Uses of Class
GeneList

Packages that use GeneList

Uses of GeneList in

Fields in declared as GeneList

(package private) static GeneList	ClusterGenes.curClusterCL ARG: current genes being clustered
(package private) static GeneList	ClusterGenes.complexClusterCL ARG: list of genes to be clustered
(package private) GeneList	ClusterGenes.mnClustersCL artificial mean K-means gene list
(package private) GeneList	ClusterGenes.Cluster.clusterCL optional list of genes in this cluster
private GeneList	ClusterGramCanvas.orderedCL gene list for rows
(package private) GeneList	ClusterSamples.mList list of genes used in pattern vector
private GeneList	CompositeDatabase.tempCD_CL temporary GeneList used in local gene list operations
(package private) GeneList	Draw2Dplot.eventHandlerCL set to gene list being used
(package private) GeneList	Draw2Dplot.dispCL associated GeneList if not null
private GeneList	DrawClusterGram.orderedCL GeneList being used
private GeneList	EditedGeneList.tmpCL temporary gene list for computations
private static GeneList	EventMenu.workingCL link to global instance of working GeneList
private GeneList	ExprProfileOverlay.exprProfileCL GeneList being used
private GeneList	ExprProfileOverlay.epOvrLayCL special [nGenes*nHP_E] CL
private GeneList	ExprProfileScrollPane.exprProfileCL GeneList being used
private GeneList	ExprProfileScrollPane.epOvrLayCL special [nGenes*nHP_E] CL
private GeneList	Filter.tmpCL temporary gene list for intersections computations
(package private) GeneList	Filter.workingCL Working gene list after run filter
(package private) GeneList	Filter.gcMemberCL "Filter by GeneClass membership"
(package private) GeneList	Filter.HP_XY_t_TestCL "Filter genes by HP-X,HP-Y t-Test" i.e.
(package private) GeneList	Filter.HP_XYsets_t_TestCL "Filter genes by HP-X,HP-Y sets t-Test" i.e.
(package private) GeneList	Filter.HP_XYsets_KS_TestCL "Filter genes by HP-X,HP-Y sets Kolmagorove-Smirnov -Test" i.e.
(package private) GeneList	Filter.OCL_F_TestCL "Filter genes by current Ordered Condition List F-Test" i.e.
(package private) GeneList	Filter.spotCVCL "Use Spot CV filter"
(package private) GeneList	Filter.spotIntensThrCL "Threshold: spot intensity [RI1:RI2]"
(package private) GeneList	Filter.intensityThrCL "Threshold: intensity [I1:I2]"
(package private) GeneList	Filter.ratioThrCL "Threshold: ratio [R1:R2]"
(package private) GeneList	Filter.ratioCy3Cy5ThrCL "Threshold: ratio [CR1:CR2]"
(package private) GeneList	Filter.HP_EclustersCL "Filter by HP-E clusters"
(package private) GeneList	Filter.DiffHP_XYCL "Filter by Diff(HP-X,HP-Y)"
(package private) GeneList	Filter.posQuantDataCL "Filter by Positive Quant Data"
(package private) GeneList	Filter.goodSpotQualChkCL "Filter by Good Spot(QualChk) Data"
(package private) GeneList	Filter.detValueSpotDataCL "Filter by Spot (Detection Value) Data"
(package private) GeneList	Filter.nonZeroSpotDataCL "Filter by non-zero Spot Data"
(package private) GeneList	Filter.highestRatiosCL "Highest ratios"
(package private) GeneList	Filter.lowestRatiosCL "Lowest ratios"
(package private) GeneList	Filter.clusteredGenesCL "Tightly clustered genes"
(package private) GeneList	Filter.displayCL "Spots in the display list"
(package private) GeneList	Filter.KmeansNodesCL "Genes in primary K-means nodes"
(package private) GeneList	Filter.ratioHistCL "Ratio histogram selected genes"
(package private) GeneList	Filter.intensHistCL "Intensity histogram selected genes"
(package private) GeneList	GeneBitSet.ml Associated Master GeneList if any, else null
(package private) GeneList	GeneClass.allGenesCL special list of all genes
(package private) GeneList	GeneClass.allNamedGenesCL special list of all named genes
(package private) GeneList	GeneClass.similarESTsCL special list of ESTs similar to genes
(package private) GeneList	GeneClass.ESTsCL special list of unknown ESTs
(package private) GeneList	GeneClass.allGenesAndESTsCL special list of All genes and ESTs
(package private) GeneList	GeneClass.goodGenesCL special list of good genes
(package private) GeneList	GeneClass.replicateGenesCL special list of replicate genes
(package private) GeneList	GeneClass.housekeepingGenesCL special list of all housekeeping genes
(package private) GeneList	GeneClass.calDNACL special list of calibration DNA
(package private) GeneList	GeneClass.yourPlatesCL special list of "your plate" genes
(package private) GeneList	GeneClass.emptyWellCL special list of "EmptyWell" genes
(package private) GeneList	GeneClass.userFilterGeneSetCL "Filter by user Filter Gene Set"
(package private) GeneList	GeneClass.editedCL "edited gene list"
(package private) GeneList	GeneClass.normCL "Normalization genes"
(package private) GeneList[]	GeneClass.geneClassCLS Gene index lists for each gene class.
(package private) GeneList	GeneGeneDist.dataCL Gene list to generate geneEPvector
private static GeneList[]	GeneList.geneSets list of all gene lists
private static GeneList	GeneList.tempSetCL temporary GeneList used in set operations
(package private) GeneList	MAExplorer.clLst Global instance of GeneList contains gene (clone) list tables
(package private) static GeneList	MJAbase.mlLst link to global GeneClass instance
(package private) static GeneList	MaeJavaAPI.mlLst link to global GeneClass instance
(package private) GeneList	Maps.midStaticCL map: mid index to list of genes i.e.
(package private) GeneList	Maps.gidStaticCL map: GridCoords gid index to list of genes.
(package private) GeneList	ShowExprProfilesPopup.mlToUse Master GeneList being used

