - remove gene from the editedCL by gene.
removeGeneFromEditedCL(int) - Method in class EditedGeneList
removeGeneFromEditedCL() - remove gene from the editedCL by mid.
removeGeneFromGeneBitset(String, int) - Method in class MJAgeneList
removeGeneFromGeneBitset() - remove gene MID from Gene bitset, ignore if already there
removeGeneFromGeneList(String, int, String[]) - Method in class MJAgeneList
removeGeneFromGeneList() - remove gene MID from GeneList, ignore if not there
removeLocalParameter() - Method in class PopupCondChooser
removeLocalParameter() - remove parameter locally for all conditions
removeLocalParameter() - Method in class PopupOrderedCondChooser
removeLocalParameter() - remove parameter locally for all conditions
removeMissingEntries() - Method in class MaInfoTable
removeMissingEntries() - remove missing entries if not enabled to view
removeMsg - Variable in class PopupCondChooser.ChoiceList
specific msg to be displayed about what is being removed interface parameter or condition
removeMsg - Variable in class PopupOrderedCondChooser.ChoiceList
specific msg to be displayed about what is being removed interface parameter or condition
removeNamedOrderedCondList(String) - Method in class Condition
removeNamedOrderedCondList() - remove existing named ordered list of conditions if it exists.
removeNamedOrderedCondList(String) - Method in class MJAcondition
removeNamedOrderedCondList() - remove existing named ordered list of conditions the ordered list exists.
removeOCLButton - Variable in class PopupOrderedCondChooser
remove order cond list
removeOCLLocally() - Method in class PopupOrderedCondChooser
removeOCLLocally() - remove user specified condition locally.
removeOverlayMap(String) - Static method in class MJAplot
removeOverlayMap() - remove named scatterplot overlay map.
removeOverlayMap(String) - Static method in class OverlayMap
removeOverlayMap() - remove named scatterplot overlay map.
removePlugin(MAEPlugin) - Static method in class MAEPlugin.MAEPlugin
removePlugin () - unloads plugin and removes it from the MAexplorer menu.
removePluginMenu(MenuItem) - Method in class MaeJavaAPI
removePluginMenu() - remove plugin from the menubar.
removePluginMenu(MenuItem) - Method in interface MAEPlugin.MAEStub
remove plugin menu
removePopupByKey(String) - Method in class MJApopupRegistry
removePopupByKey() - remove instance of MAEPlugin by keyName
removePopupByKey(String) - Method in class PopupRegistry
removePopupByKey() - remove popup by unique key if existing instance
removePreviousClusterMethod(int) - Method in class ClusterGenes
removePreviousClusterMethod() - remove any popups and data structures from previous cluster method if it was active.
removeSampleFromCondList(int, String) - Method in class MJAcondition
removeSampleFromCondList() - remove sample from named condition list
removeUserBS(String) - Method in class GeneBitSet
removeUserBS() - remove user GeneBitSet by name from userBS[] database Do NOT remove the gct.nSpecialGC bit sets at the front of the list.
remSamples - Variable in class PopupCondChooser.CondData
list of remainder samples
remSamplesTmp - Variable in class PopupCondChooser
remaining sample names of condition before edit
remTextArea - Variable in class PopupCondChooserGUI
REMAINDER objs
remTextArea - Variable in class PopupOrderedCondChooserGUI
REMAINDER objs
remTextAreaLabel - Variable in class PopupCondChooserGUI
label under remTextArea
remTextAreaLabel - Variable in class PopupOrderedCondChooserGUI
label under remTextArea
remTitle - Variable in class PopupCondChooser
title of remainder samples TextArea for PopupCondChooserGUI
remTitle - Variable in class PopupOrderedCondChooser
title of remainder TextArea for PopupOrderedCondChooserGUI
renameCondList(String, String, boolean) - Method in class Condition
renameCondList() - rename conditionName if it exists to newCondName
renameCondList(String, String, boolean) - Method in class MJAcondition
renameCondList() - rename userListName if it exists to newListName.
reorderColors(int[], int, int, int) - Method in class MedianCut
reorderColors() - Change ordering of 5-bit colors in each word of int[] so we can sort on the 'longDim' color
replaceItem(List, String) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
replaceItem() -
replicateGenesCL - Variable in class GeneClass
special list of replicate genes
report - Variable in class ShowSpreadsheetPopup
Report instance to show
Report - class Report.
The class generates a popup report window for either HP sample or Gene reports.
Report(MAExplorer, String, int, int, String, int) - Constructor for class Report
Report() - constructor for Report
reportBasePath - Static variable in class RevalBase
path of {client project} Report/ directory
reportFileName - Static variable in class RevalBase
path of Text report file in Report/ if doing a "SaveAs" of TextArea
reportHierClusterTree() - Method in class ClusterGenes
reportHierClusterTree() - popup report of hierarchical clusters tree.
reportKmeansNodes() - Method in class ClusterGenes
reportKmeansNodes() - popup expression profile report of K-means nodes
reportLabel - Variable in class MenuBarFrame
report label must be global variable
reportMenu - Variable in class MenuBarFrame
"Report" menu
reportMode - Variable in class MAExplorer
Report type mode: RPT_xxxx.
reportMode - Variable in class Report
Report mode
reportRatioStr - Variable in class MAExplorer
either "F1/F2", "Cy3/Cy5", or "Cy5/Cy3"
reportText - Variable in class RtestBase
text for TextArea
reportTextArea - Variable in class RtestBase
Text area to draw reportText that is returned from performing the eval of the .R script
reRunClusterAnalysis() - Method in class StateScrollers
reRunClusterAnalysis() - rerun cluster analysis after changed state.
reRunImageOptimizer() - Method in class StateScrollers
reRunImageOptimizer() - rerun pseudoarray image optimization after changed state.
resetChooserGUI() - Method in class ChooserGUI
resetChooserGUI() - reset original data to working data, reset ta1 and ta2 text areas.
resetDefaultstate() - Method in class MAExplorer
resetDefaultstate() - Reinitialize global user state.
resetEditRLObuttons(boolean) - Method in class PopupEditRscript
resetEditRLObuttons() - enable/disable Edit Buttons.
resetEnumeration() - Method in class GeneBitSet
resetEnumeration() - reset the gene bit set eumeration count to 0
resetImageAndState() - Method in class MAExplorer
resetImageAndState() - Re initialize whenever restart
resetKeyEventHandler(String[], int) - Method in class KeyEventHandler
resetKeyEventHandler() - Reset data within KeyEventHandler.
resetMouseEventHandler(String[]) - Method in class MouseEventHandler
resetMouseEventHandler() - reset the alphaList
resetMouseEventHandler(String[], int) - Method in class ChooserGUI.MouseEventHandler
resetMouseEventHandler() - reset MouseEventHandler for text area
resetMouseEventHandler(String[], int) - Method in class PopupCondChooserGUI.MouseEventHandler
resetMouseEventHandler() - reset MouseEventHandler for text area
resetMouseEventHandler(String[], int) - Method in class PopupOrderedCondChooserGUI.MouseEventHandler
resetMouseEventHandler() - reset MouseEventHandler for text area
resetPipeline(int) - Method in class GenNormalizationPlugin
resetPipeline() - reset filter at start of data Normalization.
resetPipeline(int) - Method in interface MAEPlugin.Normalization
resetPipeline() - reset filter at start of data Normalization.
resetPipeline(int) - Method in class MAEPlugin.analysis.NormalizationPlugin
resetPipeline() - reset filter at start of data Normalization.
resetPipeline(int) - Method in class MAEPlugin.analysis.FilterPlugin
resetPipeline() - reset filter at start of test of all genes (if required).
resetPopupCondChooserGUI() - Method in class PopupCondChooserGUI
resetPopupCondChooserGUI() - reset original data to working data, reset remTextArea and selTextArea text areas.
resetPopupOrderedCondChooserGUI() - Method in class PopupOrderedCondChooserGUI
resetPopupOrderedCondChooserGUI() - reset original data to working data, reset remTextArea and selTextArea text areas.
resizeLAXfileData() - Method in class UserState
resizeLAXfileData() - resize MAExplroer.lax file data for MAExplorer.
responseCode - Variable in class JavaCGIBridge
set when return from server
responseMsg - Variable in class JavaCGIBridge
 
restoreColorOrder(int[], int, int, int) - Method in class MedianCut
restoreColorOrder() - Restore the 5-bit colors to original order
restoreCondLists() - Method in class UserState
restoreCondLists() - read user HP condition lists from stand-alone file.
restoreGeneSets() - Method in class UserState
restoreGeneSets() - read user gene bit sets from stand-alone file.
restoreUserGeneSet(int) - Static method in class UserState
restoreUserGeneSet() - restore user gene bit set by set number [FUTURE]
restoreUserGeneSetUPW(String, String, int) - Static method in class UserState
restoreUserGeneSetUPW() - restore user gene bit set by set nbr [FUTURE]
resultMode - Variable in class Guesser
what type of finish was requested: either SINGLE_GENE or MULTIPLE_GENE
resultStr - Variable in class Guesser
return user results from guesser
resultSubList - Variable in class Guesser
if passing results back as sublist
return_it - Variable in class SStextArray
 
returnItem - Variable in class PopupCondChooser.ChoiceList
return selected item when done button is pressed after remove button is pressed
returnItem - Variable in class PopupOrderedCondChooser.ChoiceList
return selected item when done button is pressed after remove button is pressed
returnListOfCondsForOCL(String) - Method in class Condition
returnListOfCondsForOCL() - return list of conditions
reuseGUIframeFlag - Variable in class MAExplorer
Flag: set if reuse main GUI frame
reuseXYcoordsFlag - Variable in class MAExplorer
Flag: reuse HP[1] Quant xy coords for speedup
rEval - Static variable in class MJAReval
Reval instance
Reval - class Reval.
Class Reval is used to evaluate R scripts with data supplied from MAExplorer via the MJAReval API.
Reval(MaeJavaAPI, int) - Constructor for class Reval
Reval() - constructor for initial database allocation
rEvalBase - Static variable in class RLO
 
RevalBase - class RevalBase.
Class RevalBase is an abstract base class used to define the base infrastructure for evaluating R scripts (using the R program) using data supplied from a client program.
RevalBase(String, String, String, int) - Constructor for class RevalBase
RevalBase() - constructor for initial database allocation
reverseSelections(List) - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
reverseSelections() -
REVISION - Static variable in class PopupCondChooser
 
REVISION - Static variable in class PopupOrderedCondChooser
 
REVISION - Static variable in class RtestBase
 
rgb - Variable in class WriteGifEncoderHashitem
 
rgb15(int) - Method in class MedianCut
rgb15() - convert from 24-bit (ignore alpha) to 15-bit color.
rgd - Variable in class RtestBase
R demo code generator
rgd - Variable in class PopupEditRscript
R demo code generator
RgenDemo - class RgenDemo.
Class RgenDemo - generate a R demo script based on the current RLO genRbits that are set.
RgenDemo(Rtest) - Constructor for class RgenDemo
RgenDemo() - Constructor
rightEdge - Variable in class ClusterGramCanvas
right edge of box array
rlo - Variable in class RevalBase
instance of the RLO database.
RLO - class RLO.
This class is used to specify the .R script LayOuts (RLO) analyses.
RLO_VERSION - Static variable in class RevalBase
current RLO version number for I/O
RLO() - Constructor for class RLO
RLO() - constructor instance to create empty RLO
RLO(RevalBase, int) - Constructor for class RLO
RLO() - constructor for initial database allocation
RLObasePath - Static variable in class RevalBase
path of {client installation} RLO/ directory
rloID - Variable in class RgenDemo
RLO to use
rloID - Variable in class PopupEditRscript
sequence # of description
rloMenuNameLabel - Variable in class PopupEditRscript
current RLO being edited
rloMenuNameMsg - Variable in class PopupEditRscript
RLO edit menuName msg
rloMenuNames - Variable in class MenuBarFrame
RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree
rloPopup - Static variable in class EventMenu
RLO report popup if it exists
rloReportLoggingFile - Variable in class RevalBase
Name of RLO Report logging by creating subdirectory {project}/Report/{RLOname}-yymmdd.hhmmss/ to store the RLO output files copied to Report/
RLORlibr - Static variable in class RevalBase
Clients R project RLORlibr/ directory lives.
rloRscriptNames - Variable in class MenuBarFrame
RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree
rloSmnu - Variable in class MenuBarFrame
Menu stub to add/modify R(Plugin | RLO methods (submenu)) menu items
rloTitleLabel - Variable in class PopupEditRscript
title label
rloTitleMsg - Variable in class PopupEditRscript
RLO edit title label msg
rLUT - Variable in class MedianCut
[0:255] Red Color map look up table
rmax - Variable in class MC_Cube
 
rmin - Variable in class MC_Cube
 
rmvAllButton - Variable in class ChooserGUI
mv ALL Selected entries to Remainder
rmvAllButton - Variable in class PopupCondChooserGUI
Move ALL Selected entries to Remainder
rmvAllButton - Variable in class PopupOrderedCondChooserGUI
Move ALL Selected entries to Remainder
rmvAllObjs() - Method in class ChooserGUI
rmvAllObjs() - move all objects from (SELECTED) ta2 to ta1 (REMAINDER).
rmvAllObjs() - Method in class PopupCondChooserGUI
rmvAllObjs() - move all objects from (SELECTED) selTextArea to remTextArea (REMAINDER).
rmvAllObjs() - Method in class PopupOrderedCondChooserGUI
rmvAllObjs() - move all objects from (SELECTED) selTextArea to remTextArea (REMAINDER).
rmvAnnButton - Variable in class PopupOrderedCondChooser
remove annotation
rmvConditionFromOrderedCondList(Condition, String) - Method in class Condition
rmvConditionFromOrderedCondList() - remove condition from named ordered condition list.
rmvConditionFromOrderedCondList(String, String) - Method in class MJAcondition
rmvConditionFromOrderedCondList() - remove condition from named ordered condition list.
rmvCondList(String, boolean, boolean) - Method in class Condition
rmvCondList() - remove conditionName from the list of Condition lists if it exists.
rmvDupIMAGEstr(String) - Method in class Util
rmvDupIMAGEstr() - remove duplicate "IMAGE:xxxx:" prefix from string.
rmvFinalSubDirectory(String, String, boolean) - Static method in class Util
rmvFinalSubDirectory() - remove trailing ".../dir/" if it exists otherwise return original string.
rmvGene(Gene) - Method in class GeneList
rmvGene() - remove Gene from gene list and bitSet.
rmvHPfromCondList(MaHybridSample) - Method in class Condition
rmvHPfromCondList() - remove Sample from condition list
rmvHPfromElist(MaHybridSample) - Method in class SampleSets
rmvHPfromElist() - remove HP sample from HP-E list
rmvHPfromXset(MaHybridSample) - Method in class SampleSets
rmvHPfromXset() - remove HP sample from HP-X set
rmvHPfromYset(MaHybridSample) - Method in class SampleSets
rmvHPfromYset() - remove HP sample from HP-Y set
rmvIMAGEstr(String) - Method in class Util
rmvIMAGEstr() - - remove "IMAGE:" prefix from string.
rmvItem(int) - Method in class GeneBitSet
rmvItem() - remove Item (i.e.
rmvParamButton - Variable in class PopupCondChooser
remove condition parameter
rmvPopupFromReg(Object, int) - Method in class PopupRegistry
rmvPopupFromReg() - remove popup from maepList[].
rmvPopupFromReg(ShowExprProfilesPopup) - Method in class PopupRegistry
rmvPopupFromReg() - remove popup from ShowExprProfilesPopup seppList[].
rmvPopupFromReg(ShowPlotPopup) - Method in class PopupRegistry
rmvPopupFromReg() - remove popup instance from ShowPlotPopup sppList[].
rmvPopupFromReg(ShowSpreadsheetPopup) - Method in class PopupRegistry
rmvPopupFromReg() - remove popup from ShowSpreadsheetPopup ssspList[].
rmvPopupFromReg(ShowStringPopup) - Method in class PopupRegistry
rmvPopupFromReg() - remove popup from ShowStringPopup ssptList[].
rmvRLO(int) - Method in class MJAReval
rmvRLO() - remove the RLO from the analyses database
rmvRLO(int) - Method in class RevalBase
rmvRLO() - remove the RLO from the analyses database
rmvRLO(int) - Method in class RLO
rmvRLO() - remove the RLO from the analyses database This removes the .rlo file from the RLO/ directory and the .R script file from the R/ directory.
rmvRtnChars(String) - Method in class MJAutil
rmvRtnChars() - remove return chars.
rmvRtnChars(String) - Static method in class RevalBase
rmvRtnChars() - remove return chars.
rmvRtnChars(String) - Method in class Rtest
rmvRtnChars() - remove return chars.
rmvRtnChars(String) - Method in class RtestBase
rmvRtnChars() - remove return chars.
rmvRtnChars(String) - Static method in class Util
rmvRtnChars() - remove return chars.
rmvScroller(String) - Method in class StateScrollers
rmvScroller() - remove a particular scroller by scroller name
rName - Variable in class Report
Report name
rOfileTypeMenu - Static variable in class RevalBase
R output file types menu entries
rOfileTypeName - Static variable in class RevalBase
R output file types names
rOfileTypeStdOut - Static variable in class RevalBase
Special StdOut Output File type needed for RevalBase class
rOfileTypeVal - Static variable in class RevalBase
R output file types values
root - Variable in class SStextArray
 
rootDummy - Variable in class SStextArray
 
rowLabel - Variable in class ClusterGramCanvas
row labels (Master_ID + MasterGeneName)
rowMID - Variable in class ClusterGramCanvas
row MID index
rows - Variable in class ShowSpreadsheetPopup
rows
rowSeparator - Variable in class JavaCGIBridge
The row separator.
rPB_useVanillaBit - Static variable in class RevalBase
Special process bit needed for RevalBase class
rProcessBitMenu - Static variable in class RevalBase
Process Bits to use Menu entries
rProcessBitName - Static variable in class RevalBase
R2Client actions names
rProcessBitVal - Static variable in class RevalBase
Process Bits to use values
RPT_FMT_DYN - Static variable in class MAExplorer
Report format mode: dynamic spreadsheet report
RPT_FMT_DYN - Static variable in class MJAbase
Report format mode: dynamic spreadsheet report
RPT_FMT_TAB_DELIM - Static variable in class MAExplorer
Report format mode: tab-delimited report as TextArea
RPT_FMT_TAB_DELIM - Static variable in class MJAbase
Report format mode: tab-delimited report as TextArea
RPT_NONE - Static variable in class MAExplorer
Report mode: no report
RPT_NONE - Static variable in class MJAbase
Report mode: no report
RPT_TBL_ALL_GENES_CLUSTER - Static variable in class MAExplorer
Report mode: all genes clustering statistics
RPT_TBL_ALL_GENES_CLUSTER - Static variable in class MJAbase
Report mode: all genes clustering statistics
RPT_TBL_CALIB_DNA_STAT - Static variable in class MAExplorer
Report mode: array samples Calibration DNA statistics
RPT_TBL_CALIB_DNA_STAT - Static variable in class MJAbase
Report mode: array samples Calibration DNA statistics
RPT_TBL_CUR_GENE_CLUSTER - Static variable in class MAExplorer
Report mode: current gene clustering statistics
RPT_TBL_CUR_GENE_CLUSTER - Static variable in class MJAbase
Report mode: current gene clustering statistics
RPT_TBL_EDITED_GENE_LIST - Static variable in class MAExplorer
Report mode: Edited Gene List
RPT_TBL_EDITED_GENE_LIST - Static variable in class MJAbase
Report mode: Edited Gene List
RPT_TBL_EXPR_PROFILE - Static variable in class MAExplorer
Report mode: expression profiles of filtered genes [CHECK]
RPT_TBL_EXPR_PROFILE - Static variable in class MJAbase
Report mode: expression profiles of filtered genes [CHECK]
RPT_TBL_FILTERED_GENES - Static variable in class MAExplorer
Report mode: data Filtered genes
RPT_TBL_FILTERED_GENES - Static variable in class MJAbase
Report mode: data Filtered genes
RPT_TBL_GENE_CLASS - Static variable in class MAExplorer
Report mode: genes in current GencClass
RPT_TBL_GENE_CLASS - Static variable in class MJAbase
Report mode: genes in current GencClass
RPT_TBL_HIER_CLUSTER - Static variable in class MAExplorer
Report mode: hierarchical clusters gene statistics
RPT_TBL_HIER_CLUSTER - Static variable in class MJAbase
Report mode: hierarchical clusters gene statistics
RPT_TBL_HIGH_F1F2 - Static variable in class MAExplorer
Report mode: highest N current HP F1/F2 ratio genes
RPT_TBL_HIGH_F1F2 - Static variable in class MJAbase
Report mode: highest N current HP F1/F2 ratio genes
RPT_TBL_HIGH_RATIO - Static variable in class MAExplorer
Report mode: highest N HP-X/HP-Y ratio genes
RPT_TBL_HIGH_RATIO - Static variable in class MJAbase
Report mode: highest N HP-X/HP-Y ratio genes
RPT_TBL_HP_DB_INFO - Static variable in class MAExplorer
Report mode: array report of extra Info samples data (DEPRICATED)
RPT_TBL_HP_DB_INFO - Static variable in class MJAbase
Report mode: array report of extra Info samples data (DEPRICATED)
RPT_TBL_HP_HP_CORR - Static variable in class MAExplorer
Report mode: HP vs HP correlation coefficient for only filtered genes
RPT_TBL_HP_HP_CORR - Static variable in class MJAbase
Report mode: HP vs HP correlation coefficient for only filtered genes
RPT_TBL_HP_MN_VAR_STAT - Static variable in class MAExplorer
Report mode: array samples mean and variance statistics
RPT_TBL_HP_MN_VAR_STAT - Static variable in class MJAbase
Report mode: array samples mean and variance statistics
RPT_TBL_HP_XY_SET_STAT - Static variable in class MAExplorer
Report mode: array samples set statistics
RPT_TBL_HP_XY_SET_STAT - Static variable in class MJAbase
Report mode: array samples set statistics
RPT_TBL_KMEANS_CLUSTER - Static variable in class MAExplorer
Report mode: K-means clustering statistics
RPT_TBL_KMEANS_CLUSTER - Static variable in class MJAbase
Report mode: K-means clustering statistics
RPT_TBL_LOW_F1F2 - Static variable in class MAExplorer
Report mode: lowest N current HP F1/F2 ratio genes
RPT_TBL_LOW_F1F2 - Static variable in class MJAbase
Report mode: lowest N current HP F1/F2 ratio genes
RPT_TBL_LOW_RATIO - Static variable in class MAExplorer
Report mode: lowest N HP-X/HP-Y ratio genes
RPT_TBL_LOW_RATIO - Static variable in class MJAbase
Report mode: lowest N HP-X/HP-Y ratio genes
RPT_TBL_MAE_PRJ_DB - Static variable in class MAExplorer
Report mode: project database
RPT_TBL_MAE_PRJ_DB - Static variable in class MJAbase
Report mode: project database
RPT_TBL_MN_KMEANS_CLUSTER - Static variable in class MAExplorer
Report mode: mean clusters for K-means clusters statistics
RPT_TBL_MN_KMEANS_CLUSTER - Static variable in class MJAbase
Report mode: mean clusters for K-means clusters statistics
RPT_TBL_NAMED_GENES - Static variable in class MAExplorer
Report mode: all named genes
RPT_TBL_NAMED_GENES - Static variable in class MJAbase
Report mode: all named genes
RPT_TBL_NORMALIZATION_GENE_LIST - Static variable in class MAExplorer
Report mode:Normalization gene list statistics
RPT_TBL_NORMALIZATION_GENE_LIST - Static variable in class MJAbase
Report mode:Normalization gene list statistics
RPT_TBL_OCL_STAT - Static variable in class MAExplorer
Report mode: Ordered Condition List gene statistics
RPT_TBL_OCL_STAT - Static variable in class MJAbase
Report mode: Ordered Condition List gene statistics
RPT_TBL_SAMPLES_DB_INFO - Static variable in class MAExplorer
Report mode: array report of SamplesDB
RPT_TBL_SAMPLES_DB_INFO - Static variable in class MJAbase
Report mode: array report of SamplesDB
RPT_TBL_SAMPLES_WEB_LINKS - Static variable in class MAExplorer
Report mode: array report with active Web links
RPT_TBL_SAMPLES_WEB_LINKS - Static variable in class MJAbase
Report mode: array report with active Web links
rptFontSize - Variable in class MAExplorer
Report font size: "8pt", "10pt", or "12pt"
rReport - Variable in class RevalBase
Report text that results from running an R script.
Rscript - Variable in class RgenDemo
The complete generated .R script
RscriptBasePath - Static variable in class RevalBase
path of {client installation} R/ directory
RscriptName - Variable in class RLO
Name of .R script file
RscriptName - Variable in class RgenDemo
Current Rscript file for current RLO
RscriptName - Variable in class PopupEditRscript
Name of .R script file
RscriptText - Variable in class PopupEditRscript
.R text
rSq - Static variable in class MathMAE
RTN: correlation coefficient
rSqHP_HP - Variable in class CompositeDatabase
[1:nRows][1:nCols] rSq, HP vs HP correlation coefficient
rStdout - Variable in class RevalBase
Stdout (and stderr) text that results from running an R script.
rt - Variable in class RgenDemo
Rtest instance
rt - Variable in class RtestBase
 
rtb - Variable in class PopupEditRscript
instance of the parent
Rtest - class Rtest.
Class Rtest - evaluate R scripts with data supplied from MAExplorer via the MJA API.
Rtest(MaeJavaAPI) - Constructor for class Rtest
Rtest() - Constructor
RtestBase - class RtestBase.
Class RtestBase - evaluate R scripts with data supplied from Client program via the MJAReval API.
RtestBase(MJAReval, String, String, String, String, String) - Constructor for class RtestBase
RtestBase() - Constructor
rtList - Variable in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog.PluginList
 
run() - Method in class JavaCGIBridge
run() - This run thread asynchronously POSTs and GETs data from URL and places the contents into the threadCGIData variable.
run() - Method in class MAExplorer
run() - main loop which does checking for various things [1] Check if want to repaint based on spot list change.
runClusterAnalysis - Variable in class StateScrollers
 
runDataFilter() - Method in class MJAfilter
runDataFilter() - re-run the data filter (don't update popups).
runFilter - Variable in class StateScrollers
 
runImageOptimizer - Variable in class StateScrollers
 
runKmeansClusterAnalysis - Variable in class StateScrollers
 
runLoopDelayMsec - Variable in class MAExplorer
Flicker delay for run() loop delay also used for flicker
runRscriptWithR() - Method in class MJAReval
runRscriptWithR() - compute report string by running R script through the R program.
runRscriptWithR() - Method in class RevalBase
runRscriptWithR() - compute report string by running R script through R.
runT - Variable in class MAExplorer
main thread for run()
RuserBasePath - Static variable in class RevalBase
user's home directory for e.g.env "R_USER" or "HOME" or "C:/R/", etc.

