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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--java.awt.Component | +--java.awt.Container | +--java.awt.Window | +--java.awt.Frame | +--MenuBarFrame
The class builds the MAExplorer GUI including a menu bar in a new Frame. We have to use a new Frame so we can get a MenuBar for the standalone GUI. It also has the Action (MenuItem) and Item (CheckBoxMenuItem) event listeners for the menu and passes the event commands back to the @see EventMenu classe to handle.
The builtin checkbox menu items are given (currently) individual variables. We track all all menu entries in order to be able to invoke commands from the program (in addition to user interaction with the GUI): 1. Menu Items are tracked in (menuActionLabelList[0:nCmds-1], and menuActionCmdList[0:nCmds-1]). 2.Checkbox menu items are tracked in (chkBoxMenuLabelList[0:nCBcmds-1] and chkBoxMenuItemList[0:nCBcmds-1])
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.
EventMenu
, Serialized FormInner classes inherited from class java.awt.Frame |
java.awt.Frame.AccessibleAWTFrame |
Inner classes inherited from class java.awt.Window |
java.awt.Window.AccessibleAWTWindow |
Inner classes inherited from class java.awt.Container |
java.awt.Container.AccessibleAWTContainer |
Inner classes inherited from class java.awt.Component |
java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock |
Field Summary | |
(package private) java.awt.Menu |
analysisMenu
"Analysis" menu |
(package private) java.lang.String |
aTitle
i.e. |
private Config |
cfg
link to global Config instance |
(package private) static java.awt.CheckboxMenuItem[] |
chkBoxMenuItemList
[MAX_CHKBOX_CMDS] list of checkboxItem cmds menu items corresponding to names |
(package private) static java.lang.String[] |
chkBoxMenuLabelList
[MAX_CHKBOX_CMDS] list of checkboxItem cmds menu labels |
(package private) java.awt.Menu |
clusterMenu
"Cluster" menu |
(package private) java.awt.Button |
curGeneTextButton
enter cur. |
(package private) java.awt.Frame |
dialogFrame
dialog frame created but not displayed until needed |
(package private) java.awt.Menu |
editMenu
"Edit" menu |
(package private) ExprProfilePopup |
exprProfilePopup
command pops it up |
(package private) java.awt.Menu |
fileMenu
"File" menu |
(package private) java.awt.Menu |
filterMenu
"Filter" menu |
(package private) java.awt.Menu |
geneClassMenu
"GeneClass" menu |
(package private) PopupGeneGuesser |
gnMidGuesser
create when needed |
(package private) boolean |
hasStopButtonFlag
set if stopButton has "STOP!" label |
(package private) java.awt.Menu |
helpMenu
"Help" menu |
(package private) java.awt.Label |
HP_Xlabel
GUI label for current HP-X |
(package private) java.awt.Label |
HP_Ylabel
GUI label for current HP-Y |
(package private) java.awt.Panel |
HPlabelPanel
holds HP-X & -Y labels, STOP button |
(package private) boolean |
hpMenuChooserIsPoppedUp
if chooser was popped up |
(package private) PopupHPmenuGuesser |
hpMenuGuesser
HP menu guesser: create when needed |
(package private) boolean |
hpMenuGuesserIsPoppedUp
if guesser was popped up |
(package private) java.lang.String |
hpMenuToUpdateFromChooser
Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-" |
(package private) java.lang.String |
hpMenuToUpdateFromGuesser
Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-" |
private MAExplorer |
mae
link to global instance |
(package private) boolean |
masterIDguesserIsPoppedUp
if guesser was popped up |
(package private) static int |
MAX_CHKBOX_CMDS
max number of menu checkbox items allowed |
(package private) static int |
MAX_CMDS
max number of menu items allowed |
(package private) static int |
MAX_MENU_STUBS
|
(package private) static java.awt.MenuBar |
mbar
menu bar |
(package private) java.awt.Font |
mediumFontLbl
current global medium font |
(package private) static java.lang.String[] |
menuActionCmdList
[MAX_CMDS] list of menuItem (short-form) commands for event handler |
(package private) static java.lang.String[] |
menuActionLabelList
[MAX_CMDS] list of menuItem commands labels |
(package private) java.awt.CheckboxMenuItem |
miCLHCMavgPGMALnk
Menu: (Analysis | Cluster | Hierarchical) use average-arithmetic linkage for hier.clustering |
(package private) java.awt.CheckboxMenuItem |
miCLHCMavgPGMCLnk
Menu: (Analysis | Cluster | Hierarchical) average-centroid linkage for hier.clustering |
(package private) java.awt.CheckboxMenuItem |
miCLHCMnextMinLnk
Menu: (Analysis | Cluster | Hierarchical) next-min for linkage hier.clustering |
(package private) java.awt.CheckboxMenuItem |
miCLHCMunWtAvg
Menu: (Analysis | Cluster | Hierarchical) unweighted/weighted average for hier.clustering |
(package private) java.awt.CheckboxMenuItem |
miCLHCMuseClusterDistCache
Menu: (Analysis | Cluster | Hierarchical) use Cluster dist-dist cache matrix for hier.clustering |
(package private) java.awt.CheckboxMenuItem |
miCLHCMuseShortClusterDistCache
Menu: (Analysis | Cluster | Hierarchical) use 16-bit short vs 32-bit float for hier.clustering |
(package private) java.awt.CheckboxMenuItem |
miCLMdispKmeansNodes
Menu: (Analysis | Cluster) cluster by K-means |
(package private) java.awt.CheckboxMenuItem |
miCLMfindSimGenesDisp
Menu: (Analysis | Cluster) cluster by finding similar genes |
(package private) java.awt.CheckboxMenuItem |
miCLMhierClusterDisp
Menu: (Analysis | Cluster) cluster by hierarchical clustering |
(package private) java.awt.CheckboxMenuItem |
miCLMnormHP
Menu: (Analysis | Cluster | Hierarchical) normalize EP by HP sample for hier.clustering |
(package private) java.awt.CheckboxMenuItem |
miCLMsimGeneCountsDisp
Menu: (Analysis | Cluster) cluster by finding similar gene counts |
(package private) java.awt.CheckboxMenuItem |
miCLMuseCorrCoeffDist
Menu: (Analysis | Cluster) cluster using correlation coefficient else Euclidean distance |
(package private) java.awt.CheckboxMenuItem |