Methods in that return GeneList

(package private) GeneList	GeneClass.getGeneListOfGeneClass(java.lang.String geneClassName) getGeneListOfGeneClass() - return a Gene List for the gene class
(package private) GeneList	GeneClass.getGeneListOfCurrentGeneClass() getGeneListOfCurrentGeneClass() - get the current GeneClass Gene List
(package private) GeneList	GeneList.getGeneListByName(java.lang.String geneListName) getGeneListByName() - get GeneList if geneListName is a valid GeneList cName.
(package private) static GeneList	MJAbase.lookupGeneListByName(java.lang.String geneListName) lookupGeneListByName() - lookup GeneList by name Only used by MJA classes.

Methods in with parameters of type GeneList

(package private) boolean	ClusterGenes.createClusterMethod(GeneList complexClusterCL, int nbrOfClusters, MaHybridSample[] msEPlist, int nEPmsList, int method, boolean resetFlag) createClusterMethod() - create instance of new cluster method
(package private) void	ClusterGenes.sortKmeansClusterList(GeneList srcCL, GeneList dstCL) sortKmeansClusterList() - sort K-means srcCL to dstCL by Node number.
(package private) boolean	ClusterGramCanvas.updateData(GeneList orderedCL, HierClustNode tree) updateData() - update expression profile with new gene data
(package private) void	CompositeDatabase.calcRatioHists(int nList, float[] d1List, float[] d2List, GeneList ml) calcRatioHists() - compute ratio histogram of d1List[]/d2List[] data.
(package private) boolean	CompositeDatabase.calcHistOfF1F2Ratios(GeneList ml, MaHybridSample ms) calcHistOfF1F2Ratios() - compute histogram of F1/F2 ratios for spots which are selected in the GeneList ml.
(package private) boolean	CompositeDatabase.calcHistOfHP_XYratios(GeneList ml, boolean useXYsetsFlag) calcHistOfHP_XYRatios() - compute histogram of HP-X/-Y (or 'sets') spot ratios of filtered data
(package private) boolean	CompositeDatabase.setIntensHistCLfromIntenRange(GeneList resultCL, MaHybridSample ms, float intensLB, float intensUB, boolean outsideRangeFlag) setIntensHistCLfromIntensRange() - set GeneList of (F1+F2)/2 in intensity range
(package private) boolean	CompositeDatabase.setRatioHistCLfromF1F2Ratios(GeneList resultCL, MaHybridSample ms, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromF1F2Ratios() - set GeneList of F1/F2 ratios in ratio range
(package private) boolean	CompositeDatabase.setRatioHistCLfromHP_XYratios(GeneList resultCL, MaHybridSample msX, MaHybridSample msY, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromHP_XYRatios() - set GeneList of X/Y ratios in ratio range
(package private) boolean	CompositeDatabase.setRatioHistCLfromHP_XYsetRatios(GeneList resultCL, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromHP_XYsetRatios() - set GeneList of X/Y set ratios in ratio range
(package private) int	CompositeDatabase.getNormHP_XandYdata(float[] xList, float[] yList, int[] propList, GeneList ml, MaHybridSample msX, MaHybridSample msY, boolean setPropsFlag, boolean filterByMLflag) getNormHP_XandYdata() - get normalized list spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
(package private) int	CompositeDatabase.getRawHP_XandYdata(float[] xData, float[] yData, float[] xBkgd, float[] yBkgd, int[] propList, GeneList ml, MaHybridSample msX, MaHybridSample msY, boolean setPropsFlag, boolean filterByMLflag) getRawHP_XandYdata() - get list raw spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
(package private) int	CompositeDatabase.getHP_XandYsetData(float[] xList, float[] yList, int[] propList, GeneList ml, boolean setPropsFlag, boolean filterByMLflag) getHP_XandYsetData() - get list spot (HP-X,HP-Y) sets data passing the data filter mae.fc.workingCL.
(package private) void	Draw2Dplot.update2Dplot(java.lang.String vertCaption, java.lang.String horizCaption, java.lang.String title, java.lang.String topTitle, java.lang.String title1, java.lang.String title2, java.lang.String title3, java.lang.String aText, int xText, int yText, double scaleX, double scaleY, double minX, double maxX, double minY, double maxY, boolean draw45lineFlag, boolean draw180lineFlag, float[] xList, float[] yList, int[] propList, GeneList dispCL, int nList, int[] mapPntToMid) update2Dplot() - set data for plot and then update the plot.
