Uses of Class
MAExplorer

Packages that use MAExplorer

Uses of MAExplorer in

Fields in declared as MAExplorer

(package private) MAExplorer	ArrayScroller.mae link to global MAExplorer instance
private static MAExplorer	ChooserGUI.mae link to global MAExplorer instance
(package private) MAExplorer	ChooserGUI.MouseEventHandler.mae
private static MAExplorer	ClusterGenes.mae link to global MAExplorer instance
(package private) static MAExplorer	ClusterGramCanvas.mae link to global MAExplorer instance
private MAExplorer	ClusterSamples.mae link to global MAExplorer instance
private MAExplorer	CompositeDatabase.mae link to global MAExplorer instance
private static MAExplorer	Condition.mae link to global MAExplorer instance
private MAExplorer	Config.mae link to global instance of MAExplorer
(package private) MAExplorer	Draw2Dplot.mae link to global instance
private MAExplorer	DrawClusterGram.mae link to global instance
private MAExplorer	DrawHistogram.mae link to global MAExplorer instance
private MAExplorer	DrawPseudoImage.mae link to global MAExplorer instance
private MAExplorer	DrawRatioHistogram.mae link to global instance
private MAExplorer	DrawScatterPlot.mae link to global instance
private MAExplorer	EditedGeneList.mae link to global MAExplorer instance
private static MAExplorer	EventMenu.mae link to global MAExplorer instance
private MAExplorer	ExprProfile.mae link to global MAExplorer instance
(package private) MAExplorer	ExprProfileCanvas.mae instance of MAExplorer so we can clear flags indicating the user did a manual quit()
private MAExplorer	ExprProfileOverlay.mae links to global MAExplorer instance
(package private) MAExplorer	ExprProfilePanel.mae link to global MAExplorer instance
private MAExplorer	ExprProfilePopup.mae link to global MAExplorer instance
private MAExplorer	ExprProfileScrollPane.mae link to global MAExplorer instance
private MAExplorer	FileIO.mae link to global MAExplorer instance
private MAExplorer	Filter.mae link to global MAExplorer instance
private static MAExplorer	Gene.mae link to global MAExplorer instance
private static MAExplorer	GeneBitSet.mae link to global MAExplorer instance
private MAExplorer	GeneClass.mae link to global instance
private static MAExplorer	GeneGeneDist.mae link to global MAExplorer instance
private MAExplorer	GeneList.mae link to global MAExplorer instance
private static MAExplorer	GetParams.mae link to global MAExplorer instance
private MAExplorer	GipoTable.mae link to global MAExplorer instance
private static MAExplorer	GridCoords.mae link to global MAExplorer instance
(package private) MAExplorer	Guesser.mae link to global instance
(package private) MAExplorer	KeyEventHandler.mae instance of MAExplorer
(package private) MAExplorer	MouseEventHandler.mae instance of MAExplorer
private MAExplorer	HPxyData.mae link to global MAExplorer instance
private static MAExplorer	HierClustNode.mae link to global MAExplorer instance
(package private) static MAExplorer	MJAbase.mae link to global MAExplorer instance
private MAExplorer	MaHPquantTable.mae link to global MAExplorer instance
(package private) MAExplorer	MaHybridSample.mae link to global MAExplorer instance
private MAExplorer	MaInfoTable.mae link to global MAExplorer instance
(package private) static MAExplorer	MaeJavaAPI.mae link to global MAExplorer instance
private MAExplorer	Maps.mae link to global MAExplorer instance
private MAExplorer	MenuBarFrame.mae link to global instance
private MAExplorer	OverlayMap.mae link to global instance
private MAExplorer	OverlayMap.dp link to global instance
private MAExplorer	PopupBinOprDialogQuery.mae link to MAExplorer instance
private MAExplorer	PopupDialogQuery.mae link to global instance to MAExplorer
private MAExplorer	PopupHPChooser.mae link to global MAExplorer instance
private MAExplorer	PopupLoginDialogQuery.mae link to global instance of MAExplorer
private MAExplorer	PopupRegistry.mae link to global MAExplorer instance
private MAExplorer	Report.mae link to global MAExplorer instance
(package private) static MAExplorer	Reval.mae Global link
private MAExplorer	SampleSets.mae link to global MAExplorer instance
private MAExplorer	PopupScrollableSelector.mae
private MAExplorer	SamplesTable.mae link to global instance of MAExplorer
private MAExplorer	ScrollableImageCanvas.mae link to global instance of MAExplorer
(package private) MAExplorer	ShowExprProfilesPopup.mae
private MAExplorer	ShowPlotPopup.mae link to global MAExplorer instance
private MAExplorer	ShowSpreadsheetPopup.mae link to global MAExplorer instance
private MAExplorer	ShowStringPopup.mae link to global MAExplorer nstance
private static MAExplorer	SpotData.mae link to global MAExplorer instance
private static MAExplorer	SpotFeatures.mae link to global MAExplorer instance
(package private) MAExplorer	SpreadSheet.mae link to global MAExplorer instance
(package private) MAExplorer	SSspreadPanel.mae
(package private) MAExplorer	SSstatusBar.mae max number col with alphabet
private MAExplorer	StateScrollers.mae link to global MAExplorer instance
private MAExplorer	Statistics.mae link to global instance of MAExplorer
(package private) MAExplorer	Table.mae link to global instance of MAExplorer
private MAExplorer	UserState.mae link to global instance of MAExplorer
(package private) static MAExplorer	Util.mae link to global MAExplorer instance

