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• calcAllTermsEnrichment() : broad.pda.gene.functionalAnnotation
• calcLightSilhouette() : broad.pda.geneexpression.clustering.Kmeans
• calcSilhouette() : broad.pda.geneexpression.clustering.Kmeans
• calcTermEnrichment() : broad.pda.gene.functionalAnnotation
• calculateApproximatePVal() : broad.core.math.ScanStatistics
• calculateBamEnrichments() : broad.pda.seq.rap.CollectAnnotationEnrichments
• calculateDiscreteAnnotationEnrichments() : broad.pda.seq.rap.CollectAnnotationEnrichments
• calculateGc() : broad.pda.seq.rap.GCContent
• calculateGlobalPvalue() : umms.core.model.score.BasicScanStatisticScore
• calculateLocalPvalue() : umms.core.model.score.BasicScanStatisticScore
• calculateNormalizationFactors() : umms.esat.ESAT , umms.esat.ESATDistanceCalculator
• calculatePVal() : broad.core.math.ScanStatistics , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.PoissonEnrichmentScore
• calculateScore() : jaligner.Alignment
• callKLPeaks() : broad.pda.seq.rap.RAPPeakCaller
• callSkellamPeaks() : broad.pda.seq.rap.RAPPeakCaller
• Cell() : jaligner.Cell
• centroidOf() : broad.core.motif.PositionWeightMatrix
• changeBackground() : broad.core.siphy.EvolutionaryModel
• checkOrientation() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• checkScore() : jaligner.Alignment
• chiSquareDistance() : broad.core.math.EmpiricalDistribution
• chol() : Jama.Matrix
• CholeskyDecomposition() : Jama.CholeskyDecomposition
• Chromosome() : broad.pda.feature.genome.Chromosome
• ChromosomeInconsistencyException() : umms.core.alignment.ChromosomeInconsistencyException
• chromosomeLength() : broad.pda.seq.segmentation.AlignmentDataModelStats
• ChromosomeWithBubblesJGraphT() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• chunk() : broad.core.sequence.Sequence
• CisVsTrans() : broad.pda.differentialExpression.CisVsTrans
• ClassifyAgilentLincProbes() : broad.pda.geneexpression.agilent.ClassifyAgilentLincProbes
• cleanIsoforms() : broad.pda.gene.GeneWithIsoforms
• cleanup() : broad.pda.seq.rap.CollectAnnotationEnrichments
• clear() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.datastructures.IntervalTree< V > , broad.core.multiplealignment.MAFAlignment , broad.core.parser.StringParser , broad.core.siphy.TreeScalerIO , broad.pda.annotation.BEDFileParser
• clearAttribute() : broad.core.annotation.GFF
• clearFullIntervalTreeAsAlignmentsCached() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• clone() : Jama.Matrix
• cloneRegions() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• close() : broad.core.datastructures.JCSCache.JCSNodeIterator , broad.pda.samtools.PairedEndReadIterator , broad.pda.samtools.SAMPairedEndFileReader , broad.pda.samtools.WrappedIterator , broad.pda.seq.fastq.FastqParser , broad.pda.seq.segmentation.WrappedIGVIterator , umms.core.coordinatesystem.ShuffledIterator< T extends Annotation > , umms.core.general.CloseableFilterIterator< T > , umms.core.model.AlignmentModel.FilteredIterator , umms.core.model.AlignmentModel.NodeIterator , umms.core.model.AlignmentModel.WrapAlignmentCountIterator , umms.core.model.JCSAlignmentModel.FilteredIterator , umms.core.model.JCSAlignmentModel.NodeIterator , umms.core.model.JCSAlignmentModel.WrapAlignmentCountIterator , umms.core.model.score.WindowScoreIterator< T extends WindowScore > , umms.core.readers.PairedEndReader , umms.core.writers.PairedEndWriter
• CloseableFilterIterator() : umms.core.general.CloseableFilterIterator< T >
• closeFilterRejectWriters() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• closeTo1() : broad.core.math.MathUtil
• CLUSTAL() : jaligner.formats.CLUSTAL
• Cluster() : broad.pda.geneexpression.clustering.Cluster
• cluster() : broad.pda.geneexpression.clustering.HierarchicalClustering
• CLUtil() : broad.core.util.CLUtil
• colapse() : broad.pda.gene.GeneWithIsoforms
• collapse() : umms.core.annotation.AbstractAnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation >
• collapseByIntersection() : broad.core.util.CollapseByIntersection
• CollapsedGeneLengths() : umms.esat.CollapsedGeneLengths
• CollapseGenesByIntersection() : broad.core.util.CollapseByIntersection
• collapseOverlappers() : umms.core.utils.AnnotationUtils
• CollapseProbesByMinPValue() : broad.pda.geneexpression.agilent.CollapseProbesByMinPValue
• CollapseProjections() : broad.pda.differentialExpression.CollapseProjections
• collapseSingleExonTranscripts() : broad.pda.annotation.BEDFileParser
• collectResults() : broad.pda.seq.rap.CollectAnnotationEnrichments