S

saCodeBase - Static variable in class MAExplorer
Stand-alone PARAM "saCodeBase" overrides default
sampDB - Variable in class MAExplorer
The "Samples.txt" database list of the H.P.s in the entire database.
sampDB - Variable in class Report
link to global SamplesTable instance
sampDBfile - Variable in class Config
PARAM "samplesDBfile"
sample - Variable in class MAEPlugin.analysis.NormalizationPlugin
 
sampleDBrow - Variable in class StageNames
row of membrane table
sampleID - Variable in class MaHybridSample
English name of the sample
sampleIntensityRangeMode - Variable in class MAExplorer
Sample intensity range mode for threshold: RANGE_INSIDE, RANGE_OUTSIDE
sampleMenu - Variable in class MenuBarFrame
"Sample" command menu
SampleSets - class SampleSets.
The SampleSets class maintains the set of all HP samples, the HP-X set, HP-Y set and the HP-E list.
SampleSets(MAExplorer) - Constructor for class SampleSets
SampleSets() - constructor to create the sample lists.
SamplesTable - class SamplesTable.
The SamplesTable class is database for the Samples DB Table.
SamplesTable(MAExplorer, String) - Constructor for class SamplesTable
SamplesTable() - constructor to read Samples DB and set up table.
saveAllCondsToMaeState() - Method in class PopupCondChooser
saveAllCondsToMaeState() - save all conditions to MAExplorer state
saveAllCondsToMaeState() - Method in class PopupOrderedCondChooser
saveAllCondsToMaeState() - save all conditions to MAExplorer state
saveAllDemoRLOsButton - Variable in class RtestBase
Save All Demo RLOs button if "Show Demo RLOs" is set.
saveasButton - Variable in class RtestBase
"SaveAs" window button
saveAsButton - Variable in class ShowExprProfilesPopup
 
saveAsButton - Variable in class ShowPlotPopup
"SaveAs" GIF image button
saveAsButton - Variable in class ShowStringPopup
"SaveAs" .txt button
saveAsButton - Variable in class LogTextFrame
Save Log As button to save the log data as a new named Report/XXXX.txt file
saveAsGIF - Variable in class DrawClusterGram
Save display as GIF file
saveAsGIF - Variable in class ExprProfilePopup
Save display as GIF file
saveAsGifFile(String) - Method in class ShowPlotPopup
saveAsGifFile() - save plot canvas in oGifFileName
saveAsTxtFile() - Method in class LogTextFrame
saveAsTxtFile() - save logTextStr data in .txt file logFileName
saveAsTxtFile(String) - Method in class ShowStringPopup
saveAsTxtFile() - save textReport data in .txt file oTxtFileName
saveButton - Variable in class PopupCondChooser
save
saveButton - Variable in class PopupOrderedCondChooser
save to MAExplorer
saveCmdHistory(String) - Method in class MJAutil
saveCmdHistory() - print msg to showMsg1() and also save in command history and message logs if logging is enabled.
saveCmdHistory(String) - Static method in class Util
saveCmdHistory() - print msg to showMsg1() and also save in command history and message logs if logging is enabled as well.
saveCmdHistory(String, boolean) - Static method in class MJAutil
saveCmdHistory() - save msg in command history and message logs if logging is enabled.
saveCmdHistory(String, boolean) - Static method in class Util
saveCmdHistory() - save msg in command history and message logs if logging is enabled.
saveCondState(PopupCondChooser.CondData[], int) - Method in class PopupCondChooser
saveCondState() - saves all condition sample and param (N,V) data to MAE via MJAcondition.
saveCondState(PopupOrderedCondChooser.OclListData[], int) - Method in class PopupOrderedCondChooser
saveCondState() - saves all conditions and ocl param (N,V) data to MAE via MJAcondition.
saveData() - Method in class PopupCondChooser.CondParamEditForm
saveData() - Save value data from textFields to cd.value[] if changed.
saveData() - Method in class PopupOrderedCondChooser.CondParamEditForm
saveData() - Save value data from textFields to oclLd.value[] if changed.
savedMsg - Variable in class ShowStringPopup
message after Saved Txt into file
saveFlag - Variable in class PopupCondChooser
see if saved ok
saveFlag - Variable in class PopupOrderedCondChooser
see if saved ok
saveKmeansClustersAsGeneSets() - Method in class ClusterGenes
saveKmeansClustersAsGeneSets() - save K-means clusters in named Gene BitSets.
saveMsgHistory(String, boolean) - Method in class MJAutil
saveMsgHistory() - save msg in message logs if logging is enabled.
saveMsgHistory(String, boolean) - Static method in class Util
saveMsgHistory() - save msg in message logs if logging is enabled.
saveNamedHPlist(Condition, int) - Method in class UserState
saveNamedHPlist() - save the named sample HP list (i.e.
saveNamedOCLlist(int) - Method in class UserState
saveNamedOCLlist() - save the named OCL list (i.e.
saveReportAsTextFileFlag - Variable in class PopupCondChooser
Flag enabled if doing "SaveAs"
saveReportAsTextFileFlag - Variable in class PopupOrderedCondChooser
Flag enabled if doing "SaveAs"
saveReportAsTextFileFlag - Variable in class RtestBase
Flag enabled if doing "SaveAs"
saveRLOButton - Variable in class PopupEditRscript
"Save RLO" window button
saveStateFile(String, String, String) - Method in class UserState
saveStateFile() - save the user state in a file.
saveTextReport(String) - Method in class RtestBase
saveTextReport() - Saves reportText to file
saveUserGeneSet(int) - Method in class UserState
saveUserGeneSet() - save user gene bit set by set number.
saveUserGeneSetUPW(String, String, int) - Method in class UserState
saveUserGeneSetUPW() - save user gene bit set by set number [FUTURE]
sbActive - Variable in class StateScrollers
Flags: true if scroll bars are active
sbBar - Variable in class StateScrollers
list of scroll bars
sbCurValue - Variable in class StateScrollers
current & initial (STATE) values of scrollbar
sbGTidx - Variable in class StateScrollers
corresponding GT scroller integer bounds
sbLblName - Variable in class StateScrollers
label of Name to left of scrollbar
sbLblValue - Variable in class StateScrollers
label of Values to right of scrollbar
sbLowerBound - Variable in class StateScrollers
Note: lower bounds in STATE space
sbLTidx - Variable in class StateScrollers
corresponding LT scroller integer bounds
sbMouseMsg - Static variable in class StateScrollers
messages for mouseover of label
sbName - Static variable in class StateScrollers
list of state scroller label names
sbNonLinearScale - Variable in class StateScrollers
Flags for using a nonlinear vernier in the SCROLLER CONTROLs
sbPrecision - Variable in class StateScrollers
# of digits in scroller value labels
sbSize - Variable in class ExprProfileOverlay
width of scroll bar control
sbSize - Variable in class ExprProfileScrollPane
width of scroll bar control
sbSize - Variable in class StateScrollers
size of scale in Scroller space
sbUpperBound - Variable in class StateScrollers
Note: upper bounds in STATE space
scaleCalDNA - Variable in class MaHybridSample
scale factor for scaling by calDNA
scaleCalDNAto65K - Variable in class MaHybridSample
scale factor for scaling by calDNA but max for all HPs is 65K
scaleDataToMaxIntensFlag - Variable in class MAExplorer
normalize to maximum intensity
scaleIntensData(float) - Method in class MJAgene
scaleIntensData() - scale raw intensity data as fct of normalization mode.
scaleIntensData(float) - Method in class MaHybridSample
scaleIntensData() - scale raw intensity data as function of normalization mode.
scaleIntensData(float, int) - Method in class MJAgene
scaleIntensData() - scale raw intensity data as fct of normalization mode.
scaleIntensData(float, int) - Method in class MaHybridSample
scaleIntensData() - scale raw intensity data as function of normalization mode.
scaleIntensityData(float) - Method in class GenNormalizationPlugin
scaleIntensityData() - scale raw intensity data as fct of normalization mode.
scaleIntensityData(float) - Method in interface MAEPlugin.Normalization
scaleIntensityData() - scale raw intensity data as fct of normalization mode.
scaleIntensityData(float) - Method in class MAEPlugin.analysis.NormalizationPlugin
scaleIntensityData() - scale raw intensity data as fct of normalization mode.
scaleIntensityData(float, float, int, int, int) - Method in class GenNormalizationPlugin
scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis.
scaleIntensityData(float, float, int, int, int) - Method in interface MAEPlugin.Normalization
scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis.
scaleIntensityData(float, float, int, int, int) - Method in class MAEPlugin.analysis.NormalizationPlugin
scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis.
scaleIntensityData(float, int, int, int) - Method in class GenNormalizationPlugin
scaleIntensityData() - scale raw intensity data as fct of normalization mode.
scaleIntensityData(float, int, int, int) - Method in interface MAEPlugin.Normalization
scaleIntensityData() - scale raw intensity data as fct of normalization mode.
scaleIntensityData(float, int, int, int) - Method in class MAEPlugin.analysis.NormalizationPlugin
scaleIntensityData() - scale raw intensity data as fct of normalization mode.
scaleMapX - Variable in class ClusterGramCanvas
position of scale map X
scaleMapY - Variable in class ClusterGramCanvas
position of scale map Y
scaleToMaxIV - Variable in class MaHybridSample
total array: maxFV/maxRIscale factor to compute max range
scaleUseGeneSet - Variable in class MaHybridSample
scale factor for 'User Filter Gene set'
scaleUseGeneSetTo65K - Variable in class MaHybridSample
scale factor for 'User Filter Gene Set' but max for all HPs is 65K
scaleX - Variable in class Draw2Dplot
scale factor X-axis
scaleY - Variable in class Draw2Dplot
scale factor X-axis
scalingButton - Variable in class ShowPlotPopup
[DEPRICATED] Linear/Log button
scHeight - Variable in class ScrollableImageCanvas
pImage: iHeight+extraHeight of the actual canvas
screenGoodGenesFlag - Variable in class MaHPquantTable
flag: if calc glob-stats on only GoodGenes
scrHeight - Variable in class MAExplorer
Horizontal screen size
scriptChoice - Variable in class RtestBase
Choice to select an R script to use from analysis[0:nAnalyses-1].
scriptSpecificRoptions - Variable in class RLO
Optional script Specific R startup options.
scriptSpecificRoptions - Variable in class PopupEditRscript
Optional script Specific R startup options.
ScrollableImageCanvas - class ScrollableImageCanvas.
This class supports a scrollable image canvas for the pseudoarray image.
ScrollableImageCanvas(MaHybridSample, int, int, ArrayScroller) - Constructor for class ScrollableImageCanvas
ScrollableImageCanvas() - constructor for scrollable pseudoarray image canvas.
scrPos - Variable in class StateScrollers
Normal position for showing selected state.
scrWidth - Variable in class MAExplorer
Horizontal screen size
scWidth - Variable in class ScrollableImageCanvas
pImage: iWidth+extraWidth of the actual canvas
sCy35 - Variable in class SampleSets
"Cy3/Cy5" based on mae.cfg.fluoresLbl[12]
sCy53 - Variable in class SampleSets
"Cy5/Cy3" based on mae.cfg.fluoresLbl[12]
sd - Variable in class MAExplorer
Global instance of spot data object
sdDataV - Static variable in class HierClustNode
Dynamic node: [0:nDataV-1] global StdDev data for samples h
sdDist - Variable in class ClusterGenes.Cluster
stdDev distance to meanDP
sdEP - Variable in class ClusterGenes.Cluster
stdDev expr profile (to meanEP) of cluster
sdHPri - Variable in class MaHybridSample
total array: rawIntens StdDev, all genes in HP w/o bkgrd
sdHPri1 - Variable in class MaHybridSample
total array: rawIntens f1 StdDev, all genes in HP w/o bkgrd
sdHPri2 - Variable in class MaHybridSample
total array: rawIntens f2 StdDev, all genes in HP w/o bkgrd
sdWithinClusterDist - Variable in class ClusterGenes
[1:maxKmeansNodes] StdDev within-cluster distance between K-means clusters
sdX - Static variable in class MathMAE
RTN: standard deviation X
sdY - Static variable in class MathMAE
RTN: standard deviation Y
searchStr - Variable in class KeyEventHandler
typed in tf
selCol - Variable in class ClusterGramCanvas
selected column set by event handler mouse on click
selCond - Variable in class PopupOrderedCondChooser.OclListData
list of selected conditions for current condition being edited
selCondTmp - Variable in class PopupOrderedCondChooser
selected conditions before edit
selDist - Variable in class ClusterGramCanvas
distance selected by clicking on dendrogram
selectedIndex - Variable in class PopupCondChooser.ChoiceList
index of which item is selected.
selectedIndex - Variable in class PopupOrderedCondChooser.ChoiceList
index of which item is selected.
selectedPanel - Variable in class ChooserGUI
SELECTED list
selectedPanel - Variable in class PopupCondChooserGUI
SELECTED list
selectedPanel - Variable in class PopupOrderedCondChooserGUI
SELECTED list
selectMeh - Variable in class PopupCondChooserGUI
handle mouse events for text areas for selTextArea RIGHT
selectMeh - Variable in class PopupOrderedCondChooserGUI
handle mouse events for text areas for selTextArea RIGHT
selectObject(int, int) - Method in class ClusterGramCanvas
selectObject() - test mouse cursor to select row or box if within any box
selLabelName - Variable in class PopupCondChooserGUI
label for REMAINDER RIGHT text area
selLabelName - Variable in class PopupOrderedCondChooserGUI
label for REMAINDER RIGHT text area
selMID - Variable in class ClusterGramCanvas
set by event handler on click
selObjList - Variable in class ChooserGUI
SELECTED list to be returned
selObjList - Variable in class PopupCondChooserGUI
SELECTED list of sample object names to be returned
selObjList - Variable in class PopupOrderedCondChooserGUI
SELECTED list of cond object names to be returned
selObjListSize - Variable in class ChooserGUI
SELECTED list size
selObjListSize - Variable in class PopupCondChooserGUI
SELECTED list size
selObjListSize - Variable in class PopupOrderedCondChooserGUI
SELECTED list size
selRow - Variable in class ClusterGramCanvas
selected row set by event handler mouse on click
selSamples - Variable in class PopupCondChooser.CondData
list of selected samples for current condition being edited
selSamplesTmp - Variable in class PopupCondChooser
selected sample names of condition before edit
selTextArea - Variable in class PopupCondChooserGUI
SELECTED obj list
selTextArea - Variable in class PopupOrderedCondChooserGUI
SELECTED obj list
selTextAreaLabel - Variable in class PopupCondChooserGUI
label under selTextArea
selTextAreaLabel - Variable in class PopupOrderedCondChooserGUI
label under selTextArea
selTitle - Variable in class PopupCondChooser
title of selected samples TextArea for PopupCondChooserGUI
selTitle - Variable in class PopupOrderedCondChooser
title of selected TextArea for PopupOrderedCondChooserGUI
send(OutputStream, String) - Static method in class JavaCGIBridge
send() - helper routine to send a string to output stream.
sepp - Variable in class ExprProfileOverlay
Parent window
sepp - Variable in class ExprProfileScrollPane
Parent window
seppKey - Variable in class PopupRegistry
[0:nSEPP-1] ExprProfilePopup key names
seppList - Variable in class PopupRegistry
[0:nSEPP-1] list of active Expr Profile popups
seppPropBits - Variable in class PopupRegistry
[0:nSEPP-1] bits requesting notification of ExprProfilePopup list of changes
set_abortFlag(boolean) - Method in class MJAstate
set_abortFlag() - set "abortFlag" flag status
set_addExprProfileFlag(boolean) - Method in class MJAreport
set_addExprProfileFlag() - set flag: add EP ratios in gene REPORTS
set_addHP_XYstatFlag(boolean) - Method in class MJAreport
set_addHP_XYstatFlag() - set flag: add HP_XY statistics in gene REPORTS
set_Clone_ID(int, String) - Method in class MJAgene
set_Clone_ID() - set Clone_ID for specified gene, if exists
set_clusterNodeNbr(int, int) - Method in class MJAgene
set_clusterNodeNbr() - set clusterNodeNbr for specified gene, if exists The cluster node # is the cluster number that a gene belongs to.
set_dbEST3ID(int, String) - Method in class MJAgene
set_dbEST3ID() - set dbEST3 ID for specified gene, if exists
set_dbEST5ID(int, String) - Method in class MJAgene
set_dbEST5ID() - set dbEST5 ID for specified gene, if exists
set_doGCflag(boolean) - Method in class MJAstate
set_doGCFlag() - set "doGCflag" flag status to invoke the Garbage Collector when have time as determined by main idle loop.
set_duplMIDlist(int, int[]) - Method in class MJAgene
set_duplMIDlist() - set list of MIDs for duplicate genes for specified gene, if exists
set_GenBankAcc3ID(int, String) - Method in class MJAgene
set_GenBankAcc3ID() - set GenBank Acc 3' ID for specified gene, if exists
set_GenBankAcc5ID(int, String) - Method in class MJAgene
set_GenBankAcc5ID() - set GenBank Acc 5' ID for specified gene, if exists
set_GenBankAccID(int, String) - Method in class MJAgene
set_GenBankAccID() - set GenBankAcc ID for specified gene, if exists
set_Gene_Name(int, String) - Method in class MJAgene
set_Gene_Name() - set Gene_Name for specified gene
set_Generic_ID(int, String) - Method in class MJAgene
set_Generic_ID() - set Generic_ID for specified gene, if exists
set_genomicDB_URLs(int, String[], String[], String[], String[]) - Method in class MJAgenomicDB
set_genomicDB_URLs() - set user-defined genomic DB URLs
set_GenomicID(int, String[]) - Method in class MJAgene
set_GenomicID() - seta list of additional genomic IDs for the default gene, if exists.
set_hierClusterUnWeightedAvgFlag(boolean) - Method in class MJAcluster
set_hierClusterUnWeightedAvgFlag() - set hier-clustering averaging method flag.
set_isZscoreNorm(boolean) - Method in class MJAstate
set_isZscoreNormFlag() - set "isZscoreNorm" flag status using one of the Zscore normalizations.
set_LocusID(int, String) - Method in class MJAgene
set_LocusID() - set LocusLinkID for specified gene, if exists
set_Master_ID(int, String) - Method in class MJAgene
set_Master_ID() - set Master_ID for specified gene
set_MasterGeneName(int, String) - Method in class MJAgene
set_MasterGeneName() - set MasterGeneName for specified gene
set_nDuplGenes(int, int) - Method in class MJAgene
set_nDuplGenes() - # duplicate genes in duplMIDlist[] for specified gene, if exists
set_nGeneClustersCnt(int, int) - Method in class MJAgene
set_nGeneClustersCnt() - set nGeneClustersCnt for specified gene, if exists The centroid gene of a cluster is flagged by containing the # of genes in that cluster.
set_nGenomicID(int, int[]) - Method in class MJAgene
set_nGenomicID() - set # additional genomic IDs in the GenomicID[] list for the specified gene, if exists.
set_NratiosToReport(int) - Method in class MJAfilter
set_NratiosToReport() - set # of ratios to report
set_plate_col(int, String) - Method in class MJAgene
set_plate_col) - set original plate_col for specified gene, if exists
set_plate_row(int, String) - Method in class MJAgene
set_plate_row() - set original plate_row for specified gene, if exists
set_plate(int, String) - Method in class MJAgene
set_plate() - set original plate for specified gene, if exists
set_properties(int, int) - Method in class MJAgene
set_properties() - set properties for specified gene, if exists
set_pValue(int, float) - Method in class MJAgene
set_pValue() - set pValue for specified gene, if exists
set_pValueThr(float) - Method in class MJAfilter
set_pValueThr() - set Sample p-Value for t-Test Filter threshold
set_SwissProtID(int, String) - Method in class MJAgene
set_SwissProtID() - set SwissProt ID for specified gene, if exists
set_thrClusterDist(float) - Method in class MJAfilter
set_thrClusterDist() - set Sample gene-gene cluster distance threshold
set_thrCR1(float) - Method in class MJAfilter
set_thrCR1() - set Sample Cy3/Cy5 lower limit CR1 threshold
set_thrCR2(float) - Method in class MJAfilter
set_thrCR2() - set Sample Cy3/Cy5 lower limit CR2 threshold
set_thrDiff(float) - Method in class MJAfilter
set_thrDiff() - set Sample diff (HP-X,HP-Y) Filter threshold
set_thrI1(float) - Method in class MJAfilter
set_thrI1() - set Sample Intensity lower limit I1 threshold
set_thrI2(float) - Method in class MJAfilter
set_thrI2() - set Sample Intensity lower limit I2 threshold
set_thrNbrClusters(int) - Method in class MJAfilter
set_thrNbrClusters() - set # of clusters in K-means clustering
set_thrPercentOK(float) - Method in class MJAfilter
set_thrPercentOK() - set % of samples meeting Spot Intensity criteria threshold
set_thrQualCheck(float) - Method in class MJAfilter
set_thrQualCheck() - set Sample QualCheck threshold
set_thrR1(float) - Method in class MJAfilter
set_thrR1() - set Sample Ratio lower limit R1 threshold
set_thrR2(float) - Method in class MJAfilter
set_thrR2() - set Sample Ratio lower limit R2 threshold
set_thrSI1(float) - Method in class MJAfilter
set_thrSI1() - set Spot Intensity lower limit SI1 threshold
set_thrSI2(float) - Method in class MJAfilter
set_thrSI2() - set Spot Intensity lower limit SI2 threshold
set_thrSpotCV(float) - Method in class MJAfilter
set_thrSpotCV() - set Sample spot Coefficient Of Variation Filter threshold
set_UGclusterName(int, String) - Method in class MJAgene
set_UGclusterName() - set UGclusterName for specified gene
set_Unigene_ID(int, String) - Method in class MJAgene
set_Unigene_ID() - set Unigene_ID for specified gene, if exists
set_updatePseudoImgFlag(boolean) - Method in class MJAstate
set_updatePseudoArrayImageFlag() - set "updatePseudoArrayImage" flag status.
set_useEPrawIntensityValuesFlag(boolean) - Method in class MJAreport
set_useEPrawIntensityValuesFlag() - set flag: use Raw intensity for EP ratios in gene REPORTS
set_useGeneSetFilterFlag(boolean) - Method in class MJAfilter
set_useGeneSetFilterFlag() - set filter by user gene set membership status
set2DplotSubtitles(String, String, String, String) - Method in class Draw2Dplot
set2DplotSubtitles() - set info1,2,3,4 subtitles for plot.
setActiveFilter(FilterPlugin) - Method in class MAEPlugin.analysis.FilterPlugin
setActiveFilter() - Bean-style method for setting the activeFilterPluginList.
setActiveNormalization(Normalization) - Method in class MAEPlugin.analysis.NormalizationPlugin
setActiveNormalization() - Bean-style method for setting the activeNormalization.
setAllGenRbits(int) - Method in class MJAReval
setAllGenRbits() - set GenR Bits using R_GENR_xxxx bits for current RLO.
setAllProcessBits(int) - Method in class MJAReval
setAllProcessBits() - set Process Bits bits for current RLO.
setAllProcessBits(int) - Method in class RevalBase
setAllProcessBits() - set Process Bits using R_PB_xxxx bits for current RLO.
setArrayScrollerSize(int, int) - Method in class ArrayScroller
setArrayScrollerSize() - set the Image Scroller size
setBottomSeparator(String) - Method in class JavaCGIBridge
setBottomSeparator() - Sets the bottom separator for the object.
setBoxSizes(Graphics) - Method in class ClusterGramCanvas
setBoxSizes() - set box sizes based on font metrics.
setCalcEPdataFlag(boolean) - Method in class HPxyData
setCalcEPdataFlag() - set the also calculate EP data when do updates.
setCellFontAndColor(int, int) - Method in class SSspreadPanel
setCellFontAndColor() - use dataFont or cellUrlFont depending on cell(r,c)
setClassNameReplacementChar(char) - Method in class MAEPlugin.JarClassLoader
setClassNameReplacementChar() - remap class name.
setClusterDisplayState(CheckboxMenuItem, boolean) - Static method in class EventMenu
setClusterDisplayState() - set the cluster display checkbox state.
setCondInOrderedCondList(String, String[], int) - Method in class MJAcondition
setCondInOrderedCondList() - replace existing conditions with new list
setCondListLength(int, String) - Method in class MJAcondition
setCondListLength() - Set # of samples in the condition list
setCondListsNames(String[], int) - Method in class MJAcondition
setCondListsNames() - Set list of active condition lists names
setCondListsSizes(int[]) - Method in class MJAcondition
setCondListsSizes() - Set list of active condition lists sizes
setCondParamNames(String[]) - Method in class MJAcondition
setCondParamNames() - set list of condition parameter names for all conditions.
setCondParamValue(String, String[]) - Method in class MJAcondition
setCondParamValue() - set list of parameter values for specific condition NOTE: the # of parameter values must match the number of parameter names.
setCurCondition(String) - Method in class MJAcondition
 
