- a -

• absFold() : broad.core.math.Statistics
• absoluteToRelativePosition() : umms.core.annotation.Gene
• absoluteValue() : broad.core.math.Statistics
• AbstractListScore() : umms.core.model.score.AbstractListScore
• AbstractPairedEndAlignment() : umms.core.alignment.AbstractPairedEndAlignment
• AbstractWindowScore() : umms.core.model.score.WindowScore.AbstractWindowScore
• accept() : broad.core.annotation.GenomicAnnotationFilter< T extends LightweightGenomicAnnotation >
• acceptRead() : broad.pda.seq.rap.rna.CollectRnaSeqMetrics
• acidAt() : jaligner.Sequence
• add() : broad.core.datastructures.MatrixWithHeaders , broad.core.math.EmpiricalDistribution , jaligner.Alignment , umms.core.alignment.AlignmentPair , umms.core.annotation.AnnotationList< T extends Annotation >
• addAlignment() : umms.core.writers.PairedEndWriter
• addAll() : broad.core.math.EmpiricalDistribution , umms.core.annotation.AnnotationList< T extends Annotation >
• AddAllIsoforms() : broad.pda.gene.GeneWithIsoforms
• AddAllIsoNotIncludedforms() : broad.pda.gene.GeneWithIsoforms
• addAnnotation() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• addAnnotationSet() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• addAnnotationToGraph() : umms.core.scripture.OrientedChromosomeTranscriptGraph
• addAnnotationToLastTrack() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• addAttribute() : broad.core.annotation.GFF , umms.core.annotation.Gene
• addAttributeValues() : broad.core.annotation.GFF
• addBlock() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.BED , broad.core.annotation.GenomicAnnotation , broad.core.multiplealignment.MAFAlignment , broad.core.sequence.SequenceRegion
• addBlocks() : broad.core.multiplealignment.MAFAlignment , umms.core.annotation.BasicAnnotation
• addBooleanArg() : broad.core.parser.CommandLineParser
• addBrowserLine() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• addColumn() : broad.core.datastructures.MatrixWithHeaders , broad.core.motif.PositionWeightMatrix
• addConservedPi() : broad.core.siphy.PiHMM
• addContainedIsoform() : broad.pda.gene.GeneWithIsoforms
• addDistribution() : broad.core.math.EmpiricalDistribution
• addDoubleArg() : broad.core.parser.CommandLineParser
• addEdge() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.graph.Path , umms.core.scripture.OrientedChromosomeTranscriptGraph
• addEdgeAddingMissingVertices() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• addEdges() : broad.pda.seq.graph.Path
• addExtraField() : umms.core.annotation.Gene
• addExtraScore() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• addFilter() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• addFilters() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• addFloatArg() : broad.core.parser.CommandLineParser
• addIntArg() : broad.core.parser.CommandLineParser
• addInterval() : umms.core.annotation.CompoundInterval
• addIsoform() : broad.pda.annotation.Locus
• AddIsoform() : broad.pda.gene.GeneWithIsoforms
• addIsoform() : umms.core.annotation.Gene
• addListener() : broad.core.siphy.TreeScalerIO
• addMatch() : broad.core.motif.meme.MemeMotif
• addNewEdge() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• addPairedEnd() : broad.pda.seq.graph.Path
• addPairedEndEdges() : broad.pda.seq.graph.Path
• addPseudoCounts() : broad.core.motif.PositionWeightColumn , broad.core.motif.PositionWeightMatrix , broad.core.motif.PositionWeightMatrixIO
• addPsuedocounts() : broad.core.math.EmpiricalDistribution
• addPWMColumn() : broad.core.motif.meme.MemeMotif
• addRecord() : umms.core.writers.PairedEndWriter
• addRefSeq() : broad.pda.annotation.BEDFileParser
• addRefSeqSet() : broad.pda.annotation.BEDFileParser
• addRow() : broad.core.datastructures.MatrixWithHeaders
• addScore() : broad.pda.datastructures.Alignments
• addSequence() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , umms.core.annotation.Gene