miCLMuseLSQmagNorm
Menu: (Analysis | Cluster | hierarchical ) cluster using LSQ magnitude normalization else ... |
(package private) java.awt.CheckboxMenuItem |
miCLMuseMedianKmeans
Menu: (Analysis | Cluster | cluster by K-means) cluster using K-medians else use K-means |
(package private) java.awt.CheckboxMenuItem |
miEMautoScrollerPopup
Menu: (Edit | User Edited Gene List') [DEPRICATED] |
(package private) java.awt.CheckboxMenuItem |
miEMclusterWorkingCL
Menu: (Edit | Preferences) Cluster Filtered Genes, else all genes |
(package private) java.awt.CheckboxMenuItem |
miEMeditAdd
Menu: (Edit | User Edited Gene List') add gene to 'Edited Gene List' |
(package private) java.awt.CheckboxMenuItem |
miEMeditNop
Menu: (Edit | User Edited Gene List') don't edit 'Edited Gene List' |
(package private) java.awt.CheckboxMenuItem |
miEMeditRmv
Menu: (Edit | User Edited Gene List') delete gene to 'Edited Gene List' |
(package private) java.awt.CheckboxMenuItem |
miEMshowEditedGenes
Menu: (Edit | User Edited Gene List') Show 'Edited Gene List' |
(package private) java.awt.CheckboxMenuItem |
miFEMenableFIOcache
Menu: (Edit | Preferences) enable using cache for Web database |
(package private) java.awt.CheckboxMenuItem |
miFEMuseWebDB
Menu: (Edit | Preferences) access data from Web database |
(package private) java.awt.CheckboxMenuItem |
miFRM_EGLfilter
Menu: (Analysis | Filter) Filter by EGL gene membership |
(package private) java.awt.CheckboxMenuItem |
miFRMclusterHP_Efilter
Menu: (Analysis | Filter) Filter by Cluster test |
(package private) java.awt.CheckboxMenuItem |
miFRMcvModeE
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample |
(package private) java.awt.CheckboxMenuItem |
miFRMcvModeMS
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample |
(package private) java.awt.CheckboxMenuItem |
miFRMcvModeXANDYsets
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X and HP-Y 'sets' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMcvModeXORYsets
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X or HP-Y 'sets' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMcvModeXset
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X 'set' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMcvModeXY
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample |
(package private) java.awt.CheckboxMenuItem |
miFRMcvModeYset
Menu: (Analysis | Filter | CV threshold sliders) test current HP-Y 'set' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMCy3Cy5RatioRngIn
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) in range |
(package private) java.awt.CheckboxMenuItem |
miFRMCy3Cy5RatioRngOut
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) outside of range |
(package private) java.awt.CheckboxMenuItem |
miFRMdetValueSpotModeE
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-E 'list' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMdetValueSpotModeMS
Menu: (Analysis | Filter | use Spot Detection Valuedata) test current HP sample |
(package private) java.awt.CheckboxMenuItem |
miFRMdetValueSpotModeXANDYsets
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y 'set' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMdetValueSpotModeXY
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y samples |
(package private) java.awt.CheckboxMenuItem |
miFRMfTestOCLFilter
Menu: (Analysis | Filter) Filter by cur. |
(package private) java.awt.CheckboxMenuItem |
miFRMgeneClassMbrFilter
Menu: (Analysis | Filter) Filter by GeneClass membership |
(package private) java.awt.CheckboxMenuItem |
miFRMgoodGeneListFilter
Menu: (Analysis | Filter) Filter by good genes membership |
(package private) java.awt.CheckboxMenuItem |
miFRMgoodSpotModeE
Menu: (Analysis | Filter | use Good Spot data) test current HP-E 'list' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMgoodSpotModeMS
Menu: (Analysis | Filter | use Good Spot data) test current HP sample |
(package private) java.awt.CheckboxMenuItem |
miFRMgoodSpotModeXANDYsets
Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y 'set' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMgoodSpotModeXORYsets
Menu: (Analysis | Filter | use Good Spot data) |
(package private) java.awt.CheckboxMenuItem |
miFRMgoodSpotModeXY
Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y samples |
(package private) java.awt.CheckboxMenuItem |
miFRMgrayRngIn
Menu: (Analysis | Filter | by intensity range test) within range |
(package private) java.awt.CheckboxMenuItem |
miFRMgrayRngOut
Menu: (Analysis | Filter | by intensity range test) outside range |
(package private) java.awt.CheckboxMenuItem |
miFRMhighXYratioFilter
Menu: (Analysis | Filter) Filter by high ratio range test |
(package private) java.awt.CheckboxMenuItem |
miFRMhistIntensRngFilter
Menu: (Analysis | Filter) Filter by intensity histogram bin |
(package private) java.awt.CheckboxMenuItem |
miFRMhistRatioRngFilter
Menu: (Analysis | Filter) Filter by ratio histogram bin |
(package private) java.awt.CheckboxMenuItem |
miFRMksTestXYsetsFilter
Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' KS-Test |
(package private) java.awt.CheckboxMenuItem |
miFRMlowXYratioFilter
Menu: (Analysis | Filter) Filter by low ratio range test |
(package private) java.awt.CheckboxMenuItem |
miFRMOnlyGenesWithNonZeroDensityFlag
Menu: (Analysis | Filter | use only genes with non-zero intensity) |
(package private) java.awt.CheckboxMenuItem |
miFRMposQuantModeE
Menu: (Analysis | Filter | use positive quantified data) test current HP-E 'list' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMposQuantModeMS
Menu: (Analysis | Filter | use positive quantified data) test current HP sample |
(package private) java.awt.CheckboxMenuItem |
miFRMposQuantModeXY
Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y samples |
(package private) java.awt.CheckboxMenuItem |
miFRMposQuantModeXYsets
Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y 'set' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMratioRngIn
Menu: (Analysis | Filter | by ratio range test) in range |
(package private) java.awt.CheckboxMenuItem |
miFRMratioRngOut
Menu: (Analysis | Filter | Filter by ratio range test) outside of range |
(package private) java.awt.CheckboxMenuItem |
miFRMreplicateGenesFilter
Menu: (Analysis | Filter) Filter by replicate genes membership |
(package private) java.awt.CheckboxMenuItem |
miFRMspotCVfilter
Menu: (Analysis | Filter) Filter by spot CV test |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensCompareModeALL
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ALL selected samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensCompareModeANY
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ANY selected samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensCompareModeAT_LEAST
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT LEAST (n) selected samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensCompareModeAT_MOST
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT MOST (n) selected samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensCompareModePRODUCT
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have PRODUCT selected samples less than threshold |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensCompareModeSUM
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have SUM selected samples less than threshold |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensModeE
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-E 'list' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensModeMS
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP sample |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensModeXANDYsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y 'sets' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensModeXORYsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X or HP-Y 'sets' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensModeXsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X 'sets' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensModeXY
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensModeYsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-Y 'sets' samples |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensRngIn
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) within range test |
(package private) java.awt.CheckboxMenuItem |
miFRMspotIntensRngOut
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) outside range test |
(package private) java.awt.CheckboxMenuItem |
miFRMthrCy3Cy5Ratio
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) enabled |
(package private) java.awt.CheckboxMenuItem |
miFRMthrGray
Menu: (Analysis | Filter | by intensity range test) enabled |
(package private) java.awt.CheckboxMenuItem |
miFRMthrRatio
Menu: (Analysis | Filter | by ratio range test) enabled |
(package private) java.awt.CheckboxMenuItem |
miFRMthrSpotIntens
Menu: (Analysis | Filter | Filter by spot intensity [SI1:SI2] sliders) Filter by spot intensity range test |
(package private) java.awt.CheckboxMenuItem |
miFRMtTestXYfilter
Menu: (Analysis | Filter) Filter by HP-X and HP-Y F1+F2 t-Test |
(package private) java.awt.CheckboxMenuItem |
miFRMtTestXYsetsFilter
Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' t-Test |
(package private) java.awt.CheckboxMenuItem |
miFRMuseCVmeanElseMax
Menu: (Analysis | Filter | CV threshold sliders) use the CV mean else the CV max in computation |
(package private) java.awt.CheckboxMenuItem |
miFRMuseDetValueSpotDataFlag
Menu: (Analysis | Filter | use Spot Detection Value data) |
(package private) java.awt.CheckboxMenuItem |
miFRMuseDiffFilter
Menu: (Analysis | Filter) Filter by difference test |
(package private) java.awt.CheckboxMenuItem |
miFRMuseGeneSetFilter
Menu: (Analysis | Filter) Filter by user gene set membership |
(package private) java.awt.CheckboxMenuItem |
miFRMuseGoodSpotDataFlag
Menu: (Analysis | Filter | use Good Spot data) |
(package private) java.awt.CheckboxMenuItem |
miFRMusePosQuantDataFlag
Menu: (Analysis | Filter | use positive quantified data) |
(package private) java.awt.CheckboxMenuItem |
miHPMuseHPxySets
Menu: (Samples) use HP-X and HP-Y 'sets' of multiple samples else use individual HP-X and HP-Y samples. |
(package private) java.awt.CheckboxMenuItem |
miNRMbkgrdCorr
(Analysis | Normalization) use background correction |
(package private) java.awt.CheckboxMenuItem |
miNRMCalDNAnorm
(Analysis | Normalization | Calibration DNA genes) |
(package private) java.awt.CheckboxMenuItem |
miNRMgeneSetNorm
(Analysis | Normalization | User defined gene set genes) |
(package private) java.awt.CheckboxMenuItem |
miNRMgoodSpotsStats
(Analysis | Normalization) use per-sample Good Spots data for global array statistics |
(package private) java.awt.CheckboxMenuItem |
miNRMhousekeepNorm
(Analysis | Normalization | Housekeeping genes) |
(package private) java.awt.CheckboxMenuItem |
miNRMlogMedianNorm
(Analysis | Normalization | Normalize by logMedian ) |
(package private) java.awt.CheckboxMenuItem |
miNRMmedianNorm
(Analysis | Normalization | Median) |
(package private) java.awt.CheckboxMenuItem |
miNRMnoNorm
(Analysis | Normalization } No normalization) |
(package private) java.awt.CheckboxMenuItem |
miNRMratioMedianCorrection
(Analysis | Normalization) use ratio median correction for the Cy3 and Cy5 channels |
(package private) java.awt.CheckboxMenuItem |
miNRMscaleToMaxIntens
(Analysis | Normalization | Normalize to maximum intensity (65K) |
(package private) java.awt.CheckboxMenuItem |
miNRMtestGenericNormPlugin
only if mae.DBUG_GENERIC_NORM_PLUGIN is set, then (Analysis | Normalization | Test Generic Norm Plugin) |
(package private) java.awt.CheckboxMenuItem |
miNRMZscoreMeanAbsDevLogNorm