setCurGene(int) - Method in class DrawScatterPlot
setCurGene() - set current gene and update data in displays
setCurGene(int) - Method in class ExprProfileOverlay
setCurGene() - set current gene from mid if it is not -1.
setCurGene(int) - Method in class ExprProfileScrollPane
setCurGene() - set current gene if mid is not -1
setCurOCL(String) - Method in class MJAcondition
 
setCurrentGene(int, int, int, boolean) - Method in class ClusterGramCanvas
setCurrentGene() - set current gene from (xCursor,yCursor) in ClusterGram.
setCurrentGeneClassName(String) - Method in class GeneClass
setCurrentGeneClassName() - set the "current GeneClass"
setCurrentGeneFromMID(int) - Method in class MJAgene
setCurrentGeneFromMID() - set the Current Gene to the specified mid.
setCurrentGenes(int) - Method in class CompositeDatabase
setCurrentGenes() - set current genes to those in the GeneClass database if the curGenesMode is true.
setCurrentRLO(int) - Method in class MJAReval
setCurrentRLO() - set the current RLO analysis method by id
setCurrentRLO(int) - Method in class RevalBase
setCurrentRLO() - set the current RLO analysis method by id
setCurrentRLO(int) - Method in class RLO
setCurrentRLO() - set the current RLO analysis by id
setCurrentSample(int) - Method in class MJAgene
setCurrentSample() - set the sample to be used for subsequent gene or spot data accesses in that array
setCVmodeState(CheckboxMenuItem) - Static method in class EventMenu
setCVmodeState() - set theCV mode checkbox state.
setCy3Cy5RatioRangeState(CheckboxMenuItem) - Static method in class EventMenu
setCy3Cy5RatioRangeState() - set the Cy3/Cy5 Ratio Range checkbox state.
setCy3Cy5RatiosCL(GeneList, GeneList, MaHybridSample, boolean) - Method in class Filter
setCy3Cy5RatiosCL() - Set GeneList of thresholded genes for Cy3/Cy5 ratio range where the threshold for rangeType [CR1:CR2] and rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
setData(char, String, String[], int, int, int, String, Font) - Method in class Guesser
setData() - for single list.
setDataToClip(float, float, float, float) - Method in class Draw2Dplot
setDataToClip() - set (cx1,cx2,cy1,cy2) data to clip from((x1,x2,y1,y2)
setDbEstURL(String) - Method in class MJAstate
setDbEstURL() - set the url
setDbugFlag(boolean) - Method in class MJAReval
setDbugFlag() set debugging flag to print to stdout if required
setDbugFlag(boolean) - Method in class RevalBase
setDbugFlag() - set debugging flag to print to stdout if required
setDefaultGene(int) - Method in class MJAgene
setDefaultGene() - define the default gene by the Master Gene ID mid for interrogation by the get_XXXX() methods.
setDefaultThreadJavaCGIBridgeTimeOut(int) - Static method in class JavaCGIBridge
setDefaultThreadJavaCGIBridgeTimeOut() - set communication time out Static method sets the default communication time out in milliseconds for the class.
setDefaultURLs(String) - Method in class Config
setDefaultURLs() - set default URLs based on species
setDefParam(String, boolean) - Method in class GetParams
setDefParam() - set value or default if
setDefParam(String, Color) - Method in class GetParams
setDefParam() - set value or default if
setDefParam(String, double) - Method in class GetParams
setDefParam() - set double value or default value if <APPLET> <PARAM NAME=tag VALUE=val>
setDefParam(String, double, double, double) - Method in class GetParams
setDefParam() - set double value or default value if <APPLET> <PARAM NAME=tag VALUE=val>
setDefParam(String, float) - Method in class GetParams
setDefParam() - set floag value or default value if <APPLET> <PARAM NAME=tag VALUE=val>
setDefParam(String, float, float, float) - Method in class GetParams
setDefParam() - set float value or default value if <APPLET> <PARAM NAME=tag VALUE=val>
setDefParam(String, int) - Method in class GetParams
setDefParam() - set value or default value if 1.
setDefParam(String, int, int, int) - Method in class GetParams
setDefParam() - set int value or default value if <APPLET> <PARAM NAME=tag VALUE=val>
setDefParam(String, String) - Method in class GetParams
setDefParam() - set String value or default value if <APPLET> <PARAM NAME=tag VALUE=val>
setDetValueQuantData(GeneList, GeneList, int) - Method in class Filter
setDetValueQuantData() - filter out genes failing Detection Value quant values.
setDetValueSpotModeState(CheckboxMenuItem) - Static method in class EventMenu
setDetValueSpotModeState() - set the Spot detection value data mode checkbox state.
setDiffHP_XYCL(GeneList, GeneList, float) - Method in class Filter
setDiffHP_XYCL() - Filter genes by diff(HP-X,HP-Y) GEQ diffThr.
setDoMeanPlotsFlag(boolean) - Method in class MJAexprProfile
setDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots
setEditState(CheckboxMenuItem) - Static method in class EventMenu
setEditState() - set the edit checkbox state.
setEGL(String[], String) - Method in class PopupGeneGuesser
setEGL() - process the selected text for setting EGL, popdown the guesser
setEGLfromGeneListStr(String[]) - Method in class EditedGeneList
setEGLfromGeneListStr() - set the EGL from the gene list string names.
setEGLfromListFlag - Variable in class Guesser
if set then group copy to EGL
setEGLtoSubTreeGenes(int[]) - Method in class ClusterGramCanvas
setEGLtoSubTreeGenes() - Copy genes to E.G.L.
setEnablePopupScrollbars(boolean) - Method in class StateScrollers
setEnablePopupScrollbars() - hide or show popup all scrollbars
setEnumerateNodes() - Static method in class HierClustNode
setEnumerateNodes() - Set the top node of the tree
setEPcanvasDrawingOptions(boolean, int, int) - Method in class ExprProfileOverlay
setEPcanvasDrawingOptions() - set err-bar and zoom status and then repaint.
setEPcanvasDrawingOptions(boolean, int, int) - Method in class ExprProfileScrollPane
setEPcanvasDrawingOptions() - set err-bar & zoom status and then repaint.
setEPmaxMeanSampleData(float) - Method in class MJAexprProfile
setEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles.
setFieldData(String[], int) - Method in class SimpleTable
setFieldData() - set new field[] list for table
setFieldSeparator(String) - Method in class JavaCGIBridge
setFieldSeparator() - Sets the field separator for the object.
setFlag(boolean) - Method in class MAEPlugin.MAEPlugin
setFlag() - set the menu status (CheckBox) menuFlag
setFontsFromState() - Method in class Draw2Dplot
setFontsFromState() - set the regular fonts from the state variables
setFontsFromState() - Method in class DrawPseudoImage
setFontsFromState() - set the regular and header fonts from the state variables
setFullGEOplatformDataTableURL(String) - Method in class MJAproperty
setFullGEOplatformDataTableURL() - set URL for current full GEO platform data table
setGbid2LocusLinkURL(String) - Method in class MJAstate
setGbid2LocusLinkURL() - set the url
setGenBankAccURL(String) - Method in class MJAstate
setGenBankAccURL() - set the url
setGenBankCloneURL(String) - Method in class MJAstate
setGenBankCloneURL() - set the url
setGenBankCloneURLepilogue(String) - Method in class MJAstate
setGenBankCloneURLepilogue() - set the url
setGene(Gene, int) - Method in class GeneList
setGene() - set Gene to specific gene list mList[idx].
setGeneBitsetData(String, long[], int) - Method in class MJAgeneList
setGeneBitsetData() - set bitData for GeneBitSet by GeneBitSet name.
setGeneCardURL(String) - Method in class MJAstate
setGeneCardURL() - set the url
setGeneData(float) - Method in class Gene
setGeneData() - set gene quantified data
setGeneData(float, float, float) - Method in class Gene
setGeneData() - set quantified gene data, data1 and data2
setGeneData(float, float, float, float) - Method in class Gene
setGeneData() - set quantified gene data, data1 and data2
setGeneData1AndData2(float, float) - Method in class Gene
setGeneData1AndData2() - set quantified gene data1 and data2
setGeneDist(float) - Method in class Gene
setGeneDist() - set gene cluster distance (only used if clustering).
setGeneListBySpotCV(GeneList, GeneList, float, int) - Method in class Filter
setGeneListBySpotCV() - do test of coefficient of variation against threshold.
setGeneListByStringList(String, String[]) - Method in class MJAgeneList
setGeneListByStringList() - set GeneList by "," delimited list of MID indices
setGeneListData(String, int[]) - Method in class MJAgeneList
setGeneListData() - set GeneList list of gene index data by existing GeneList name.
setGeneListData(String, int[], int) - Method in class MJAgeneList
setGeneListData() - set GeneList list of gene index data by existing GeneList name.
setGeneListFromGeneNameArray(String[]) - Method in class GeneList
setGeneListFromGeneNameArray() - set the GeneList from array of gene names.
setGeneMIDfromXYcoord(int, int, int) - Method in class MJAgene
setGeneMIDfromXYcoord() - set current gene MID from XY coordinates for a spot in the pseudoarray image for that sample.
setGeneProperty(int) - Method in class Gene
setGeneProperty() - set C_xxxx gene properties.
setGenomicData(int) - Method in class SpotFeatures
setGenomicData() - get genomic data from GID gene into local variables of spotFeatures.
setGenRbit(int) - Method in class MJAReval
setGenRbit() - set specific GenR Bit(s) for current RLO.
setGEOplatformID(String) - Method in class MJAproperty
setGEOplatformID() - set current GEO platform ID for this database.
setGoodSpotModeState(CheckboxMenuItem) - Static method in class EventMenu
setGoodSpotModeState() - set the Good Spot data mode checkbox state.
setGoodSpotQuantData(GeneList, GeneList, int) - Method in class Filter
setGoodSpotQuantData() - filter out genes failing QualChk quant values.
setHistogramData(String, String, String, float, float, float, float, float, int, int[], int) - Method in class DrawHistogram
setHistogramData() - draw histogram of hist[0:nHist-1].
setHistogramRatiosData(String, String, String, String, String, double, double, int, int[], double[], int) - Method in class DrawRatioHistogram
setHistogramRatiosData() - draw histogram of rg.ratioHist[].
setHistoryFileLogging(String, boolean, boolean) - Static method in class Util
setHistoryFileLogging() - set up history file logging.
setHistoryLoggingState(boolean, boolean) - Method in class Util
setHistoryLoggingState() - set the history logging state on/off.
setHP_EclustersCL(GeneList, GeneList, float) - Method in class Filter
setHP_EclustersCL() - Filter genes by HP-E clusters LEQ clusterDist
setHP_XY_t_TestCL(GeneList, GeneList, MaHybridSample, MaHybridSample, float) - Method in class Filter
setHP_XY_t_TestCL() - set GeneList of genes passing HP-X,HP-Y t-Test with a pValue better than pValueThr.
Compute the means and std deviations using the f1,f2 values for each sample.
setHP_XYlabels() - Method in class MenuBarFrame
setHP_XYlabels() - set the GUI HP-X: and HP-Y: labels as singles or multiple (Class names)
setHP_XYsets_KS_TestCL(GeneList, GeneList, float) - Method in class Filter
setHP_XYsets_KS_TestCL() - set GeneList of genes passing HP-X,HP-Y sets KS-Test (Kolmogorov-Smirnov) with a pValue better than pValueThr.
[CHECK] how do we handle this if not in HP-XY 'set' mode?GeneList
setHP_XYsets_t_TestCL(GeneList, GeneList, float) - Method in class Filter
setHP_XYsets_t_TestCL() - set GeneList of genes passing HP-X,HP-Y sets t-Test with a pValue better than pValueThr.
[CHECK] how do we handle this if not in HP-XY 'set' mode?GeneList
setHPlistsFromPARAM() - Method in class SampleSets
setHPlistsFromPARAM() - set msList{X|Y|E}[] from PARAM cfg.{X|Y|E}list.
setHPXflag - Variable in class DrawPseudoImage
set HP-X (HP-Y) if click on sample name
setHPxyModStrings() - Method in class SampleSets
setHPxyModStrings() - set up (sMod, sModX, sModY, sModXY) state strings.
setIMAGE2GenBankURL(String) - Method in class MJAstate
setIMAGE2GenBankURL() - set the url
setIMAGE2unigeneURL(String) - Method in class MJAstate
setIMAGE2unigeneURL() - set the url
setImgPos(int, int) - Method in class ArrayScroller
setImgPos() - set the Image position (x,y).
setImgPos(MaHybridSample, int, int) - Method in class ScrollableImageCanvas
setImgPos() - set the Image position.
setImgPos(Point) - Method in class ArrayScroller
setImgPos() - set the Image position Point xyImg.
setInputFilesData(String[], int[]) - Method in class MJAReval
setInputFilesData() - set current RLO list of input data (fileName,dataType)
setInputFilesData(String[], int[]) - Method in class RevalBase
setInputFilesData() - set current RLO list of input data (fileName,dataType)
setIntensHistCLfromIntenRange(GeneList, MaHybridSample, float, float, boolean) - Method in class CompositeDatabase
setIntensHistCLfromIntensRange() - set GeneList of (F1+F2)/2 in intensity range
setIntensityCompareModeSlider(int) - Static method in class EventMenu
setIntensityCompareModeSlider() - set intensity compare mode Percent SI slider
setIntensityRangeState(CheckboxMenuItem) - Static method in class EventMenu
setIntensityRangeState() - set the Intensity Range checkbox state.
setItem(int) - Method in class GeneBitSet
setItem() - set bit in gene bit set corresponding to item (i.e.
setJarResources(JarResources) - Method in class MAEPlugin.MAEPlugin
setJarResources() - sets the JarResources object to get to the contents of the Jar object.
setListData(int, int, int, int, String[], String[]) - Method in class ChooserGUI
setListData() - copy original data for REMAINDER and SELECTED lists.
setListData(int, int, int, int, String[], String[]) - Method in class PopupCondChooserGUI
setListData() - copy original data for REMAINDER and SELECTED lists.
setListData(int, int, int, int, String[], String[]) - Method in class PopupOrderedCondChooserGUI
setListData() - copy original data for REMAINDER and SELECTED lists.
setListOfEsamples(int[]) - Method in class MJAsampleList
setListOfEsamples() - set int[] list of samples in HP-E 'list' list.
setListOfGEOplatformsURL(String) - Method in class MJAproperty
setListOfGEOplatformsURL() - set URL for list of current GEO platforms
setListOfXsamples(int[]) - Method in class MJAsampleList
setListOfXsamples() - set int[] list of samples in HP-X 'set' list.
setListOfYsamples(int[]) - Method in class MJAsampleList
setListOfYsamples() - set int[] list of samples in HP-Y 'set' list.
setLocusLinkURL(String) - Method in class MJAstate
setLocusLinkURL() - set the url
setLogHistoryWindowVisible(boolean) - Static method in class Util
setLogHistoryWindowVisible() - make the popup window visible or invisible
setLogMsgWindowVisible(boolean) - Static method in class Util
setLogMsgWindowVisible() - make the popup window visible or invisible
setLogWindowVisible(boolean) - Method in class LogTextFrame
setLogWindowVisible() - make the popup window visible or invisible
setMAdbURL(String) - Method in class MJAstate
setMAdbURL() - set the url
setMAEstateFromChooserData() - Method in class PopupHPChooser
setMAEstateFromChooserData() - restore MAE state from chooser data.
setMAEStub(MAEStub) - Method in class MAEPlugin.MAEPlugin
setMAEStub() - get the menu stub for this instance of plugin
setMedMinerURL(String) - Method in class MJAstate
setMedMinerURL() - set the url
setMedMinerURLepilogue(String) - Method in class MJAstate
setMedMinerURLepilogue() - set the url
setMenuHook(Menu) - Method in class MaeJavaAPI
setMenuHook() - set menu hook for the plugin
setMenuHook(Menu) - Method in interface MAEPlugin.MAEStub
setMenuHook() - method to set access root menu
setMenuHook(MenuItem) - Method in class MAEPlugin.MAEPlugin
setMenuHook() - set menu Item hook to put our instance of plugin
setMenuInsertionPointName(String) - Method in class MAEPlugin.MAEPlugin
setMenuInsertionPointName() - set the name of menu insertion point.
setMenuItem(MenuItem) - Method in class MAEPlugin.MAEPlugin
setMenuItem() - get menu item for this instance of the plugin
setMenuLabel(String) - Method in class MAEPlugin.MAEPlugin
setMenuLabel() - changes the label on the mennItem
setMsgFileLogging(String, boolean, boolean) - Static method in class Util
setMsgFileLogging() - set up message file logging.
setMsgLoggingState(boolean, boolean) - Method in class Util
setMsgLoggingState() - set the messages logging state on/off.
setName(String) - Method in class Report
setName() - set Report name
setName(String) - Method in class UserState
setName() - set UserState name
setNbrCondLists(int) - Method in class MJAcondition
setNbrCondLists() - Set # of active condition lists
setNonZeroQuantData(GeneList, GeneList) - Method in class Filter
setNonZeroQuantData() - filter out genes with 0.0 quant values in any HP-EP samples.
setNormalizationState(boolean) - Method in class MaeJavaAPI
setNormalizationState() - update Normalization state based on normalization method selected in non-plugin menus
setNormalizationState(boolean) - Method in interface MAEPlugin.MAEStub
setNormalizationState() - alias to: EventMenu.setNormalizationState used by: NormalizationPlugin
setNormalizationState(CheckboxMenuItem, String) - Static method in class EventMenu
setNormalizationState() - set the normalization checkbox state.
setNormalizationStateFromPlugin(String) - Static method in class EventMenu
setNormalizationStateFromPlugin() - set normalization state from MAEPlugin
setNormalizationStateFromPlugin(String) - Method in class MaeJavaAPI
setNormalizationStateFromPlugin() - set normalization state FROM the plugin.
setNormalizationStateFromPlugin(String) - Method in interface MAEPlugin.MAEStub
setNormalizationStateFromPlugin() - used by: NormalizationPlugin
setNormToOneFlag(boolean) - Method in class MJAexprProfile
setNormToOneFlag() - flag of normalize expression profile to 1.0 flag
setObjCoordFromMaster_ID(String) - Method in class CompositeDatabase
setObjCoordFromMaster_ID() - set gene xxxOBJ values from Master_ID name
setObjCoordFromMID(int, Object) - Method in class CompositeDatabase
setObjCoordFromMID() - set gene xxxOBJ values from MID for current HP sample.
setObjPos(int, int) - Method in class ArrayScroller
setObjPos) - set the object position (x,y).
setObjPos(int, int) - Method in class ScrollableImageCanvas
setObjPos() - set the object position (xObj,yObj).
setObjPos(Point) - Method in class ArrayScroller
setObjPos() - set the object position xyObj.
setObjState(MaHybridSample, int, int) - Method in class ScrollableImageCanvas
setObjState() - change the object position
setOBJtoGID(int, MaHybridSample) - Method in class CompositeDatabase
setOBJtoGID() - set the current gene xxxOBJ values to the specified GID.
setOCL_F_TestCL(GeneList, GeneList, float) - Method in class Filter
setOCL_F_TestCL() - set GeneList of genes passing F-test on current OCL (Ordered Condition List) with a pValue better than pValueThr.
setOclParamNames(String[]) - Method in class MJAcondition
setOclParamNames() - set list of ocl parameter names for all conditions.
setOclParamValue(String, String[]) - Method in class MJAcondition
setOclParamValue() - set list of ocl parameter values for specific condition NOTE: the # of parameter values must match the number of parameter names.
setOfileTypeDB(String[], String[], int[]) - Method in class MJAReval
setOfileTypeDB() - set R output file-types (name,menu,type) database.
setOfileTypeDB(String[], String[], int[]) - Method in class RevalBase
setOfileTypeDB() - set the R output file-types (name,menu,type) database.
setOperation(int[], int) - Method in class MAEPlugin.analysis.FilterPlugin
setOperation() - used in Filter intersection chain to process additional MAEPlugin filter tests.
setOutputFilesData(String[], int[]) - Method in class MJAReval
setOutputFilesData() - set current RLO list of output data (fileName,dataType)
setOutputFilesData(String[], int[]) - Method in class RevalBase
setOutputFilesData() - set current RLO list of output data (fileName,dataType)
setOverlayMapData(String, float[], int) - Static method in class MJAplot
setOverlayMapData() - set xy data into named scatterplot overlay map
setOverlayMapData(String, float[], int) - Static method in class OverlayMap
setOverlayMapData() - set xy data into named scatterplot overlay map
setOverlayMapDisplayChars(String, char[]) - Static method in class MJAplot
setOverlayMapDisplayChars() - set overlay characters for named scatterplot overlay map
setOverlayMapDisplayChars(String, char[]) - Static method in class OverlayMap
setOverlayMapDisplayChars() - set overlay characters for named scatterplot overlay map
setOverlayMapDisplayColor(String, Color) - Static method in class MJAplot
setOverlayMapDisplayColor() - set named scatterplot overlay map display color
setOverlayMapDisplayColor(String, Color) - Static method in class OverlayMap
setOverlayMapDisplayColor() - set named scatterplot overlay map display color
setOverlayMapDisplayType(String, int) - Static method in class MJAplot
setOverlayMapDisplayType() - set line type for named scatterplot overlay map
setOverlayMapDisplayType(String, int) - Static method in class OverlayMap
setOverlayMapDisplayType() - set line type for named scatterplot overlay map
setPirURL(String) - Method in class MJAstate
setPirURL() - set the url
setplateData(String, String, String) - Method in class Gene
setplateData() - set gene plate data (plate, plate_row, plate_col)
setPlotEPclusterMeansData(boolean) - Method in class ShowExprProfilesPopup
setPlotEPclusterMeansData() - set expression profile to plot Cluster means data
setPlotEPmeansData(int, int[], float[][], float[][], boolean) - Method in class ExprProfileOverlay
setPlotEPmeansData() - set expression profile to plot mean data for each panel
setPlotEPmeansData(int, int[], float[][], float[][], boolean) - Method in class ExprProfileScrollPane
setPlotEPmeansData() - set EP to plot means for each panel
setPlotEPmeansData(int, int, float, float[], float[], boolean) - Method in class ExprProfileCanvas
setPlotEPmeansData() - set expression profile data so plot mean EP data.
setPlotEPmeansData(int, int, float, float[], float[], boolean) - Method in class ExprProfilePanel
setPlotEPmeansData() - set expression profile to plot means data.
setPlotState(CheckboxMenuItem) - Static method in class EventMenu
setPlotState() - set the Plot checkbox state.
setPluginHashState(String, String, Object) - Method in class MJAstate
setPluginHashState() - set state object value from MAEPlugin hash state storage.
setPopupEditVisible(boolean) - Method in class PopupEditRscript
setPopupEditVisible() - enable/disable popup edit RLO window
setPosQuantModeState(boolean) - Method in class MJAnormalization
setPosQuantModeState() - set Positive Quantified Intensity state [MAEPlugin] forced implementation via MAEStub.
setPosQuantModeState(CheckboxMenuItem) - Static method in class EventMenu
setPosQuantModeState() - set the Postive Quant data mode checkbox state.
setPostiveQuantData(GeneList, GeneList, int) - Method in class Filter
setPostiveQuantData() - filter out genes with negative quant values.
setProcessBit(int) - Method in class MJAReval
setProcessBit() - set specific Process Bit(s) for current RLO.
setProcessBitsDB(String[], String[], int[]) - Method in class MJAReval
setProcessBitsDB() - set the Export/Import ProcessBits (name,menu,type) database.
setProcessBitsDB(String[], String[], int[]) - Method in class RevalBase
setProcessBitsDB() - set the Export/Import ProcessBits (name,menuOn,menuOFF,type) database.
setPseudoArrayColorSpectrumMap(Color[], float[]) - Static method in class Util
setPseudoArrayColorSpectrumMap() - set pseudoarray color map spectrum data.
setPseudoArrayRatioColorMap(Color[], float[], int) - Static method in class Util
setPseudoArrayRatioColorMap() - set pseudoarray ratios color map data.
setPseudoColorRange() - Method in class DrawPseudoImage
setPseudoColorRange() - set isZscoreLog flag and pseudocolor range.
setR2ClientActionDB(String[], String[], int[]) - Method in class MJAReval
setR2ClientActionDB() - set R to client Actions (name,menu,type) DB.
setR2ClientActionDB(String[], String[], int[]) - Method in class RevalBase
setR2ClientActionDB() - set the R to client Actions (name,menu,type) database.
setR2ClientActionsData(String[], String[], int[]) - Method in class MJAReval
setR2ClientActionsData() - set cur.
setR2ClientFileNames - Variable in class RLO
List of output file names used to set R to Client data if any, null if none
setR2ClientFileNames - Variable in class PopupEditRscript
List of output file names used to set R to client data if any, null if none
setR2ClientFilesData(String[], String[], int[]) - Method in class RevalBase
setR2ClientFilesData() - set cur.
setR2ClientObjNames - Variable in class RLO
List of client object names used to set R to Client data if any, null if none.
setR2ClientObjNames - Variable in class PopupEditRscript
List of Client object names used to set R to client data if any, null if none.
setR2ClientObjTypes - Variable in class RLO
List of R_SET_R2CLIENT__xxxx types of output files if any, null if none.
setR2ClientObjTypes - Variable in class PopupEditRscript
List of R_SET_R2Client_xxxx types of output files if any, null if none.
setRangeMaps() - Method in class StateScrollers
setRangeMaps() - set norm dependent scrollers based normalization method.
setRangeMapsFromState() - Method in class StateScrollers
setRangeMapsFromState() - set normalization dependent scrollers based on norm.
setRatioColor(float, Color[], float[], int) - Static method in class Util
setRatioColor() - map data ratio to color in current color scheme Color is in(ratioMin : ratioMax].
setRatioColor(float, int) - Method in class ClusterGramCanvas
setRatioColor() - map data ratio to color (used to color a box).
setRatioHistCLfromF1F2Ratios(GeneList, MaHybridSample, float, float, boolean) - Method in class CompositeDatabase
setRatioHistCLfromF1F2Ratios() - set GeneList of F1/F2 ratios in ratio range
setRatioHistCLfromHP_XYratios(GeneList, MaHybridSample, MaHybridSample, float, float, boolean) - Method in class CompositeDatabase
setRatioHistCLfromHP_XYRatios() - set GeneList of X/Y ratios in ratio range
setRatioHistCLfromHP_XYsetRatios(GeneList, float, float, boolean) - Method in class CompositeDatabase
setRatioHistCLfromHP_XYsetRatios() - set GeneList of X/Y set ratios in ratio range
setRatioRangeState(CheckboxMenuItem) - Static method in class EventMenu
setRatioRangeState() - set the Ratio Range checkbox state.
setRatiosGeneList(GeneList, GeneList, int, boolean, boolean) - Method in class Filter
setRatiosGeneList() set ratiosCL by reportMode and sort by specified direction.
setRdataTypeDB(String[], String[], int[]) - Method in class MJAReval
setRdataTypeDB() - set the export-types (name,menu,type) database.
setRdataTypeDB(String[], String[], int[]) - Method in class RevalBase
setRdataTypeDB() - set the export-types (name,menu,type) database.
setReportFontSizeState(CheckboxMenuItem) - Static method in class EventMenu
setReportFontSizeState() - set the Report Font Size checkbox state.
setReportFormatState(CheckboxMenuItem) - Static method in class EventMenu
setReportFormatState() - set the Report Format checkbox state.
setRLO(int, String, String, String, String[], int[], int, int, String[], int[], String[], String[], int[], String) - Method in class MJAReval
setRLO() - set R LayOut (RLO) instance to the RLO database.
setRLO(int, String, String, String, String[], int[], int, int, String[], int[], String[], String[], int[], String) - Method in class RevalBase
setRLO() - set R LayOut (RLO) instance to the RLO database.
setRLO(int, String, String, String, String[], int[], int, int, String[], int[], String[], String[], int[], String) - Method in class RLO
setRLO() - set R LayOut (RLO) instance to the RLO database.
setRLOdbFromRLOedit() - Method in class PopupEditRscript
setRLOdbFromRLOedit() - set the RLO database from the edit state for current RLO.
setRLOeditFromRLOdb() - Method in class PopupEditRscript
setRLOeditFromRLOdb() - set the local RLO edit state from current RLO.
setRLOreportLoggingFlag(boolean) - Method in class MJAReval
setRLOreportLoggingFlag() - set RLO Report logging flag for creating subdirectory in {project}/Report/{RLOname}-yymmdd.hhmmss/ to store the RLO output files copied to Report/
setRLOreportLoggingFlag(boolean) - Method in class RevalBase
setRLOreportLoggingFlag() - set RLO Report logging flag for creating subdirectory in {project}/Report/{RLOname}-yymmdd.hhmmss/ to store the RLO output files copied to Report/
setRoutput2ClientObjects() - Method in class Reval
setRoutput2ClientObjects() - copy data for any R2Mae Action entries in the RLO.
setRoutput2ClientObjects() - Method in class RevalBase
setRoutput2ClientObjects() - copy data for any entries in the RLO.
setRowData(String[], int, int) - Method in class SimpleTable
setRowData() - set new row data[] for specific row in the table
setRowSeparator(String) - Method in class JavaCGIBridge
setRowSeparator() - Sets the row separator for the object.
setSample(Object) - Method in interface MAEPlugin.Normalization
setSample() - set the sample object
setSample(Object) - Method in class MAEPlugin.analysis.NormalizationPlugin
setSample() - method used to set primary variables from the sample.
setSampleCurScaledExtrema(int, float, float, float, float) - Method in class MJAsample
setSampleCurScaledExtrema() - set sample's current normalized scaled intensity extrema.
setSampleF1F2Extrema(int, float, float, float, float) - Method in class MJAsample
setSampleF1F2Extrema() - set list of sample's normalized F1F2 intensity extrema.
setSampleNameMethod(int) - Static method in class MJAsample
setSampleNameMethod() - sets the sample name method to the name domain to be used.
setSamplesInCondList(String, String[], int) - Method in class MJAcondition
setSamplesInCondList() - Set list of sample numbers in named condition.
setScrollBar(int, int) - Method in class ArrayScroller
setScrollBar() - set the scroll bars (x,y) position for this image.
setScrollBarPos(int) - Method in class ExprProfileScrollPane
setScrollBarPos() - set the scroll barPosition for this panel.
setScrollBarPos(int) - Method in class SSscrollHorizontal
setScrollBarPos() - reset scroller bar, not used now
setScrollBarPosition(int) - Method in class SSscrollVertical
setScrollBarPosition() - reset scroller bar, not used now
setScrollPageSteps(int, int) - Method in class ArrayScroller
setScrollPageSteps() - set scroll bar pagestep and steps
setSIcompareModeState(CheckboxMenuItem) - Static method in class EventMenu
setSIcompareModeState() - set the spot intensity compare mode checkbox state.
setSImodeState(CheckboxMenuItem) - Static method in class EventMenu
setSImodeState() - set the spot intensity mode checkbox state.
setSIrangeState(CheckboxMenuItem) - Static method in class EventMenu
setSIrangeState() - set the spot intensity Range checkbox state.
setSIthresholdsCL(GeneList, GeneList) - Method in class Filter
setSIthresholdsCL() - set GeneList of Spot Iintensity thresholded range where the threshold for rangeType [ST1:ST2] and rangeMode is RANGE_INSIDE, RANGE_OUTSIDE.
setSpotData(MaHybridSample, int, int, int, float) - Static method in class SpotData
setSpotData() - set the default STATIC spot data by (x,y).
setSpotData(MaHybridSample, Point, int, float) - Static method in class SpotData
setSpotData() - set the default STATIC spot data by Point xy.
setSpotData1(MaHybridSample, Point, int, float) - Static method in class SpotData
setSpotData1() - set the default STATIC spot data by Point xy.
setSpotData2(MaHybridSample, Point, int, float) - Static method in class SpotData
setSpotData2() - set the default STATIC spot data by Point xy.
setState(boolean) - Method in class MAEPlugin.CheckBoxMenuPlugin
setState() - utility to set the checkbox state
setState(boolean) - Method in interface MAEPlugin.Normalization
setState() - set the state of the checkbox
setSTOPbuttonState(boolean, boolean) - Method in class MenuBarFrame
setSTOPbuttonState() - enable/disable STOP button & clear abortFlag.
setSwissProtURL(String) - Method in class MJAstate
setSwissProtURL() - set the url
setText(SStextCell, SStextArray, int, int, int, int, String[][], int[], String[][], boolean) - Method in class SSstatusBar
setText() - set the cells coordinate position in the display.statusBar.
setText1(String, boolean) - Method in class ArrayScroller
setText1() - change the text1 msg for the panel.
setText1(String, boolean, Color, Color) - Method in class ArrayScroller
setText1() - change the text1 field in the panel with fg, bg colors You can save the msg as the title.
setText2(String) - Method in class ArrayScroller
setText2() - change the text2 field in the panel.
setText2(String, Color, Color) - Method in class ArrayScroller
setText2() - change the text2 field in the panel with fg, bg colors
setText3(String) - Method in class ArrayScroller
setText3() - change the text3 field in the panel.
setText3(String, Color, Color) - Method in class ArrayScroller
setText3() - change the text3 field in the panel with fg, bg colors
setThreadJavaCGIBridgeTimeOut(int) - Method in class JavaCGIBridge
setThreadJavaCGIBridgeTimeOut() - actual communication time out in msec.
setThresholdsCL(GeneList, GeneList, MaHybridSample, MaHybridSample, boolean) - Method in class Filter
setThresholdsCL() - set GeneList of thresholded F1,F2 or HP_X,HP_Y intensity or ratio range where the threshold for rangeType [T1:T2] or [R1:R2] and rangeMode is RANGE_INSIDE, RANGE_OUTSIDE.
setThresholdValueBySliderIdx(int, float) - Method in class StateScrollers
setThresholdValueBySliderIdx() - set slider threshold value by slider index
setTitles(String, String) - Method in class ChooserGUI
setTitles() - set titles for REMAINDER and SELECTED text areas
setTitles(String, String) - Method in class PopupCondChooserGUI
setTitles() - set titles for REMAINDER and SELECTED text areas
setTitles(String, String) - Method in class PopupOrderedCondChooserGUI
setTitles() - set titles for REMAINDER and SELECTED text areas
setTopSeparator(String) - Method in class JavaCGIBridge
setTopSeparator() - Sets the top separator for the object.
setUniGeneClusterIdURL(String) - Method in class MJAstate
setUniGeneClusterIdURL() - set the url
setUniGeneURL(String) - Method in class MJAstate
setUniGeneURL() - set the url
setupAllBasePaths(String) - Method in class MJAReval
setupAllBasePaths() - generate all base paths of directories
setupAllBasePaths(String) - Method in class RevalBase
setupAllBasePaths() - generate all base paths of directories
setupClientDemoRLOdb() - Method in class RgenDemo
setupClientDemoRLOdb() - create MJARevalr analyses[0:nAnalyses-1] database.
setupColorRatioRange(float, Color[], float[], int, boolean) - Static method in class Util
setupColorRatioRange() - setup ratio color map iteratively w/spacing delta.
setupColorSpectrumRange(Color[], float[], int, boolean) - Static method in class Util
setupColorSpectrumRange() - setup spectrumcolor map data range [0.0:1.0].
setupCondData() - Method in class PopupCondChooser
setupCondData() - get remainder and selected condition data, & parameters from MJA (indirectly from mae) and set up the cd[] array of conditions data.
setupCondData() - Method in class PopupOrderedCondChooser
setupCondData() - get remainder and selected condition data, & parameters from MJA (indirectly from mae) and set up the oclLd[] array of ordered condition data.
setupConstants() - Method in class MJAbase
setupConstants() - copy constants from apropriate variables.
setupData() - Method in class ClusterGramCanvas
setupData() - setup additional data arrays for ClusterGram
setupData(int) - Method in class ExprProfile
setupData() - setup the data arrays for the other computations
setupDataStruct(boolean) - Method in class HPxyData
setupDataStruct() - setup or change array allocations
setupDefaultGeneClass_GeneBitSets() - Method in class GeneClass
setupDefaultGeneClass_GeneBitSets() - called at end of init() to set up gene sets.
setupEPdata(int) - Method in class HPxyData
setupEPdata() - setup the HP-EP data arrays.
setupFieldIndexes() - Method in class ConfigTable
setupFieldIndexes() - setup indexes for commonly found fields.
setupFieldIndexes() - Method in class GipoTable
setupFieldIndexes() - lookup field name indexes for GIPO Table fields
setupFieldIndexes() - Method in class MaHPquantTable
setupFieldIndexes() - setup indexes for common Table fields for speedups.
setupFieldIndexes() - Method in class MaInfoTable
setupFieldIndexes() - setup indexes for common fields for speedups
setupFieldIndexes() - Method in class SamplesTable
setupFieldIndexes() - set up indexes for common fields for speedups
setupFullpathFilenames() - Method in class Config
setupFullpathFilenames() - add the full path to the file names
setupGenRcheckboxesStates() - Method in class PopupEditRscript
setupGenRcheckboxesStates() - set all genRbits checkbox states based on RLO state
setupGSstateMJAbase(MAExplorer) - Method in class MJAbase
MJAbase() - constructor for Gather Scatter API for MAExplorer to access MAExplorer data in a uniform interface.
setupHP_XYEchooserLists() - Method in class PopupHPChooser
setupHP_XYEchooserLists() - setup working HP-(X,Y,E) chooser lists.
setupHPmenuItemList() - Method in class PopupHPmenuGuesser
setupHPmenuItemList() - set lists of HP menu items for Guesser.
setupHybSampleData() - Method in class MaHybridSample
setupHybSampleData() - setup for .quant file for this hybridized sample.
setupKmeansHPstats() - Method in class ClusterGenes
setupKmeansHPstats() - compute summary K-means node HP statistics for each HP sample in each Node and assign mnClustersCL to the nKmeansNodes primary nodes.
setupMapLookupTables() - Method in class GipoTable
setupMapLookupTables() - reparse FGRC to GipoTable table row idx from tData[][].
setupNameTypeDB() - Method in class Reval
setupNameTypeDB() - setup the RLO (name,type) input, output, action, processBits database
setupPathBase(MAExplorer) - Static method in class Config
setupPathBase() - set mae.(fileBasePath, isWorkingMAE) from codeBase.
setupProcessCheckboxesStates() - Method in class PopupEditRscript
setupProcessCheckboxesStates() - set all processBits checkbox states based on RLO state
setupProjDirItemList() - Method in class PopupProjDirGuesser
setupProjDirItemList() - set lists of project Dir items for Guesser.
setupQuantImageTextQGridCoords() - Method in class MaHPquantTable
setupQuantImageTextQGridCoords() - for .quant data to draw in PseudoImage
setupRbinPath(boolean) - Method in class RevalBase
setupRbinPath() - setup RbinBasePath by analyzing OS env vars and OS name.
setupSpecialGeneLists() - Method in class GeneClass
setupSpecialGeneLists() - set up default special gene class cases.
setupTableFieldNameMap() - Method in class ConfigTable
setupTableFieldNameMap() - map user to MAE field names
setupXYdata(int) - Method in class HPxyData
setupXYdata() - setup the data arrays depending on useHPxySetDataFlag.
setupXYlabels() - Method in class HPxyData
setupXYlabels() - set the XY labels based on samples selected.
setupXYQandCorrectSkew() - Method in class MaHPquantTable
setupXYQandCorrectSkew() - set XY coords and correct XY skew if actual xy coords.
setUseAllScrollersFlag(boolean) - Method in class StateScrollers
setUseAllScrollersFlag() - set the state to display all scrollers by flag.
setUserFilterGeneList(String, boolean) - Method in class MJAgeneList
setUserFilterGeneList() - set the "User Filter Gene Set" by GeneList name.
setUserNormalizeGeneList(String, boolean) - Method in class MJAgeneList
setUserNormalizeGeneList() - set the "Normalize by 'User Gene set'" by GeneList name.
setUseSPLUSelseRengineFlag(boolean) - Method in class MJAReval
setUseSPLUSelseRengineFlag() - specify if use R or S-PLUS statistics engine
setViewerDisplayState(CheckboxMenuItem, String) - Static method in class EventMenu
setViewerDisplayState() - set the viewer display checkbox state.
setViewport(float, float, float, float) - Method in class Draw2Dplot
setViewport() - set the viewport (vx1,vx2,vy1,vy2) between two points.
setWaitCursor(boolean) - Method in class MJApopupRegistry
setWaitCursor() - set wait cursor ON/OFF to clock or standard cursor
setWaitCursor(boolean) - Method in class PopupRegistry
setWaitCursor() - if true set wait cursor, else set default cursor.
setWaitCursor(boolean) - Method in class Reval
setWaitCursor() - turn wait cursor on and off
setWaitCursor(boolean) - Method in class RevalBase
setWaitCursor() - turn wait cursor on and off
setZscoreNormalizationState() - Static method in class EventMenu
setZscoreNormalizationState() - set Zscore normalization state and adjust sliders if required.
sf - Variable in class MAExplorer
Global instance of spot feature info
sg - Variable in class MAExplorer
Global instance of Staging names for menus etc
sGenomicIDreq - Variable in class Config
PARAM ID required entries ("GenomicIDreq"+i).
sGenomicMenu - Variable in class Config
PARAM menu entries "GenomicMenu"+i.
sGenomicURL - Variable in class Config
PARAM URL entries "GenomicURL"+i
sGenomicURLepilogue - Variable in class Config
PARAM: URL entries "GenomicURLepilogue"+i
sh - Variable in class SpreadSheet
horizontal spreadsheet scroller instance
sh - Variable in class SSspreadPanel
 