Methods in with parameters of type MAExplorer

(package private) static void	ClusterGenes.findAllGeneClusterCounts(MAExplorer maE, float clusterDistThr) findAllGeneClusterCounts() - # genes such that geneDist LEQ geneDistThr.
(package private) static int	ClusterGenes.findClustersOfGene(MAExplorer maE, Gene geneToTest, float clusterDistThr, boolean doSortFlag) findClustersOfGene() - find all HP-E gene clusters LT clusterDist.
(package private) static void	Config.setupPathBase(MAExplorer mae) setupPathBase() - set mae.(fileBasePath, isWorkingMAE) from codeBase.
private void	MJAbase.setupGSstateMJAbase(MAExplorer mae) MJAbase() - constructor for Gather Scatter API for MAExplorer to access MAExplorer data in a uniform interface.
(package private) void	MaeJavaAPI.initStateAndMJAchildren(MAExplorer mae) initStateAndMJAchildren() - init the children classes.
(package private) static void	PopupGeneGuesser.sortGeneNameAndCloneIDLists(MAExplorer mae) sortGeneNameAndCloneIDLists() - sort lists of Master_IDs & Gene_Names for use with the guesser.
private static void	PopupGeneGuesser.preSortLists(MAExplorer mae) 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 .
(package private) boolean	StageNames.getMenuTreeFromSamplesTable(MAExplorer mae) getMenuTreeFromSamplesTable() - build tree from Samples.txt Table
private boolean	Table.createFileTable(MAExplorer mae, java.lang.String fileName, java.lang.String msg, java.lang.String[] overideFieldNames, boolean dontReadHeaderLineFlag) createFileTable() - create table from file on this Table.

Constructors in with parameters of type MAExplorer

ArrayScroller(MAExplorer mae, java.lang.String name, java.lang.String title, int iWidth, int iHeight, int preferredWidth, int preferredHeight, int magnification)
ArrayScroller() - constructor.

ChooserGUI(MAExplorer mae, ChooserGUI remoteC_GUI, int taRows, int taCols, java.awt.Font titleFont, java.awt.Font labelFont, java.awt.Font dataFont, java.lang.Object parentWindow, boolean addChangePosFlag)
ChooserGUI() - constructor for base class of Chooser GUI

ChooserGUI.MouseEventHandler(MAExplorer mae, ChooserGUI cGUI, java.awt.TextArea ta, java.lang.String[] alphaList, int size)
MouseEventHandler() - constructor

ChooserGUI.MouseEventHandler(MAExplorer mae, java.awt.TextArea ta)
MouseEventHandler() - constructor

ClusterGenes(MAExplorer mae)
ClusterGenes() - constructor to create instance of new cluster method

ClusterGramCanvas(MAExplorer mae, DrawClusterGram dcg, GeneList orderedCL, HierClustNode tree)
ClusterGramCanvas() - Constructor to display expresion profile in canvas

ClusterSamples(MAExplorer mae, GeneList mList, MaHybridSample[] msList, int nMSlist)
ClusterSamples() - constructor

CompositeDatabase(MAExplorer mae)
CompositeDatabase() - constructor to set up data structures.

Condition(MAExplorer maE, java.lang.String condName, boolean intitalParamFlag)
Condition() - constructor to create a new named sample Condition list.

Config(MAExplorer mae, java.lang.String configFile)
Config() - constructor to make it accessible.

ConfigTable(MAExplorer mae, java.lang.String fileName)
ConfigTable() - constructor to read the configuration table file.

