- w -

• Wilcox2Sample() : broad.core.math.Wilcox2Sample
• WindowAllScore() : umms.core.model.score.WindowAllScore
• windowIterator() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• WindowScoreIterator() : umms.core.model.score.WindowScoreIterator< T extends WindowScore >
• within() : broad.pda.datastructures.Alignments
• WrapAlignmentCountIterator() : umms.core.model.AlignmentModel.WrapAlignmentCountIterator , umms.core.model.JCSAlignmentModel.WrapAlignmentCountIterator
• WrappedIGVIterator() : broad.pda.seq.segmentation.WrappedIGVIterator
• WrapSamRecord() : umms.core.alignment.SingleEndAlignment.WrapSamRecord
• write() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.datastructures.IntervalTree< V > , broad.core.datastructures.MatrixWithHeaders , broad.core.math.EmpiricalDistribution , broad.core.motif.PositionWeightColumn , broad.core.motif.PositionWeightMatrix , broad.core.motif.PositionWeightMatrixIO , broad.core.multiplealignment.FastaMultipleAlignmentIO , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MAFIO , broad.core.multiplealignment.MultipleAlignment , broad.core.multiplealignment.MultipleAlignmentIO , broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO , broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO , broad.core.sequence.FastaSequenceIO , broad.core.siphy.EvolutionaryModelParameters , broad.pda.annotation.GTFFileParser , broad.pda.datastructures.Alignments , broad.pda.datastructures.AlignmentsReader , broad.pda.datastructures.LocationAwareMatrix , broad.pda.geneexpression.clustering.HierarchicalClustering , broad.pda.geneexpression.PaGEJava , broad.pda.seq.fastq.FastqSequence , Jama.Matrix , umms.core.scripture.BuildScriptureCoordinateSpace
• writeAllAntisenseAlignmentsToBed() : umms.core.alignment.FeatureSequenceAlignment
• writeAllSenseAlignmentsToBed() : umms.core.alignment.FeatureSequenceAlignment
• writeAsText() : broad.core.sequence.FastaQualityIndex
• writeBarcodeCount() : broad.pda.seq.fastq.SplitFastqByIndex
• writeBED() : broad.pda.annotation.BEDFileParser
• writeBEDWithScores() : broad.pda.annotation.BEDFileParser
• writeBox() : broad.core.datastructures.MatrixWithHeaders
• writeChunks() : broad.pda.seq.fastq.FastqParser
• writeCLS() : broad.core.datastructures.MatrixWithHeaders , broad.pda.geneexpression.agilent.MakeCLSFromDescription
• writeClusters() : broad.pda.geneexpression.clustering.Kmeans
• writeClustersCentroids() : broad.pda.geneexpression.clustering.Kmeans
• writeColoumnNamesToFile() : broad.core.datastructures.MatrixWithHeaders
• writeConnections() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• writeDistanceFromCentroids() : broad.pda.geneexpression.clustering.Kmeans
• writeDistanceFromInputCentroids() : broad.pda.geneexpression.clustering.Kmeans
• writeFasta() : broad.pda.rnai.ExtractSequence , broad.pda.seq.clip.FastaExtendPeaks
• writeFull() : broad.core.siphy.TreeScalerIO
• writeFullAsGenomeGraphUsingLogPval() : broad.core.siphy.TreeScalerIO
• writeFullBED() : broad.pda.annotation.BEDFileParser
• writeFullBed() : broad.pda.annotation.BEDFileParser
• writeFullBED() : broad.pda.annotation.BEDFileParser , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• writeGCT() : broad.core.datastructures.MatrixWithHeaders , broad.core.util.ParseGCTFile
• writeGCTAndCLS() : broad.core.datastructures.MatrixWithHeaders
• writeGCTWithHeaders() : broad.core.datastructures.MatrixWithHeaders
• writeGeneralStats() : broad.core.overlaputils.GeneSetIntersect
• writeGMT() : broad.core.datastructures.MatrixWithHeaders , broad.core.util.GMTParser
• writeGMTFile() : broad.core.util.ParseGCTFile
• writeGraph() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.scripture.OrientedChromosomeTranscriptGraph
• writeIndex() : broad.core.multiplealignment.MAFAlignment
• writeIntergenicGenome() : broad.pda.gene.transcriptsNullModel
• writeLeftJustifiedField() : broad.core.util.CLUtil
• writeNormalizedMatrix() : umms.esat.ESAT , umms.esat.ESATDistanceCalculator
• writeOverlap() : broad.core.overlaputils.GeneSetIntersect
• writeRecordsWithMinLength() : broad.core.sequence.FastaSequenceIO
• writeResult() : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• writeResults() : broad.pda.differentialExpression.RunDifferentialExpression , broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• writeRightJustifiedField() : broad.core.util.CLUtil
• writeRowNamesToFile() : broad.core.datastructures.MatrixWithHeaders
• writeScanPvalsFragmentEndPileupsAllRegionsWig() : broad.pda.seq.clip.Pileup
• writeSeparateFiles() : broad.pda.countreads.FastqLibraryStats
• writeSequenceId() : broad.core.sequence.FastaSequenceIO
• writeSilhouetteRes() : broad.pda.geneexpression.clustering.Kmeans
• writeSingleSampleScanPeaks() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• writeSizes() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• writeSortedBED() : broad.pda.annotation.BEDFileParser
• writeSortedBEDWithScores() : broad.pda.annotation.BEDFileParser
• writeTermsEnrichments() : broad.pda.gene.functionalAnnotation
• writeUNIPROBE() : broad.core.motif.PositionWeightMatrix , broad.core.motif.PositionWeightMatrixIO
• writeWigEachPosition() : broad.core.math.PermutationDistribution
• writeWindowsWithPvalue() : broad.core.math.PermutationDistribution