shareUserState(String, String, String) - Method in class UserState
shareUserState() - share/unshare user state with other user [FUTURE]
sHelpMenu - Variable in class Config
PARAM menu entries "HelpMenu"+i
sHelpURL - Variable in class Config
PARAM URL entries "HelpURL"+i
shiftMod - Variable in class ScrollableImageCanvas
SHIFT/Mouse
shortenGeneList() - Method in class GeneList
shortenGeneList() - shorten the mList[] to save space.
shortWidthFlag - Variable in class ClusterGramCanvas
flag: plot narrower boxes
show() - Method in class MAEPlugin.popup.PluginUnLoader.UnloaderDialog
show() - necessary override to allow refresh of hash and lists in window
showCurrentRplots() - Static method in class EventMenu
showCurrentRplots() - show plots generated if any with last R eval.
showCurrentRplots() - Method in class RtestBase
showCurrentRplots() - show plots generated if any with last R eval.
showData(String, Color, Color) - Method in class RtestBase
showData() - draw data in GUI data line
showDemoRLOsCheckbox - Variable in class RtestBase
Show Demo RLOs checkbox toggles showDemoRLOsFlag.
showDemoRLOsFlag - Variable in class RtestBase
Flag show Demo RLOs in menu - toggled by showDemoRLOsCheckbox
showedGeneMouseOverFlag - Variable in class ScrollableImageCanvas
displayed Gene MouseOver
showedHPmouseOverFlag - Variable in class ScrollableImageCanvas
displayed HP MouseOver
showEGLButton - Variable in class ShowExprProfilesPopup
 
showEGLflag - Variable in class MAExplorer
Display Flag: show edited gene list
showEGLlinesFlag - Variable in class ShowExprProfilesPopup
 
showEPsubset - Variable in class DrawClusterGram
show expression profiles for nEPgenes at current ClusterGram position curCGrow
showErrBarsCheckBox - Variable in class ExprProfilePopup
checkbox to show error bars
showErrBarsCheckBox - Variable in class ShowExprProfilesPopup
 
showErrBarsFlag - Variable in class ExprProfileCanvas
draw error bars for each line
showErrBarsFlag - Variable in class ExprProfileOverlay
pass through to EP panel
showErrBarsFlag - Variable in class ExprProfileScrollPane
pass through to EP panel
showErrBarsFlag - Variable in class ShowExprProfilesPopup
Flag allowing the plotting of error bars
ShowExprProfilesPopup - class ShowExprProfilesPopup.
The class pops up a window to display a list of expression profiles for the data filtered genes.
ShowExprProfilesPopup(MAExplorer, GeneList, int[], float[][], float[][], int, boolean, String, String, int, boolean, boolean, boolean) - Constructor for class ShowExprProfilesPopup
ShowExprProfilesPopup() - Constructor.
showFeatures(String, String) - Static method in class Util
showFeatures() - print features to txtField2 and txtField3
showFilteredLinesButton - Variable in class ShowExprProfilesPopup
 
showFilteredLinesFlag - Variable in class ShowExprProfilesPopup
 
showGeneMsgsAndPlot() - Method in class ExprProfileOverlay
showGeneMsgsAndPlot() - show quant genomic data messages in MSG and in plot
showGeneMsgsAndPlot(int) - Method in class DrawScatterPlot
showGeneMsgsAndPlot() - show quant&NCBI data messages in MSG and in plot
showGeneMsgsAndPlot(int, int) - Method in class ClusterGramCanvas
showGeneMsgsAndPlot() - show quant & genomic data messages in MSG & in plot
showGeneOfInterest(int, int) - Method in class ExprProfileScrollPane
showGeneOfInterest() - show quant and genomic data if click on a point in plot
showGeneOfInterest(int, int, boolean) - Method in class DrawScatterPlot
showGeneOfInterest() - show quant&NCBI data if click on a point in plot
showGeneOfInterest(int, int, boolean) - Method in class ExprProfileOverlay
showGeneOfInterest() - show quant and genomic data if click on point in plot
showGeneReport(Gene[], int, int, String, int, String, boolean, int, int) - Method in class Report
showGeneReport() - show gene report with top maxGene's.
showGuiMsg(String, Color, Color) - Method in class RtestBase
showGuiMsg() - draw text in GUI message line
showHelpCheckbox - Variable in class PopupEditRscript
Show Help message text box.
showHelpFlag - Variable in class PopupEditRscript
Flag to display help message
showHP_E_assignmentsPopup() - Method in class SampleSets
showHP_E_assignmentsPopup() - make popup display of HP_E list of samples.
showHP_XY_assignmentsPopup() - Method in class SampleSets
showHP_XY_assignmentsPopup() - make popup display of HP_X and HP-Y sample lists
showHPnames - Variable in class DrawClusterGram
show list of Samples
showImageMousePos(MouseEvent, String, int, int) - Method in class ScrollableImageCanvas
showImageMousePos() - show the mouse positions in the image.
showKmeansDataFlag - Variable in class ExprProfileCanvas
report K-means data else just CloneID & name
showMouseCoords(String, int, int, int) - Method in class ScrollableImageCanvas
showMouseCoords() - show the mouse coordinates for DEBUGGING
showMsg(String) - Method in class MJAutil
showMsg() - display string in text field 1 in main window.
showMsg(String) - Method in class MaeJavaAPI
showMsg() - display string in text field 1 in main window.
showMsg(String) - Method in class Reval
showMsg() - display message in client GUI
showMsg(String) - Method in class RevalBase
showMsg() - display message in client GUI
showMsg(String) - Method in class Rtest
showMsg() - display message in client GUI
showMsg(String) - Method in class RtestBase
showMsg() - display message in client GUI
showMsg(String) - Static method in class Util
showMsg() - print msg to showStatus() and to txtField1
showMsg(String) - Method in interface MAEPlugin.MAEStub
showMsg() - alias to: Util.showMsg(String); used by: (all).
showMsg1(String) - Method in class MJAutil
showMsg1() - display string in text field 1 in main window.
showMsg1(String, boolean, Color, Color) - Static method in class Util
showMsg1() - print msg to showStatus() and to txtField1 and change color
showMsg1(String, Color, Color) - Method in class MJAutil
showMsg1() - display string in text field 1 in main window.
showMsg1(String, Color, Color) - Static method in class Util
showMsg1() - print msg to showStatus() and to txtField1 and change color
showMsg2(String) - Method in class MJAutil
showMsg2() - display string in text field 2 in main window.
showMsg2(String) - Static method in class Util
showMsg2() - print msg2 to txtField2
showMsg2(String, Color, Color) - Method in class MJAutil
showMsg2() - display string in text field 2 in main window.
showMsg2(String, Color, Color) - Static method in class Util
showMsg2() - print msg2 to txtField2 and change color
showMsg3(String) - Method in class MJAutil
showMsg3() - display string in text field 3 in main window.
showMsg3(String) - Static method in class Util
showMsg3() - print msg3 to txtField3
showMsg3(String, Color, Color) - Method in class MJAutil
showMsg3() - display string in text field 3 in main window.
showMsg3(String, Color, Color) - Static method in class Util
showMsg3() - print msg3 to txtField3 ALSO: side effect of setting cursor to WAIT_CURSOR if the(fg,bg) is not(black,white).
showNbrFilteredGenes() - Method in class Filter
showNbrFilteredGenes() - update Msg3 status line with the number of genes passing filter
showNonFilteredGenesFlag - Variable in class Draw2Dplot
show grayed out non-filtered genes
showNonFilteredGenesFlag - Variable in class ShowPlotPopup
flag: toggle non-Filtered genes button
showPEmsg(String) - Method in class PopupEditRscript
showPEmsg() - draw text in Popup Edit message line
showPEmsg(String, Color, Color) - Method in class PopupEditRscript
showPEmsg() - draw text in Popup Edit message line
ShowPlotPopup - class ShowPlotPopup.
The class popups a plot window containing one of several types of plots.
ShowPlotPopup(MAExplorer, int, String, String, int, int) - Constructor for class ShowPlotPopup
ShowPlotPopup() - constructor to create a spreadsheet from raw data with URL spec.
showPlotsButton - Variable in class RtestBase
"Show generated plot(s)" window button
showPopupSpreadsheetGeneReport(Table, Table, Gene[], int, int, String, int, String, int[], boolean) - Method in class Report
showPopupSpreadsheetGeneReport() - show gene report with top maxGene's.
showReducedFilteredGenesMsg(String, String, int) - Static method in class ClusterGenes
showReducedFilteredGenesMsg() - show 'reduce the# of filtered genes' msg
showRLOButton - Variable in class RtestBase
"Show RLO" window button
showRscriptButton - Variable in class RtestBase
"Show R script" current R script button
ShowSpreadsheetPopup - class ShowSpreadsheetPopup.
The ShowSpreadsheetPopup class pops up a scrollable dynamic spreadsheet.
ShowSpreadsheetPopup(MAExplorer, Report, String[], String[][], int, int, int, int, String, String, String[], int[], String[][], String, int, boolean) - Constructor for class ShowSpreadsheetPopup
ShowSpreadsheetPopup() - constructor to create a spreadsheet from raw data with URL spec.
ShowSpreadsheetPopup(MAExplorer, Report, Table, String, String, String, int, boolean) - Constructor for class ShowSpreadsheetPopup
ShowSpreadsheetPopup() - constructor to create a spreadsheet from table without URL spec.
ShowStringPopup - class ShowStringPopup.
The class creates and displays a scrollable string text area in a popup window.
ShowStringPopup(MAExplorer, String, int, int, String, String, int, int, String, int, String) - Constructor for class ShowStringPopup
ShowStringPopup() - Constructor.
showValidSpotInfo(Point, MaHybridSample) - Method in class SpotFeatures
showValidSpotInfo() - show spot gene info if valid obj else no-op
sHPsetCy53 - Variable in class SampleSets
may have " some HPs ("+sCy53+") swapped"
shrinkCube(MC_Cube) - Method in class MedianCut
shrinkCube() - Encloses "cube" with a tight-fitting cube by updating the (rmin,gmin,bmin) and (rmax,gmax,bmax) members of "cube".
siCanvas - Variable in class ArrayScroller
instance of the scrollable image canvas
similarESTsCL - Variable in class GeneClass
special list of ESTs similar to genes
simpleLookupRprogramPath() - Static method in class MJAReval
simpleLookupRprogramPath() - lookup RbinBasePath by analyzing OS env vars and OS name.
simpleLookupRprogramPath() - Static method in class RevalBase
simpleLookupRprogramPath() - lookup RbinBasePath by analyzing OS env vars and OS name.
simpleLookupSPLUSprogramPath() - Static method in class RevalBase
simpleLookupSPLUSprogramPath() - lookup SPlusBinBasePath by analyzing OS env vars and OS name.
SimpleTable - class SimpleTable.
The SimpleTable class creates an empty table of size tRows and tCols.
SimpleTable() - Constructor for class SimpleTable
SimpleTable() - constructor for creating empty table.
SimpleTable(String, String, String, int, int) - Constructor for class SimpleTable
 
