- s -

• SameOrientationFilter() : umms.core.readFilters.SameOrientationFilter
• SAMFormatFullBED() : broad.pda.seq.alignment.AlignmentUtils
• SAMFragmentWriter() : broad.pda.samtools.SAMFragmentWriter
• SAMPairedEndFileReader() : broad.pda.samtools.SAMPairedEndFileReader
• sample() : broad.core.siphy.EvolutionaryModel
• sampleColumns() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• SampleData() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• scaleNorm() : broad.core.datastructures.MatrixWithHeaders
• scaleRegion() : broad.core.siphy.TreeScaler
• scaleTree() : broad.core.siphy.TreeScaler
• scaleTreeWithSampling() : broad.core.siphy.TreeScaler
• scan() : broad.core.siphy.ConservedPWMScanner , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , umms.core.annotation.AbstractAnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• scanGenome() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scanPRate() : broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scanRegion() : broad.core.motif.PWMUtils , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• ScanStatisticScore() : umms.core.model.score.ScanStatisticScore
• score() : broad.core.siphy.PositionWeightMatrixModel
• scoreAnnotations() : broad.pda.seq.alignment.AlignmentUtils
• scoreGene() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scoreGenes() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scoreListByTStatistic() : broad.pda.geneexpression.ScoreDiffGenes
• ScoreMotifInstances() : broad.core.motif.misc.ScoreMotifInstances
• scoreMotifs() : broad.core.motif.misc.ComputeConservedMotifs
• scorePaths() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scorePathsForOnlyRPKM() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scoreSegment() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scoreSegments() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• scoreWindow() : broad.pda.seq.protection.SampleData
• scoreWindowWithFragmentLengthFilter() : broad.pda.seq.protection.SampleData
• scramble() : broad.core.sequence.Sequence
• SearchException() : broad.core.motif.SearchException
• selectHighScoringIsoform() : broad.pda.gene.GeneTools
• SelectLongestIntronChainCandidate() : broad.pda.annotation.Locus
• selectRandIsoSubset() : broad.pda.annotation.Locus , broad.pda.gene.GeneWithIsoforms
• Sequence() : broad.core.sequence.Sequence , jaligner.Sequence
• SequenceMotif() : broad.core.motif.SequenceMotif
• SequenceMotifCluster() : broad.core.motif.SequenceMotifCluster
• SequenceParserException() : jaligner.util.SequenceParserException
• SequenceRegion() : broad.core.sequence.SequenceRegion
• SequenceRegionWindow() : broad.core.sequence.SequenceRegionWindow
• set() : broad.core.datastructures.MatrixWithHeaders , jaligner.Cell , Jama.Matrix
• setA() : broad.core.annotation.BasicTwoSubjectAnnotation
• setAddToReadName() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setAlignedSequences() : broad.core.multiplealignment.MAFAlignment
• setAlignment() : broad.core.siphy.TreeScaler
• setAlignmentChunkSize() : broad.core.siphy.ConservedPWMScanner
• setAlignmentDataModel() : broad.pda.seq.segmentation.AlignmentDataModelStats
• setAlignPos() : broad.core.motif.PositionWeightMatrix
• setAlpha() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setAlphabetSize() : broad.core.siphy.EvolutionaryModel
• setAnnotationList() : broad.core.annotation.BasicGenomicAnnotationReader
• setAsSafeToLoad() : broad.pda.seq.alignment.StoredAlignmentStats
• setAsUnsafeToLoad() : broad.pda.seq.alignment.StoredAlignmentStats
• setAtEnd() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setAttribute() : umms.core.alignment.AbstractPairedEndAlignment
• setAttributes() : broad.core.annotation.GFF
• setAvergeNumberOfReads() : broad.pda.seq.segmentation.GeneScore
• setB() : broad.core.annotation.BasicTwoSubjectAnnotation
• setBackgroundModel() : broad.core.siphy.ConservedPWMScanner
• setBackgroundNucleotideFreqs() : broad.core.siphy.EvolutionaryModelParameters
• setBedScore() : broad.pda.gene.GeneWithIsoforms , umms.core.annotation.Gene
• setBinomialScore() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setBlastHit() : broad.core.primer3.HairpinKmer
• setBlocks() : broad.core.multiplealignment.MAFAlignment
• setBlockSizeStarts() : broad.core.annotation.BED
• setBoundariesFromAnnoations() : broad.core.annotation.BasicLightweightAnnotation
• setCapacity() : broad.core.sequence.Sequence
• setCDS() : umms.core.annotation.Gene
• setCDSEnd() : umms.core.annotation.Gene