Draw2Dplot(MAExplorer mae, int plotMode, ShowPlotPopup spp, ExprProfileOverlay epov, java.lang.String title, int nPoints, int nLineGroup, boolean useXaxisIntNbrFlag)
Draw2Dplot() - constructor

DrawClusterGram(MAExplorer mae, ShowPlotPopup spp, java.awt.Panel titlePanel, HierClustNode tree, GeneList orderedCL, java.lang.String title, int plotMode, boolean keepFlagsOnClosing)
DrawClusterGram() - Create popup grid of ClusterGram plots.

DrawHistogram(MAExplorer mae, ShowPlotPopup spp, java.lang.String mTitle, java.lang.String horizVariableCaption, int plotMode)
DrawHistogram() - constructor to create an intensity histogram.

DrawPseudoImage(MAExplorer mae)
DrawPseudoImage() - constructor

DrawRatioHistogram(MAExplorer mae, ShowPlotPopup spp, int plotMode)
DrawRatioHistogram() - constructor to draw ratio histogram

DrawScatterPlot(MAExplorer mae, ShowPlotPopup spp, int plotMode)
DrawScatterPlot() - constructor to create scatter plot

EditedGeneList(MAExplorer mae)
EditedGeneList() - constructor

EventMenu(MAExplorer mae)
EventMenu() - constructor for event menu instance

ExprProfile(MAExplorer mae, int mid, boolean normToOneFlag)
ExprProfile() - Constructor to create expresion profile object

ExprProfileCanvas(MAExplorer mae, int mid, java.lang.String title, java.awt.Font font, int preferredWidth, int preferredHeight, boolean showKmeansDataFlag, boolean drawLabelsFlag)
ExprProfileCanvas() - Constructor to display an expression profile in a canvas.

ExprProfileOverlay(MAExplorer mae, ShowExprProfilesPopup sepp, GeneList exprProfileCL, java.lang.String title, int preferredPanelWidth, boolean showKmeansDataFlag)
ExprProfileOverlay() - Create popup overlay plot of ExprProfiles.

ExprProfilePanel(MAExplorer mae, int mid, java.lang.String title, java.awt.Font font, int preferredWidth, int preferredHeight, boolean showKmeansDataFlag, boolean drawLabelsFlag)
ExprProfilePanel() - Constructor to display expression profile in canvas.

ExprProfilePopup(MAExplorer mae, int mid, java.lang.String title, java.awt.Font font, int preferredWidth, int preferredHeight, boolean drawLabelsFlag)
ExprProfilePopup() - Constructor to popup expression profile window.

ExprProfileScrollPane(MAExplorer mae, ShowExprProfilesPopup sepp, GeneList exprProfileCL, java.lang.String title, int preferredPanelWidth, boolean showKmeansDataFlag)
ExprProfileScrollPane() - Create a popup grid of ExprProfile plots.

FileIO(MAExplorer mae)
FileIO() - constructor to create fio instance and to close the log file.

Filter(MAExplorer mae, int maxGenes)
Filter() - constructor to initialize data filter and initial gene lists.

Filter(MAExplorer mae)
Filter() - constructor to initialize data filter but not initial gene lists

Gene(MAExplorer maE)
Gene() - constructor to set up global mae instance - MUST BE CALLED FIRST!!! Note: we only need the mae instance to setup the map instance.

GeneBitSet(MAExplorer maE, int maxItems, GeneList ml)
GeneBitSet() - constructor to create a GeneBitSet without a name.

GeneBitSet(MAExplorer maE, int maxItems, java.lang.String bName, GeneList ml)
GeneBitSet() - constructor to create a named GeneBitSet.

GeneClass(MAExplorer mae)
GeneClass() - constructor to create gene class database

GeneGeneDist(MAExplorer mae)
GeneGeneDist() - constructor

GeneList(MAExplorer mae, int maxGeneListSize)
GeneList() - constructor to specify list sizes with both mList[] and bitSet.

GeneList(MAExplorer mae, int maxGeneListSize, java.lang.String cName)
GeneList() - constructor to make new Gene named list with both mList[] and bitSet.

GeneList(MAExplorer mae, int maxGeneListSize, java.lang.String cName, boolean createMlistFlag)
GeneList() - constructor to make new Gene named list with bitSet but optional mList[].

GetParams(MAExplorer mae)
GetParams() - constructor

GipoTable(MAExplorer mae, java.lang.String fileName)
GipoTable() - constructor to read the GIPO table.

GridCoords(MAExplorer mae)
GridCoords() - constructor which builds (f,g,r,c) - (gid or cid) mapping tables.

Guesser(MAExplorer mae, boolean genericFlag, boolean setEGLfromListFlag)
Guesser() - constructor for Guesser.