SimpleTable(String, String, String, int, int, String[], String[][]) - Constructor for class SimpleTable
SimpleTable() - constructor for creating a table popupated with fields and data.
SINGLE_GENE - Static variable in class Guesser
flag for single gene finish
sit1 - Variable in class MAExplorer
PARAM "SI1" 0 or MIN_INTENSITY (spot Intens.)
sit2 - Variable in class MAExplorer
PARAM "SI2" MAX_INTENSITY
sleepFlag - Variable in class PopupBinOprDialogQuery
wait for button to be pushed
sleepFlag - Variable in class PopupDialogQuery
wait for button to be pushed
sleepFlag - Variable in class PopupLoginDialogQuery
flag to wait for button to be pushed
sleepMsec(int) - Method in class MJAutil
sleepMsec() - sleep nMsec where nMsec must be >= 0 milliseconds.
sleepMsec(int) - Static method in class Util
sleepMsec() - sleep nMsec where nMsec must be >= 0 milliseconds.
SLIDER - Static variable in class PopupRegistry
Property bit type: Notify bit if Slider changed
sList - Variable in class PopupHPChooser
List of ALL initial samples in DB
sListEo - Variable in class PopupHPChooser
initial HP-E list on starting chooser
sListrE - Variable in class PopupHPChooser
rem(E) = msListo - msListEo
sListrXY - Variable in class PopupHPChooser
rem(X+Y) = msListo - msListXo - msListYo
sListXo - Variable in class PopupHPChooser
initial HP-X sample list on starting chooser
sListYo - Variable in class PopupHPChooser
initial HP-Y sample list on starting chooser
smallFont - Variable in class DrawHistogram
font used for lableing
smallFont - Variable in class DrawRatioHistogram
font used for lableing
smallFont - Variable in class ScrollableImageCanvas
small char font - 12pt
smallFontLbl - Variable in class MenuBarFrame
current global small font
sMod - Variable in class SampleSets
prefix title "" or " 'set'"
sModX - Variable in class SampleSets
HP-X epilog "", sHPsetCy53, sCy35, sCy53
sModXY - Variable in class SampleSets
either sModX or sModY depending on mode
sModY - Variable in class SampleSets
HP-Y epilog "", sHPsetCy53, sCy35, sCy53
sMsg - Variable in class RgenDemo
Return string.
snHPDatabaseFileID - Variable in class MAExplorer
(opt) list of DB file ID [1:snHPnbr]
snHPFullStageText - Variable in class MAExplorer
list for buildingn menus [1:snHPnbr]
snHPMenuText - Variable in class MAExplorer
list for building menus [1:snHPnbr]
snHPName - Variable in class MAExplorer
slist of tage HP name [1:snHPnbr]
snHPnbr - Variable in class MAExplorer
# of entries in the Stage name list
snHPSampleID - Variable in class MAExplorer
list of free form sample names [1:snHPnbr]
snImageFile - Variable in class MAExplorer
list of image files to read [1:snHPnbr]
snNeedLogin - Variable in class MAExplorer
(opt) sample requires login
snPrjName - Variable in class MAExplorer
list of Project names [1:snHPnbr]
snSwapCy5Cy3Data - Variable in class MAExplorer
swap (Cy3,Cy5) field data for (Cy5,Cy3) for this HP
sock - Variable in class JavaCGIBridge
socket for fine-grain control
sortArray(String[], boolean) - Method in class MJAsort
sortArray() - bubble sort string array either ASCENDING or DESCENDING.
sortArray(String[], boolean) - Static method in class RevalBase
sortArray() - bubble sort string array either ASCENDING or DESCENDING.
sortArray(String[], boolean) - Static method in class SortMAE
sortArray() - bubble sort string array either ASCENDING or DESCENDING.
sortAsendDesendFlag - Variable in class SSspreadPanel
keep track of desend/ascending
sortDirection - Variable in class Report
Sort direction: assending or descending
sortedAlphaListStr - Variable in class Guesser
concatenated string for sorting
sortedClassIDListStr - Static variable in class PopupGeneGuesser
sorted list of clone_id
sortedGeneAndCloneIDListsFlag - Variable in class MAExplorer
true if alphaList[] geneNames and numericList[] gene xxxx_IDs are sorted
sortedGeneNameListStr - Static variable in class PopupGeneGuesser
sorted list of geneName
sortedHPmenuItemListStr - Static variable in class PopupHPmenuGuesser
sorted list of HP menu name
sortedProjDirItemListStr - Static variable in class PopupProjDirGuesser
sorted list of HP menu name
sortGeneList(Gene[], int, boolean) - Static method in class Gene
sortGeneList() - bubble sort gene list by associated gene.data field
sortGeneNameAndCloneIDLists(MAExplorer) - Static method in class PopupGeneGuesser
sortGeneNameAndCloneIDLists() - sort lists of Master_IDs & Gene_Names for use with the guesser.
sortKmeansClusterList(GeneList, GeneList) - Method in class ClusterGenes
sortKmeansClusterList() - sort K-means srcCL to dstCL by Node number.
SortMAE - class SortMAE.
The SortMAE class contains a variety of sorting methods.
SortMAE() - Constructor for class SortMAE
 
sortMenuEntriesByStage(StageNames[], int) - Method in class StageNames
sortMenuEntriesByStage() - sort HPmnuEntry[] by Stage.
sortNearestGenes(int) - Method in class ClusterGenes
sortNearestGenes() - sort nearest gene list for gene # c by min.
sortSpreadsheet(int, int, int, int, String[][]) - Method in class SSspreadPanel
sortSpreadsheet() - sort entire spread sheet based on column clicked.
sortStrArray(String[]) - Method in class MJAsort
sortStrArray() - create a sorted String[] array.
sortStrArray(String[]) - Static method in class SortMAE
sortStrArray() - create a sorted String[] array.
sortStrArray(String[], int) - Method in class MJAsort
sortStrArray() - create a sorted String[] array with len specified.
sortStrArray(String[], int) - Static method in class SortMAE
sortStrArray() - create a sorted String[] array with length specified.
sourceJ - Variable in class StageNames
index for sourceNames[]
sourceNames - Variable in class StageNames
List unique source name entries for various entities in Samples tbl
southPanel - Variable in class ArrayScroller
opt.
sp - Variable in class SpreadSheet
link to local SSspreadPanel instance
spaces - Variable in class PopupBinOprDialogQuery
spaces
spaces - Variable in class PopupDialogQuery
DEF_COL_SIZE spaces
spaces - Variable in class PopupLoginDialogQuery
variable holding spaces
spaces - Variable in class RtestBase
Spaces
SPACING_BETWEEN_SPOTS - Static variable in class MaHPquantTable
(opt) spacing between spots
sPanel - Variable in class ShowPlotPopup
Panel that holds scrollable canvas
specificCreateInputFileProblem - Variable in class RevalBase
If createInputDataFiles() failed, this is a suggestion on how to fix the problem.
spectrumColor - Variable in class DrawPseudoImage
color table used for PseudoArray image color spectrum color mapping
spectrumRange - Variable in class DrawPseudoImage
range of values for values used in PseudoArray image color spectrum mapping
sPluginCallAtStartup - Variable in class Config
PARAM menu entries "PluginCallAtStartup"+i.
sPluginClassFile - Variable in class Config
PARAM menu entries "PluginClassFile"+i.
sPluginMenuName - Variable in class Config
PARAM menu entries "PluginMenuName"+i.
sPluginMenuStubName - Variable in class Config
PARAM menu entries "PluginMenuStubName"+i.
SPlusBasePath - Static variable in class RevalBase
base path to S-Plus executable e.g.
SPlusBinBasePath - Static variable in class RevalBase
base bin Path to S-Plus executable if it exists.
spotCVCL - Variable in class Filter
"Use Spot CV filter"
spotCVthr - Variable in class Config
Threshold PARAM: Spot CV threshold 2*|f1-f2|/(f1+f2) for Filter
SpotData - class SpotData.
The SpotData class is used as a static object to hold gene (HP-X,HP-Y), (f1,f2) spot quantified data and (x,y) coordiantes for a particular hybridized sample HP or pairs of samples (HP-X and HP-Y).
SpotData(MAExplorer) - Constructor for class SpotData
SpotData() - constructor to capture mae.
SpotFeatures - class SpotFeatures.
The SpotFeatures class and methods to get spot feature String information.
SpotFeatures(MAExplorer) - Constructor for class SpotFeatures
SpotFeatures() - constructor
spotIntensCompareMode - Variable in class MAExplorer
Spot Intensity compare mode for threshold: COMPARE_xxxx
spotIntensFilterFlag - Variable in class MAExplorer
filter genes by spot Intensity threshold
spotIntensRangeMode - Variable in class MAExplorer
Spot intensity range mode for thresholds RANGE_OUTSIDE, RANGE_INSIDE
spotIntensTestMode - Variable in class MAExplorer
spot intensity test mode: SS_MODE_xxxx
spotIntensThrCL - Variable in class Filter
"Threshold: spot intensity [RI1:RI2]"
spotRad - Variable in class MAExplorer
PARAM "SpotRadius"
spp - Variable in class Draw2Dplot
if ShowPlotPopup is the parent, else null
spp - Variable in class DrawClusterGram
Parent popup window instance
spp - Variable in class DrawHistogram
ARG: parent window
spp - Variable in class DrawRatioHistogram
link to global instance
spp - Variable in class DrawScatterPlot
parent window
sppKey - Variable in class PopupRegistry
[0:nSPP-1] ShowPlotPopup key names
sppList - Variable in class PopupRegistry
[0:nSPP-1] list of active Plot popups
sppPropBits - Variable in class PopupRegistry
[0:nSPP-1] bits requesting notification of ShowPlotPopup of change
spreadPanel - Variable in class SSscrollHorizontal
 
spreadPanel - Variable in class SSscrollVertical
 
SpreadSheet - class SpreadSheet.
This SpreadSheet class implements a dynamic spread sheet data structures.
SpreadSheet(ShowSpreadsheetPopup, MAExplorer, int, int, String[][], int, int, int, String, Font, Font, Font, int[], String[][]) - Constructor for class SpreadSheet
Spreadsheet() - creates a new Panel with BoderLayout and adds a new SSspreadPanel (the grid itself) w/ horizontal and vertical scrollbars.
ss - Variable in class ShowSpreadsheetPopup
SpreadSheet objecyt
SS_MODE_ELIST - Static variable in class MAExplorer
HP data Filter subset mode: F1F2 HP-E list - hps.msListE[]
SS_MODE_ELIST - Static variable in class MJAbase
HP data Filter subset mode: F1F2 HP-E list
SS_MODE_MS - Static variable in class MAExplorer
HP data Filter subset mode: F1F2 current HP - mae.ms
SS_MODE_MS - Static variable in class MJAbase
HP data Filter subset mode: F1F2 current HP
SS_MODE_XANDY_SETS - Static variable in class MAExplorer
HP data Filter subset mode: F1F2 HP-X AND HP-Y sets - hps.msListX(Y)[]
SS_MODE_XANDY_SETS - Static variable in class MJAbase
HP data Filter subset mode: F1F2 HP-X and HP-Y sets
SS_MODE_XORY_SETS - Static variable in class MAExplorer
HP data Filter subset mode: F1F2 HP-X or HP-Y sets - hps.msListX(Y)[]
SS_MODE_XORY_SETS - Static variable in class MJAbase
HP data Filter subset mode: F1F2 HP-X or HP-Y sets
SS_MODE_XSET - Static variable in class MAExplorer
HP data Filter subset mode: F1F2 HP-X sets - hps.msListX[]
SS_MODE_XSET - Static variable in class MJAbase
HP data Filter subset mode: F1F2 HP-X sets
SS_MODE_XY - Static variable in class MAExplorer
HP data Filter subset mode: F1F2 HP-X and HP-Y - mae.msX and mae.msY
SS_MODE_XY - Static variable in class MJAbase
HP data Filter subset mode: F1F2 HP-X and HP-Y
SS_MODE_YSET - Static variable in class MAExplorer
HP data Filter subset mode: F1F2 HP-Y sets - hps.msListY[]
SS_MODE_YSET - Static variable in class MJAbase
HP data Filter subset mode: F1F2 HP-Y sets
ssp - Variable in class SpreadSheet
link to global instance of SpreadsheetPopup
ssp - Variable in class SSspreadPanel
pass down globals
ssp - Variable in class SSstatusBar
popup browser flag
sspKey - Variable in class PopupRegistry
[0:nSSP-1] ShowStringPopup key names
sspList - Variable in class PopupRegistry
[0:nSSP-1] list of active String popups
sspPropBits - Variable in class PopupRegistry
[0:nSSP-1] bits requesting notification of ShowStringPopup of changes
sspTime - Variable in class PopupRegistry
[0:nSPP-1] String Popup timeout seconds
SSscrollHorizontal - class SSscrollHorizontal.
 
SSscrollHorizontal(SSspreadPanel) - Constructor for class SSscrollHorizontal
SSscrollHorizontal() - a horizontal scrollbar for the SpreadSheet
SSscrollVertical - class SSscrollVertical.
 
SSscrollVertical(SSspreadPanel) - Constructor for class SSscrollVertical
SSscrollVertical() - a vertical scrollbar for the SpreadSheet
ssspKey - Variable in class PopupRegistry
[0:nSSSP-1] ShowSpreadsheetPopup key names
ssspList - Variable in class PopupRegistry
[0:nSSSP-1] list of active spreadsheet popup popups
ssspPropBits - Variable in class PopupRegistry
[0:nSSSP-1] bits requesting notification of ShowSpreadsheetPopup of change
SSspreadPanel - class SSspreadPanel.
 
SSspreadPanel(MAExplorer, int, int, String[][], int, int, int, Font, Font) - Constructor for class SSspreadPanel
SSspreadPanel() - constructor, inits the grid with values without the URL font and fields.
SSspreadPanel(String[][], ShowSpreadsheetPopup, MAExplorer, int, int, int, int, int, Font, Font, Font, int[], String[][]) - Constructor for class SSspreadPanel
SSspreadPanel() - constructor, panel holding (row,col) matrix of TextFields with the URL font and fields.
SSstatusBar - class SSstatusBar.
 
SSstatusBar(ShowSpreadsheetPopup, MAExplorer, int, int) - Constructor for class SSstatusBar
SSstatusBar() - constructor, add the components for statusbar set here
SStextArray - class SStextArray.
 
SStextArray(int, int) - Constructor for class SStextArray
SStextArray() - constructor, creates an (r,c) "array" of SStextCell
SStextCell - class SStextCell.
 
SStextCell() - Constructor for class SStextCell
SStextCell() - Constructor, inits a TextField of length for all other values 0
SStextCell(int) - Constructor for class SStextCell
SStextCell() - Constructor, inits a TextField of length, all other values 0
stageJ - Variable in class StageNames
index for stageNames[]
stageLabel - Variable in class StageNames
itemLabel to be used in menu
stageNames - Variable in class StageNames
List unique stage name entries for various entities in Samples tbl
StageNames - class StageNames.
The class sets up staging names for building menus and sample labels.
StageNames(int, int, int, int, int, int, int, int, String) - Constructor for class StageNames
StageNames() - constructor with data
StageNames(MAExplorer) - Constructor for class StageNames
StageNames() - initial global constructor with no data
standarizeDataVector() - Static method in class HierClustNode
standarizeDataVector() - compute standardized dataV[] using (dataV[h]-mnDataV[h])/sdDataV[h] for ALL terminal objects [0:nObj-1].
start() - Method in class MAExplorer
start() - (re)create GUI if needed, read PARAMs & start run thread.
startPopupDialog(String, int) - Method in class PopupBinOprDialogQuery
startPopupDialog() - create a hidden dialog panel within a frame.
startPopupDialog(String, int) - Method in class PopupDialogQuery
startPopupDialog() - create a hidden dialog panel within a frame.
startPopupDialog(String, int) - Method in class PopupLoginDialogQuery
startPopupDialog() - create a hidden dialog panel within a frame.
startRow - Variable in class ShowSpreadsheetPopup
ARG: start of table data to use, counts from 0 ?
startupDir - Static variable in class MAExplorer
Standalone startup Directory where startupFile is found
startupFile - Static variable in class MAExplorer
Standalone startup DB .mae file
startupFileExistsFlag - Static variable in class MAExplorer
Flag that indicates if the database startup .mae file exists
startupRscriptFileName - Static variable in class RevalBase
name of current batch R startup script file to exec() by the OS
stat - Variable in class Filter
link to global Statistics instance
stat - Variable in class MAExplorer
Global instance of parametric & non-parametric stats
stat - Variable in class MaHybridSample
link to global Statistics instance
stat - Variable in class Report
link to global Statistics instance
stateScr - Static variable in class EventMenu
link to global StateScrollers instance
stateScr - Variable in class MAExplorer
holds popup state scrollers - note: created in MenuBarFrame!
StateScrollers - class StateScrollers.
The class builds a popup window dynamic grid of threshold parameter scrollers.
StateScrollers(MAExplorer, String) - Constructor for class StateScrollers
StateScrollers() - constructor to build the GUI with pop up menus
Statistics - class Statistics.
The class contains various parametric and non-parametric probability statistics methods.
Statistics() - Constructor for class Statistics
Statistics() - constructor
Statistics(MAExplorer) - Constructor for class Statistics
Statistics() - constructor
status - Variable in class SSspreadPanel
[RC] & full cell contents displayed @top
statusCanvas - Variable in class DrawClusterGram
status canvas
StatusCanvas - class StatusCanvas.
 
StatusCanvas(DrawClusterGram, int, int) - Constructor for class StatusCanvas
StatusCanvas () - constructor
statusCanvasHeight - Variable in class DrawClusterGram
height size of status canvas
statVertOffset - Variable in class ClusterGramCanvas
offset of status canvas if drawing it at top of GIF image canvas, else 0
stdDev - Variable in class MaHybridSample
Filter hist: std deviation raw intensity
stdDev - Variable in class Statistics
stdDev[0:nConditions-1] of data for computations, set by calcMeanAndVariance() if calcStdDevFlag set on call
stdDevCalDNA - Variable in class MaHybridSample
stddev 'calibration DNA' intensity
stdDevEdata - Variable in class HPxyData
std deviation HP-EP list data
stdDevH - Variable in class Statistics
histogram data stdDev set by calcHistStats()
stdDevUseGeneSet - Variable in class MaHybridSample
stddev 'User Filter Gene Set' intensity
stdDevXdata - Variable in class HPxyData
std deviation intensity HP-X set data
stdDevYdata - Variable in class HPxyData
std deviation HP-Y set data
stdizeByMnStdFlag - Static variable in class HierClustNode
flag: standardize all array dataV[h] by mnDataV[h]/sdDataV[h]
steps - Variable in class ArrayScroller
prewired scroller steps
sTitle - Variable in class RgenDemo
Title is the "Method: current RLO menu name
stop() - Method in class MAExplorer
stop() - stop the thread.
stopButton - Variable in class MenuBarFrame
If hasStopButtonFlag is set (i.e.
stopLblName - Variable in class MenuBarFrame
either "STOP!" or " "
storeDataBufParser(String, String, String[], boolean) - Method in class Table
storeDataBufParser() - Put data into Table tData[r][c] and tFields[c], given a String from the whole file.
strainJ - Variable in class StageNames
index for strainNames[]
strainNames - Variable in class StageNames
List unique strain name entries for various entities in Samples tbl
strDataIsSortedFlag - Variable in class PopupGeneGuesser
set once it is sorted
strDataIsSortedFlag - Static variable in class PopupHPmenuGuesser
Flag that is set once it is sorted
strDataIsSortedFlag - Static variable in class PopupProjDirGuesser
flag: set once data is sorted
stringValidFlag - Variable in class PopupCondChooser.PopupTextField
This is set if the name the user types is valid
stringValidFlag - Variable in class PopupOrderedCondChooser.PopupTextField
This is set if the name the user types is valid
stubMenus - Variable in class MenuBarFrame
list of Menu Stubs in Menu tree
stubNames - Variable in class MenuBarFrame
list of Names of Stubs in Menu tree
subAlphaList - Variable in class Guesser
sub strings for guesser
subMenuNbr - Variable in class StageNames
submenu # correspndg to Source
sumCBdist - Variable in class HierClustNode
Dynamic node: sum of CB distances
sumDistSq - Variable in class HierClustNode
Dynamic node: sum of distances squared
sv - Variable in class SpreadSheet
vertical spreadsheet scroller instance
sv - Variable in class SSspreadPanel
scroll bars
svgFile - Variable in class RgenDemo
Current SVG file for current RLO, if specified
swapCy5Cy3AndReCalcStats() - Method in class MaHybridSample
swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics for this sample.
swapCy5Cy3AndReCalcStats(int) - Method in class MJAsample
swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics for sample.
swapCy5Cy3DataFlag - Variable in class MaHPquantTable
 
swapCy5Cy3DataFlag - Variable in class MaHybridSample
flag: swapped Cy3 (Field1) and Cy5 (Field 2) data
swapRowsColsFlag - Variable in class MAExplorer
PARAM flip array rows & columns
SwissProt - Variable in class Gene
Swiss-Prot ID if it exists
SwissProt - Variable in class SpotFeatures
lookup SwissProtID
SwissProtIdx - Variable in class GipoTable
index for "SwissProtID"
swissProtURL - Variable in class Config
base addr PARAM "swissProtURL"
swissProtViewerFlag - Variable in class MAExplorer
Swiss-Prot page popup browser Mode
switchAlphaList(int) - Method in class Guesser
switchAlphaList() - switch alphaList to alphaListMode (for gene guesser).
syncCanvasAccess() - Method in class ScrollableImageCanvas
syncCanvasAccess() - update canvas access
syncScrollerAccess() - Method in class ArrayScroller
syncScrollerAccess() - update the image scroller and sync canvas access to current HP's pseudoarray image, ms, msX, msY

T

t - Variable in class Statistics
CALC: t or t' statistic set by calcTandPvalues()
t1 - Variable in class MAExplorer
PARAM "I1" 0 or MIN_INTENSITY (gene "intens")
t2 - Variable in class MAExplorer
PARAM "I2" MAX_INTENSITY
ta - Variable in class ChooserGUI.MouseEventHandler
TextArea list of best guesses
ta - Variable in class Guesser
TextArea list of best guesses
ta - Variable in class KeyEventHandler
TextArea list of best guesses
ta - Variable in class MouseEventHandler
TextArea list of best guesses
ta - Variable in class PopupCondChooserGUI.MouseEventHandler
TextArea list of best guesses
ta - Variable in class PopupOrderedCondChooserGUI.MouseEventHandler
TextArea list of best guesses
TA_COLS - Static variable in class StateScrollers
size of mouseover TextArea
TA_ROWS - Static variable in class StateScrollers
size of mouseover TextArea
ta1 - Variable in class ChooserGUI
REMAINDER objs
ta1Label - Variable in class ChooserGUI
label under ta1
ta2 - Variable in class ChooserGUI
SELECTED obj list
ta2Label - Variable in class ChooserGUI
label under ta2
tabDelimReportFile - Variable in class RgenDemo
 