(Analysis | Normalization | Normalize by Zscore of log (AbsDev) ) |
(package private) java.awt.CheckboxMenuItem |
miNRMZscoreMeanStdDevLogNorm
(Analysis | Normalization | Normalize by Zscore of log (StdDev) ) |
(package private) java.awt.CheckboxMenuItem |
miNRMZscoreNorm
(Analysis | Normalization | Zscore ) |
(package private) java.awt.CheckboxMenuItem |
miPEPlistType
(Analysis | Plot | Expression Profile) Menu Expression Profile list type (overlay or grid). |
(package private) java.awt.CheckboxMenuItem |
miPLGMuseSPLUSasComputingEngine
Menu: (Plugins | Use S-PLUS, else R, as computing engine [CB]) |
(package private) java.awt.CheckboxMenuItem |
miPLGMuseTimeStampReports
Menu: (Plugins | Save SRLO reports in time-stampled folder [CB]) |
(package private) java.awt.CheckboxMenuItem |
miPMdualXYpseudoImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor dual HP-X and HP-Y as Field 1 and Field 2 grids |
(package private) java.awt.CheckboxMenuItem |
miPMflickerXY
Menu:(Analysis | Plot | Show Microarray) use Flicker of HP-X and HP-Y samples in intensity mode |
(package private) java.awt.CheckboxMenuItem |
miPMlowRangeZoom
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor low range zoom |
(package private) java.awt.CheckboxMenuItem |
miPMplotPseudoF1F2Img
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Cy3/Cy5 ratio or Zdiff |
(package private) java.awt.CheckboxMenuItem |
miPMplotPseudoHP_EP_CV_valueImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-EP 'list' CV-value |
(package private) java.awt.CheckboxMenuItem |
miPMplotPseudoHP_F1F2_RYGImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(Cy5)-Yellow-Green(Cy3) Cy3/Cy5 ratio or Zdiff |
(package private) java.awt.CheckboxMenuItem |
miPMplotPseudoHP_XY_pValueImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor (HP-X,HP-Y) 'sets' p-value |
(package private) java.awt.CheckboxMenuItem |
miPMplotPseudoHP_XY_RYGImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(X)-Yellow-Green(Y) HP-X/Y ratio or Zdiff |
(package private) java.awt.CheckboxMenuItem |
miPMplotPseudoHP_XYImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-X/Y ratio or Zdiff |
(package private) java.awt.CheckboxMenuItem |
miPMplotPseudoImg
Menu:(Analysis | Plot | Show Microarray) use Pseudograyscale intensity |
(package private) java.awt.CheckboxMenuItem |
miPRtblFontSize10pt
Menu: (Analysis | Report) font size is 10 pt |
(package private) java.awt.CheckboxMenuItem |
miPRtblFontSize12pt
Menu: (Analysis | Report) font size is 12 pt |
(package private) java.awt.CheckboxMenuItem |
miPRtblFontSize8pt
Menu: (Analysis | Report) font size is 8 pt |
(package private) java.awt.CheckboxMenuItem |
miTMtblFmtAddEPdata
Menu: (Analysis | Report) add Expr-Profile data to Table |
(package private) java.awt.CheckboxMenuItem |
miTMtblFmtAddHP_XYsetStat
Menu: (Analysis | Report) add HP-XY set statistics data to Table |
(package private) java.awt.CheckboxMenuItem |
miTMtblFmtAddOCLstatistics
Menu: (Analysis | Report) add OCL statistics data to Table |
(package private) java.awt.CheckboxMenuItem |
miTMtblFmtClickable
Menu: (Analysis | Report) use Dynamic clickable table format |
(package private) java.awt.CheckboxMenuItem |
miTMtblFmtTabDelim
Menu: (Analysis | Report) use Tab-Delimited table format |
(package private) java.awt.CheckboxMenuItem |
miTMtblFmtUseRawEPdata
Menu: (Analysis | Report) use raw Expr-Profile data in Table |
(package private) java.awt.CheckboxMenuItem |
miTMtblFontSize10pt
Menu: (Analysis | Report) font size is 10 pt |
(package private) java.awt.CheckboxMenuItem |
miTMtblFontSize12pt
Menu: (Analysis | Report) font size is 12 pt |
(package private) java.awt.CheckboxMenuItem |
miTMtblFontSize8pt
Menu: (Analysis | Report) font size is 8 pt |
(package private) java.awt.CheckboxMenuItem |
miVMdbESTviewer
Menu:(View) enable popup GenBank browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMGang
Menu:(View) show gang scrolling for duplicated grids of spots |
(package private) java.awt.CheckboxMenuItem |
miVMgenBankViewer
Menu:(View) enable popup GenBank browser for new current gene |
(package private) java.awt.CheckboxMenuItem[] |
miVMgenomicViewer
sGenomicMenu[cfg.nGenomicMenus] menu items as determined from Config DB |
(package private) java.awt.CheckboxMenuItem |
miVMlocusLinkViewer
Menu:(View) enable popup LocusLink gene browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMmAdbViewer
Menu:(View) enable popup mAdb gene browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMmedMinerViewer
Menu:(View) enable popup MedMiner browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMomimViewer
Menu:(View) enable popup OMIM browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMpirViewer
Menu:(View) enable popup PIRs browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMPresentView
Menu:(View) enable Presentation view that increases font sizes |
(package private) java.awt.CheckboxMenuItem |
miVMshowEditedGenes
Menu:(View) show EGL genes |
(package private) java.awt.CheckboxMenuItem |
miVMshowFilteredSpots
Menu:(View) show Filtered genes and spots |
(package private) java.awt.CheckboxMenuItem |
miVMshowHistoryLog
Menu:(View) enable popup command history log |
(package private) java.awt.CheckboxMenuItem |
miVMshowMsgLog
Menu:(View) enable popup message history log |
(package private) java.awt.CheckboxMenuItem |
miVMswissProtViewer
Menu:(View) enable popup SwissProt browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMuniGeneViewer
Menu:(View) enable popup UniGene browser for new current gene |
(package private) java.awt.CheckboxMenuItem |
miVMuseDichromasy
Menu:(View) enable Dichromasy colors that may be useful for some colorblind researchers instead of default color schemes. |
(package private) java.awt.CheckboxMenuItem |
miVMuseMouseOver
Menu:(View) enable mouse-over information for mouse over selected genes |
(package private) java.awt.Checkbox |