(package private) void	DrawClusterGram.updateCGplot(GeneList orderedCL, HierClustNode tree) updateCGplot() - update ClusterGram plots using new GeneList.
(package private) void	ExprProfileOverlay.updateData(GeneList exprProfileCL, java.lang.String title) updateData() - update exprression profile scroller with new gene data.
(package private) void	ExprProfileScrollPane.updateData(GeneList exprProfileCL, java.lang.String title) updateData() - update expression profile scroller with new gene data.
(package private) boolean	Filter.setPostiveQuantData(GeneList posQuantDataCL, GeneList genesToTestCL, int posQuantTestMode) setPostiveQuantData() - filter out genes with negative quant values.
(package private) boolean	Filter.setGoodSpotQuantData(GeneList goodSpotDataCL, GeneList genesToTestCL, int goodSpotTestMode) setGoodSpotQuantData() - filter out genes failing QualChk quant values.
(package private) boolean	Filter.setDetValueQuantData(GeneList detValueSpotDataCL, GeneList genesToTestCL, int detValueSpotTestMode) setDetValueQuantData() - filter out genes failing Detection Value quant values.
(package private) boolean	Filter.setNonZeroQuantData(GeneList nonZeroSpotDataCL, GeneList genesToTestCL) setNonZeroQuantData() - filter out genes with 0.0 quant values in any HP-EP samples.
(package private) boolean	Filter.setRatiosGeneList(GeneList ratiosCL, GeneList genesToTestCL, int maxGenesToRpt, boolean useHP_XYratio, boolean sortDirection) setRatiosGeneList() set ratiosCL by reportMode and sort by specified direction.
(package private) boolean	Filter.setGeneListBySpotCV(GeneList cvResultCL, GeneList genesToTestCL, float spotCVthr, int cvTestMode) setGeneListBySpotCV() - do test of coefficient of variation against threshold.
(package private) boolean	Filter.setHP_XY_t_TestCL(GeneList t_TestResultCL, GeneList genesToTestCL, MaHybridSample msX, MaHybridSample msY, float pValueThr) 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.
(package private) boolean	Filter.setHP_XYsets_t_TestCL(GeneList t_TestResultCL, GeneList genesToTestCL, float pValueThr) 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
(package private) boolean	Filter.setHP_XYsets_KS_TestCL(GeneList KS_TestResultCL, GeneList genesToTestCL, float pValueThr) 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
(package private) boolean	Filter.setOCL_F_TestCL(GeneList OCL_F_TestResultCL, GeneList genesToTestCL, float pValueThr) setOCL_F_TestCL() - set GeneList of genes passing F-test on current OCL (Ordered Condition List) with a pValue better than pValueThr.
(package private) boolean	Filter.setHP_EclustersCL(GeneList passedCL, GeneList genesToTestCL, float clusterDistThr) setHP_EclustersCL() - Filter genes by HP-E clusters LEQ clusterDist
(package private) boolean	Filter.setDiffHP_XYCL(GeneList passedCL, GeneList genesToTestCL, float diffThr) setDiffHP_XYCL() - Filter genes by diff(HP-X,HP-Y) GEQ diffThr.
(package private) boolean	Filter.setSIthresholdsCL(GeneList genesToTestCL, GeneList resultCL) setSIthresholdsCL() - set GeneList of Spot Iintensity thresholded range where the threshold for rangeType [ST1:ST2] and rangeMode is RANGE_INSIDE, RANGE_OUTSIDE.
(package private) boolean	Filter.setThresholdsCL(GeneList genesToTestCL, GeneList passedCL, MaHybridSample msX, MaHybridSample msY, boolean testGrayFlag) 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.
(package private) boolean	Filter.setCy3Cy5RatiosCL(GeneList genesToTestCL, GeneList passedCL, MaHybridSample msX, boolean useCy5Cy3flag) setCy3Cy5RatiosCL() - Set GeneList of thresholded genes for Cy3/Cy5 ratio range where the threshold for rangeType [CR1:CR2] and rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
private void	GeneBitSet.allocGeneBitSet(int maxItems, java.lang.String bName, GeneList ml) allocGeneBitSet() - create named GeneBitSet by allocating bit set structures.