• setCDSRegion() : umms.core.annotation.Gene
• setCDSStart() : umms.core.annotation.Gene
• setCharAt() : broad.core.sequence.Sequence
• setChromosome() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• setChromosomeLength() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• setChunkSize() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setClusterDistanceFunction() : broad.pda.geneexpression.clustering.HierarchicalClustering
• setCol() : jaligner.Cell
• setColumn() : broad.core.datastructures.MatrixWithHeaders , Jama.Matrix
• setColumns() : broad.pda.datastructures.LocationAwareMatrix
• setCoordinateSpace() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setCount() : umms.core.model.score.CountScore , umms.core.model.score.EndInWindowCountScore , umms.core.model.score.StartInWindowCountScore
• setCountNormalizer() : broad.pda.seq.segmentation.AlignmentDataModelStats
• setCountScore() : broad.pda.datastructures.Alignments , umms.core.annotation.Gene
• setCtrlCoordSpace() : umms.core.model.score.MultiScore
• setCtrlCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore
• setCtrlRegionCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore
• setCtrlRegionTotal() : umms.core.model.score.PoissonEnrichmentScore
• setCtrlTotal() : umms.core.model.score.PoissonEnrichmentScore
• setCurrentSequenceId() : broad.core.sequence.AbstractFastaParser
• setData() : broad.core.datastructures.MatrixWithHeaders
• setDataDimensions() : broad.pda.datastructures.LocationAwareMatrix
• setDenominatorCount() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• setDenominatorRegionTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• setDenominatorScanPVal() : umms.core.model.score.WindowAllScore
• setDenominatorTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• setDescription() : broad.pda.seq.fastq.FastqSequence , jaligner.Sequence
• setDiagonal() : jaligner.TracebackNode
• setDuplicateFlag() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• setDuplicateReadFlag() : umms.core.alignment.SingleEndAlignment.WrapSamRecord
• setEnd() : broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• setEndStateTransitionProbability() : broad.core.hmm.MarkovModel< T >
• setEnrichment() : broad.pda.seq.segmentation.GeneScore
• setEstimationWindow() : broad.core.siphy.TreeScalerIO
• setExonScores() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• setExpressionScanPvalueCutoff() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.MultiSampleScanPeakCaller , broad.pda.seq.protection.SampleData
• setExtend() : jaligner.Alignment
• setExtensionFactor() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setExtraFields() : broad.pda.gene.GeneWithIsoforms , broad.pda.seq.protection.MultiSampleScanPeakCaller , umms.core.annotation.Gene
• setFeature() : broad.core.annotation.GFF
• setFilterByStrand() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setFindMaxContiguous() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setFirstRead() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setFirstReadTranscriptionStrand() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setFivePrimeBuffer() : broad.core.annotation.BasicGenomicAnnotation
• setForwardStrand() : broad.core.sequence.Sequence
• setFragmentFlag() : umms.core.readers.PairedEndReader
• setFragmentStrand() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• setFrame() : broad.core.annotation.GFF
• setFromCounts() : broad.core.motif.PositionWeightColumn
• setFullyContainedNumberOfReads() : broad.pda.seq.segmentation.GeneScore , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.ScanStatisticScore
• setGaps() : jaligner.Alignment
• setGene() : umms.core.model.score.MultiScore
• setGeneLength() : broad.pda.seq.segmentation.GeneScore
• setGlobalLength() : umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.PoissonEnrichmentScore , umms.core.model.score.ScanStatisticScore
• setGroup() : broad.core.annotation.GFF
• setHasIndel() : umms.core.alignment.SingleEndAlignment
• setHeader() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• setId() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , jaligner.formats.Format , jaligner.Sequence
• setIdentity() : jaligner.Alignment
• setIgnoreList() : broad.core.siphy.ConservedPWMScanner
• setInitialStateTransitionProbability() : broad.core.hmm.MarkovModel< T >
• setIOHelper() : broad.core.multiplealignment.MultipleAlignment
• setIsFirstMate() : umms.core.alignment.SingleEndAlignment