mouseOverCheckBox
Show Mouse-over info |
(package private) static int |
nCBcmds
# of menu CheckBoxMenuItem item cmds [0:nCBcmds-1] |
(package private) static int |
nCmds
# of menu item commands [0:nCmds-1] |
(package private) int |
nMenuStubs
# of menu stubs in the list |
(package private) java.awt.Menu |
normMenu
"Normalization" menu |
(package private) int |
nRLOs
# of RLO entries in the menu |
(package private) PopupBinOprDialogQuery |
pBOdq
holds popup BinOpr dialog query |
(package private) PopupDialogQuery |
pdq
holds popup dialog query |
(package private) java.awt.Menu |
plotMenu
"Plot" menu |
(package private) java.awt.Menu |
pluginsMenu
"Plugins" menu |
(package private) PopupProjDirGuesser |
projDirGuesser
Project Guesser: create when needed |
(package private) boolean |
projDirGuesserIsPoppedUp
if guesser was popped up |
(package private) java.lang.String |
projDirToUpdateFromGuesser
prj dir result set in event handler |
(package private) java.awt.Panel |
ps
holds above chkboxes & scrollbar panels |
(package private) java.awt.Label |
reportLabel
report label must be global variable |
(package private) java.awt.Menu |
reportMenu
"Report" menu |
(package private) java.lang.String[] |
rloMenuNames
RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree |
(package private) java.lang.String[] |
rloRscriptNames
RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree |
(package private) java.awt.Menu |
rloSmnu
Menu stub to add/modify R(Plugin | RLO methods (submenu)) menu items |
(package private) java.awt.Menu |
sampleMenu
"Sample" command menu |
(package private) java.awt.Font |
smallFontLbl
current global small font |
(package private) java.awt.Button |
stopButton
If hasStopButtonFlag is set (i.e. |
(package private) java.lang.String |
stopLblName
either "STOP!" or " " |
(package private) java.awt.Menu[] |
stubMenus
list of Menu Stubs in Menu tree |
(package private) java.lang.String[] |
stubNames
list of Names of Stubs in Menu tree |
(package private) java.lang.String |
title
title for frame |
(package private) java.awt.Font |
useFontLbl
current global font to use font |
(package private) java.awt.Menu |
viewMenu
"View" menu |
(package private) int |
x0
ULHC X of MenuBarFrame window |
(package private) int |
y0
ULHC X of MenuBarFrame window |
Fields inherited from class java.awt.Frame |
base, CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, frameSerializedDataVersion, HAND_CURSOR, icon, ICONIFIED, mbManagement, menuBar, MOVE_CURSOR, N_RESIZE_CURSOR, nameCounter, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, ownedWindows, resizable, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, serialVersionUID, state, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR, weakThis |
Fields inherited from class java.awt.Window |
active, dbg, focusMgr, inputContext, inputContextLock, OPENED, ownedWindowList, showWithParent, warningString, windowListener, windowSerializedDataVersion |
Fields inherited from class java.awt.Container |
component, containerListener, containerSerializedDataVersion, dispatcher, layoutMgr, listeningBoundsChildren, listeningChildren, maxSize, ncomponents, printing, printingThreads |
Fields inherited from class java.awt.Component |
accessibleContext, actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, changeSupport, componentListener, componentListenerK, componentOrientation, componentSerializedDataVersion, containerListenerK, cursor, dropTarget, enabled, eventMask, focusListener, focusListenerK, font, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, name, nameExplicitlySet, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, privateKey, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, x, y |
Fields inherited from interface java.awt.image.ImageObserver |
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
(package private) |
MenuBarFrame(MAExplorer mae)
MnuBarFrame() - constructor used with the Applet. |
(package private) |
MenuBarFrame(MAExplorer mae,
java.lang.String title,
int x0,
int y0)
MenuBarFrame() - constructor for main GUI window and menubar. |
Method Summary | |
void |
actionPerformed(java.awt.event.ActionEvent e)
actionPerformed() - handle action events for Buttons and menu commands. |
(package private) int |
addMenuBar()
addMenuBar() - add menubar with menus to the frame |
private void |
addMenuStubToMenuStubList(java.lang.String name,
java.awt.Menu menuStub)
addMenuStubToMenuStubList() - add menu position to Menu Stub List. |
(package private) void |
addRLOsubmenuTree()
addRLOsubmenuTree() - add RLO R scripts submenu tree to rloSmnu if RLOs exist. |
(package private) void |
addSetHP_XYEsubmenuTree(java.awt.Menu subMenu,
java.lang.String hpPostfixStr)
addSetHP_XYEsubmenuTree() - add HP sample submenu tree to submenu if submenus exist. |
(package private) void |
buildMenuGUI(int x0,
int y0,
int width,
int height)
buildMenuGUI() - build the GUI with pop up menus |
(package private) void |
callAllStartupPlugins()
callAllStartupPlugins() - call all Plugins initialized at Startup. |
(package private) void |
createDialogQueryFrames()
createDialogQueryFrames() - create all popup dialog frames |
(package private) void |
enableMenus(java.lang.String opr)
enableMenus() - enable/disable all menus, checkboxes, typein fields etc. |
private java.awt.Menu |
findMenuStubByName(java.lang.String name)
findMenuStubByName() - find menu stub associated with name in Menu Stub List. |
private void |
insertPluginMenuEntries()
insertPluginMenuEntries() - insert Plugin menus if any at proper stubs. |
void |
itemStateChanged(java.awt.event.ItemEvent e)
itemStateChanged() - handle item state changed events. |
void |
keyPressed(java.awt.event.KeyEvent e)
keyPressed() - get key Pressed event - look for ESCAPE key to set STOP flag |
void |
keyReleased(java.awt.event.KeyEvent e)
keyReleased() - get key Released event |
void |
keyTyped(java.awt.event.KeyEvent e)
keyTyped() - get key typed event - look for ESCAPE key to set STOP flag |
private java.awt.CheckboxMenuItem |
makeChkBoxMenuItem(java.awt.Menu pm,
java.lang.String sLabel,
java.lang.String sCmd,
int shortcut,
boolean value)
makeChkBoxMenuItem() - make CheckboxMenuItem entry in popup menu list. |
private void |
makeMenuItem(java.awt.Menu pm,
java.lang.String sLabel,
java.lang.String sCmd,
int shortcut)
makeMenuItem() - make menuItem entry in menu list. |
private java.awt.Menu |
makeSubMenu(java.awt.Menu pm,
java.lang.String sLabel,
java.lang.String sCmd,
int shortcut)
makeSubMenu() - make submenu entry in menu list. |
(package private) void |
redoMenuBar()
redoMenuBar() - redo the menubar if restarted a new database with different entries. |
(package private) void |
setHP_XYlabels()
setHP_XYlabels() - set the GUI HP-X: and HP-Y: labels as singles or multiple (Class names) |
(package private) void |
setSTOPbuttonState(boolean flag,
boolean isEnabledFlag)
setSTOPbuttonState() - enable/disable STOP button & clear abortFlag. |
void |
windowActivated(java.awt.event.WindowEvent e)
|
void |
windowClosed(java.awt.event.WindowEvent e)
|
void |
windowClosing(java.awt.event.WindowEvent e)
windowClosing() - close the window |
void |
windowDeactivated(java.awt.event.WindowEvent e)
|
void |
windowDeiconified(java.awt.event.WindowEvent e)
|
void |
windowIconified(java.awt.event.WindowEvent e)
|
void |
windowOpened(java.awt.event.WindowEvent e)
|
Methods inherited from class java.awt.Frame |
|
Methods inherited from class java.awt.Window |
addOwnedWindow, addWindowListener, adjustListeningChildren, applyResourceBundle, applyResourceBundle, connectOwnedWindow, dispatchEventImpl, dispose, eventEnabled, getFocusOwner, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getOwnedWindows, getOwner, getToolkit, getWarningString, hide, isActive, isShowing, nextFocus, ownedInit, pack, postEvent, postWindowEvent, preProcessKeyEvent, processEvent, processWindowEvent, removeOwnedWindow, removeWindowListener, resetGC, setCursor, setFocusOwner, setWarningString, show, toBack, toFront, transferFocus |
Methods inherited from class java.awt.Container |
add, add, add, add, add, addContainerListener, addImpl, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventToSelf, doLayout, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getInsets, getLayout, getMaximumSize, getMinimumSize, getMouseEventTarget, getPreferredSize, getWindow, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, numListening, paint, paintComponents, paintHeavyweightComponents, postsOldMouseEvents, preferredSize, print, printComponents, printHeavyweightComponents, processContainerEvent, proxyEnableEvents, proxyRequestFocus, remove, remove, removeAll, removeContainerListener, setFont, setLayout, update, validate, validateTree |
Methods inherited from class java.awt.Component |
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus |
Methods inherited from class java.lang.Object |
clone, equals, getClass, hashCode, notify, notifyAll, registerNatives, wait, wait, wait |
Methods inherited from interface java.awt.MenuContainer |
getFont, postEvent |
Field Detail |
private MAExplorer mae
private Config cfg
java.lang.String title
static java.awt.MenuBar mbar
static final int MAX_CMDS
static final int MAX_CHKBOX_CMDS
static int nCmds
static java.lang.String[] menuActionLabelList
static java.lang.String[] menuActionCmdList
static int nCBcmds
static java.lang.String[] chkBoxMenuLabelList
static java.awt.CheckboxMenuItem[] chkBoxMenuItemList
static final int MAX_MENU_STUBS
int nMenuStubs
java.lang.String[] stubNames
java.awt.Menu[] stubMenus
java.awt.Menu rloSmnu
int nRLOs
java.lang.String[] rloMenuNames
java.lang.String[] rloRscriptNames
java.lang.String aTitle
int x0
int y0
java.awt.Label reportLabel
java.awt.Font smallFontLbl
java.awt.Font mediumFontLbl
java.awt.Font useFontLbl
ExprProfilePopup exprProfilePopup
java.awt.Frame dialogFrame
PopupDialogQuery pdq
PopupBinOprDialogQuery pBOdq
java.awt.Panel HPlabelPanel
java.awt.Panel ps
java.awt.Button stopButton
java.awt.Checkbox mouseOverCheckBox
java.awt.Button curGeneTextButton
boolean masterIDguesserIsPoppedUp
PopupGeneGuesser gnMidGuesser
boolean hasStopButtonFlag
boolean hpMenuChooserIsPoppedUp
boolean hpMenuGuesserIsPoppedUp
java.lang.String stopLblName
java.lang.String hpMenuToUpdateFromGuesser
java.lang.String hpMenuToUpdateFromChooser
PopupHPmenuGuesser hpMenuGuesser
PopupProjDirGuesser projDirGuesser
boolean projDirGuesserIsPoppedUp
java.lang.String projDirToUpdateFromGuesser
java.awt.Menu analysisMenu
java.awt.Menu fileMenu
java.awt.Menu sampleMenu
java.awt.Menu geneClassMenu
java.awt.Menu normMenu
java.awt.Menu editMenu
java.awt.Menu filterMenu
java.awt.Menu viewMenu
java.awt.Menu plotMenu
java.awt.Menu clusterMenu
java.awt.Menu reportMenu
java.awt.Menu pluginsMenu
java.awt.Menu helpMenu
java.awt.CheckboxMenuItem miFEMuseWebDB
java.awt.CheckboxMenuItem miFEMenableFIOcache
java.awt.CheckboxMenuItem miHPMuseHPxySets
java.awt.CheckboxMenuItem miNRMhousekeepNorm
java.awt.CheckboxMenuItem miNRMgeneSetNorm
java.awt.CheckboxMenuItem miNRMCalDNAnorm
java.awt.CheckboxMenuItem miNRMZscoreNorm
java.awt.CheckboxMenuItem miNRMmedianNorm
java.awt.CheckboxMenuItem miNRMlogMedianNorm
java.awt.CheckboxMenuItem miNRMZscoreMeanStdDevLogNorm
java.awt.CheckboxMenuItem miNRMZscoreMeanAbsDevLogNorm
java.awt.CheckboxMenuItem miNRMscaleToMaxIntens
java.awt.CheckboxMenuItem miNRMnoNorm
java.awt.CheckboxMenuItem miNRMtestGenericNormPlugin
java.awt.CheckboxMenuItem miNRMgoodSpotsStats
java.awt.CheckboxMenuItem miNRMbkgrdCorr
java.awt.CheckboxMenuItem miNRMratioMedianCorrection
java.awt.CheckboxMenuItem miEMshowEditedGenes
java.awt.CheckboxMenuItem miEMeditNop
java.awt.CheckboxMenuItem miEMeditAdd
java.awt.CheckboxMenuItem miEMeditRmv
java.awt.CheckboxMenuItem miEMautoScrollerPopup
java.awt.CheckboxMenuItem miEMclusterWorkingCL