Table - class Table.
This class creates a table object with no data or data read from a tab-delimited file.
Table(MAExplorer, int, int, String, String) - Constructor for class Table
Table() - constructor for creating empty table of (nRows,nCols).
Table(MAExplorer, String, String) - Constructor for class Table
Table() - constructor for creating table from file
Table(MAExplorer, String, String, String[], boolean) - Constructor for class Table
Table() - constructor for creating table from file
Table(SimpleTable) - Constructor for class Table
Table() - constructor for creating table from a SimpleTable
taCols - Variable in class ChooserGUI
columns/text area
taCols - Variable in class Guesser
size of TextArea
taCols - Variable in class PopupCondChooserGUI
columns/text area
taCols - Variable in class PopupGeneGuesser
default size of text area
taCols - Variable in class PopupHPChooser
TextArea cols dimensions
taCols - Variable in class PopupHPmenuGuesser
default size of text area
taCols - Variable in class PopupOrderedCondChooserGUI
columns/text area
taCols - Variable in class PopupProjDirGuesser
working column size of text area
tagCol - Variable in class ShowSpreadsheetPopup
tag col for current clicked cell color
tagRow - Variable in class ShowSpreadsheetPopup
tag row for current clicked cell color
TARGET_SIZE - Static variable in class Draw2Dplot
target Size for selecting a line
TARGET_SIZE - Static variable in class DrawHistogram
target Size for selecting a line
TARGET_SIZE - Static variable in class DrawRatioHistogram
target Size for selecting a line
TARGET_SIZE - Static variable in class ExprProfileCanvas
target Size for selecting a line
targetColor - Variable in class ScrollableImageCanvas
cross-hairs color
taRows - Variable in class ChooserGUI
rows/text area
taRows - Variable in class Guesser
size of TextArea
taRows - Variable in class PopupCondChooserGUI
rows/text area
taRows - Variable in class PopupGeneGuesser
default size of text area
taRows - Variable in class PopupHPChooser
TextArea rows dimensions
taRows - Variable in class PopupHPmenuGuesser
default size of text area
taRows - Variable in class PopupOrderedCondChooserGUI
rows/text area
taRows - Variable in class PopupProjDirGuesser
working row size of text area
taStr1 - Variable in class ChooserGUI
label for SELECTED LEFT text area
taStr2 - Variable in class ChooserGUI
label for REMAINDER RIGHT text area
tblFmtMode - Variable in class MAExplorer
Report table format mode: RPT_FMT_xxxx
tblFmtMode - Variable in class Report
Table format mode: spreadsheet or tab-delim
tCols - Variable in class ShowSpreadsheetPopup
ARG: # cols in Table data
tCols - Variable in class SimpleTable
# of columns/row in the table
tData - Variable in class ShowSpreadsheetPopup
ARG: user Table data [0:maxRows-1][0:maxCols-1]
tData - Variable in class SimpleTable
row vectors of data [0:tRows-1][0:tCols-1]
tempBasePath - Static variable in class RevalBase
path of {client project} Temp/ directory
tempCD_CL - Variable in class CompositeDatabase
temporary GeneList used in local gene list operations
templateValue - Variable in class PopupEditRscript
selected template value # from R_DATA_TYPE_xxxx Note: this is the type of the 1st input file
tempSetBL - Static variable in class GeneBitSet
temporary bit set used in set operations
tempSetCL - Static variable in class GeneList
temporary GeneList used in set operations
termEnumCnt - Static variable in class HierClustNode
# terminal nodes enumerated in order
testCy3Cy5SamplesRange(float, float) - Method in class MJAfilter
testCy3Cy5SamplesRange() - test cy3/cy5 [CR1:CR2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
testGenericNormPluginFlag - Variable in class MAExplorer
If DBUG_GENERIC_NORM_PLUGIN, then debug GenericNormalizationPlugin within the code.
TestPlugin - class TestPlugin.
The TestPlugin class may be invoked from MAExplorer when debugging MAEPlugins.
TestPlugin(MaeJavaAPI) - Constructor for class TestPlugin
TestPlugin() - constructor to invoke user's test Plugin code.
TestPluginCode - class TestPluginCode.
This is a dummy class meant to be used with TestPluginCode for testing MAEPlugins.
TestPluginCode(MAExplorer) - Constructor for class TestPluginCode
TestPluginCode() - constructor to capture mae.
testSamplesRange(float, float, boolean) - Method in class MJAfilter
testSamplesRange() - for testing [I1:I2] or [R1:R2] for current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
testSpotIntensityRange(float) - Method in class MJAfilter
testSpotIntensityRange() - for testing spot intensity [ST1:ST2] in current rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
text_font - Variable in class LogTextFrame
text font in TextArea
textarea - Variable in class ShowStringPopup
Text area GUI for main report
textBkGrdColor - Variable in class LogTextFrame
background color of text area
textField - Variable in class PopupDialogQuery
place text to be edited here
textField1 - Variable in class PopupBinOprDialogQuery
place text to be edited here
textField2 - Variable in class PopupBinOprDialogQuery
place text to be edited here
textField3 - Variable in class PopupBinOprDialogQuery
place text to be edited here
textFieldWizard - Variable in class PopupEditRscript
Wizard title text fields [0:MAX_WIZ_ROWS-1]
textHP - Variable in class MaHybridSample
title for each HP grid
textReport - Variable in class ShowStringPopup
copy of text in textArea
textValueChanged(TextEvent) - Method in class PopupCondChooser.CondParamEditForm
textValueChanged() - service text changed by setting the value changed flag.
textValueChanged(TextEvent) - Method in class PopupOrderedCondChooser.CondParamEditForm
textValueChanged() - service text changed by setting the value changed flag.
textValueChanged(TextEvent) - Method in class PopupEditRscript
textValueChanged() - event handler for TextArea
tf - Variable in class Guesser
Text field for User input
tf - Variable in class KeyEventHandler
User types in here
tf - Variable in class MouseEventHandler
User types in here
tfGL - Variable in class PopupCondChooser.CondParamEditForm
TextFields GridLayout to create condition form
tfGL - Variable in class PopupOrderedCondChooser.CondParamEditForm
TextFields GridLayout to create condition form
tFields - Variable in class ShowSpreadsheetPopup
ARG: [maxCols] Table field names from user
tFields - Variable in class SimpleTable
names of table fields
tfPanel - Variable in class PopupCondChooser.CondParamEditForm
TextFields go here
tfPanel - Variable in class PopupOrderedCondChooser.CondParamEditForm
TextFields go here
TH_EQ - Static variable in class ShowPlotPopup
threshold Button tests "= "
TH_GT - Static variable in class ShowPlotPopup
threshold Button tests "> "
TH_IN - Static variable in class ShowPlotPopup
threshold Button tests "<>"
TH_LT - Static variable in class ShowPlotPopup
threshold Button tests "< "
TH_OUT - Static variable in class ShowPlotPopup
threshold Button tests "><"
threadCanRunMethodExecute - Variable in class JavaCGIBridge
This is a flag that makes it so that the run() method is at least semi-private for Threading.
threadCGIData - Variable in class JavaCGIBridge
This is the returned URL data.
threadCompleted - Variable in class JavaCGIBridge
This is a flag indicating whether the URL data was retrieved inside the thread or not.
threadFormVar - Variable in class JavaCGIBridge
The HTML form data for the URL that data is retrieved from.
threadJavaCGIBridgeTimeOut - Variable in class JavaCGIBridge
This is the actual CGI Timeout value in milliseconds for the instantiated object.
threadURL - Variable in class JavaCGIBridge
The URL That data is retrieved from.
TIMEOUT - Static variable in class PopupRegistry
Property bit type: set if timeout and kill itself after TIMEOUT_DELAY milliseconds
TIMEOUT_DELAY - Static variable in class PopupRegistry
# msec.
timeStampReportDir - Variable in class RevalBase
time stamp dir for reports
timeStr() - Static method in class Util
timeStr() - return a new daytime HH:MM:SS string of the current time.
title - Variable in class ArrayScroller
current title for window
title - Variable in class ChooserGUI
title for entire GUI window
title - Variable in class Draw2Dplot
ARGS: horizontal caption
title - Variable in class DrawClusterGram
title for window
title - Variable in class DrawHistogram
title
title - Variable in class DrawRatioHistogram
title
title - Variable in class ExprProfileCanvas
ARG: opt.
title - Variable in class ExprProfileOverlay
title for entire EP.
title - Variable in class ExprProfileScrollPane
title for entire EP.
title - Variable in class Guesser
title of window
title - Variable in class MenuBarFrame
title for frame
title - Variable in class PopupCondChooserGUI
title for entire GUI window
title - Variable in class PopupHPChooser
title of popup chooser window
title - Variable in class PopupOrderedCondChooserGUI
title for entire GUI window
title - Variable in class PopupScrollableSelector
# of elements in the list
title - Variable in class ShowExprProfilesPopup
ARG: for PopupRegistry
title - Variable in class ShowPlotPopup
ARG: title of popup plot
title - Variable in class ShowSpreadsheetPopup
ARG: title of spreadsheet
title - Variable in class SimpleTable
Optional title of table
title - Variable in class SpreadSheet
ARG: user title
title - Variable in class StateScrollers
holds title string for state scroller GUI
title - Variable in class Statistics
for data used in histogram set by calcHistStats()
title - Variable in class LogTextFrame
text to beas popup window title
title1 - Variable in class Draw2Dplot
ARGS:
title2 - Variable in class Draw2Dplot
ARGS:
title3 - Variable in class Draw2Dplot
ARGS:
titleFont - Variable in class ChooserGUI
font used by title
titleFont - Static variable in class ExprProfileCanvas
 
titleFont - Variable in class PopupCondChooser
font for labels
titleFont - Variable in class PopupCondChooserGUI
font used by title
titleFont - Variable in class PopupHPChooser
font for title of popup chooser window
titleFont - Variable in class PopupOrderedCondChooser
font for labels
titleFont - Variable in class PopupOrderedCondChooserGUI
font used by title
titleFont - Variable in class RtestBase
fonts for labeling full image title etc.
titleLabel - Variable in class Guesser
title label
titleLabel - Variable in class StateScrollers
Label for title
titleLbl - Variable in class PopupScrollableSelector
 
titlePanel - Variable in class DrawClusterGram
titlePanel of parent
titlePanel - Variable in class Guesser
place for title
titlePanel - Variable in class SpreadSheet
title panel for of spreadsheet
titleX - Variable in class DrawRatioHistogram
X title
titleY - Variable in class DrawRatioHistogram
Y title
tmpCL - Variable in class EditedGeneList
temporary gene list for computations
tmpCL - Variable in class Filter
temporary gene list for intersections computations
topEdge - Variable in class ClusterGramCanvas
top edge of box array
topEditPanel - Variable in class PopupEditRscript
 
topNode - Static variable in class HierClustNode
top node of the tree
topNodeID - Static variable in class HierClustNode
top Node of tree
toPoint - Variable in class ScrollableImageCanvas
mouseDragged record
topPanel - Variable in class RtestBase
top panel holding the buttonPanel and the msgTA TextField
topSeparator - Variable in class JavaCGIBridge
The top of data separator.
topSubMenuNames - Variable in class SampleSets
The following are the order of the top level menus in the menu tree.
topTitle - Variable in class Draw2Dplot
ARGS:
toString() - Method in class Gene
toString() - generate prettyprint gene data string
toString(boolean) - Method in class GridCoords
toString() - convert grid coordinate instance to string name
toString(int, String) - Method in class Reval
toString() - create string representing the R LayOut (RLO) of the instance.
toString(int, String, String) - Method in class RevalBase
toString() - create string representing the R LayOut (RLO) of the RLO instance
toString(String, boolean) - Method in class ChooserGUI
toString() - pretty-print instance of this ChooserGUI
toString(String, boolean) - Method in class PopupCondChooserGUI
toString() - pretty-print instance of this PopupCondChooserGUI
toString(String, boolean) - Method in class PopupOrderedCondChooserGUI
toString() - pretty-print instance of this PopupOrderedCondChooserGUI
toString(String, boolean, boolean, boolean) - Method in class HierClustNode
toString() - convert value of a node to a String.
tot1S - Static variable in class SpotData
total bkgrd corrected intensity of a spot
tot2S - Static variable in class SpotData
total bkgrd corrected intensity of a spot
totQ - Variable in class MaHybridSample
list of raw intensity data/spot, unscaled
totS - Static variable in class SpotData
total bkgrd corrected intensity of a spot
tree - Variable in class ClusterGramCanvas
hierarchical cluster tree
tree - Variable in class DrawClusterGram
cluster tree
trimWhitespace() - Method in class SimpleTable
trimWhitespace() - trim Table tData[][] and tFields[] data.
tRows - Variable in class ShowSpreadsheetPopup
ARG: # rows in Table data
tRows - Variable in class SimpleTable
# of rows/Table
tSize - Static variable in class ScrollableImageCanvas
target Size
tTestFct - Variable in class RgenDemo
Optional t-test function code if required by addTtestFlag
tTestXYfilterFlag - Variable in class MAExplorer
filter genes passing HP-X/-Y t-test
tTestXYsetsFilterFlag - Variable in class MAExplorer
filter genes passing HP-X/-Y sets t-test
txt - Variable in class SSstatusBar
 
txtField1 - Variable in class ArrayScroller
image title placed above canvas
txtField2 - Variable in class ArrayScroller
genomic info placed above canvas
txtField3 - Variable in class ArrayScroller
additional genomic info placed above canvas
txtOld - Variable in class SSstatusBar
 

U

UGclusterName - Variable in class Gene
opt.
UGclusterName - Variable in class SpotFeatures
lookup "UGclusterName" name
uName - Variable in class UserState
user name from dialog handler
Unigene_cluster_IDidx - Variable in class GipoTable
index for "Unigene cluster ID"
Unigene_cluster_nameIdx - Variable in class GipoTable
index for "Unigene cluster name"
Unigene_ID - Variable in class Gene
NCBI Unigene cluster if it exists
Unigene_ID - Variable in class SpotFeatures
lookup "Unigene_ID" name
uniGeneClusterIdURL - Variable in class Config
base addr PARAM "uniGeneClusterIdURL"
unigeneSpecies - Variable in class Config
PARAM "species" UniGene Species code
uniGeneURL - Variable in class Config
base addr PARAM "uniGeneURL"
uniGeneViewerFlag - Variable in class MAExplorer
UniGene popup browser Mode
union(Condition, Condition, String) - Method in class Condition
union() - compute union of two conditions cond1 and cond2.
union(GeneBitSet, GeneBitSet, GeneBitSet) - Method in class GeneBitSet
union() - compute union of GeneBitSets sets (b1 & b2) ==> b3.
union(GeneList, GeneList, GeneList) - Method in class GeneList
union() - compute union of gene lists (c1 & c2) ==> c3.
union(String, String, String) - Method in class MJAcondition
union() - compute resultCond= Union (Condition 1, Condition 2)
UNIQUE - Static variable in class PopupRegistry
Property bit type: set if this is a unique popup
uniqueInsert(String[], String[], int, String, Hashtable) - Method in class MJAsort
uniqueInsert() - insert s1 at end of sList1[] and UC of s1 in sList1UC[] if s1 is not already in sList1[].
uniqueInsert(String[], String[], int, String, Hashtable) - Static method in class SortMAE
uniqueInsert() - insert s1 at end of sList1[] and UC of s1 in sList1UC[] if s1 is not already in sList1[].
uniqueInsert(String[], String[], String[], int, String, String, Hashtable) - Method in class MJAsort
uniqueInsert() - insert s1,s2 at end of sList1[], sList2[] lists if s1 is not already in sList1[].
uniqueInsert(String[], String[], String[], int, String, String, Hashtable) - Static method in class SortMAE
uniqueInsert() - insert s1,s2 at end of sList1[], sList2[] lists if s1 is not already in sList1[].
uniqueInsertionSort(String[], String[], int, String) - Static method in class SortMAE
uniqueInsertionSort() - insertion sort newStr into sList[] if unique.
uniqueInsertionSort(String[], String[], int, String, Hashtable) - Method in class MJAsort
uniqueInsertionSort() - insertion sort newStr into sList[] if unique.
uniqueInsertionSort(String[], String[], String[], int, String, String) - Static method in class SortMAE
uniqueInsertionSort() - insertion bubble sort s1,s2 into sList1[], sList2[] if s1 is unique.
uniqueInsertionSort(String[], String[], String[], int, String, String, Hashtable) - Method in class MJAsort
uniqueInsertionSort() - insertion bubble sort s1,s2 into sList1[], sList2[] if s1 is unique.
unloaderDialog - Variable in class MAEPlugin.popup.PluginUnLoader
Reference to the Dialog that will load files
unMountPlugin(String) - Method in class MAEPlugin.popup.PluginUnLoader
unMountPlugin() - unloads the plugin from the MAE application.
unpackTreeDgramLists(HierClustNode) - Method in class ClusterGramCanvas
unpackTreeDgramLists() - extract dGram arrays for drawing dendrograms
unWeightedAvgFlag - Static variable in class HierClustNode
flag: unweighted/weighted avg calc method
up - Variable in class MC_Cube
 
