Uses of Class
Gene

Packages that use Gene

Uses of Gene in

Fields in declared as Gene

(package private) static Gene	ClusterGenes.curGene current gene being clustered
(package private) Gene	ClusterGenes.initialSeedGene initial seed gene - either 1st or current Obj gene
(package private) Gene[]	ClusterGenes.Cluster.mList ordered list of genes in this cluster
private Gene	ExprProfileOverlay.bestGene gene if mouse event
private Gene	ExprProfileScrollPane.bestGene gene if mouse event
(package private) Gene[]	GeneList.mList instance: (opt) sorted list of Gene objects.
(package private) Gene	MAExplorer.gene Global instance of Gene
private Gene	MJAgene.gene
private Gene	MJAgene.defaultGene

Methods in that return Gene

(package private) Gene[]

GeneList.getGeneList() getGeneList() - get gene mList[] data as Gene[].

Methods in with parameters of type Gene

(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) boolean	EditedGeneList.removeGeneFromEditedCL(Gene gene) removeGeneFromEditedCL() - remove gene from the editedCL by gene.
(package private) boolean	EditedGeneList.addGeneToEditedCL(Gene gene) addGeneToEditedCL() - add gene to editedCL if not in CL by gene
(package private) boolean	EditedGeneList.addGeneByRegion(Gene gene) addGenesByRegion() - add genes to editedCL if they are in the region in the pseudoarray image or scatterplot [TODO]
(package private) static void	Gene.sortGeneList(Gene[] cList, int nClist, boolean sortAssendingFlag) sortGeneList() - bubble sort gene list by associated gene.data field
(package private) float	GeneGeneDist.clusterDistance(Gene geneI, Gene geneJ) clusterDistance() - compute genes(I,J) cluster distance for HP-E samples.
(package private) boolean	GeneList.setGene(Gene c, int idx) setGene() - set Gene to specific gene list mList[idx].
(package private) boolean	GeneList.addGene(Gene c) addGene() - add Gene to gene list bitSet, and mList[] if it exists.
(package private) boolean	GeneList.rmvGene(Gene c) rmvGene() - remove Gene from gene list and bitSet.
(package private) boolean	GeneList.isGeneInGeneList(Gene c) isGeneInGeneList() - test if gene is in GeneList.
private Table	Report.createTableOfExprProfiles(Gene[] mList, int nC, boolean normByHP_Xflag) createTableOfExprProfiles() - make Table of expression profiles for mList[0:nC-1]
private Table	Report.createTableOfOCL_Fstat(Gene[] mList, int nC) createTableOfOCL_Fstat() - make Table of OCL F-test for mList[0:nC-1] If the OCL F-Test filter is active, then report F-test statistics
private Table	Report.createTableOfHP_XYstat(Gene[] mList, int nC) createTableOfHP_XYstat() - make Table of HP_XYstatistics for mList[0:nC-1] If the t-Test filter is active, then report t-test statistics If the KS-Test filter is active, then report KS-test statistics
private Table	Report.createTableKmeansClusterStats(Gene[] mList, int nC) createTableKmeansClusterStats() - make Table of Kmeans clusters for mList[0:nC-1]
private java.lang.String	Report.createStrReportOfOCL_FstatData(Gene[] mList, int nC) createStrReportOfOCL_FstatData() - make String report of OCL F-test for mList[0:nC-1] If the OCL F-Test filter is active, then report F-test statistics.
private java.lang.String	Report.cvGene2TabDelimStr(Gene gene, int i, java.lang.String dataName, boolean showGeneName, Table epTbl, Table hpxyTbl) cvGene2TabDelimStr() - convert a gene to printable tab-delimited string
private void	Report.showGeneReport(Gene[] mListOrig, int nMlistOrig, int maxGenesReported, java.lang.String title, int sortDirection, java.lang.String dataName, boolean showGeneName, int tblFmtMode, int reportMode) showGeneReport() - show gene report with top maxGene's.
private Table	Report.createTotURLgeneRptTbl(Table kcTbl, Gene[] mListOrig, int nMlistOrig, int maxGene, java.lang.String title, int sortDirection, java.lang.String dataName, int[] cellFormat, boolean showGeneName) createTotURLgeneRptTbl() - generate total URL gene report table
private SimpleTable	Report.createTotGeneRptTbl(Gene[] mListOrig, int nMlistOrig, int maxGene, java.lang.String title, int sortDirection, java.lang.String dataName, boolean showGeneName, int reportMode) createTotGeneRptTbl() - generate total gene report table.
private void	Report.showPopupSpreadsheetGeneReport(Table kcTbl, Table kcUrlTbl, Gene[] mListOrig, int nMlistOrig, int maxGene, java.lang.String title, int sortDirection, java.lang.String dataName, int[] cellFormat, boolean showGeneName) showPopupSpreadsheetGeneReport() - show gene report with top maxGene's.

Constructors in with parameters of type Gene

ClusterGenes.Cluster(int id, int nGenes, int nEP, java.lang.String cName, Gene[] mList)
Cluster() - constructor.