java.awt.CheckboxMenuItem miVMshowEditedGenes
java.awt.CheckboxMenuItem miVMshowFilteredSpots
java.awt.CheckboxMenuItem miVMPresentView
java.awt.CheckboxMenuItem miVMGang
java.awt.CheckboxMenuItem miVMuseMouseOver
java.awt.CheckboxMenuItem miVMgenBankViewer
java.awt.CheckboxMenuItem miVMdbESTviewer
java.awt.CheckboxMenuItem miVMuniGeneViewer
java.awt.CheckboxMenuItem miVMomimViewer
java.awt.CheckboxMenuItem miVMmAdbViewer
java.awt.CheckboxMenuItem miVMlocusLinkViewer
java.awt.CheckboxMenuItem miVMmedMinerViewer
java.awt.CheckboxMenuItem miVMswissProtViewer
java.awt.CheckboxMenuItem miVMpirViewer
java.awt.CheckboxMenuItem miVMuseDichromasy
java.awt.CheckboxMenuItem miVMshowMsgLog
java.awt.CheckboxMenuItem miVMshowHistoryLog
java.awt.CheckboxMenuItem[] miVMgenomicViewer
java.awt.CheckboxMenuItem miFRMgeneClassMbrFilter
java.awt.CheckboxMenuItem miFRMuseGeneSetFilter
java.awt.CheckboxMenuItem miFRMgoodGeneListFilter
java.awt.CheckboxMenuItem miFRMreplicateGenesFilter
java.awt.CheckboxMenuItem miFRMhistRatioRngFilter
java.awt.CheckboxMenuItem miFRMhistIntensRngFilter
java.awt.CheckboxMenuItem miFRM_EGLfilter
java.awt.CheckboxMenuItem miFRMspotCVfilter
java.awt.CheckboxMenuItem miFRMclusterHP_Efilter
java.awt.CheckboxMenuItem miFRMuseDiffFilter
java.awt.CheckboxMenuItem miFRMtTestXYfilter
java.awt.CheckboxMenuItem miFRMtTestXYsetsFilter
java.awt.CheckboxMenuItem miFRMksTestXYsetsFilter
java.awt.CheckboxMenuItem miFRMfTestOCLFilter
java.awt.CheckboxMenuItem miFRMhighXYratioFilter
java.awt.CheckboxMenuItem miFRMlowXYratioFilter
java.awt.CheckboxMenuItem miFRMthrSpotIntens
java.awt.CheckboxMenuItem miFRMspotIntensRngIn
java.awt.CheckboxMenuItem miFRMspotIntensRngOut
java.awt.CheckboxMenuItem miFRMspotIntensModeMS
java.awt.CheckboxMenuItem miFRMspotIntensModeXY
java.awt.CheckboxMenuItem miFRMspotIntensModeXsets
java.awt.CheckboxMenuItem miFRMspotIntensModeYsets
java.awt.CheckboxMenuItem miFRMspotIntensModeXORYsets
java.awt.CheckboxMenuItem miFRMspotIntensModeXANDYsets
java.awt.CheckboxMenuItem miFRMspotIntensModeE
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeALL
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeANY
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_MOST
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_LEAST
java.awt.CheckboxMenuItem miFRMspotIntensCompareModePRODUCT
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeSUM
java.awt.CheckboxMenuItem miFRMthrGray
java.awt.CheckboxMenuItem miFRMgrayRngIn
java.awt.CheckboxMenuItem miFRMgrayRngOut
java.awt.CheckboxMenuItem miFRMthrRatio
java.awt.CheckboxMenuItem miFRMratioRngIn
java.awt.CheckboxMenuItem miFRMratioRngOut
java.awt.CheckboxMenuItem miFRMthrCy3Cy5Ratio
java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngIn
java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngOut
java.awt.CheckboxMenuItem miFRMcvModeMS
java.awt.CheckboxMenuItem miFRMcvModeXY
java.awt.CheckboxMenuItem miFRMcvModeXset
java.awt.CheckboxMenuItem miFRMcvModeYset
java.awt.CheckboxMenuItem miFRMcvModeXORYsets
java.awt.CheckboxMenuItem miFRMcvModeXANDYsets
java.awt.CheckboxMenuItem miFRMcvModeE
java.awt.CheckboxMenuItem miFRMuseCVmeanElseMax
java.awt.CheckboxMenuItem miFRMusePosQuantDataFlag
java.awt.CheckboxMenuItem miFRMposQuantModeMS
java.awt.CheckboxMenuItem miFRMposQuantModeXY
java.awt.CheckboxMenuItem miFRMposQuantModeXYsets
java.awt.CheckboxMenuItem miFRMposQuantModeE
java.awt.CheckboxMenuItem miFRMuseGoodSpotDataFlag
java.awt.CheckboxMenuItem miFRMgoodSpotModeMS
java.awt.CheckboxMenuItem miFRMgoodSpotModeXY
java.awt.CheckboxMenuItem miFRMgoodSpotModeXORYsets
java.awt.CheckboxMenuItem miFRMgoodSpotModeXANDYsets
java.awt.CheckboxMenuItem miFRMgoodSpotModeE
java.awt.CheckboxMenuItem miFRMuseDetValueSpotDataFlag
java.awt.CheckboxMenuItem miFRMOnlyGenesWithNonZeroDensityFlag
java.awt.CheckboxMenuItem miFRMdetValueSpotModeMS
java.awt.CheckboxMenuItem miFRMdetValueSpotModeXY
java.awt.CheckboxMenuItem miFRMdetValueSpotModeXANDYsets
java.awt.CheckboxMenuItem miFRMdetValueSpotModeE
java.awt.CheckboxMenuItem miPMplotPseudoImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_RYGImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_F1F2_RYGImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_XYImg
java.awt.CheckboxMenuItem miPMplotPseudoF1F2Img
java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_pValueImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_EP_CV_valueImg
java.awt.CheckboxMenuItem miPMdualXYpseudoImg
java.awt.CheckboxMenuItem miPMflickerXY
java.awt.CheckboxMenuItem miPMlowRangeZoom
java.awt.CheckboxMenuItem miPEPlistType
java.awt.CheckboxMenuItem miCLMfindSimGenesDisp
java.awt.CheckboxMenuItem miCLMsimGeneCountsDisp
java.awt.CheckboxMenuItem miCLMhierClusterDisp
java.awt.CheckboxMenuItem miCLMdispKmeansNodes
java.awt.CheckboxMenuItem miCLMuseMedianKmeans
java.awt.CheckboxMenuItem miCLMuseCorrCoeffDist
java.awt.CheckboxMenuItem miCLMuseLSQmagNorm
java.awt.CheckboxMenuItem miCLHCMavgPGMALnk
java.awt.CheckboxMenuItem miCLHCMavgPGMCLnk
java.awt.CheckboxMenuItem miCLHCMnextMinLnk
java.awt.CheckboxMenuItem miCLHCMunWtAvg
java.awt.CheckboxMenuItem miCLMnormHP
java.awt.CheckboxMenuItem miCLHCMuseClusterDistCache
java.awt.CheckboxMenuItem miCLHCMuseShortClusterDistCache
java.awt.CheckboxMenuItem miTMtblFontSize8pt
java.awt.CheckboxMenuItem miTMtblFontSize10pt
java.awt.CheckboxMenuItem miTMtblFontSize12pt
java.awt.CheckboxMenuItem miPRtblFontSize8pt
java.awt.CheckboxMenuItem miPRtblFontSize10pt
java.awt.CheckboxMenuItem miPRtblFontSize12pt
java.awt.CheckboxMenuItem miTMtblFmtTabDelim
java.awt.CheckboxMenuItem miTMtblFmtClickable
java.awt.CheckboxMenuItem miTMtblFmtAddEPdata
java.awt.CheckboxMenuItem miTMtblFmtUseRawEPdata
java.awt.CheckboxMenuItem miTMtblFmtAddHP_XYsetStat
java.awt.CheckboxMenuItem miTMtblFmtAddOCLstatistics
java.awt.CheckboxMenuItem miPLGMuseSPLUSasComputingEngine