upButton - Variable in class ChooserGUI
move SELECTED entry up if possible
upButton - Variable in class PopupCondChooserGUI
Move SELECTED entry up if possible
upButton - Variable in class PopupOrderedCondChooserGUI
Move SELECTED entry up if possible
UPDATE - Static variable in class ClusterGenes
bit property: cause PopupRegistry to force a update of a cluster window
update(Graphics) - Method in class MAExplorer
update() - redraw graphics
update(Graphics) - Method in class PopupCondChooser
update() - update window
update(Graphics) - Method in class PopupOrderedCondChooser
update() - update window
update(Graphics) - Method in class RtestBase
update() - update window
update(Graphics) - Method in class PopupEditRscript
update() - update window
update(Graphics) - Method in class ScrollableImageCanvas
update() - update, without background, the scrollable canvas
update(Observable, Object) - Method in class DelFileWalker
update() - delete file
update2Dplot(String, String, String, String, String, String, String, String, int, int, double, double, double, double, double, double, boolean, boolean, float[], float[], int[], GeneList, int, int[]) - Method in class Draw2Dplot
update2Dplot() - set data for plot and then update the plot.
updateAllClustersGeneReport() - Static method in class ClusterGenes
updateAllClustersGeneReport() - update all filtered clusters gene report
updateAllPluginsJarFiles() - Method in class UserState
updateAllPluginsJarFiles() - update all MAEPlugins from server in the /Plugins directory This prompts for the user to verify they want to update all plugins jar files.
updateAssocTextField(String) - Method in class Guesser
updateAssocTextField() - update the associated text field
updateAssocTextField(String) - Method in class PopupGeneGuesser
updateAssocTextField() - update the associated text field
updateAssocTextField(String) - Method in class PopupHPmenuGuesser
updateAssocTextField() - update the associated text field
updateAssocTextField(String) - Method in class PopupProjDirGuesser
updateAssocTextField() - update the associated text field
updateAssocTextFieldCaretPos(int) - Method in class Guesser
updateAssocTextFieldCaretPos() - update associated text field caret position
updateAssocTextFieldCaretPos(int) - Method in class PopupGeneGuesser
updateAssocTextFieldCaretPos() - update assoc text field caret position
updateAssocTextFieldCaretPos(int) - Method in class PopupHPmenuGuesser
updateAssocTextFieldCaretPos() - update assoc text field caret position.
updateAssocTextFieldCaretPos(int) - Method in class PopupProjDirGuesser
updateAssocTextFieldCaretPos() - update assoc text field caret position
updateBothTextAreas() - Method in class ChooserGUI
updateBothTextAreas() - update both text areas ta1 and ta2
updateBothTextAreas() - Method in class PopupCondChooserGUI
updateBothTextAreas() - update both text areas remTextArea and selTextArea
updateBothTextAreas() - Method in class PopupOrderedCondChooserGUI
updateBothTextAreas() - update both text areas remTextArea and selTextArea
updateCGplot(GeneList, HierClustNode) - Method in class DrawClusterGram
updateCGplot() - update ClusterGram plots using new GeneList.
updateCurGene(int) - Method in class ClusterGramCanvas
updateCurGene() - set current gene by MID from PopupRegistry
updateCurGene(int) - Method in class DrawClusterGram
updateCurGene()- update the current gene in the ClusterGram
updateCurGene(int) - Method in class ExprProfileOverlay
updateCurGene() - update the current gene in the expression profile plot list
updateCurGene(int) - Method in class ExprProfileScrollPane
updateCurGene()- update the current gene in the EP plot list.
updateCurGene(int) - Method in class GenNormalizationPlugin
updateCurGene() - update any data since current gene has changed.
updateCurGene(int) - Method in interface MAEUpdateListener
updateCurGene() - update (plot,report,string) popups w/current gene.
updateCurGene(int) - Method in class PopupCondChooser
updateCurGene() - update any data since current gene has changed.
updateCurGene(int) - Method in class PopupOrderedCondChooser
updateCurGene() - update any data since current gene has changed.
updateCurGene(int) - Method in class Report
updateCurGene() - update report if current gene changed and this type of report requires it.
updateCurGene(int) - Method in class RtestBase
updateCurGene() - update any data since current gene has changed.
updateCurGene(int) - Method in class ShowExprProfilesPopup
updateCurGene() - update expression profile plot list if current gene changed and this type of string report requires it.
updateCurGene(int) - Method in class ShowSpreadsheetPopup
updateCurGene() - update plot if current gene changed and this type of report requires it.
updateCurGene(int) - Method in class ShowStringPopup
updateCurGene() - update string report if current gene changed and this type of string report requires it.
updateCurGene(int) - Method in class MAEPlugin.analysis.NormalizationPlugin
updateCurGene() - abstract method end-users must implement to use the API.
updateCurGene(int) - Method in class MAEPlugin.connection.ConnectionPlugin
updateCurGene() - abstract method end-users must implement to use the API.
updateCurGene(int) - Method in class MAEPlugin.popup.PopupPlugin
updateCurGene() - abstract method end-users must implement to use the API.
updateCurGene(int) - Method in class MAEPlugin.popup.PluginLoader
updateCurGene() - update any data since current gene has changed.
updateCurGene(int) - Method in class MAEPlugin.popup.PluginUnLoader
updateCurGene() - update any data since current gene has changed.
updateCurGene(int, int, Object) - Method in class PopupRegistry
updateCurGene() - update (plot,report,string,MAEPlugin) popups with the current gene.
updateCurGene(int, Object) - Method in class ShowPlotPopup
updateCurGene() - update plot if current gene changed and this type of plot requires it.
updateCurGeneInImageAndReg(int) - Method in class MJApopupRegistry
updateCurGeneInImageAndReg() - update current gene in PseudoArray image and registry If the current gene is defined (i.e.
updateCurGeneInImageAndReg(String) - Method in class PopupRegistry
updateCurGeneInImageAndReg() - update current gene in pseudoarray image and notify the PopupRegistry.
updateData(GeneList, HierClustNode) - Method in class ClusterGramCanvas
updateData() - update expression profile with new gene data
updateData(GeneList, String) - Method in class ExprProfileOverlay
updateData() - update exprression profile scroller with new gene data.
updateData(GeneList, String) - Method in class ExprProfileScrollPane
updateData() - update expression profile scroller with new gene data.
updateData(int) - Method in class ExprProfile
updateData() - update expression profile with new gene data
updateData(int, boolean) - Method in class HPxyData
updateData() - update HP XY data with new gene data and calculate (mn,StdDev,CV) statistics, and update the labels (suitable for display)
updateData(int, boolean, int, float, float[], float[]) - Method in class ExprProfile
updateData() - update expression profile with new gene and mean data
updateData(int, String, boolean) - Method in class ExprProfileCanvas
updateData() - update expression profile plot with new gene data.
updateData(int, String, boolean) - Method in class ExprProfilePanel
updateData() - update expression profile with new gene data if a legal gene MID.
updateData(int, String, boolean) - Method in class ExprProfilePopup
updateData() - update expression profile with new gene data.
updateDataAndStat(int) - Method in class HPxyData
updateDataAndStat() - update HP XY data with new data and calculate (mn,StdDev,CV) statistics.
updateEPplots(GeneList) - Method in class ShowExprProfilesPopup
updateEPplots() - update expression profile plots using new GeneList.
updateEPtitles() - Method in class ExprProfileScrollPane
updateEPtitles() - generate array of titles for drawing in expression profile plots
updateFilter() - Method in class GenNormalizationPlugin
updateFilter() - update any dependent data since Filter has changed.
updateFilter() - Method in interface MAEUpdateListener
updateFilter() - update popups using Filter workingCL changes for (plot,report,string,EPOverlayPlot) popups.
updateFilter() - Method in class MJAfilter
updateFilter() - re-run the data filter and then update all popup registry windows that depend on the working gene set.
updateFilter() - Method in class PopupCondChooser
updateFilter() - update any dependent data since Filter has changed.
updateFilter() - Method in class PopupOrderedCondChooser
updateFilter() - update any dependent data since Filter has changed.
updateFilter() - Method in class RtestBase
updateFilter() - update any dependent data since Filter has changed.
updateFilter() - Method in class MAEPlugin.analysis.NormalizationPlugin
updateFilter() - abstract method end-users must implement to use the API.
updateFilter() - Method in class MAEPlugin.connection.ConnectionPlugin
updateFilter() - abstract method end-users must implement to use the API.
updateFilter() - Method in class MAEPlugin.popup.PopupPlugin
updateFilter() - abstract method end-users must implement to use the API.
updateFilter() - Method in class MAEPlugin.popup.PluginLoader
updateFilter() - update any dependent data since Filter has changed.
updateFilter() - Method in class MAEPlugin.popup.PluginUnLoader
updateFilter() - update any dependent data since Filter has changed.
updateFilter(GeneList) - Method in class PopupRegistry
updateFilter() - update popups using Filter workingCL changes for (plot,report,string,MAEPlugin) popups.
updateFilter(GeneList) - Method in class Report
updateFilter() - update report if Filter using new GeneList ml.
updateFilter(GeneList) - Method in class ShowExprProfilesPopup
updateFilter() - update expression profile plots using new GeneList ml.
updateFilter(GeneList) - Method in class ShowPlotPopup
updateFilter() - update plot if Filter changed and this type of plot requires it.
updateFilter(GeneList) - Method in class ShowSpreadsheetPopup
updateFilter() - update plot if Filter changed and this type of report requires it.
updateFilter(GeneList) - Method in class ShowStringPopup
updateFilter() - update string report if Filter changed and this type of string report requires it.
updateFilterScrollerUseCounter(String, boolean) - Method in class MJAfilter
updateFilterScrollerUseCounter() - "add" or "remove" use of a particular scroller by scroller name.
updateFilterScrollerUseCounter(String, boolean) - Method in class StateScrollers
updateFilterScrollerUseCounter() - "add" or "remove" use of a particular scroller by scroller name.
updateGeneClustersOfCurrentGeneReport() - Static method in class ClusterGenes
updateGeneClustersOfCurrentGeneReport() - update current gene cluster report
updateHierarchicalClusters() - Method in class ClusterGenes
updateHierarchicalClusters() - create or update Hierarchical clusters
updateHistogramPlot() - Method in class DrawHistogram
updateHistogramPlot() - set hist state and do repaint to draw it.
updateInfo(ChooserGUI, int, String) - Method in class PopupHPChooser
updateInfo() - update the info text fields for selected HP Note: this should be called from ChooseGUI when an entry is picked.
updateInfo(int, String) - Method in class ChooserGUI
updateInfo() - update info for index entry in parentWindow if any
updateInfo(int, String) - Method in class PopupCondChooserGUI
updateInfo() - update info for index entry in parentWindow if any
updateInfo(int, String) - Method in class PopupOrderedCondChooserGUI
updateInfo() - update info for index entry in parentWindow if any
updateInfo(String) - Method in class PopupCondChooser
updateInfo() - update the info text fields for selected HP.
updateInfo(String) - Method in class PopupOrderedCondChooser
updateInfo() - update the info text fields for selected HP.
updateKmeansClusters() - Method in class ClusterGenes
updateKmeansClusters() - update an existing Kmeans cluster window
updateLabels() - Method in class GenNormalizationPlugin
updateLabels() - update any dependent data since global labels have changed.
updateLabels() - Method in interface MAEUpdateListener
updateLabels() - update popups using Label changes for (plot,report,string) popups.
updateLabels() - Method in class PopupCondChooser
updateLabels() - update any dependent data since global labels have changed.
updateLabels() - Method in class PopupOrderedCondChooser
updateLabels() - update any dependent data since global labels have changed.
updateLabels() - Method in class PopupRegistry
updateLabels() - update popups using Label changes for (plot,report,string,MAEPlugin) popups.
updateLabels() - Method in class Report
updateLabels() - update plot if labels changed and this type of report requires it.
updateLabels() - Method in class RtestBase
updateLabels() - update any dependent data since global labels have changed.
updateLabels() - Method in class ShowExprProfilesPopup
updateLabels() - update string report if labels changed and this type of plot requires it.
updateLabels() - Method in class ShowPlotPopup
updateLabels() - update string report if labels changed and this type of plot requires it.
updateLabels() - Method in class ShowSpreadsheetPopup
updateLabels() - update string report if labels changed and this type of report requires it.
updateLabels() - Method in class ShowStringPopup
updateLabels() - update string report if labels changed and this type of string report requires it.
updateLabels() - Method in class MAEPlugin.analysis.NormalizationPlugin
updateLabels() - abstract method end-users must implement to use the API.
updateLabels() - Method in class MAEPlugin.connection.ConnectionPlugin
updateLabels() - abstract method end-users must implement to use the API.
updateLabels() - Method in class MAEPlugin.popup.PopupPlugin
updateLabels() - abstract method end-users must implement to use the API.
updateLabels() - Method in class MAEPlugin.popup.PluginLoader
updateLabels() - update any dependent data since global labels have changed.
updateLabels() - Method in class MAEPlugin.popup.PluginUnLoader
updateLabels() - update any dependent data since global labels have changed.
updateListCondLists() - Method in class Condition
updateListCondLists() - update existing Condition list window, else nop
updateListCondLists() - Method in class MJAcondition
updateListCondLists() - update existing Condition list window if active.
updateListGeneBitSets() - Method in class GeneBitSet
updateListGeneBitSets() - update existing "UserGeneSets" popup window
updateMAEprojectDB(String, String, String, String) - Method in class UserState
updateMAEprojectDB() - update 'install-dir'/maeProjects.txt DB file.
updateMAERlibrFiles() - Method in class UserState
updateMAERlibrFiles() - download MAExplorer/lib/MAERlibr/* files into MAExplorer program install area.
updateMAERlibrFilesViaZip() - Method in class UserState
updateMAERlibrFilesViaZip() - Download and install library files via MAERlibr.zip file.
updateMAExplorerJarFile() - Method in class UserState
updateMAExplorerJarFile() - update MAExplorer.jar into program install area.
updatePlot() - Method in class ShowPlotPopup
updatePlot() - update the popup plot
updatePopupDialog(String, String) - Method in class PopupLoginDialogQuery
updatePopupDialog() - display/unhide popup dialog frame set new values.
updatePopupDialog(String, String, String[], int) - Method in class PopupDialogQuery
updatePopupDialog() - display/unhide popup dialog frame and set new values.
updatePopupDialog(String, String, String, String, String, String, String) - Method in class PopupBinOprDialogQuery
updatePopupDialog() - display/unhide popup dialog frame and set new vals Remove recreate actionListeners & components
updatePseudoImgFlag - Variable in class MAExplorer
update pseudo image - not saved in the State
updateRatioHistogramPlot() - Method in class DrawRatioHistogram
updateRatioHistogramPlot() - set ratioHist state & do repaint to draw it.
updateRmethodsFiles() - Method in class UserState
updateRmethodsFiles() - download MAExplorer/{R/,RLO/,lib/MAERlibr/} methods files into MAExplorer program install area.
updateSampleBins() - Method in class DrawHistogram
updateSampleBins() - map hist[0:nHist-1] to binXXX[0:MAXBINS-1].
updateScaling() - Method in class ShowPlotPopup
updateScaling() - set scaling mode in proper sub-object for plotMode.
updateScaling(boolean) - Method in class DrawHistogram
updateScaling() - set scaling mode in proper sub-object.
updateScaling(boolean) - Method in class DrawRatioHistogram
updateScaling() - set scaling mode in proper sub-object.
updateScaling(boolean, boolean) - Method in class Draw2Dplot
updateScaling() - set scaling mode in proper sub-object.
updateScatterPlot() - Method in class DrawScatterPlot
updateScatterPlot() - refresh scatter plot Note: prevBestMID could be -1 or -2.
updateScrolledRegion(float, float) - Method in class DrawHistogram
updateScrolledRegion() - update scrolled region to plot
updateScrolledRegion(float, float, float, float) - Method in class Draw2Dplot
updateScrolledRegion() - update scrolled region to plot.
updateSelTextArea() - Method in class ChooserGUI
updateSelTextAreas() - update selected text area ta2 (SELECTED)
updateSelTextArea() - Method in class PopupCondChooserGUI
updateSelTextAreas() - update selected text area selTextArea (SELECTED)
updateSelTextArea() - Method in class PopupOrderedCondChooserGUI
updateSelTextAreas() - update selected text area selTextArea (SELECTED)
updateSimilarGenesListCounts() - Method in class ClusterGenes
updateSimilarGenesListCounts() - this updates the cluster counts for this cycle of clustering.
updateSlider() - Method in class GenNormalizationPlugin
updateSlider() - update any dependent data sincea threshold slider has changed.
updateSlider() - Method in interface MAEUpdateListener
updateSlider() - update popups using Slider changes for (plot,report,string) popups.
updateSlider() - Method in class PopupCondChooser
updateSlider() - update any dependent data sincea threshold slider has changed.
updateSlider() - Method in class PopupOrderedCondChooser
updateSlider() - update any dependent data sincea threshold slider has changed.
updateSlider() - Method in class PopupRegistry
updateSlider() - update popups using Slider changes for (plot,report,string,MAEPlugin) popups.
updateSlider() - Method in class Report
updateSlider() - update report if Slider changed and this type of report requires it.
updateSlider() - Method in class RtestBase
updateSlider() - update any dependent data sincea threshold slider has changed.
updateSlider() - Method in class ShowExprProfilesPopup
updateSlider() - update expression profile plot list if Slider changed and Filter.workingCL is the current EP list.
updateSlider() - Method in class ShowPlotPopup
updateSlider() - update plot if Slider changed and this type of plot requires it.
updateSlider() - Method in class ShowSpreadsheetPopup
updateSlider() - update plot if Slider changed and this type of report requires it.
updateSlider() - Method in class ShowStringPopup
updateSlider() - update string report if Slider changed and this type of string report requires it.
updateSlider() - Method in class MAEPlugin.analysis.NormalizationPlugin
updateSlider() - abstract method end-users must implement to use the API.
updateSlider() - Method in class MAEPlugin.connection.ConnectionPlugin
updateSlider() - abstract method end-users must implement to use the API.
updateSlider() - Method in class MAEPlugin.popup.PopupPlugin
updateSlider() - abstract method end-users must implement to use the API.
updateSlider() - Method in class MAEPlugin.popup.PluginLoader
updateSlider() - update any dependent data sincea threshold slider has changed.
updateSlider() - Method in class MAEPlugin.popup.PluginUnLoader
updateSlider() - update any dependent data sincea threshold slider has changed.
updateSOMclusters() - Method in class ClusterGenes
updateSOMclusters() - [FUTURE] create or update Self Organizing Maps clusters.
updateStdGenePartitions() - Method in class GeneClass
updateStdGenePartitions() - setup all of the special gene sets.
updateTable - Variable in class Report
Table used for updating a report
updateText(String) - Method in class ShowStringPopup
updateText() - update text in popup window
updateTextReportText(String, Object) - Method in class MJAreport
updateTextReportText() - update text in popup report window
updateTitle(String) - Method in class ShowStringPopup
updateTitle() - update popup window title
updateTitleMsgs() - Method in class PopupEditRscript
updateTitleMsgs() - update the title messages
upDownPanel - Variable in class ChooserGUI
panel with up/down buttons
upDownPanel - Variable in class PopupCondChooserGUI
panel with up/down buttons
upDownPanel - Variable in class PopupOrderedCondChooserGUI
panel with up/down buttons
upperHorzBounds - Variable in class SSscrollHorizontal
upper bounds on scroller
upperVertBounds - Variable in class SSscrollVertical
upper bounds on scroller
upPoint - Variable in class MaHybridSample
[FUTURE] for dragging- could be used for defining rubber-band regions
urlArg - Variable in class JavaCGIBridge
may need because of HttpURLConnection
urlPopupFlag - Variable in class ShowSpreadsheetPopup
popup browser flag
urlPopupFlag - Variable in class SpreadSheet
popup browser flag
urlPopupFlag - Variable in class SSspreadPanel
popup browser flag
urlPopupFlag - Variable in class SSstatusBar
 
urlViewerFlag - Variable in class ShowSpreadsheetPopup
button for browser control
us - Variable in class MAExplorer
Global instance of User State methods
US_VERSION - Static variable in class UserState
User Set version # for file format compatibility
useAbove - Variable in class ChooserGUI
optional label if not to use ta1 from above
useAbove - Variable in class PopupCondChooserGUI
optional label if not to use remTextArea from above
useAbove - Variable in class PopupOrderedCondChooserGUI
optional label if not to use remTextArea from above
useAllScrollersFlag - Variable in class StateScrollers
Flag: force all scrollers to appear even if not used...
useArgListFlag - Static variable in class EventMenu
processing by eval method not GUI.
useBkgrdFlag - Variable in class Reval
status of (a.processBits & lookupProcessBitsDBvalue("Use-background-data"))!=0)
useClusterCountsDispFlag - Variable in class MAExplorer
show gene clusters count
useClusterDistCacheFlag - Static variable in class HierClustNode
flag: cache distance matrix.
useClusterDistCacheFlag - Variable in class MAExplorer
use cluster cache else recompute each time
useClusterDistFlag - Variable in class MAExplorer
cluster distance thresholding
useColNbrFlag - Variable in class ClusterGramCanvas
flag: 1, 2, 3, ...
useCorrCoeffFlag - Static variable in class HierClustNode
flag: use corr.
useCorrCoeffFlag - Variable in class MAExplorer
use correlation coeffieient instead of Euclidian distance when clustering
useCVmeanElseMaxFlag - Variable in class MAExplorer
use mean of CV else use max in CV filter
useCy5OverCy3Flag - Variable in class MAExplorer
PARAM "useCy5/Cy3" else Cy3/Cy5
useDetValueSpotDataFlag - Variable in class MAExplorer
filter genes with Spot (Detection value) data
useDichromasyFlag - Variable in class MAExplorer
PARAM "useDichromasy" alt.
useDiffFilterFlag - Variable in class MAExplorer
filter genes by abs diff(HP-X,HP-Y)
useEditedCLflag - Variable in class MAExplorer
filter genes on Edited Gene List
useEPoverlayFlag - Variable in class MAExplorer
Flag: Plot EP list as overlay 2Dplot else scrollable Grid of EPs
useEPrawIntensValFlag - Variable in class MAExplorer
use Raw intensity for EP ratios in gene REPORTS
useEPrawIntensValFlag - Variable in class Report
 
useF1F2dataFlag - Variable in class Reval
status of (a.processBits & lookupProcessBitsDBvalue("Use-F1-F2-channels"))!=0)
useF1F2dataFlag - Variable in class RgenDemo
get x and y data from separate channels if lookupProcessBitsDBvalue("Use-F1-F2-channels") is set
useFilterCounters - Variable in class StateScrollers
# of filters dependent on each slider.
useFilterFlag - Variable in class Reval
status of (a.processBits & lookupProcessBitsDBvalue("Use-filter"))
useFontLbl - Variable in class MenuBarFrame
current global font to use font
useFullHPStageNameFlag - Variable in class ClusterGramCanvas
flag: use full HP stage name for COL name
useGeneSetBS(GeneList, String, String) - Method in class GeneBitSet
useGeneSetBS() - assign the specified GeneBitSet by name to GeneList ml.
useGeneSetFilterFlag - Variable in class MAExplorer
filter genes by useGeneSet mbrship
useGeneSetIndex - Static variable in class GeneList
GeneSet to use for Current Gene Class.
useGenRbit - Static variable in class RgenDemo
Rscript generation GUI for DEMO only: add separate method generators
useGenRbit - Variable in class PopupEditRscript
Rscript generation GUI for DEMO only: add separate method generators
useGenRcheckbox - Variable in class PopupEditRscript
Rscript generation GUI for DEMO only: add separate method generators
useGenRname - Static variable in class RgenDemo
Rscript generation GUI for DEMO only: add separate method generators
useGenRname - Variable in class PopupEditRscript
Rscript generation GUI for DEMO only: add separate method generators
useGoodGeneCLflag - Variable in class MAExplorer
filter by genes in Good Genes List
useGoodSpotDataFlag - Variable in class MAExplorer
filter genes with Good Spot (QualChk) data
useGoodSpotsForGlobalStatsFlag - Variable in class MAExplorer
use Good Spots data for computing global array statistics for normalization purposes on a per array basis, otherwise use all spot data.
useHierClusterDispFlag - Variable in class MAExplorer
show hierarchical clusters
useHighRatiosFilterFlag - Variable in class MAExplorer
"Use highest X/Y ratios filter"
useHPsetsFlag - Variable in class Reval
 
useHPxySetDataFlag - Variable in class HPxyData
flag: get data from msListX/Y else msX/Y
useHPxySetDataFlag - Variable in class MAExplorer
use HP-X,Y 'sets msListX/Y else HP-X,HP-Y msX/Y
useIntensHistCLflag - Variable in class MAExplorer
filter genes on Intensity hist bin
useKmeansClusterCntsDispFlag - Variable in class MAExplorer
show K-means clusters
useLowRatiosFilterFlag - Variable in class MAExplorer
"Use lowest X/Y ratios filter"
useLSQmagNormFlag - Variable in class MAExplorer
norm geneEPvect[] to 1.0 for clustering
useMeanHPeListDataFlag - Variable in class MAExplorer
[TODO] use mean HP-E 'list' data else single current HP sample data
useMeanHPeListDataFlag - Variable in class Reval
 
useMedianForKmeansClusteringFlag - Variable in class MAExplorer
set true if use median instead of means of clusters in K-means clustering.
useMouseOverFlag - Variable in class MAExplorer
PARAM "useMouseOver" for popup tracking balloons
useOnlyGenesWithNonZeroDensityFlag - Variable in class MAExplorer
filter by genes with non-zero intensity - problem when do log() transform
usePosQuantDataFlag - Variable in class MAExplorer
filter genes with positive quant data
usePseudoXYcoordsFlag - Variable in class MAExplorer
PARAM use Pseudo XY coords else actual
useRatioDataFlag - Variable in class MAExplorer
PARAM "useRatioData" Cy3/Cy5 else Intensity
useRatioHistCLflag - Variable in class MAExplorer
filter genes on Ratio histogram bin
useRawDataFlag - Variable in class Reval
status of (a.processBits & lookupProcessBitsDBvalue("Use-raw-data"))
userBS - Static variable in class GeneBitSet
[1:maxUserBS] user assignable gene bit sets.
userDir - Static variable in class RevalBase
 
userDir - Variable in class RtestBase
 
useReplicateGenesFlag - Variable in class MAExplorer
filter by genes with at least 1 replicate
userFilterGeneSetCL - Variable in class GeneClass
"Filter by user Filter Gene Set"
useRLOloggingFlag - Variable in class MAExplorer
Flag: use time-stamped RLO logging files folders, else just Report/
useRLOloggingFlag - Variable in class RevalBase
Flag for RLO Report logging by creating subdirectory in {project}/Report/{RLOname}-yymmdd.hhmmss/ to store the RLO output files copied to Report/
userName - Variable in class JavaCGIBridge
possibly used for Authentication
userName - Variable in class MAExplorer
Dialog: current user login name
userPasswd - Variable in class MAExplorer
Dialog: current user password
UserState - class UserState.
The UserState class is used to read and write the user state.
UserState(MAExplorer, String) - Constructor for class UserState
UserState() - constructor
userStateIdx - Variable in class MAExplorer
current user state index
userStateName - Variable in class MAExplorer
current user state name
useRYGcolorsFlag - Variable in class DrawPseudoImage
flag: color for ratio data.
useShortCacheFlag - Static variable in class HierClustNode
flag: use short else float cache
useShortClusterDistCacheFlag - Variable in class MAExplorer
use short else float cluster cache, can save memory if really needed
useSimGeneClusterDispFlag - Variable in class MAExplorer
show a cluster of similar genes for current gene
useSPLUSasComputingEngineFlag - Variable in class MAExplorer
Flag: Use S-PLUS, else R, as computing engine
useSPlusFlag - Variable in class RevalBase
Flag to use S-Plus, else use R.
useSpotCVfilterFlag - Variable in class MAExplorer
filter by Spot CV filter is enabled
useTest - Variable in class Statistics
CALC: 'B' or 'T' - t-test to use set by calcTandPvalues()
useWebDBflag - Variable in class MAExplorer
Flag: stand-alone PARAM "useWebDB" try WebDB before local directories
useXaxisIntNbrFlag - Variable in class Draw2Dplot
flag: label all vert lines w/int #
usingNgenesFlag - Variable in class RgenDemo
optional flag that we defined nGenes in R if the analysis involves the nGenes R variable.
usingProxy() - Method in class JavaCGIBridge
usingProxy() - impimplements abstract method for HttpURLconnection.
util - Static variable in class EventMenu
link to global Util instance
util - Variable in class MAExplorer
Global instance of Utility class
util - Static variable in class MJAbase
link to global Util instance
util - Static variable in class MaeJavaAPI
link to global Util instance
util - Variable in class StateScrollers
link to global Util instance
Util - class Util.
The Util class contains common utility functions used by the rest of MAExplorer.
Util(MAExplorer) - Constructor for class Util
Util() - constructor for Utility package

V

validateHybSample(String) - Method in class MaHybridSample
validateHybSample() - validate if login is required for this sample for this project.
validateInFileListsSize(int) - Method in class PopupEditRscript
validateInFileListsSize() - grow or create RLO Input File lists size
validateLoginAtServer(String, String, String) - Method in class UserState
validateLoginAtServer() - validate login at MAE web server.
validateOutFileListsSize(int) - Method in class PopupEditRscript
validateOutFileListsSize() - grow or create RLO Output File lists Sizes
validateR2ClientlistsSize(int) - Method in class PopupEditRscript
validateR2ClientlistsSize() - grow or create R2Client lists Sizes
validateUserProject(String, String, String) - Method in class UserState
validateUserProject() - validate this HybSample login for this project.
validPrj - Variable in class MAExplorer
[0:n-1] login verified projects
value - Variable in class PopupCondChooser.CondData
list of condition values
value - Variable in class PopupOrderedCondChooser.OclListData
list of condition values
valueChangedFlag - Variable in class PopupCondChooser
if something is changed, need to save it so keep track
valueChangedFlag - Variable in class PopupCondChooser.CondData
A value has changed, data will need to be saved
valueChangedFlag - Variable in class PopupCondChooser.CondParamEditForm
a value was changed for THIS condition in one or more parametes, so data will need to be saved.
valueChangedFlag - Variable in class PopupCondChooserGUI
value changed
valueChangedFlag - Variable in class PopupOrderedCondChooser
if something is changed, need to save it so keep track
valueChangedFlag - Variable in class PopupOrderedCondChooser.OclListData
A value has changed, data will need to be saved
valueChangedFlag - Variable in class PopupOrderedCondChooser.CondParamEditForm
a value was changed for THIS condition in one or more parametes, so data will need to be saved.
valueChangedFlag - Variable in class PopupOrderedCondChooserGUI
value changed
valueList - Variable in class SampleSets
list for Cy5/Cy3 swap
valueList - Variable in class PopupScrollableSelector
[0:nList-1] values
variance - Variable in class Statistics
variance[0:nConditions-1] of data for computations, set by calcMeanAndVariance()
VERSION - Static variable in class MAExplorer
Compiled Version constant for use in version comparison etc.
VERSION - Static variable in class PopupCondChooser
 
VERSION - Static variable in class PopupOrderedCondChooser
 
VERSION - Static variable in class RtestBase
 
verStr - Static variable in class MAExplorer
Compiled Date/Revision constants
vertCaption - Variable in class Draw2Dplot
ARGS: vertical caption
vertCaption - Variable in class DrawHistogram
vertical caption
vertCaption - Variable in class DrawRatioHistogram
vertical caption
verticallyStackedFlag - Variable in class Reval
status of (a.processBits & lookupProcessBitsDBvalue("Use-vert-stacked-data"))!=0)
verticallyStackedFlag - Variable in class RgenDemo
Check if vertical stacking if processBits lookupProcessBitsDBvalue("Use-vert-stacked-data") is set
vertLabelX - Variable in class ClusterGramCanvas
vertical label ULHC
vertLabelY1 - Variable in class ClusterGramCanvas
top y for vert label
vertLabelY2 - Variable in class ClusterGramCanvas
bottom y for vert label
vertLBscr - Variable in class ShowPlotPopup
vertical LowerBound scrollbar for canvas
vertUBscr - Variable in class ShowPlotPopup
vertical UpperBound scrollbar for canvas
viewFilteredSpotsFlag - Variable in class MAExplorer
Flag: show Filtered spots
viewMenu - Variable in class MenuBarFrame
"View" menu
virCols - Variable in class SpreadSheet
virtual column sizes of prepDataEdit[0:rows-1][0:cols-1] This also inclues the field names in the top row and the row # in the left column
virCols - Variable in class SSspreadPanel
ARG: "virtual screen" size
virCols - Variable in class SSstatusBar
 
virCols - Variable in class SStextArray
size of visible grid
virRows - Variable in class SpreadSheet
virtual row size of prepDataEdit[0:rows-1][0:cols-1] This also inclues the field names in the top row and the row # in the left column
virRows - Variable in class SSspreadPanel
ARG: "virtual screen" size that is visible
virRows - Variable in class SSstatusBar
 
virRows - Variable in class SStextArray
size of visible grid
virtualHdrPos - Variable in class ShowSpreadsheetPopup
location of col clicked in virData
visibleScr - Variable in class ShowPlotPopup
scrollbar's 'visible' amount
visited - Variable in class HierClustNode
Dynamic node: set to true if visited in tree traversal
vLB - Variable in class ExprProfileOverlay
lower expression value to display
vs - Variable in class ArrayScroller
opt.
vs - Variable in class ExprProfileScrollPane
vertical scroll bar
vsL - Variable in class ExprProfileOverlay
lower bound vertical scroll bar
vsU - Variable in class ExprProfileOverlay
upper bound vertical scroll bar
vUB - Variable in class ExprProfileOverlay
upper expression value to display
vx1 - Variable in class Draw2Dplot
viewport x1 for clipping divider
vx2 - Variable in class Draw2Dplot
viewport x2 for clipping divider
vy1 - Variable in class Draw2Dplot
viewport y1 for clipping divider
vy2 - Variable in class Draw2Dplot
viewport y2 for clipping divider

W

walk(File, boolean) - Method in class DelFileWalker
walk() - get file names from dir, visit each file
WARNING_MSG - Static variable in class PopupCondChooser
Error codes for reportMsg()
WARNING_MSG - Static variable in class PopupOrderedCondChooser
Error codes for reportMsg()
width - Variable in class PopupBinOprDialogQuery
size of frame
width - Variable in class PopupDialogQuery
size of frame
width - Variable in class PopupLoginDialogQuery
size of frame
width - Variable in class WriteGifEncoder
 
width - Variable in class MedianCut
width size of image
Width - Variable in class WriteGifEncoder
 
wIdx - Variable in class GeneBitSet
index of bitWord = bitData[wIdx]
wildCard(String, String[], int) - Method in class Guesser
wildCard() - search for * and return the sublist
windowActivated(WindowEvent) - Method in class ChooserGUI
 
windowActivated(WindowEvent) - Method in class DrawClusterGram
 
windowActivated(WindowEvent) - Method in class ExprProfilePopup
 
windowActivated(WindowEvent) - Method in class Guesser
 
windowActivated(WindowEvent) - Method in class MenuBarFrame
 
windowActivated(WindowEvent) - Method in class PopupBinOprDialogQuery
 
windowActivated(WindowEvent) - Method in class PopupCondChooser
 
windowActivated(WindowEvent) - Method in class PopupCondChooser.CondDialogBox
 
windowActivated(WindowEvent) - Method in class PopupCondChooser.PopupTextField
 
windowActivated(WindowEvent) - Method in class PopupCondChooser.ChoiceList
 
windowActivated(WindowEvent) - Method in class PopupCondChooserGUI
 
windowActivated(WindowEvent) - Method in class PopupDialogQuery
 
windowActivated(WindowEvent) - Method in class PopupHPChooser
 
windowActivated(WindowEvent) - Method in class PopupLoginDialogQuery
 
windowActivated(WindowEvent) - Method in class PopupOrderedCondChooser
 
windowActivated(WindowEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
 
windowActivated(WindowEvent) - Method in class PopupOrderedCondChooser.PopupTextField
 
windowActivated(WindowEvent) - Method in class PopupOrderedCondChooser.ChoiceList
 
windowActivated(WindowEvent) - Method in class PopupOrderedCondChooserGUI
 
windowActivated(WindowEvent) - Method in class RtestBase
 
windowActivated(WindowEvent) - Method in class PopupEditRscript
 
windowActivated(WindowEvent) - Method in class PopupScrollableSelector
 
windowActivated(WindowEvent) - Method in class ShowExprProfilesPopup
 
windowActivated(WindowEvent) - Method in class ShowPlotPopup
 
windowActivated(WindowEvent) - Method in class ShowSpreadsheetPopup
 
windowActivated(WindowEvent) - Method in class ShowStringPopup
 
windowActivated(WindowEvent) - Method in class StateScrollers
 
windowActivated(WindowEvent) - Method in class LogTextFrame
 
windowClosed(WindowEvent) - Method in class ChooserGUI
 
windowClosed(WindowEvent) - Method in class DrawClusterGram
 
windowClosed(WindowEvent) - Method in class ExprProfilePopup
 
windowClosed(WindowEvent) - Method in class Guesser
 
windowClosed(WindowEvent) - Method in class MenuBarFrame
 
windowClosed(WindowEvent) - Method in class PopupBinOprDialogQuery
 
windowClosed(WindowEvent) - Method in class PopupCondChooser
 
windowClosed(WindowEvent) - Method in class PopupCondChooser.CondDialogBox
 
windowClosed(WindowEvent) - Method in class PopupCondChooser.PopupTextField
 
windowClosed(WindowEvent) - Method in class PopupCondChooser.ChoiceList
 
windowClosed(WindowEvent) - Method in class PopupCondChooserGUI
 
windowClosed(WindowEvent) - Method in class PopupDialogQuery
 
windowClosed(WindowEvent) - Method in class PopupHPChooser
 
windowClosed(WindowEvent) - Method in class PopupLoginDialogQuery
 
windowClosed(WindowEvent) - Method in class PopupOrderedCondChooser
 
windowClosed(WindowEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
 
windowClosed(WindowEvent) - Method in class PopupOrderedCondChooser.PopupTextField
 
windowClosed(WindowEvent) - Method in class PopupOrderedCondChooser.ChoiceList
 
windowClosed(WindowEvent) - Method in class PopupOrderedCondChooserGUI
 
windowClosed(WindowEvent) - Method in class RtestBase
 
windowClosed(WindowEvent) - Method in class PopupEditRscript
 
windowClosed(WindowEvent) - Method in class PopupScrollableSelector
 
windowClosed(WindowEvent) - Method in class ShowExprProfilesPopup
 
windowClosed(WindowEvent) - Method in class ShowPlotPopup
 
windowClosed(WindowEvent) - Method in class ShowSpreadsheetPopup
 
windowClosed(WindowEvent) - Method in class ShowStringPopup
 
windowClosed(WindowEvent) - Method in class StateScrollers
 
windowClosed(WindowEvent) - Method in class LogTextFrame
 
windowClosing(WindowEvent) - Method in class ChooserGUI
windowclosing() - close the window
windowClosing(WindowEvent) - Method in class DrawClusterGram
windowClosing() - closing down the window, get rid of the frame.
windowClosing(WindowEvent) - Method in class ExprProfilePopup
windowClosing() - closing down the window, get rid of the frame.
windowClosing(WindowEvent) - Method in class Guesser
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class MenuBarFrame
windowClosing() - close the window
windowClosing(WindowEvent) - Method in class PopupBinOprDialogQuery
windowClosing() - close down the window on PC only.
windowClosing(WindowEvent) - Method in class PopupCondChooser
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class PopupCondChooser.CondDialogBox
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class PopupCondChooser.PopupTextField
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class PopupCondChooser.ChoiceList
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class PopupCondChooserGUI
windowclosing() - close the window
windowClosing(WindowEvent) - Method in class PopupDialogQuery
windowClosing() - close down the window on PC only.
windowClosing(WindowEvent) - Method in class PopupHPChooser
windowClosing() - close the window
windowClosing(WindowEvent) - Method in class PopupLoginDialogQuery
windowClosing() - close down the window on PC only.
windowClosing(WindowEvent) - Method in class PopupOrderedCondChooser
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class PopupOrderedCondChooser.PopupTextField
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class PopupOrderedCondChooser.ChoiceList
windowClosing() - close down the window - assume false.
windowClosing(WindowEvent) - Method in class PopupOrderedCondChooserGUI
windowclosing() - close the window
windowClosing(WindowEvent) - Method in class RtestBase
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class PopupEditRscript
windowClosing() - close down the window after saving the RLO
windowClosing(WindowEvent) - Method in class PopupScrollableSelector
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class ShowExprProfilesPopup
windowClosing() - closing down the window, get rid of the frame.
windowClosing(WindowEvent) - Method in class ShowPlotPopup
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class ShowSpreadsheetPopup
windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class ShowStringPopup
windowClosing() - closing down the window, get rid of the frame.
windowClosing(WindowEvent) - Method in class StateScrollers
windowClosing() - close the window - don't allow unless doing ALL scrollers.
windowClosing(WindowEvent) - Method in class LogTextFrame
windowClosing() - close the log window
windowDeactivated(WindowEvent) - Method in class ChooserGUI
 
windowDeactivated(WindowEvent) - Method in class DrawClusterGram
 
windowDeactivated(WindowEvent) - Method in class ExprProfilePopup
 
windowDeactivated(WindowEvent) - Method in class Guesser
 
windowDeactivated(WindowEvent) - Method in class MenuBarFrame
 
windowDeactivated(WindowEvent) - Method in class PopupBinOprDialogQuery
 
windowDeactivated(WindowEvent) - Method in class PopupCondChooser
 
windowDeactivated(WindowEvent) - Method in class PopupCondChooser.CondDialogBox
 
windowDeactivated(WindowEvent) - Method in class PopupCondChooser.PopupTextField
 
windowDeactivated(WindowEvent) - Method in class PopupCondChooser.ChoiceList
 
windowDeactivated(WindowEvent) - Method in class PopupCondChooserGUI
 
windowDeactivated(WindowEvent) - Method in class PopupDialogQuery
 
windowDeactivated(WindowEvent) - Method in class PopupHPChooser
 
windowDeactivated(WindowEvent) - Method in class PopupLoginDialogQuery
 
windowDeactivated(WindowEvent) - Method in class PopupOrderedCondChooser
 
windowDeactivated(WindowEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
 
windowDeactivated(WindowEvent) - Method in class PopupOrderedCondChooser.PopupTextField
 
windowDeactivated(WindowEvent) - Method in class PopupOrderedCondChooser.ChoiceList
 
windowDeactivated(WindowEvent) - Method in class PopupOrderedCondChooserGUI
 
windowDeactivated(WindowEvent) - Method in class RtestBase
 
windowDeactivated(WindowEvent) - Method in class PopupEditRscript
 
windowDeactivated(WindowEvent) - Method in class PopupScrollableSelector
 
windowDeactivated(WindowEvent) - Method in class ShowExprProfilesPopup
 
windowDeactivated(WindowEvent) - Method in class ShowPlotPopup
 
windowDeactivated(WindowEvent) - Method in class ShowSpreadsheetPopup
 
windowDeactivated(WindowEvent) - Method in class ShowStringPopup
 
windowDeactivated(WindowEvent) - Method in class StateScrollers
 
windowDeactivated(WindowEvent) - Method in class LogTextFrame
 
windowDeiconified(WindowEvent) - Method in class ChooserGUI
 
windowDeiconified(WindowEvent) - Method in class DrawClusterGram
 
windowDeiconified(WindowEvent) - Method in class ExprProfilePopup
 
windowDeiconified(WindowEvent) - Method in class Guesser
 
windowDeiconified(WindowEvent) - Method in class MenuBarFrame
 
windowDeiconified(WindowEvent) - Method in class PopupBinOprDialogQuery
 
windowDeiconified(WindowEvent) - Method in class PopupCondChooser
 
windowDeiconified(WindowEvent) - Method in class PopupCondChooser.CondDialogBox
 
windowDeiconified(WindowEvent) - Method in class PopupCondChooser.PopupTextField
 
windowDeiconified(WindowEvent) - Method in class PopupCondChooser.ChoiceList
 
windowDeiconified(WindowEvent) - Method in class PopupCondChooserGUI
 
windowDeiconified(WindowEvent) - Method in class PopupDialogQuery
 
windowDeiconified(WindowEvent) - Method in class PopupHPChooser
 
windowDeiconified(WindowEvent) - Method in class PopupLoginDialogQuery
 
windowDeiconified(WindowEvent) - Method in class PopupOrderedCondChooser
 
windowDeiconified(WindowEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
 
windowDeiconified(WindowEvent) - Method in class PopupOrderedCondChooser.PopupTextField
 
windowDeiconified(WindowEvent) - Method in class PopupOrderedCondChooser.ChoiceList
 
windowDeiconified(WindowEvent) - Method in class PopupOrderedCondChooserGUI
 
windowDeiconified(WindowEvent) - Method in class RtestBase
 
windowDeiconified(WindowEvent) - Method in class PopupEditRscript
 
windowDeiconified(WindowEvent) - Method in class PopupScrollableSelector
 
windowDeiconified(WindowEvent) - Method in class ShowExprProfilesPopup
 
windowDeiconified(WindowEvent) - Method in class ShowPlotPopup
 
windowDeiconified(WindowEvent) - Method in class ShowSpreadsheetPopup
 
windowDeiconified(WindowEvent) - Method in class ShowStringPopup
 
windowDeiconified(WindowEvent) - Method in class StateScrollers
 
windowDeiconified(WindowEvent) - Method in class LogTextFrame
 
windowIconified(WindowEvent) - Method in class ChooserGUI
 
windowIconified(WindowEvent) - Method in class DrawClusterGram
 
windowIconified(WindowEvent) - Method in class ExprProfilePopup
 
windowIconified(WindowEvent) - Method in class Guesser
 
windowIconified(WindowEvent) - Method in class MenuBarFrame
 
windowIconified(WindowEvent) - Method in class PopupBinOprDialogQuery
 
windowIconified(WindowEvent) - Method in class PopupCondChooser
 
windowIconified(WindowEvent) - Method in class PopupCondChooser.CondDialogBox
 
windowIconified(WindowEvent) - Method in class PopupCondChooser.PopupTextField
 
windowIconified(WindowEvent) - Method in class PopupCondChooser.ChoiceList
 
windowIconified(WindowEvent) - Method in class PopupCondChooserGUI
 
windowIconified(WindowEvent) - Method in class PopupDialogQuery
 
windowIconified(WindowEvent) - Method in class PopupHPChooser
 
windowIconified(WindowEvent) - Method in class PopupLoginDialogQuery
 
windowIconified(WindowEvent) - Method in class PopupOrderedCondChooser
 
windowIconified(WindowEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
 
windowIconified(WindowEvent) - Method in class PopupOrderedCondChooser.PopupTextField
 
windowIconified(WindowEvent) - Method in class PopupOrderedCondChooser.ChoiceList
 
windowIconified(WindowEvent) - Method in class PopupOrderedCondChooserGUI
 
windowIconified(WindowEvent) - Method in class RtestBase
 
windowIconified(WindowEvent) - Method in class PopupEditRscript
 
windowIconified(WindowEvent) - Method in class PopupScrollableSelector
 
windowIconified(WindowEvent) - Method in class ShowExprProfilesPopup
 
windowIconified(WindowEvent) - Method in class ShowPlotPopup
 
windowIconified(WindowEvent) - Method in class ShowSpreadsheetPopup
 
windowIconified(WindowEvent) - Method in class ShowStringPopup
 
windowIconified(WindowEvent) - Method in class StateScrollers
 
windowIconified(WindowEvent) - Method in class LogTextFrame
 
windowOpened(WindowEvent) - Method in class ChooserGUI
 
windowOpened(WindowEvent) - Method in class DrawClusterGram
 
windowOpened(WindowEvent) - Method in class ExprProfilePopup
 
windowOpened(WindowEvent) - Method in class Guesser
 
windowOpened(WindowEvent) - Method in class MenuBarFrame
 
windowOpened(WindowEvent) - Method in class PopupBinOprDialogQuery
 
windowOpened(WindowEvent) - Method in class PopupCondChooser
 
windowOpened(WindowEvent) - Method in class PopupCondChooser.CondDialogBox
 
windowOpened(WindowEvent) - Method in class PopupCondChooser.PopupTextField
 
windowOpened(WindowEvent) - Method in class PopupCondChooser.ChoiceList
 
windowOpened(WindowEvent) - Method in class PopupCondChooserGUI
 
windowOpened(WindowEvent) - Method in class PopupDialogQuery
 
windowOpened(WindowEvent) - Method in class PopupHPChooser
 
windowOpened(WindowEvent) - Method in class PopupLoginDialogQuery
 
windowOpened(WindowEvent) - Method in class PopupOrderedCondChooser
 
windowOpened(WindowEvent) - Method in class PopupOrderedCondChooser.CondDialogBox
 
windowOpened(WindowEvent) - Method in class PopupOrderedCondChooser.PopupTextField
 
windowOpened(WindowEvent) - Method in class PopupOrderedCondChooser.ChoiceList
 
windowOpened(WindowEvent) - Method in class PopupOrderedCondChooserGUI
 
windowOpened(WindowEvent) - Method in class RtestBase
 
windowOpened(WindowEvent) - Method in class PopupEditRscript
 
windowOpened(WindowEvent) - Method in class PopupScrollableSelector
 
windowOpened(WindowEvent) - Method in class ShowExprProfilesPopup
 
windowOpened(WindowEvent) - Method in class ShowPlotPopup
 
windowOpened(WindowEvent) - Method in class ShowSpreadsheetPopup
 
windowOpened(WindowEvent) - Method in class ShowStringPopup
 
windowOpened(WindowEvent) - Method in class StateScrollers
 
windowOpened(WindowEvent) - Method in class LogTextFrame
 
withinClusterKmeansStatistics() - Method in class ClusterGenes
withinClusterKmeansStatistics() - compute mean & StdDev within cluster stats
wizardChoice - Variable in class PopupEditRscript
Wizard choice widget
wizardNames - Variable in class PopupEditRscript
List of Wizard options
wizardNbr - Variable in class PopupEditRscript
default wizard to use at startup index wizardNames[]
wizardPanel - Variable in class PopupEditRscript
Wizard Panel
wkCLbitSet - Static variable in class EventMenu
link to global instance of working GeneBitSet
workingCL - Static variable in class EventMenu
link to global instance of working GeneList
workingCL - Variable in class Filter
Working gene list after run filter
writeData(String, String, String) - Method in class FileIO
writeData() - write data to a URL or local file depending on file name prefix.
writeFile(String) - Method in class WriteGifEncoder
writeFile() - write the Gif encoded image to output file
writeFileCGIurl - Variable in class Config
base addr PARAM "writeFileCGIurl"
writeFileFromUrl(String, String, String) - Method in class FileIO
writeFileFromUrl() - write string data to http URL, using JavaCGIBridge.
writeFileToDisk(String, String) - Method in class FileIO
writeFileToDisk() - write string data to a local disk file.
writeGif(FileOutputStream) - Method in class WriteGifEncoder
writeGif() - Saves the image as a GIF file.
WriteGifEncoder - class WriteGifEncoder.
The WriteGifEncoder class writes out an Image object as a named GIF file.
WriteGifEncoder(Image) - Constructor for class WriteGifEncoder
WriteGifEncoder() - Constructs using 24-bit Image.
WriteGifEncoder(int, int, byte[], byte[], byte[], byte[]) - Constructor for class WriteGifEncoder
WriteGifEncoder() - Constructs a new WriteGifEncoder.
WriteGifEncoderHashitem - class WriteGifEncoderHashitem.
 
WriteGifEncoderHashitem(int, int, int, boolean) - Constructor for class WriteGifEncoderHashitem
WriteGifEncoderHashitem() - constructor
writeMAEstartupFile(String, String, boolean) - Method in class UserState
writeMAEstartupFile() - write the .mae startup DB File.
writePermanentRLOdatabase() - Method in class MJAReval
writePermanentRLOdatabase() - write RLO entries to the permanent /RLO/ database.
writePermanentRLOdatabase() - Method in class RevalBase
writePermanentRLOdatabase() - write RLO entries to the permanent /RLO/ database.
writeRdataTableFile(SimpleTable, String) - Method in class Reval
writeRdataTableFile() - write the MAE table data as R input file
writeRLOfile(String, int) - Method in class MJAReval
writeRLOfile() - write RLO by .rlo file name for the specified RLO (rloID).
writeRLOfile(String, int) - Method in class RevalBase
writeRLOfile() - write RLO by .rlo file name for specified RLO (rloID).
writeString(FileOutputStream, String) - Static method in class WriteGifEncoder
writeString() - write string to the file.
writeTextToFile(String, String) - Method in class MJAreport
writeTextToFile() - save text string as text file.
writeTextToFile(String, String) - Method in class Reval
writeTextToFile() - save text string as text file.
writeTextToFile(String, String) - Method in class RevalBase
writeTextToFile() - save text string as text file.
writeTextToFile(String, String) - Method in class Rtest
writeTextToFile() - save text string as text file.
writeTextToFile(String, String) - Method in class RtestBase
writeTextToFile() - save text string as text file.

X

X_AXIS - Static variable in class MAExplorer
Code for assigning current HP to X-axis
X_GRID_OFFSET - Static variable in class MaHPquantTable
value to add to orig data coords to draw GRID labels
X_SPOTQ_OFFSET - Static variable in class MaHPquantTable
value to add to orig data coords x_textQ[].
x_textQ - Variable in class MaHybridSample
position of X grid label for PseudoImage
x0 - Variable in class MenuBarFrame
ULHC X of MenuBarFrame window
x1 - Variable in class DrawHistogram
x1 [0:MAXBINS-1] for clicking on point in list
x1 - Variable in class DrawRatioHistogram
X2 [1:nHist] for clicking on point in list
x2 - Variable in class DrawHistogram
x2 [0:MAXBINS-1] for clicking on point in list
x2 - Variable in class DrawRatioHistogram
X2 [1:nHist] for clicking on point in list
xBase - Variable in class Draw2Dplot
baseline for xxList to xPnt
xBase - Variable in class ScrollableImageCanvas
+ base address of ULHC of clipped image in image canvas used in last paint
xCmax - Variable in class MaHybridSample
total array: max X coord mapped to MAE coord
xCmin - Variable in class MaHybridSample
total array: min X coord mapped to MAE coord
xCoord - Variable in class ExprProfile
X coords for all HP-E vert lines in canvas for event handler...
xCursor - Variable in class ClusterGramCanvas
x cursor set by event handler mouse coords on click
xCursor - Variable in class ExprProfileCanvas
event handler mouse X cursor coordinates
xDataScatterPlot - Variable in class Draw2Dplot
x Data for computing ratios when clicking
xImg - Variable in class ScrollableImageCanvas
 
xLineList - Variable in class Draw2Dplot
X values for only EGL gene points [0:nGroup-1][0:maxGenes-1]
xList - Variable in class Draw2Dplot
ALL of actual X data points to draw [0:nList-1]
xList - Variable in class ExprProfileOverlay
[nGenes*nHP_E] EP overlay X coords
xList - Variable in class ExprProfileScrollPane
[nGenes*nHP_E] EP overlay coords
Xlist - Variable in class Config
HP-X set
xObj - Variable in class ScrollableImageCanvas
eventHndlr set (x,y) object position
xPlotted - Variable in class Draw2Dplot
x plot coordinate for clicking on point in list
xPnt - Variable in class Draw2Dplot
xList[] data mapped to int
xRelMap - Variable in class ScrollableImageCanvas
 
xRmax - Variable in class MaHPquantTable
max X coordinate from orig .quant data
xRmin - Variable in class MaHPquantTable
min X coordinate from orig .quant data
xScale - Variable in class Draw2Dplot
slope for xList to xPnt
xSpotOffset - Variable in class DrawPseudoImage
add to orig data coords x_textQ[]
xText - Variable in class Draw2Dplot
--
xy1S - Static variable in class SpotData
X,Y Centroid of spot 1
xy2S - Static variable in class SpotData
X,Y Centroid of spot 2
xyCQ - Variable in class MaHybridSample
(X,Y) of data from original array (if present) mapped to MAExplorer coordinate system or generated for PseudoArray Image
xyCQ - Variable in class ScrollableImageCanvas
link to ms.xyCQ[] coordinates of spots
xygStr - Static variable in class SpotFeatures
Strings generated by getSpotFeatures()
xyImgCQ_X - Variable in class MaHybridSample
(opt) X original image X coords scaled by 2.0.
xyImgCQ_Y - Variable in class MaHybridSample
(opt) X original image X coords scaled by 2.0.
xyMap - Variable in class OverlayMap
1D array [0:(nPoints*2)-1] of sequential pairs of (x,y) data in current display space for nPoints in the map instance.
xyObj - Variable in class ScrollableImageCanvas
current point (xObj,yObj) on event
xyS - Static variable in class SpotData
X,Y Centroid of a spot

Y

Y_AXIS - Static variable in class MAExplorer
Code for assigning current HP to X-axis
Y_SPOTQ_OFFSET - Static variable in class MaHPquantTable
value to add to orig data coords y_textQ[] AND to grid coords so they match spots
y_textQ - Variable in class MaHybridSample
position of Y grid label for PseudoImage
y0 - Variable in class MenuBarFrame
ULHC X of MenuBarFrame window
y1Coord - Variable in class ExprProfile
Y coord for horizontal axis for vertical line, else is label for setting current gene
yBase - Variable in class Draw2Dplot
baseline for yList to xyPnt
yBase - Variable in class ScrollableImageCanvas
+ base address of ULHC of clipped image in image canvas used in last paint
yCmax - Variable in class MaHybridSample
total array: max Y coord mapped to MAE coord
yCmin - Variable in class MaHybridSample
total array: min Y coord mapped to MAE coord
yCursor - Variable in class ClusterGramCanvas
y cursor set by event handler mouse coords on click
yCursor - Variable in class ExprProfileCanvas
event handler mouse Y cursor coordinates
yDataScatterPlot - Variable in class Draw2Dplot
y Data for computing ratios when clicking
yesMsg - Variable in class PopupCondChooser.CondDialogBox
Yes label for dialog box
yesMsg - Variable in class PopupOrderedCondChooser.CondDialogBox
Yes label for dialog box
yImg - Variable in class ScrollableImageCanvas
 
yLineList - Variable in class Draw2Dplot
Y values for only EGL gene points [0:nGroup-1][0:maxGenes-1]
yList - Variable in class Draw2Dplot
ALL of actual Y data points to draw [0:nList-1]
yList - Variable in class ExprProfileOverlay
[nGenes*nHP_E] EP overlay Y coords
yList - Variable in class ExprProfileScrollPane
[nGenes*nHP_E] EP overlay coords
Ylist - Variable in class Config
HP-Y set
yObj - Variable in class ScrollableImageCanvas
eventHndlr set (x,y) object position
yourPlateName - Variable in class Config
PARAM "yourPlateName" (opt) your plate name
yourPlatesCL - Variable in class GeneClass
special list of "your plate" genes
yPlotted - Variable in class Draw2Dplot
y plot coordinate for clicking on point in list
yPnt - Variable in class Draw2Dplot
yList[] data mapped to int
yRelMap - Variable in class ScrollableImageCanvas
 
yRmax - Variable in class MaHPquantTable
max Y coordinate from orig .quant data
yRmin - Variable in class MaHPquantTable
min Y coordinate from orig .quant data
yScale - Variable in class Draw2Dplot
slope for yList to yPnt
ySpotOffset - Variable in class DrawPseudoImage
add to orig data coords y_textQ[]
yText - Variable in class Draw2Dplot
--

Z

zoomBarsButton - Variable in class ExprProfilePopup
zoom magnification button
zoomBarsButton - Variable in class ShowExprProfilesPopup
 
zoomBarsMag - Variable in class ExprProfileCanvas
zoom magnification: by 1X, 2X, 5X, 10X, 20X mod
zoomBarsMag - Variable in class ExprProfileOverlay
zoom factor: 1X, 2X, 5X, 10X pass through to EP panel
zoomBarsMag - Variable in class ExprProfileScrollPane
1X, 2X, 5X, 10X pass through to EP panel
zoomBarsMag - Variable in class ShowExprProfilesPopup
data magnification 1X, 2X, 5X, 10X, 20X
zoomDgramButton - Variable in class DrawClusterGram
zoom in on dendrogram
zoomImage(Graphics, Image, int, int, int, int) - Method in class ScrollableImageCanvas
zoomImage() - zoom the image in the canvas.

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