• columnDensityNormalization() : broad.core.datastructures.MatrixWithHeaders
• columnDimension() : broad.core.datastructures.MatrixWithHeaders
• CombinationGenerator() : broad.core.math.CombinationGenerator
• commandLineHasDebugFlag() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• commandLineOutDir() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• CommandLineParser() : broad.core.parser.CommandLineParser
• commaSeparatedStringToList() : broad.core.siphy.ConservationUtils
• compare() : broad.core.util.ChromosomeStringComparator , jaligner.matrix.MatricesCompartor
• compareNames() : broad.pda.feature.genome.Chromosome
• compareTo() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.BasicLightweightAnnotation , broad.core.primer3.HairpinKmer , broad.core.sequence.SequenceRegion , broad.pda.feature.genome.Chromosome , broad.pda.seq.graph.Path , umms.core.alignment.FeatureSequenceAlignment.UnorderedGenePair , umms.core.annotation.AbstractAnnotation , umms.core.annotation.CompoundInterval , umms.core.annotation.Gene , umms.core.annotation.SingleInterval , umms.core.feature.GeneWindow , umms.core.model.score.CountScore , umms.core.model.score.EndInWindowCountScore , umms.core.model.score.StartInWindowCountScore
• compareToAnnotation() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• compatible() : umms.core.scripture.BuildScriptureCoordinateSpace
• complement() : broad.core.primer3.ComputeMIRScore , broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• CompoundInterval() : umms.core.annotation.CompoundInterval
• compress() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• compressMatrixByRowDescriptions() : broad.core.datastructures.MatrixWithHeaders
• compute454Flow() : broad.core.sequence.Sequence
• computeAbsFoldMatrix() : broad.pda.differentialExpression.DifferentialScoring
• ComputeConservedMotifs() : broad.core.motif.misc.ComputeConservedMotifs
• ComputeCorrelationOfReplicates() : broad.pda.geneexpression.clustering.ComputeCorrelationOfReplicates
• ComputeEnrichments() : broad.pda.seq.chip.ComputeEnrichments
• computeFoldMatrix() : broad.pda.differentialExpression.DifferentialScoring
• computeGCContent() : broad.core.sequence.Sequence
• computeGCPercent() : broad.core.primer3.ComputeOriginalScore
• computeGlobalStats() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• ComputeHypergeomtricEnrichment() : broad.pda.geneexpression.ComputeHypergeomtricEnrichment
• computeJMatrix() : broad.core.siphy.EvolutionaryModel
• ComputeKmersForRegion() : broad.core.siphy.tools.conservation.ComputeKmersForRegion
• computeLikelihood() : broad.core.siphy.EvolutionaryModel
• ComputeMaxPercentileOfElements() : broad.core.siphy.tools.conservation.ComputeMaxPercentileOfElements
• computeMaxTM() : broad.core.primer3.PrimerUtils
• computeMIRScore() : broad.core.primer3.ComputeMIRScore
• computeOriginalScore() : broad.core.primer3.ComputeOriginalScore
• computeOriginalScorePerKMer() : broad.core.primer3.ComputeOriginalScore
• computePathLogLikelihood() : broad.core.hmm.MarkovModel< T > , broad.core.siphy.PiHMM
• ComputePercentageOfKmers() : broad.core.siphy.tools.conservation.ComputePercentageOfKmers
• computePermutedZScores() : broad.core.math.Statistics
• computeProb() : broad.core.motif.PositionWeightColumn
• computeScore() : broad.core.sequence.SequenceRegionWindow
• computeScoreDistribution() : broad.core.motif.PositionWeightMatrix
• computeSequenceBGSequences() : broad.core.motif.PWMUtils
• computeSequenceComposition() : broad.core.sequence.Sequence
• computeTestStatistics() : broad.pda.differentialExpression.DifferentialScoring
• computeTM() : broad.core.primer3.PrimerUtils
• computeTM2() : broad.core.primer3.PrimerUtils
• computeTransitions() : broad.core.siphy.EvolutionaryModel
• concatAnnotationSet() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• cond() : Jama.Matrix , Jama.SingularValueDecomposition
• confidenceByColumn() : broad.core.datastructures.MatrixWithHeaders
• ConnectDisconnectedTranscripts() : umms.core.scripture.statistics.ConnectDisconnectedTranscripts
• connectVertexToGraph() : umms.core.scripture.OrientedChromosomeTranscriptGraph
• ConservedPWMScanner() : broad.core.siphy.ConservedPWMScanner
• constituentIntrons() : broad.pda.gene.GeneWithIsoforms
• constituentIsoform() : broad.pda.gene.GeneWithIsoforms
• constructWithCopy() : Jama.Matrix
• containChr() : broad.pda.annotation.BEDFileParser
• containedWithin() : broad.pda.datastructures.Alignments