java.awt.CheckboxMenuItem miPLGMuseTimeStampReports
java.awt.Label HP_Xlabel
java.awt.Label HP_Ylabel
Constructor Detail |
MenuBarFrame(MAExplorer mae, java.lang.String title, int x0, int y0)
mae
- is instance of MAExplorertitle
- is the name of the framex0
- is ULHC X position of framey0
- is ULHC Y position of frameaddMenuBar()
,
buildMenuGUI(int, int, int, int)
,
insertPluginMenuEntries()
,
Frame.setTitle(java.lang.String)
MenuBarFrame(MAExplorer mae)
mae
- is instance of MAExplorerMethod Detail |
void redoMenuBar()
addMenuBar()
,
insertPluginMenuEntries()
,
Frame.setTitle(java.lang.String)
private void addMenuStubToMenuStubList(java.lang.String name, java.awt.Menu menuStub)
"PluginMenuName"+i. E.g. "New sample report" "PluginMenuStubName"+i. E.g. "Report:sample" "PluginClassFile"+i. E.g. "NewReport.class" "PluginCallAtStartup"+i. E.g. "TRUE"
name
- is the name of the menu stubmenuStub
- is the Menu stub associated with the nameprivate java.awt.Menu findMenuStubByName(java.lang.String name)
"PluginMenuName"+i. E.g. "New sample report" "PluginMenuStubName"+i. E.g. "Report:sample" "PluginClassFile"+i. E.g. "NewReport.class" "PluginCallAtStartup"+i. E.g. "TRUE"
name
- is the name of the menu stub to look forprivate void insertPluginMenuEntries()
"PluginMenuName"+i. E.g. "New sample report" "PluginMenuStubName"+i. E.g. "Report:sample" (from legal list of Menu stub names) "PluginClassFile"+i. E.g. "NewReport.class" "PluginCallAtStartup"+i. E.g. "InstallInMenu" (1 of: "InstallInMenu", "RunOnStartup", "NoInstall")
findMenuStubByName(java.lang.String)
void callAllStartupPlugins()
"PluginMenuName"+i. E.g. "New sample report" "PluginMenuStubName"+i. E.g. "Report:sample" "PluginClassFile"+i. E.g. "NewReport.class" "PluginCallAtStartup"+i. E.g. "TRUE"
private void makeMenuItem(java.awt.Menu pm, java.lang.String sLabel, java.lang.String sCmd, int shortcut)
pm
- is the menu to install itsLabel
- is the visible labelsCmd
- is the opt Cmd name (uses sLabel if null)shortcut
- is the opt short cutprivate java.awt.Menu makeSubMenu(java.awt.Menu pm, java.lang.String sLabel, java.lang.String sCmd, int shortcut)
pm
- is the menu to install itsLabel
- is the visible labelsCmd
- is the opt Cmd name (uses sLabel if null)shortcut
- is the opt short cutprivate java.awt.CheckboxMenuItem makeChkBoxMenuItem(java.awt.Menu pm, java.lang.String sLabel, java.lang.String sCmd, int shortcut, boolean value)
pm
- is the menu to install itsLabel
- is the visible labelsCmd
- is the opt Cmd name (uses sLabel if null)shortcut
- is the opt short cutvalue
- is the initial value of the checkboxvoid addSetHP_XYEsubmenuTree(java.awt.Menu subMenu, java.lang.String hpPostfixStr)
subMenu
- to add to the treehpPostfixStr
- command string to associate with the submenu entries.makeMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int)
,
makeSubMenu(java.awt.Menu, java.lang.String, java.lang.String, int)
void addRLOsubmenuTree()
makeMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int)
,
makeSubMenu(java.awt.Menu, java.lang.String, java.lang.String, int)
int addMenuBar()
MaeJavaAPI
,
MaeJavaAPI.setMenuHook(java.awt.Menu)
,
addSetHP_XYEsubmenuTree(java.awt.Menu, java.lang.String)
,
addMenuStubToMenuStubList(java.lang.String, java.awt.Menu)
,
makeChkBoxMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int, boolean)
,
makeMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int)
,
makeSubMenu(java.awt.Menu, java.lang.String, java.lang.String, int)
void buildMenuGUI(int x0, int y0, int width, int height)
x0
- is X ULHC position of windowy0
- is Y ULHC position of windowwidth
- of windowheight
- of windowArrayScroller
,
StateScrollers
,
createDialogQueryFrames()
,
setSTOPbuttonState(boolean, boolean)
void createDialogQueryFrames()
PopupDialogQuery
,
PopupBinOprDialogQuery
void setSTOPbuttonState(boolean flag, boolean isEnabledFlag)
flag
- to abort command process if true.isEnabledFlag
- sets stop label to "STOP!" else "RUNNING"Component.repaint()
void setHP_XYlabels()
SampleSets.setHPxyModStrings()
void enableMenus(java.lang.String opr)
opr
- is "none", "all", or "basic"public void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed
in interface java.awt.event.ActionListener
e
- is action event for buttons and menu commandsEventMenu.handleActions(java.awt.event.ActionEvent)
,
FileIO.logMsgln(java.lang.String)
,
PopupGeneGuesser
,
setSTOPbuttonState(boolean, boolean)
public void itemStateChanged(java.awt.event.ItemEvent e)
itemStateChanged
in interface java.awt.event.ItemListener
e
- is checkbox event Checkbox and menu checkbox commandsEventMenu.handleItemStateChanged(java.awt.event.ItemEvent)
public void windowClosing(java.awt.event.WindowEvent e)
windowClosing
in interface java.awt.event.WindowListener
e
- is window closing eventMAExplorer.quit()
public void windowActivated(java.awt.event.WindowEvent e)
windowActivated
in interface java.awt.event.WindowListener
public void windowClosed(java.awt.event.WindowEvent e)
windowClosed
in interface java.awt.event.WindowListener
public void windowDeactivated(java.awt.event.WindowEvent e)
windowDeactivated
in interface java.awt.event.WindowListener
public void windowDeiconified(java.awt.event.WindowEvent e)
windowDeiconified
in interface java.awt.event.WindowListener
public void windowIconified(java.awt.event.WindowEvent e)
windowIconified
in interface java.awt.event.WindowListener
public void windowOpened(java.awt.event.WindowEvent e)
windowOpened
in interface java.awt.event.WindowListener
public void keyPressed(java.awt.event.KeyEvent e)
keyPressed
in interface java.awt.event.KeyListener
e
- is key pressed eventpublic void keyReleased(java.awt.event.KeyEvent e)
keyReleased
in interface java.awt.event.KeyListener
e
- is key released eventpublic void keyTyped(java.awt.event.KeyEvent e)
keyTyped
in interface java.awt.event.KeyListener
e
- is key typed event
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