• setIsToComplex() : broad.pda.seq.graph.Path
• setJnlp() : jaligner.util.Commons
• setLambda() : broad.pda.seq.segmentation.AlignmentDataModelStats
• setLeft() : jaligner.TracebackNode
• setLine() : broad.pda.datastructures.Alignments
• setLinkage() : broad.pda.geneexpression.clustering.HierarchicalClustering
• setLocalLambda() : broad.pda.seq.graph.Path , broad.pda.seq.segmentation.GeneScore
• setLocalRate() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• setLoggerLevel() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setMarkupLine() : jaligner.Alignment
• setMaskFileData() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setMatch() : umms.core.annotation.PSLRecord
• setMatrix() : broad.core.motif.PositionWeightMatrix , jaligner.Alignment , Jama.Matrix
• setMatrixFromRawData() : broad.core.motif.PositionWeightMatrix
• setMaxAllowableInsert() : umms.core.writers.PairedEndWriter
• setMinContguousSegmentSize() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setMinimumMappingQuality() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setMinimumTreeLength() : broad.core.siphy.TreeScaler
• setMinNumberOfSplices() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setMirScore() : broad.core.primer3.HairpinKmer
• setMismatch() : umms.core.annotation.PSLRecord
• setModel() : broad.core.siphy.ConservedPWMScanner , broad.core.siphy.TreeScaler
• setModelParameters() : broad.core.siphy.EvolutionaryModel
• setMotif() : broad.core.motif.SequenceMotif
• setName() : broad.core.annotation.LightweightGenomicAnnotation , broad.core.motif.PositionWeightMatrix , broad.core.sequence.SequenceRegion , broad.pda.seq.fastq.FastqSequence , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• setName1() : jaligner.Alignment
• setName2() : jaligner.Alignment
• setNcount() : umms.core.annotation.PSLRecord
• setNegativeStranded() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setNeutralModel() : broad.core.siphy.TreeScaler
• setNeutralOmegaDistribution() : broad.core.siphy.EvolutionaryModel
• setNominalPValue() : broad.pda.seq.segmentation.GeneScore
• setNormalizationStrategy() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setNum() : broad.core.motif.PositionWeightColumn
• setNumberFormatter() : broad.core.siphy.TreeScalerIO
• setNumberOfMarkers() : broad.pda.seq.segmentation.AlignmentDataModelStats
• setNumberOfReads() : broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GeneScore
• setNumeratorCount() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• setNumeratorRegionTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• setNumeratorScanPVal() : umms.core.model.score.WindowAllScore
• setNumeratorTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• setOmega() : broad.core.siphy.EvolutionaryModel
• setOmegaDistByTreeLength() : broad.core.siphy.EvolutionaryModel
• setOpen() : jaligner.Alignment
• setOrientation() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.Gene
• setOrientedEnd() : broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• setOrientedStart() : broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• setOriginalScore() : broad.core.primer3.HairpinKmer
• setOriginalSequence1() : jaligner.Alignment
• setOriginalSequence2() : jaligner.Alignment
• setPair1Parser() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setPair2Parser() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setPaired() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setParameters() : broad.core.siphy.EvolutionaryModel
• setPeakCutoffMostCommonReplicate() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setPeakTrimQuantile() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setPeakWindowCountCutoff() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setPeakWindowScanPvalCutoff() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• setPercentMaskedAllowed() : umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace
• setPercentVariantsCovered() : broad.core.primer3.HairpinKmer
• setPi() : broad.core.siphy.EvolutionaryModel
• setPIDToName() : broad.core.datastructures.MatrixWithHeaders
• setPositiveStranded() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setProgramDescription() : broad.core.parser.CommandLineParser
• setProperPairFlag() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• setPvalue() : umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.PoissonEnrichmentScore , umms.core.model.score.ScanStatisticScore
• setQueryEnd() : umms.core.annotation.PSLRecord
• setQueryGap() : umms.core.annotation.PSLRecord
• setQueryGapBases() : umms.core.annotation.PSLRecord
• setQuerySize() : umms.core.annotation.PSLRecord
• setQueryStart() : umms.core.annotation.PSLRecord
• setRateMatrix() : broad.core.siphy.EvolutionaryModelParameters
• setRead1Trim3p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setRead1Trim5p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setRead2Trim3p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setRead2Trim5p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• setReasonForUnsafe() : broad.pda.seq.alignment.StoredAlignmentStats
• setReferenceId() : broad.core.multiplealignment.MultipleAlignment
• setReferenceName() : broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• setRefGapped() : broad.core.multiplealignment.MultipleAlignment
• setRegionEnd() : broad.core.sequence.SequenceRegion
• setRegionLength() : umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore , umms.core.model.score.ScanStatisticScore
• setRegionStart() : broad.core.sequence.SequenceRegion
• setRegionTotal() : umms.core.model.score.CountScore
• setRemoveDuplicatesFlag() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• setRepMatch() : umms.core.annotation.PSLRecord
• setReversedOrientation() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion
• setRgb() : broad.core.annotation.BED
• setRow() : broad.core.datastructures.MatrixWithHeaders , jaligner.Cell , Jama.Matrix
• setRowDescription() : broad.core.datastructures.MatrixWithHeaders
• setRPKM() : broad.pda.seq.segmentation.GeneScore
• setRPKMConstant() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• setRS8Score() : broad.core.primer3.HairpinKmer
• setSampleCoordSpace() : umms.core.model.score.MultiScore
• setSampleCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore
• setSampleName() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• setSampleRegionCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore
• setSampleRegionTotal() : umms.core.model.score.PoissonEnrichmentScore
• setSampleTotal() : umms.core.model.score.PoissonEnrichmentScore
• setSAMString() : umms.core.annotation.Gene
• setScanPvalue() : broad.pda.seq.segmentation.GeneScore , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.ScanStatisticScore
• setScore() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.multiplealignment.MultipleAlignment , broad.core.sequence.SequenceRegion , broad.core.sequence.SequenceRegionWindow , broad.pda.geneexpression.clustering.Cluster , jaligner.Alignment , jaligner.Cell , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• setScores() : broad.pda.datastructures.Alignments , umms.core.model.score.AbstractListScore
• setSecondRead() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• setSeed() : umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace
• setSentinel() : broad.core.datastructures.IntervalTree< V >
• setSequence() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion , jaligner.Sequence , umms.core.annotation.Gene
• setSequence1() : jaligner.Alignment
• setSequence2() : jaligner.Alignment
• setSequenceBases() : broad.core.sequence.Sequence
• setSequenceFile() : broad.pda.feature.genome.Chromosome
• setSequenceFromChromosome() : umms.core.annotation.Gene
• setSimilarity() : jaligner.Alignment
• setSource() : broad.core.annotation.GFF , broad.core.sequence.FastaSequenceIO
• setSpacing() : broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO
• setSplicedEdges() : umms.core.alignment.SingleEndAlignment
• setSpliceWeight() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.graph.Path
• setStart() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• setStart1() : jaligner.Alignment
• setStart2() : jaligner.Alignment
• setStateTransitionProbability() : broad.core.hmm.MarkovModel< T >
• setStop() : jaligner.TracebackNode
• setStoredStats() : broad.pda.seq.segmentation.AlignmentDataModelStats
• setStrand() : broad.core.annotation.GFF
• setSubcluster() : broad.pda.geneexpression.clustering.Cluster
• setTargetGap() : umms.core.annotation.PSLRecord
• setTargetGapBases() : umms.core.annotation.PSLRecord
• setTargetSize() : umms.core.annotation.PSLRecord
• setThickEnd() : broad.core.annotation.BED
• setThickStart() : broad.core.annotation.BED
• setThreePrimeBuffer() : broad.core.annotation.BasicGenomicAnnotation
• setTotal() : umms.core.model.score.CountScore
• setTree() : broad.core.siphy.EvolutionaryModelParameters
• setTrimEnds() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setTrimQuantile() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setType() : jaligner.Sequence