KeyEventHandler(MAExplorer mae, Guesser gsr, java.awt.TextField tf, java.awt.TextArea ta, java.lang.String[] alphaList, int alphaListSize, MouseEventHandler meh)
KeyEventHandler() - constructor for key events.

MouseEventHandler(MAExplorer mae, Guesser gsr, java.awt.TextField tf, java.awt.TextArea ta, java.lang.String[] alphaList)
MouseEventHandler() - constructor

HPxyData(MAExplorer mae, int mid, boolean useHPxySetDataFlag)
HPxyData() - Constructor to create HP XY data object.

HierClustNode(MAExplorer maE, int nObj, int nDataV, int hierClustMode, boolean useCorrCoeffFlag, boolean useClusterDistCacheFlag, boolean normHCbyRatioHPflag, boolean normByHPXflag, int iDataV)
HierClustNode() - setup static variables for full hier clustering which will provide data for both a Clustergram and Dendrogram...

HierClustNode(MAExplorer maE, int nObj, int nDataV, GeneList ml, float[][] geneEPvector)
HierClustNode() - setup static variables for ONLY ClusterGram for use with K-means clustering data.

MJAbase(MAExplorer mae)
MJAbase() - constructor for Gather Scatter API for MAExplorer to access MAExplorer data in a uniform interface.

MaHPquantTable(MAExplorer mae, MaHybridSample ms, java.lang.String fileName, java.lang.String hpName, boolean swapCy5Cy3DataFlag)
MaHPquantTable() - constructor to read the .quant file table and setup MaHybridSample

MaHybridSample(MAExplorer mae, java.lang.String hybSampleName, java.lang.String sampleID, java.lang.String databaseFileID, java.lang.String oImageName, java.lang.String menuTitle, java.lang.String fullStageText, java.lang.String projectName, boolean needLoginFlag, boolean swapCy5Cy3DataFlag, int idxHybridSample)
MaHybridSample() - constuctor for an instance of a Microarray hybridized sample data

MaInfoTable(MAExplorer mae, java.lang.String fileName)
MaInfoTable() - constructor

MaeJavaAPI(MAExplorer mae)
MaeJavaAPI() - constructor for Gather Scatter API for MAExplorer to access MAExplorer data in a uniform interface.

Maps(MAExplorer mae)
Maps() - constructor that allocates mapping tables calc size from F*G*R*C These is populated @GipoTable.setupMapLookupTables().

MenuBarFrame(MAExplorer mae, java.lang.String title, int x0, int y0)
MenuBarFrame() - constructor for main GUI window and menubar.

MenuBarFrame(MAExplorer mae)
MnuBarFrame() - constructor used with the Applet.

OverlayMap(MAExplorer maE, int maxNamedOverlayMaps)
OverlayMap() - constructor named overlay map

PopupBinOprDialogQuery(MAExplorer MaE, java.awt.Frame f)
PopupBinOprDialogQuery() - Constructor

PopupDialogQuery(MAExplorer mae, java.awt.Frame f, int addButtonsCnt)
PopupDialogQuery() - Constructor

PopupGeneGuesser(MAExplorer maE, char chFirstTyped, java.awt.Font font)
PopupGeneGuesser() - constructor

PopupHPChooser(MAExplorer mae, java.awt.Font titleFont, java.awt.Font labelFont, java.awt.Font dataFont, int taRows, int taCols)
PopupHPChooser() - Constructor.

PopupHPmenuGuesser(MAExplorer mAE, char chFirstTyped, java.awt.Font font)
PopupHPmenuGuesser() - constructor assumes the HP menu item list is already sorted when it is created during MAExplorer initialization.

PopupLoginDialogQuery(MAExplorer MaE, java.awt.Frame f)
PopupLoginDialogQuery() - Constructor

PopupProjDirGuesser(MAExplorer maE, char chFirstTyped, java.awt.Font font, Table prjTbl)
PopupProjDirGuesser() - constructor for project director guesser which assumes the HP menu item list is already sorted when it is created during MAExplorer initialization.

PopupRegistry(MAExplorer mae)
PopupRegistry() - constructor to popup registry

Report(MAExplorer mae, java.lang.String rName, int reportMode, int tblFmtMode, java.lang.String popupName, int popupPropertyBits)
Report() - constructor for Report

SampleSets(MAExplorer mae)
SampleSets() - constructor to create the sample lists.

PopupScrollableSelector(MAExplorer mae, java.awt.Frame frame, java.lang.String title, java.lang.String[] nameList, boolean[] valueList, int nList)
PopupScrollableSelector() - popup selector to select boolean values.