• addSequences() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• addShortEncodedColumn() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• addShortEncodedColumnMatrix() : broad.core.multiplealignment.MultipleAlignment
• addShortEncodedRegion() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• addSourceAnnotation() : umms.core.feature.GeneWindow , umms.core.feature.GenomeWindow , umms.core.feature.Window
• addState() : broad.core.hmm.MarkovModel< T >
• addStringArg() : broad.core.parser.CommandLineParser
• addStringListArg() : broad.core.parser.CommandLineParser
• addSuffixToName() : broad.pda.gene.GeneWithIsoforms , umms.core.annotation.Gene
• addToCentroid() : broad.core.motif.PositionWeightMatrix
• addToCluster() : broad.pda.geneexpression.clustering.Cluster
• addTranscript() : broad.core.primer3.HairpinKmer
• addVertex() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.scripture.OrientedChromosomeTranscriptGraph
• addWindow() : broad.core.siphy.TreeScalerIO
• AgilentArrayStats() : broad.pda.geneexpression.agilent.AgilentArrayStats
• AgilentProbe() : broad.pda.geneexpression.agilent.AgilentProbe
• AgilentToGCT() : broad.pda.geneexpression.agilent.AgilentToGCT
• align() : jaligner.NeedlemanWunsch , jaligner.NeedlemanWunschGotoh , jaligner.SmithWatermanGotoh , umms.core.alignment.SmithWatermanAlignment
• Alignment() : jaligner.Alignment
• AlignmentCount() : umms.core.model.AlignmentModel.AlignmentCount , umms.core.model.JCSAlignmentModel.AlignmentCount
• AlignmentDataModelStats() : broad.pda.seq.segmentation.AlignmentDataModelStats
• AlignmentModel() : umms.core.model.AlignmentModel
• Alignments() : broad.pda.datastructures.Alignments
• AlignmentsReader() : broad.pda.datastructures.AlignmentsReader
• allIsoformsToBED() : broad.pda.gene.GeneWithIsoforms
• almostContains() : broad.pda.gene.GeneWithIsoforms , umms.core.annotation.Gene
• almostContainsRefSeq() : umms.core.annotation.Gene
• almostEqual() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.Gene
• almostSameStructure() : umms.core.annotation.Gene
• alwaysFalse() : umms.core.general.Predicates
• alwaysTrue() : umms.core.general.Predicates
• AMEResultReader() : broad.core.motif.meme.AMEResultReader
• and() : umms.core.general.Predicates
• annotation() : broad.core.annotation.AnnotationHandler , broad.pda.datastructures.LocationAwareMatrix
• AnnotationList() : umms.core.annotation.AnnotationList< T extends Annotation >
• AnnotationOutOfBoundsException() : umms.core.coordinatesystem.AnnotationOutOfBoundsException
• AnnotationReader() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• ANOVA() : broad.core.math.ANOVA
• anovaFStat() : broad.core.math.Statistics
• append() : broad.core.datastructures.MatrixWithHeaders , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , broad.core.sequence.FastaSequenceIO , broad.core.sequence.Sequence
• appendColumns() : broad.core.datastructures.MatrixWithHeaders
• appendRows() : broad.core.datastructures.MatrixWithHeaders , broad.pda.datastructures.LocationAwareMatrix
• areRepeatsInDeepDirHierarchy() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• array2List() : umms.esat.ESAT , umms.esat.ESATDistanceCalculator
• arrayLeftDivide() : Jama.Matrix
• arrayLeftDivideEquals() : Jama.Matrix
• arrayRightDivide() : Jama.Matrix
• arrayRightDivideEquals() : Jama.Matrix
• arrayTimes() : Jama.Matrix
• arrayTimesEquals() : Jama.Matrix
• asAnnotation() : umms.core.alignment.AbstractPairedEndAlignment
• asDouble() : broad.core.parser.StringParser
• asFloat() : broad.core.parser.StringParser
• asInt() : broad.core.parser.StringParser
• asLong() : broad.core.parser.StringParser
• asRPKM() : umms.core.model.score.CountScore
• asString() : broad.core.parser.StringParser
• average() : broad.core.math.Statistics
• AverageBranchLength() : broad.core.siphy.tools.conservation.AverageBranchLength