(package private) int	GeneBitSet.findCountAndhighMID(GeneList ml) findCountAndhighMID() - find count and highest MID in gene bit set BitData[].
(package private) boolean	GeneBitSet.cvtBStoCL(GeneList ml) cvtBStoCL() - convert GeneBitSet ml.bitSet to GeneList c1.mList[] (allocate data structures if needed).
(package private) boolean	GeneBitSet.copyBStoCL(GeneList c1Dst, GeneBitSet b2Src) copyBStoCL() - copy GeneBitSet b2Src to GeneList c1Dst.mList[].
(package private) static boolean	GeneBitSet.copyCLtoBS(GeneBitSet b1Dst, GeneList c2Src, boolean useCopyBitArrayFlag) copyCLtoBS() - copy GeneList c2Src to GeneBitSet b1Dst.
(package private) int	GeneBitSet.assignCLtoUserBS(java.lang.String userSetName, GeneList ml) assignCLtoUserBS() - assign GeneList ml to new user GeneBitSet userBS[] database.
(package private) boolean	GeneBitSet.useGeneSetBS(GeneList mlDest, java.lang.String gbsName, java.lang.String userSetNameSrc) useGeneSetBS() - assign the specified GeneBitSet by name to GeneList ml.
(package private) float[][]	GeneGeneDist.calcNormGeneVectors(GeneList dataCL, int nClist) calcNormGeneVectors() - compute HP-E intensity vector for dataCL.mList[].
(package private) boolean	GeneList.copySorted(GeneList c1, GeneList c2) copySorted() - copy GeneList mList[] sorted, and bitSets of c2 to c1.
(package private) boolean	GeneList.copy(GeneList c1, GeneList c2) copy() - copy GeneList mList[] and bitSets of c2 to c1.
(package private) boolean	GeneList.union(GeneList c1, GeneList c2, GeneList c3) union() - compute union of gene lists (c1 & c2) ==> c3.
(package private) boolean	GeneList.intersection(GeneList c1, GeneList c2, GeneList c3) intersection() - compute intersection of GeneLists (c1 & c2) ==> c3.
(package private) boolean	GeneList.difference(GeneList c1, GeneList c2, GeneList c3) difference() - compute difference of gene lists (c2 - c1)==> c3.
(package private) static int[]	MJAbase.cvtGeneList2GeneMIDlist(GeneList ml) cvtGeneList2GeneMIDlist() - convert GeneList to list of gene indexes Only used by MJA classes.
(package private) int	MaHybridSample.getF1F2Data(float[] xList, float[] yList, int[] propList, GeneList ml, boolean setPropsFlag, boolean useF1F2ratioFlag, boolean filterByMLflag) 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].
(package private) boolean	PopupRegistry.updateFilter(GeneList ml) updateFilter() - update popups using Filter workingCL changes for (plot,report,string,MAEPlugin) popups.
(package private) void	Report.updateFilter(GeneList ml) updateFilter() - update report if Filter using new GeneList ml.
private void	ScrollableImageCanvas.drawGeneList(java.awt.Graphics g, GeneList ml, int markerBits) drawGeneList() - draw a gene list on either SaveAsGif or Pseudoarray Image.
(package private) void	ShowExprProfilesPopup.updateEPplots(GeneList mlToUse) updateEPplots() - update expression profile plots using new GeneList.
(package private) void	ShowExprProfilesPopup.updateFilter(GeneList ml) updateFilter() - update expression profile plots using new GeneList ml.
(package private) void	ShowPlotPopup.updateFilter(GeneList ml) updateFilter() - update plot if Filter changed and this type of plot requires it.
(package private) void	ShowSpreadsheetPopup.updateFilter(GeneList ml) updateFilter() - update plot if Filter changed and this type of report requires it.
(package private) void	ShowStringPopup.updateFilter(GeneList ml) updateFilter() - update string report if Filter changed and this type of string report requires it.

Constructors in with parameters of type GeneList

ClusterGenes(GeneList complexClusterCL, MaHybridSample[] msEPlist, int nEPmsList)
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

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.

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

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

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.

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.

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.