• setUninformativeNodes() : broad.core.siphy.ConservationUtils
• setUnparsedRow() : broad.core.motif.PositionWeightMatrix
• setup() : broad.pda.seq.rap.rna.CollectRnaSeqMetrics
• setUp() : jaligner.TracebackNode
• setUpAlignment() : broad.core.siphy.ConservationUtils
• setUpMAF() : broad.core.siphy.ConservationUtils
• setUpWeightSplices() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• setValue1() : broad.core.datastructures.Pair< T1 >
• setValue2() : broad.core.datastructures.Pair< T1 >
• setWeighReadCountsFlag() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• setWindowLength() : umms.core.model.score.BasicScanStatisticScore
• shift() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.sequence.SequenceRegion , broad.core.siphy.StationaryDistributionIO , umms.core.alignment.AbstractPairedEndAlignment , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• shiftPosition() : broad.core.sequence.TranscribedRegions
• ShortBED() : broad.core.annotation.ShortBED
• ShortBEDReader() : broad.core.annotation.ShortBEDReader
• shuffle() : broad.core.math.MathUtil , broad.core.sequence.Sequence , broad.pda.feature.genome.Chromosome
• shuffleAndWriteAnnotations() : broad.pda.seq.rap.ShuffleBED
• ShuffledIterator() : umms.core.coordinatesystem.ShuffledIterator< T extends Annotation >
• shufflePeaks() : broad.pda.seq.rap.CollectAnnotationEnrichments
• shuffleScores() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• shuffleWithinValid() : broad.pda.feature.genome.Chromosome
• SingleEndAlignment() : umms.core.alignment.SingleEndAlignment
• SingleInterval() : umms.core.annotation.SingleInterval
• SingularValueDecomposition() : Jama.SingularValueDecomposition
• size() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.datastructures.IntervalTree< V > , broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• skellamCdf() : broad.core.math.Distribution
• skellamDensity() : broad.core.math.Distribution
• skellamLeftTail() : broad.core.math.Distribution
• skellamPvalue() : broad.core.math.Distribution
• skellamRightTail() : broad.core.math.Distribution
• SkellamScore() : broad.pda.seq.rap.SkellamScore
• slidePWM() : broad.core.siphy.ConservedPWMScanner , broad.core.siphy.TreeScaler
• slideWindowComputeOmega() : broad.core.siphy.tools.conservation.EstimateOmegaPerExon
• SmatchLike() : umms.core.alignment.SmatchLike
• SmithWatermanAlignment() : umms.core.alignment.SmithWatermanAlignment
• solve() : Jama.CholeskyDecomposition , Jama.LUDecomposition , Jama.Matrix , Jama.QRDecomposition
• solveTranspose() : Jama.Matrix
• sortColumns() : Jama.Matrix
• sortColumnsKeepingIndex() : Jama.Matrix
• sortList() : broad.core.datastructures.MatrixWithHeaders
• spearmanCorrelation() : broad.core.math.Statistics
• SplitAndTrimIndex() : broad.pda.seq.fastq.SplitAndTrimIndex
• splitByChr() : broad.pda.rnai.ExtractSequence
• SplitByName() : broad.pda.differentialExpression.SplitByName
• SplitFastqByIndex() : broad.pda.seq.fastq.SplitFastqByIndex
• SplitFile() : broad.core.siphy.tools.conservation.SplitFile
• standardizeOreintation() : broad.pda.gene.GeneWithIsoforms
• start() : broad.pda.seq.fastq.FastqParser , broad.pda.seq.fastq.FastqSplitterByBarcode
• StartInWindowCountScore() : umms.core.model.score.StartInWindowCountScore
• startTrack() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• StationaryDistributionIO() : broad.core.siphy.StationaryDistributionIO
• stdev() : broad.core.math.Statistics
• stitch() : broad.core.siphy.TreeScalerIO
• stitchList() : broad.core.annotation.BasicLightweightAnnotation
• stitchTo() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• stop() : broad.pda.seq.fastq.FastqSplitterByBarcode
• store() : broad.pda.seq.alignment.StoredAlignmentStats
• StoredAlignmentStats() : broad.pda.seq.alignment.StoredAlignmentStats
• StringParser() : broad.core.parser.StringParser
• submatrixByColumnIndex() : broad.core.datastructures.MatrixWithHeaders
• submatrixByColumnNames() : broad.core.datastructures.MatrixWithHeaders
• submatrixByColumns() : broad.pda.datastructures.LocationAwareMatrix
• submatrixByRowDescriptions() : broad.core.datastructures.MatrixWithHeaders
• submatrixByRowNames() : broad.core.datastructures.MatrixWithHeaders
• submitJobs() : broad.pda.seq.rap.CollectAnnotationEnrichments
• subsequence() : jaligner.Sequence
• sum() : broad.core.math.Statistics
• SumScore() : umms.core.model.score.SumScore
• svd() : Jama.Matrix