SamplesTable(MAExplorer mae, java.lang.String fileName)
SamplesTable() - constructor to read Samples DB and set up table.

ShowExprProfilesPopup(MAExplorer mae, GeneList mlToUse, int[] hpDataNbrA, float[][] hpDataMnA, float[][] hpDataSDA, int nMnGenes, boolean hasMeanPlotsFlag, java.lang.String title, java.lang.String popupName, int popupPropertyBits, boolean useEPoverlayFlag, boolean useLargeFrameFlag, boolean showKmeansDataFlag)
ShowExprProfilesPopup() - Constructor.

ShowPlotPopup(MAExplorer mae, int plotMode, java.lang.String title, java.lang.String popupName, int popupPropertyBits, int frmOffset)
ShowPlotPopup() - constructor to create a spreadsheet from raw data with URL spec.

ShowSpreadsheetPopup(MAExplorer mae, Report report, java.lang.String[] tFields, java.lang.String[][] tData, int lastRow, int startRow, int tRows, int tCols, java.lang.String fontSizeStr, java.lang.String title, java.lang.String[] altFieldNames, int[] cellFormat, java.lang.String[][] dataURL, java.lang.String popupName, int popupPropertyBits, boolean urlViewerFlag)
ShowSpreadsheetPopup() - constructor to create a spreadsheet from raw data with URL spec.

ShowSpreadsheetPopup(MAExplorer mae, Report report, Table t, java.lang.String fontSizeStr, java.lang.String title, java.lang.String popupName, int popupPropertyBits, boolean urlViewerFlag)
ShowSpreadsheetPopup() - constructor to create a spreadsheet from table without URL spec.

ShowStringPopup(MAExplorer mae, java.lang.String inputStr, int nRows, int nCols, java.lang.String fontSize, java.lang.String title, int optReportMode, int optMode, java.lang.String popupName, int popupPropertyBits, java.lang.String defTxtFile)
ShowStringPopup() - Constructor.

SpotData(MAExplorer mae)
SpotData() - constructor to capture mae.

SpotFeatures(MAExplorer mae)
SpotFeatures() - constructor

SpreadSheet(ShowSpreadsheetPopup ssp, MAExplorer mae, int virRows, int virCols, java.lang.String[][] prepDataOrig, int prepRows, int prepCols, int fontSize, java.lang.String title, java.awt.Font cellUrlFont, java.awt.Font cellDataFont, java.awt.Font buttonFont, int[] cellFormat, java.lang.String[][] dataURL)
Spreadsheet() - creates a new Panel with BoderLayout and adds a new SSspreadPanel (the grid itself) w/ horizontal and vertical scrollbars.

SSspreadPanel(java.lang.String[][] prepDataOrig, ShowSpreadsheetPopup ssp, MAExplorer mae, int virRows, int virCols, int prepRows, int prepCols, int fontSize, java.awt.Font cellUrlFont, java.awt.Font cellDataFont, java.awt.Font buttonFont, int[] cellFormat, java.lang.String[][] dataURL)
SSspreadPanel() - constructor, panel holding (row,col) matrix of TextFields with the URL font and fields.

SSspreadPanel(MAExplorer mae, int virRows, int virCols, java.lang.String[][] prepDataOrig, int prepRows, int prepCols, int fontSize, java.awt.Font cellDataFont, java.awt.Font buttonFont)
SSspreadPanel() - constructor, inits the grid with values without the URL font and fields.

SSstatusBar(ShowSpreadsheetPopup ssp, MAExplorer mae, int virRows, int virCols)
SSstatusBar() - constructor, add the components for statusbar set here

StageNames(MAExplorer mae)
StageNames() - initial global constructor with no data

StateScrollers(MAExplorer mae, java.lang.String title)
StateScrollers() - constructor to build the GUI with pop up menus

Statistics(MAExplorer mae)
Statistics() - constructor

Table(MAExplorer mae, java.lang.String fileName, java.lang.String msg)
Table() - constructor for creating table from file

Table(MAExplorer mae, java.lang.String fileName, java.lang.String msg, java.lang.String[] overideFieldNames, boolean dontReadHeaderLineFlag)
Table() - constructor for creating table from file

Table(MAExplorer mae, int nRows, int nCols, java.lang.String title, java.lang.String msg)
Table() - constructor for creating empty table of (nRows,nCols).

TestPluginCode(MAExplorer mae)
TestPluginCode() - constructor to capture mae.

UserState(MAExplorer mae, java.lang.String userStateName)
UserState() - constructor

Util(MAExplorer mae)
Util() - constructor for Utility package