• contains() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.multiplealignment.MAFAlignment , broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , broad.pda.annotation.BEDFileParser , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval , umms.core.annotation.SingleInterval
• containsAnnotation() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• containsAttribute() : umms.core.annotation.Gene
• containsColumn() : broad.core.datastructures.MatrixWithHeaders
• containsDataFor() : umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace
• containsExactInterval() : umms.core.annotation.CompoundInterval
• containsFullLengthUngappedMatch() : umms.core.alignment.SmithWatermanAlignment
• containsInterval() : umms.core.annotation.CompoundInterval
• containsReference() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• containsRow() : broad.core.datastructures.MatrixWithHeaders
• contiguousEndSubSequenceOverMin() : broad.core.annotation.MaximumContiguousSubsequence
• contiguousStartSubSequenceOverMin() : broad.core.annotation.MaximumContiguousSubsequence
• ContinuousDataAlignmentModel() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• convertInputToPairedEnd() : umms.core.writers.PairedEndWriter
• ConvertToDiscreteMatrix() : broad.pda.differentialExpression.ConvertToDiscreteMatrix
• convertToFasta() : broad.pda.seq.fastq.FastqParser
• convertToNumberedFasta() : broad.pda.seq.fastq.FastqParser
• convertToPairedEndFragment() : broad.pda.samtools.SAMPairedEndFileReader
• copy() : broad.core.datastructures.MatrixWithHeaders , broad.core.motif.PositionWeightMatrix , broad.core.sequence.SequenceRegion , broad.core.siphy.EvolutionaryModel , broad.core.siphy.EvolutionaryModelParameters , broad.pda.annotation.BEDFileParser , broad.pda.seq.graph.Path , jaligner.Alignment , Jama.Matrix , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.Gene
• CorrelationAgilentNanostring() : broad.pda.geneexpression.agilent.CorrelationAgilentNanostring
• CorrelationBetweenReplicates() : broad.pda.geneexpression.agilent.CorrelationBetweenReplicates
• CorrelationMatrix() : broad.pda.geneexpression.clustering.CorrelationMatrix
• count() : broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• countLessThanLambda() : broad.pda.seq.rap.SkellamScore
• CountNums() : broad.pda.geneexpression.CountNums
• countOverlappers() : broad.core.overlaputils.GeneSetIntersect
• countReads() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• CountScore() : umms.core.model.score.CountScore
• countSoftMaskedBases() : broad.core.sequence.Sequence
• countWithinExon() : broad.pda.seq.segmentation.AlignmentDataModelStats
• covariance() : broad.core.math.Statistics
• CoverageScore() : umms.core.model.score.CoverageScore
• create() : broad.core.annotation.AnnotationFactory< T extends LightweightGenomicAnnotation > , broad.core.annotation.AnnotationReaderFactory , broad.core.multiplealignment.MultipleAlignmentFactory , broad.core.multiplealignment.MultipleAlignmentIOFactory , umms.core.general.TabbedReader.Factory< T >
• createAnnotation() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.annotation.BasicAnnotationReader , broad.core.annotation.BasicGenomicAnnotationReader , broad.core.annotation.BEDGraphReader , broad.core.annotation.BEDReader , broad.core.annotation.GFFReader , broad.core.annotation.RepeatMaskerAnnotationReader , broad.core.annotation.ShortBEDReader , broad.pda.datastructures.AlignmentsReader
• createAsciiFromBinary() : broad.core.sequence.FastaQualityBinaryIO
• createBinaryFromAscii() : broad.core.sequence.FastaQualityBinaryIO
• createDefaultTwoStateChain() : broad.core.siphy.PiHMM
• createEdge() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• createFromCommandArgs() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• createFromUCSC() : broad.core.annotation.BasicLightweightAnnotation , umms.core.annotation.BasicAnnotation
• createIndex() : broad.core.multiplealignment.MAFAlignment
• createIndexFromQualityFile() : broad.core.sequence.FastaQualityIndex
• createIsoPWM() : broad.core.motif.PositionWeightMatrix
• createSizeFile() : broad.core.sequence.FastaSequenceIO
• createTwoStateChain() : broad.core.siphy.PiHMM
• createUnloadedAlignment() : broad.core.multiplealignment.MAFIO
• CrossRandModelsWithBed() : broad.pda.gene.transcriptsNullModel
• customCommandLineValidation() : broad.pda.samtools.PairedEndTDF , broad.pda.seq.rap.CollectAnnotationEnrichments , broad.pda.seq.rap.GenomeCommandLineProgram , broad.pda.seq.rap.GenomeScoringProgram , broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram , broad.pda.seq.rap.rna.TranscriptomeScoringProgram
• CV() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel