Here is a list of all class members with links to the classes they belong to:

- g -

• G_CODE : broad.core.multiplealignment.MultipleAlignment
• GAP : jaligner.Alignment , jaligner.Markups
• GAP_CODE : broad.core.multiplealignment.MultipleAlignment
• gaps() : broad.pda.feature.genome.Chromosome
• gcContent() : broad.core.sequence.Sequence
• GENE : broad.pda.seq.rap.GenomeCommandLineProgram
• Gene() : umms.core.annotation.Gene
• GENE_BED : broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
• geneAvgCoverage : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData , broad.pda.seq.protection.WindowScores
• GeneCounts() : broad.pda.seq.segmentation.GeneCounts
• generate() : jaligner.matrix.MatrixGenerator
• generateAlignment() : broad.core.siphy.PiHMM
• generateAll5Mers() : broad.core.sequence.Sequence
• generateAllKmers() : broad.core.sequence.Sequence
• generateHKYQMatrix() : broad.core.siphy.EvolutionaryModelParameters
• generateRandom() : broad.core.datastructures.JCSCache
• generateRandomSequence() : broad.core.sequence.Sequence
• generateSubregions() : broad.pda.seq.rap.PlotAggregateRegions
• GenericAlignmentDataModel() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• GenericRootedTree() : broad.core.datastructures.GenericRootedTree< T >
• genes : broad.pda.seq.protection.MultiSampleScanPeakCaller , broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• genesByChr : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData , broad.pda.seq.protection.WindowScores
• genesByName : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData , broad.pda.seq.protection.WindowScores
• GeneScore() : broad.pda.seq.segmentation.GeneScore
• geneScores : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData , broad.pda.seq.protection.WindowScores
• GeneSetEnrichment() : broad.projection.gsa.GeneSetEnrichment
• geneSpanContains() : umms.core.annotation.Gene
• GeneWindow() : umms.core.feature.GeneWindow
• GeneWithIsoforms() : broad.pda.gene.GeneWithIsoforms
• GENOME : broad.pda.samtools.PairedEndTDF
• GenomeSpaceSampleData() : broad.pda.seq.clip.GenomeSpaceSampleData , broad.pda.seq.protection.GenomeSpaceSampleData
• GenomeWindow() : umms.core.feature.GenomeWindow
• GenomeWithGaps() : broad.pda.seq.segmentation.GenomeWithGaps
• GenomeWithGaps2() : broad.pda.seq.segmentation.GenomeWithGaps2
• GenomicSpace() : umms.core.coordinatesystem.GenomicSpace
• GenomicSpanFilter() : nextgen.core.readFilters.GenomicSpanFilter
• genomicToGenomicPositionWithOffset() : umms.core.annotation.Gene
• genomicToTranscriptPosition() : umms.core.annotation.Gene
• geometricMean() : broad.core.math.Statistics
• geometricMeanMAD() : broad.core.math.Statistics
• get() : broad.core.datastructures.MatrixWithHeaders , broad.pda.annotation.BEDFileParser , Jama.Matrix
• get3PRegion() : broad.pda.annotation.BEDFileParser
• get3Prime() : broad.core.sequence.Sequence
• get3PrimeExon() : umms.core.annotation.Gene
• get3PrimeGenomicDistance() : umms.core.annotation.Gene
• get3Utr() : umms.core.annotation.Gene
• get3UTR() : umms.core.annotation.Gene
• get3UTRGene() : umms.core.annotation.Gene
• get3UtrIncludingIntrons() : umms.core.annotation.Gene
• get5PrimeExon() : umms.core.annotation.Gene
• get5UTR() : umms.core.annotation.Gene
• get5Utr() : umms.core.annotation.Gene
• get5UTRGene() : umms.core.annotation.Gene
• get5UtrIncludingIntrons() : umms.core.annotation.Gene
• getA() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getAbsFDR() : broad.core.math.FDRDistribution
• getAbsFDRMatrix() : broad.pda.differentialExpression.DifferentialExpression
• getAbsoluteEnd() : broad.core.sequence.SequenceRegion
• getAbsoluteStart() : broad.core.sequence.SequenceRegion
• getAEnd() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getAlignDir() : broad.core.motif.PositionWeightMatrix
• getAlignedSequence() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• getAlignedSequenceIds() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• getAlignedSequences() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• getAlignment() : broad.pda.seq.graph.Path , umms.core.alignment.PairedEndAlignmentFactory , umms.core.annotation.Gene
• getAlignmentChunkSize() : broad.core.siphy.ConservedPWMScanner
• getAlignmentDataModelStats() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getAlignmentEnd() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getAlignmentIdxSizeAtCreation() : broad.pda.seq.alignment.StoredAlignmentStats
• getAlignmentSizeAtCreation() : broad.pda.seq.alignment.StoredAlignmentStats
• getAlignmentStart() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getAlignmentType() : umms.core.model.JCSAlignmentModel , umms.core.readers.PairedEndReader
• getAllChromosomes() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getAllDataValues() : broad.core.math.EmpiricalDistribution
• getAllIsoformExonSet() : broad.pda.gene.GeneWithIsoforms
• getAllIsoformIntronSet() : broad.pda.gene.GeneWithIsoforms
• getAllIsoforms() : broad.pda.annotation.Locus , broad.pda.gene.GeneWithIsoforms
• getAllMerged() : broad.pda.annotation.Locus
• getAllNonRandomChromosomes() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getAllPairwiseAntisenseAlignments() : umms.core.alignment.FeatureSequenceAlignment
• getAllPairwiseSenseAlignments() : umms.core.alignment.FeatureSequenceAlignment
• getAllPaths() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getAllPositions() : umms.core.annotation.Gene
• getAllPossibleAmplicons() : broad.core.primer3.isPCRLike
• getAllPossibleTargets() : umms.core.alignment.SmatchLike
• getAlphabetSize() : broad.core.motif.PositionWeightColumn , broad.core.siphy.EvolutionaryModel
• getAMap() : broad.core.math.Loess
• getAName() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getAnnotation() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.pda.seq.clip.Pileup , umms.core.model.score.WindowScore.AbstractWindowScore , umms.core.model.score.WindowScore
• getAnnotationDirectory() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getAnnotationList() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.annotation.BasicGenomicAnnotationReader
• getAnnotationOverlappingRegion() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getAnnotationSetMap() : broad.pda.annotation.BEDFileParser
• getAnnotationsForSequence() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getAntisense() : broad.core.sequence.Sequence
• getArgString() : broad.core.parser.CommandLineParser
• getArray() : Jama.Matrix
• getArrayCopy() : Jama.Matrix
• getAsMatrix() : broad.core.multiplealignment.MultipleAlignment
• getAStart() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getAttribute() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment , umms.core.annotation.Gene
• getAttributes() : broad.core.annotation.GFF , umms.core.annotation.Gene
• getAutosomeGenomeSize() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getAutosomeNumber() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getAutosomes() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getAverageCountPerPosition() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getAverageCountPerPositionWithThreshold() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getAverageCoverage() : umms.core.annotation.AbstractAnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore , umms.core.model.score.ScanStatisticScore
• getAverageScore() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getAvergeNumberOfReads() : broad.pda.seq.segmentation.GeneScore
• getB() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getBackgroundNucleotideFreqs() : broad.core.siphy.EvolutionaryModelParameters
• getBackwardEdges() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getBackwardPaths() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getBamFile() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getBaseCoverage() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getBaseIUB() : broad.core.motif.PositionWeightColumn
• getBasesCovered() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel , umms.core.annotation.AbstractAnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getBasesCoveredPerAlignment() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getBatch() : broad.pda.geneexpression.ExpressionExperimentInfo
• getBedScore() : umms.core.annotation.Gene
• getBEnd() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getBin() : broad.core.math.EmpiricalDistribution
• getBinEnd() : broad.core.math.EmpiricalDistribution
• getBinMidPoint() : broad.core.math.EmpiricalDistribution
• getBinNumber() : broad.core.math.EmpiricalDistribution
• getBinStart() : broad.core.math.EmpiricalDistribution
• getBlastHit() : broad.core.primer3.HairpinKmer
• getBlockIterator() : broad.core.multiplealignment.MAFAlignment
• getBlocks() : broad.core.annotation.BED , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• getBlockSizeStarts() : broad.core.annotation.BED
• getBName() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getBooleanArg() : broad.core.parser.CommandLineParser
• getBStart() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• getCDNAs() : broad.pda.seq.segmentation.GenomeWithGaps
• getCDS() : umms.core.annotation.Gene
• getCDSEnd() : umms.core.annotation.Gene
• getCDSRegion() : umms.core.annotation.Gene
• getCDSStart() : umms.core.annotation.Gene
• getChildren() : umms.core.utils.AnnotationUtils
• getChr() : broad.core.sequence.SequenceRegion , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• getChrLength() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getChrLengths() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getChrNum() : umms.core.annotation.Gene
• getChromosome() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , broad.pda.feature.genome.DirectoryInstalledGenomeAssembly , broad.pda.seq.graph.Path , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.SingleEndAlignment
• getChromosomeAnnotationMap() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getChromosomeBEDs() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getChromosomeIterator() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.pda.annotation.BEDFileParser
• getChromosomeLength() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getChromosomeLengths() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getChromosomeNames() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getChromosomeNumber() : broad.pda.feature.genome.Chromosome
• getChromosomeReadIterator() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getChromosomes() : broad.pda.datastructures.LocationAwareMatrix
• getChromosomeString() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• getChromosomeTree() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getChromosomeTreeMap() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getChrReadIterator() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getChrSequence() : broad.core.sequence.SequenceUtils
• getChrSequencesFromFasta() : broad.core.sequence.FastaSequenceIO
• getChrSizesFile() : broad.core.sequence.SequenceUtils
• getChrTree() : broad.pda.annotation.BEDFileParser
• getChunkEnd() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getChunkStart() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCigarString() : umms.core.alignment.SingleEndAlignment
• getClosest() : broad.pda.datastructures.LocationAwareMatrix , umms.core.annotation.AnnotationList< T extends Annotation >
• getClosestDownstream() : broad.pda.annotation.BEDFileParser , umms.core.annotation.AnnotationList< T extends Annotation >
• getClosestNonOverlapping() : umms.core.annotation.AnnotationList< T extends Annotation >
• getClosestUpstream() : broad.pda.annotation.BEDFileParser , umms.core.annotation.AnnotationList< T extends Annotation >
• getClusterInfo() : broad.pda.geneexpression.clustering.Kmeans
• getCol() : jaligner.Cell
• getColoumnName() : broad.core.datastructures.MatrixWithHeaders
• getColumn() : broad.core.datastructures.MatrixWithHeaders , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , Jama.Matrix
• getColumnDimension() : Jama.Matrix
• getColumnNames() : broad.core.datastructures.MatrixWithHeaders
• getColumnNum() : broad.pda.geneexpression.agilent.AgilentProbe
• getColumnPackedCopy() : Jama.Matrix
• getColumnsAsVector() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• getComaptibleBetweenAny2Sets() : broad.pda.annotation.Locus
• getComaptibleIsoforms() : broad.pda.annotation.Locus
• getCombinedPvalue() : broad.core.math.FisherCombinedProbabilityTest
• getComplement() : broad.core.motif.PositionWeightColumn
• getConcatenatedSubAlignment() : broad.core.multiplealignment.MultipleAlignment
• getConsensus() : broad.core.motif.PositionWeightMatrix
• getConsensusSequence() : broad.core.motif.SequenceMotif
• getConsistencyProblems() : broad.core.hmm.MarkovModel< T >
• getContainingSequenceId() : broad.core.sequence.SequenceRegion
• getControlClass() : broad.core.util.ParseGCTFile
• getCoordinateAtPosition() : umms.core.annotation.CompoundInterval
• getCoordinateSpace() : broad.pda.seq.protection.MultiSampleScanPeakCaller , broad.pda.seq.rap.GenomeCommandLineProgram , broad.pda.seq.rap.RAPPeakCaller , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel , umms.core.model.score.ScanStatisticScore
• getCoreMotifs() : broad.core.motif.SequenceMotif
• getCount() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel , umms.core.annotation.AbstractAnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel.AlignmentCount , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel.AlignmentCount , umms.core.model.JCSAlignmentModel , umms.core.model.score.AbstractListScore , umms.core.model.score.CountScore , umms.core.model.score.EndInWindowCountScore , umms.core.model.score.StartInWindowCountScore
• getCountByBinStart() : broad.core.math.EmpiricalDistribution
• getCountExcludingRegion() : umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getCountProcessor() : umms.core.annotation.AbstractAnnotationCollection< T extends Annotation >
• getCounts() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountScore() : broad.pda.datastructures.Alignments , umms.core.annotation.Gene
• getCountsOfUniqueOverlappers() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsOnBase() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsOnWindow() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsPerAlignment() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsPerAlignmentForPolyA() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsPerAlignmentFullyContained() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsPerAlignmentUncached() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsPerAlignmentWithSameEndpointForPolyA() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsPerAnnotationtranded() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCountsPerBp() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getCountsPerPosition() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getCountsStrandedPerPosition() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getCountStrandedExcludingRegion() : umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getCountsWithinExons() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getCoverage() : broad.pda.seq.graph.Path
• getCtrlCoordSpace() : umms.core.model.score.MultiScore
• getCtrlCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore
• getCtrlLambda() : umms.core.model.score.PoissonEnrichmentScore
• getCtrlRegionCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore
• getCtrlRegionTotal() : umms.core.model.score.PoissonEnrichmentScore
• getCtrlSampleLambda() : umms.core.model.score.PoissonEnrichmentScore
• getCtrlTotal() : umms.core.model.score.PoissonEnrichmentScore
• getCumulativeProbability() : broad.core.math.EmpiricalDistribution
• getCurrentBase() : broad.core.sequence.AbstractFastaParser
• getCurrentQuality() : broad.core.sequence.FastaQualityParser
• getCurrentRelease() : jaligner.util.Commons
• getCurrentSequenceId() : broad.core.sequence.AbstractFastaParser
• getD() : Jama.EigenvalueDecomposition
• getData() : broad.core.datastructures.MatrixWithHeaders , broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getDataForAlignment() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getDataForGene() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getDataModel() : broad.core.sequence.SequenceUtils
• getDataType1() : broad.pda.enrichment.EnrichmentMetric
• getDataType2() : broad.pda.enrichment.EnrichmentMetric
• getDataTypes() : broad.pda.enrichment.EnrichmentMetric
• getDebugInfo() : umms.core.model.score.MultiScore , umms.core.model.score.ScanStatisticScore
• getDefaultFile() : umms.core.writers.PairedEndWriter
• getDenominatorCount() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getDenominatorLambda() : umms.core.model.score.WindowAllScore
• getDenominatorRegionTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getDenominatorRPKM() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getDenominatorScanPVal() : broad.pda.seq.rap.SkellamScore , umms.core.model.score.WindowAllScore
• getDenominatorTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getDensity() : broad.core.math.EmpiricalDistribution
• getDepletionBinomialPValue() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getDepletionBinomialScore() : umms.core.model.score.RatioScore
• getDescription() : broad.pda.seq.fastq.FastqSequence , jaligner.Sequence
• getDirection() : jaligner.TracebackNode
• getDistancesToClosest() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getDistanceTo() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.SingleInterval
• getDistanceTo3primeNeighbor() : broad.pda.annotation.Locus
• getDistanceTo5primeNeighbor() : broad.pda.annotation.Locus
• getDistanceToClosest() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , umms.core.annotation.AnnotationList< T extends Annotation >
• getDistributionOfHistogramValues() : broad.core.math.EmpiricalDistribution
• getDoubleArg() : broad.core.parser.CommandLineParser
• getDoublePivot() : Jama.LUDecomposition
• getdoubleronicCounts() : broad.pda.seq.segmentation.GeneCounts
• getDuplicateReadFlag() : umms.core.alignment.SingleEndAlignment.WrapSamRecord
• getEdgeList() : broad.pda.seq.graph.Path
• getEdges() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.graph.Path
• getElements() : broad.core.siphy.PhastconsReader
• getEmissionLogProbability() : broad.core.hmm.MarkovState< T >
• getEmissionProbability() : broad.core.hmm.MarkovState< T >
• getEmpiricalMaxStatisticDistribution() : broad.core.math.EmpiricalDistribution
• getEmptyEmpiricalDistribution() : broad.pda.seq.rap.BuildRatioNullDistribution
• getEncodedSequence() : broad.core.sequence.Sequence
• getEnd() : broad.core.annotation.LightweightGenomicAnnotation , broad.core.datastructures.Interval , broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.graph.Path , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• getEndVertex() : broad.pda.seq.graph.Path
• getEnrichment() : broad.pda.seq.segmentation.GeneScore , umms.core.model.score.ScanStatisticScore
• getEnrichmentBinomialPValue() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getEnrichmentBinomialScore() : umms.core.model.score.RatioScore
• getEnrichmentOverControl() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore
• getEnrichmentOverGene() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getEntireChromosome() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getEstimatedLibrarySize() : broad.pda.countreads.FastqLibraryStats
• getEstimationWindow() : broad.core.siphy.TreeScalerIO
• getEval() : broad.core.motif.meme.MemeMotif
• getExactIsoform() : broad.pda.annotation.BEDFileParser
• getExonAnnotationOverlappingRegion() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getExonicCounts() : broad.pda.seq.segmentation.GeneCounts
• getExons() : umms.core.annotation.Gene
• getExonSet() : umms.core.annotation.Gene
• getExonsScores() : umms.core.annotation.Gene
• getExonTree() : umms.core.annotation.Gene
• getExonUnion() : broad.pda.annotation.Locus
• getExperimentBarcode() : broad.pda.geneexpression.ExpressionExperimentInfo
• getExperimentHybDate() : broad.pda.geneexpression.ExpressionExperimentInfo
• getExperimentName() : broad.pda.geneexpression.ExpressionExperimentInfo
• getExperimentPlatePosition() : broad.pda.geneexpression.ExpressionExperimentInfo
• getExpressionScanPvalueCutoff() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getExtend() : jaligner.Alignment
• getExtraFields() : umms.core.annotation.Gene
• getExtraScore() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• getExtraScores() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• getFactory() : broad.core.annotation.AnnotationFactoryFactory
• getFDR() : broad.core.math.FDRDistribution , broad.pda.differentialExpression.RunDifferentialExpression
• getFDRDistribution() : broad.pda.differentialExpression.DifferentialExpression
• getFDRMatrix() : broad.pda.differentialExpression.DifferentialExpression
• getFeature() : broad.core.annotation.GFF
• getFieldCount() : broad.core.parser.StringParser
• getFileSeparator() : jaligner.util.Commons
• getFileSize() : broad.core.sequence.AbstractFastaParser
• getFinalMValues() : broad.core.math.Loess
• getFirstExon() : umms.core.annotation.Gene
• getFirstFragmentPositionStranded() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getFirstGene() : umms.core.alignment.FeatureSequenceAlignment.UnorderedGenePair
• getFirstIntersectLeftFromMedian() : broad.core.math.EmpiricalDistribution
• getFirstIntersectRightFromMedian() : broad.core.math.EmpiricalDistribution
• getFirstIntron() : umms.core.annotation.Gene
• getFirstMate() : umms.core.alignment.AbstractPairedEndAlignment
• getFirstNBPs() : broad.pda.seq.fastq.FastqSequence
• getFirstSequence() : broad.pda.rnai.ExtractSequence
• getFirstValue() : broad.core.annotation.GFF
• getFits() : broad.core.siphy.StationaryDistributionIO
• getFivePrimeBases() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion
• getFlagsAndValues() : broad.core.parser.CommandLineParser
• getFlankingBlocks() : umms.core.annotation.BasicAnnotation
• getFloatArg() : broad.core.parser.CommandLineParser
• getFoldMatrix() : broad.pda.differentialExpression.DifferentialExpression
• getFormat() : jaligner.formats.FormatFactory
• getFormats() : jaligner.formats.FormatFactory
• getForwardEdges() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getForwardTargetRegions() : umms.core.alignment.SmatchLike
• getForwardTargets() : umms.core.alignment.SmatchLike
• getFragment() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment , umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getFragmentEnd() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getFragmentEndsFromBamFile() : broad.pda.seq.clip.Pileup
• getFragmentLengthFilterData() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getFragmentLengthGeneCount() : broad.pda.seq.clip.SampleData
• getFragmentMidpoint() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getFragmentSize() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getFragmentStart() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getFragmentStrand() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getFrame() : broad.core.annotation.GFF
• getFullInfoString() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• getFullIntervalTreeAsAnnotation() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getFullPrintableAlignment() : umms.core.alignment.SmithWatermanAlignment
• getFullyContainedNumberOfReads() : broad.pda.seq.segmentation.GeneScore , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.ScanStatisticScore
• getFWER() : broad.pda.differentialExpression.FWERDistribution
• getFWERMatrix() : broad.pda.differentialExpression.DifferentialExpression
• getGappedSeqsInWindowMatrix() : broad.core.siphy.ConservationUtils
• getGappedSize() : umms.core.annotation.Gene
• getGaps() : broad.pda.seq.segmentation.GenomeWithGaps , jaligner.Alignment
• getGaps1() : jaligner.Alignment
• getGaps2() : jaligner.Alignment
• getGapsSize() : broad.core.sequence.Sequence
• getGene() : broad.pda.annotation.BEDFileParser , umms.core.model.score.MultiScore
• getGeneAverageCoverage() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getGeneByName() : broad.pda.annotation.BEDFileParser
• getGeneCount() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getGeneCounts() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getGeneCountsWithoutDatasetTotals() : broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getGeneDescription() : broad.pda.geneexpression.agilent.AgilentProbe
• getGeneExpression() : broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getGeneIDIsoMap() : broad.pda.annotation.GTFFileParser
• getGeneLength() : broad.pda.seq.segmentation.GeneScore
• getGeneName() : broad.pda.geneexpression.agilent.AgilentProbe , broad.pda.rnai.RNAiGeneAnnotation
• getGenePaths() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getGenePval() : broad.pda.seq.clip.GenomeSpaceSampleData
• getGeneRandNeighbors() : broad.pda.gene.NeighborsNullModel
• getGenes() : broad.core.sequence.TranscribedRegions
• GetGenes() : broad.pda.annotation.BEDFileParser
• getGenes() : broad.pda.seq.rap.GenomeCommandLineProgram
• getGeneScanPval() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.GenomeSpaceSampleData , broad.pda.seq.protection.SampleData
• getGenesPassingFDR() : broad.pda.differentialExpression.DifferentialExpression , broad.pda.differentialExpression.RunDifferentialExpression
• GetGenesWithIsoforms() : broad.pda.annotation.BEDFileParser
• getGenomeSequence() : broad.pda.rnai.ExtractSequence
• getGenomeSize() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getGenomicLength() : umms.core.annotation.Gene
• getGenomicRegionOverlappers() : broad.pda.annotation.BEDFileParser
• getGenomicSpace() : broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
• getGlobalCount() : umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getGlobalCountReferenceSeqs() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getGlobalEnrichment() : umms.core.model.score.BasicScanStatisticScore
• getGlobalLambda() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.MultiScore , umms.core.model.score.ScanStatisticScore
• getGlobalLength() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore , umms.core.model.score.ScanStatisticScore
• getGlobalNumReads() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getGlobalNumReadsReferenceSeqs() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getGlobalPairedFragments() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getGlobalRPKMConstant() : broad.pda.seq.alignment.StoredAlignmentStats , broad.pda.seq.segmentation.AlignmentDataModelStats
• getGraph() : broad.pda.seq.graph.Path
• getGroup() : broad.core.annotation.GFF
• getGroupIndexes() : broad.core.util.ParseGCTFile
• getGTFAttr() : broad.core.annotation.GFF
• getGTFGeneTranscriptMap() : broad.pda.annotation.GTFFileParser
• getH() : Jama.QRDecomposition
• getHeader() : broad.core.multiplealignment.MAFAlignment , broad.pda.samtools.SAMPairedEndFileReader , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment , umms.core.model.JCSAlignmentModel , umms.core.readers.PairedEndReader
• getHistogram() : broad.core.math.EmpiricalDistribution
• getId() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.motif.SequenceMotif , broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , broad.pda.enrichment.EnrichmentMetric , jaligner.formats.Format , jaligner.matrix.Matrix , jaligner.Sequence
• getIdentity() : jaligner.Alignment
• getImagEigenvalues() : Jama.EigenvalueDecomposition
• getIncidentEdges() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getIndecesForRowDescription() : broad.core.datastructures.MatrixWithHeaders
• getIndex() : broad.core.datastructures.IntervalTree< V > , broad.core.multiplealignment.MAFAlignment
• getIndexFor() : broad.core.parser.StringParser
• getIndexGroup() : broad.core.util.ParseGCTFile
• getInformationContent() : broad.core.motif.PositionWeightColumn
• getInitialStateTransitionProbabilities() : broad.core.hmm.MarkovModel< T >
• getInOrUnorientedEdges() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getInstance() : jaligner.formats.FormatFactory
• getIntArg() : broad.core.parser.CommandLineParser
• getIntervalBetweenReads() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getIntervalTree() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getIntervalTreeCached() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getIntervalTreeTruncated() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getIntervalTreeTruncatedCached() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getIntervalTreeWithIsoforoms() : broad.pda.annotation.BEDFileParser
• getIntronCounts() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getIntrons() : umms.core.annotation.Gene
• getIntronsBlocks() : umms.core.annotation.Gene
• getIntronSet() : umms.core.annotation.Gene
• getIntronTranscript() : umms.core.annotation.Gene
• getIOHelper() : broad.core.multiplealignment.MultipleAlignment
• getIsComaptibleBetweenAny2Sets() : broad.pda.annotation.Locus
• getIsComaptibleBetweenSubsets() : broad.pda.annotation.Locus
• getIsComaptibleWithRefPerSet() : broad.pda.annotation.Locus
• getIsFirstMate() : umms.core.alignment.SingleEndAlignment
• getIsoformMap() : umms.core.scripture.BuildScriptureCoordinateSpace
• getIsoforms() : umms.core.annotation.Gene
• getIsPartiallyComaptibleWithRefPerSet() : broad.pda.annotation.Locus
• getJAlignerInfo() : jaligner.util.Commons
• getKmerEndPosition() : broad.core.primer3.HairpinKmer
• getKmerSequence() : broad.core.primer3.HairpinKmer
• getKmerStartPosition() : broad.core.primer3.HairpinKmer
• getKSEnrichments() : broad.projection.gsa.GeneSetEnrichment
• getKSFDR() : broad.projection.gsa.GeneSetEnrichment
• getKSScores() : broad.projection.gsa.GSAScoring
• getKSStatistic() : broad.core.math.EmpiricalDistribution , broad.core.math.Statistics
• getL() : Jama.CholeskyDecomposition , Jama.LUDecomposition
• getLambda() : broad.pda.seq.alignment.StoredAlignmentStats , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getLargestParent() : umms.core.utils.AnnotationUtils
• getLastExon() : umms.core.annotation.Gene
• getLastExons() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getLastFragmentPositionStranded() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getLastIntron() : umms.core.annotation.Gene
• getLastModifiedAlignmentIdxTimeStampAtCreation() : broad.pda.seq.alignment.StoredAlignmentStats
• getLastModifiedAlignmentTimeStampAtCreation() : broad.pda.seq.alignment.StoredAlignmentStats
• getLastModifiedStoredTimeStamp() : broad.pda.seq.alignment.StoredAlignmentStats
• getLeaves() : broad.core.datastructures.GenericRootedTree< T >
• getLeft() : broad.pda.geneexpression.clustering.Cluster
• getLeftHighInfoStart() : broad.core.motif.PositionWeightMatrix
• getLeftNeighbor() : broad.pda.gene.NeighborAnalysis
• getLength() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.datastructures.Interval , broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , broad.pda.seq.fastq.FastqSequence , jaligner.Alignment , jaligner.TracebackNode , umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace.GeneTree , umms.core.coordinatesystem.TranscriptomeSpace
• getLengthOnReference() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• getLineSeparator() : jaligner.util.Commons
• getLlr() : broad.core.motif.meme.MemeMotif
• getLocalLambda() : broad.pda.seq.graph.Path , broad.pda.seq.segmentation.GeneScore , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.ScanStatisticScore
• getLocalRate() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getLocalRpkmConstant() : broad.pda.seq.alignment.StoredAlignmentStats
• getLocalSampleLambda() : umms.core.model.score.PoissonEnrichmentScore
• getLocationString() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion
• getLog2Ratio() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getLog2RegionRatio() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getLogger() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getLogLikelihood() : broad.core.motif.PositionWeightMatrix , broad.core.siphy.TreeScaler
• getLogLikelihoodRatio() : broad.core.siphy.Fit
• getLogProb() : broad.core.motif.PositionWeightColumn
• getLogProcessedSignal() : broad.pda.geneexpression.agilent.AgilentProbe
• getLogRatio() : broad.core.motif.PositionWeightColumn
• getLogRatioWeightedByNegEntropy() : broad.core.motif.PositionWeightColumn
• getLongestIntornChainIso() : broad.pda.annotation.Locus
• getLongestPerfectMatch() : jaligner.Alignment
• getLongestUngappedAlignment() : jaligner.Alignment
• getMap() : broad.core.math.Loess
• getMappingQuality() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment , umms.core.alignment.SingleEndAlignment.WrapSamRecord
• getMarkupLine() : jaligner.Alignment
• getMaskedRegions() : broad.pda.seq.alignment.StoredAlignmentStats
• getMaskedRegionsSize() : broad.pda.seq.segmentation.AlignmentDataModelStats
• getMatch() : umms.core.annotation.PSLRecord
• getMatches() : broad.core.motif.meme.MemeMotif , broad.core.sequence.Sequence
• getMatrices() : broad.core.motif.PositionWeightMatrixIO
• getMatrix() : broad.pda.geneexpression.clustering.HierarchicalClustering , jaligner.Alignment , Jama.Matrix
• getMax() : broad.core.math.EmpiricalDistribution
• getMaxExonsCovered() : broad.pda.annotation.Locus
• getMaxMeanEnrichments() : broad.projection.gsa.GeneSetEnrichment
• getMaxMeanFDR() : broad.projection.gsa.GeneSetEnrichment
• getMaxMeanScores() : broad.projection.gsa.GSAScoring
• getMaxPctCovered() : broad.pda.annotation.Locus
• getMaxPctGenomeCovered() : broad.pda.annotation.Locus
• getMaxScoreAcrossAllIso() : broad.pda.annotation.Locus
• getMaxScorePerSet() : broad.pda.annotation.Locus
• getMean() : broad.core.math.EmpiricalDistribution , umms.core.model.score.AbstractListScore
• getMeanOverAllRows() : broad.core.datastructures.MatrixWithHeaders
• getMedian() : umms.core.model.score.AbstractListScore
• getMedianOfAllDataValues() : broad.core.math.EmpiricalDistribution
• getMedianOverAllRows() : broad.core.datastructures.MatrixWithHeaders
• getMedianReadSize() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getMembers() : broad.pda.geneexpression.clustering.Cluster
• getMerged() : broad.pda.annotation.Locus , broad.pda.gene.GeneWithIsoforms
• getMergedAnnotationMap() : broad.pda.annotation.BEDFileParser
• getMergedCopy() : broad.pda.annotation.BEDFileParser
• getMessage() : broad.core.hmm.BadModelException
• getMethod() : broad.pda.enrichment.EnrichmentMetric
• getMiddle() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• getMidpoint() : broad.core.sequence.SequenceRegion
• getMidPoint() : broad.pda.datastructures.Alignments
• getMidpoint() : umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.utils.AnnotationUtils
• getMidpointGenomicCoords() : umms.core.annotation.Gene
• getMin() : broad.core.math.EmpiricalDistribution
• getMinimumMappingQuality() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getMinimumTreeLength() : broad.core.siphy.TreeScaler
• getMirScore() : broad.core.primer3.HairpinKmer
• getModel() : broad.core.siphy.TreeScaler
• getModelFilePath() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getModelParameters() : broad.core.siphy.EvolutionaryModel
• getMotif() : broad.core.motif.SequenceMotif
• getMotifNames() : broad.core.motif.misc.ComputeConservedMotifs
• getMotifs() : broad.core.motif.meme.MemeResultReader
• getName() : broad.core.annotation.Feature , broad.core.annotation.LightweightGenomicAnnotation , broad.core.datastructures.GenericRootedTree< T > , broad.core.hmm.MarkovState< T > , broad.core.motif.meme.MemeMotif , broad.core.motif.PositionWeightMatrix , broad.core.primer3.RestrictionEnzyme , broad.core.sequence.SequenceRegion , broad.pda.feature.genome.Chromosome , broad.pda.geneexpression.clustering.AbsolutePearsonFunction , broad.pda.geneexpression.clustering.ClusterDistanceFunction , broad.pda.geneexpression.clustering.EuclideanDistance , broad.pda.geneexpression.clustering.PearsonDistance , broad.pda.seq.fastq.FastqSequence , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• getName1() : jaligner.Alignment
• getName2() : jaligner.Alignment
• getNameGeneMap() : broad.pda.annotation.BEDFileParser
• getNanostringProbeClasses() : broad.core.datastructures.MatrixWithHeaders
• getNanostringReplicateMap() : broad.core.datastructures.MatrixWithHeaders
• getNeighborDistance() : broad.pda.gene.NeighborAnalysis
• getNeighbors() : broad.pda.gene.NeighborAnalysis
• getNext() : broad.core.math.CombinationGenerator
• getNextClosest() : broad.pda.datastructures.LocationAwareMatrix
• getNextKmer() : broad.core.motif.PositionWeightMatrix
• getNextRandom() : broad.core.math.CombinationGenerator
• getNextWindow() : broad.pda.seq.segmentation.GenomeWithGaps
• getNodeCount() : broad.pda.seq.graph.Path
• getNodeElements() : broad.core.datastructures.GenericRootedTree< T >
• getNodeLikelihoodParameterMap() : broad.core.siphy.EvolutionaryModel
• getNodePair() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.scripture.OrientedChromosomeTranscriptGraph
• getNodes() : broad.core.datastructures.GenericRootedTree< T >
• getNominalPValue() : broad.pda.seq.segmentation.GeneScore
• getNominalPValueMatrix() : broad.pda.differentialExpression.DifferentialExpression
• getNonControl1PercentileSignal() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNonControl50PercentileSignal() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNonControl99PercentileSignal() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNonRandomTotalSize() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getNormalizationFactor() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNormalizedKSEnrichments() : broad.projection.gsa.GeneSetEnrichment
• getNormalizedMaxMeanEnrichments() : broad.projection.gsa.GeneSetEnrichment
• getNormalizedScore() : umms.core.annotation.Gene
• getNormalizedSignal() : broad.pda.geneexpression.agilent.AgilentProbe
• getNullDistDegreesOfFreedom() : broad.core.math.FisherCombinedProbabilityTest
• getNum3PrimeComplementarity() : broad.core.primer3.Primer3PickingSummary
• getNum3PrimerStability() : broad.core.primer3.Primer3PickingSummary
• getNumberColumns() : broad.core.datastructures.MatrixWithHeaders
• getNumberMarkers() : broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getNumberOfAligningSequences() : broad.core.multiplealignment.MultipleAlignment
• getNumberOfBackgroundNonUniformFeaturesOverlimit() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNumberOfBackgroundPopulationOverlimit() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNumberOfBPs() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getNumberOfEdges() : broad.pda.seq.graph.Path
• getNumberOfFoundFeatures() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNumberOfIsoforms() : broad.pda.annotation.BEDFileParser , broad.pda.annotation.Locus , broad.pda.gene.GeneWithIsoforms
• getNumberOfMarkers() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getNumberOfMatches() : jaligner.Alignment
• getNumberOfMatches2() : jaligner.Alignment
• getNumberOfNonUniformFeaturesOverlimit() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNumberOfPopulationOverlimit() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNumberOfReads() : broad.pda.seq.alignment.StoredAlignmentStats , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GeneScore
• getNumberOfReadsByChr() : broad.pda.seq.segmentation.AlignmentDataModelStats
• getNumberOfSaturatedProbes() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getNumberOfSequences() : broad.pda.seq.fastq.FastqParser
• getNumberOfSplicedReads() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getNumberOfValuesLargerThan() : broad.core.math.EmpiricalDistribution
• getNumberPositions() : umms.core.annotation.Gene
• getNumberRows() : broad.core.datastructures.MatrixWithHeaders
• getNumCol() : broad.core.motif.PositionWeightMatrix
• getNumColdMeltingTemp() : broad.core.primer3.Primer3PickingSummary
• getNumColumns() : Jama.Matrix
• getNumEndPosToErase() : broad.core.motif.PositionWeightMatrix
• getNumeratorCount() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getNumeratorLambda() : umms.core.model.score.WindowAllScore
• getNumeratorRegionTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getNumeratorRPKM() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getNumeratorScanPVal() : broad.pda.seq.rap.SkellamScore , umms.core.model.score.WindowAllScore
• getNumeratorTotal() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getNumExons() : umms.core.annotation.Gene
• getNumGC() : broad.core.primer3.Primer3PickingSummary
• getNumGCClampFailures() : broad.core.primer3.Primer3PickingSummary
• getNumHotMeltingTemp() : broad.core.primer3.Primer3PickingSummary
• getNumIsoformsPerSet() : broad.pda.annotation.Locus
• getNumLeft() : broad.core.math.CombinationGenerator
• getNumMarkers() : broad.pda.seq.alignment.StoredAlignmentStats
• getNumMispriming() : broad.core.primer3.Primer3PickingSummary
• getNumNs() : broad.core.primer3.Primer3PickingSummary
• getNumOk() : broad.core.primer3.Primer3PickingSummary
• getNumOligosTested() : broad.core.primer3.Primer3PickingSummary
• getNumOverlappingAnnotations() : umms.core.annotation.AnnotationList< T extends Annotation >
• getNumOverlappingExcludedRegions() : broad.core.primer3.Primer3PickingSummary
• getNumOverlappingTargets() : broad.core.primer3.Primer3PickingSummary
• getNumPolyX() : broad.core.primer3.Primer3PickingSummary
• getNumPossibleKmers() : broad.core.motif.SequenceMotif
• getNumReads() : umms.core.model.AlignmentModel.AlignmentCount , umms.core.model.JCSAlignmentModel.AlignmentCount
• getNumRows() : Jama.Matrix
• getNumSelfComplementarityAnywhere() : broad.core.primer3.Primer3PickingSummary
• getNumSeqQuality() : broad.core.primer3.Primer3PickingSummary
• getNumStartPosToErase() : broad.core.motif.PositionWeightMatrix
• getNumUniqueReads() : broad.pda.countreads.FastqLibraryStats
• getOffset() : broad.core.sequence.AbstractFastaParser
• getOneRandomSamplePermutation() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• getOpen() : jaligner.Alignment
• getOppositeVertex() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getOrCreatePairedEndFile() : umms.core.readers.PairedEndReader
• getOrdered() : broad.pda.geneexpression.clustering.Cluster
• getOrderedAssembly() : umms.core.scripture.statistics.ConnectDisconnectedTranscripts
• getOrderedListCDT() : broad.core.util.ParseGCTFile
• getOrientation() : broad.core.annotation.GenomicAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , broad.core.sequence.TranscribedRegions , broad.pda.seq.graph.Path , umms.core.alignment.AbstractPairedEndAlignment , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• getOrientedEnd() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• getOrientedLastExon() : umms.core.annotation.Gene
• getOrientedStart() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• getOriginalBamFile() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getOriginalMValues() : broad.core.math.Loess
• getOriginalScore() : broad.core.primer3.HairpinKmer
• getOriginalSequence1() : jaligner.Alignment
• getOriginalSequence2() : jaligner.Alignment
• getOrphanNodes() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getOrphanPaths() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.scripture.OrientedChromosomeTranscriptGraph
• getOrphanVertices() : umms.core.scripture.OrientedChromosomeTranscriptGraph
• getOutOrUnorientedEdges() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getOutputFile() : umms.core.writers.PairedEndWriter
• getOverlap() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.overlaputils.GeneSetIntersect , broad.core.primer3.HairpinKmer , broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.Gene
• getOverlappers() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.siphy.StationaryDistributionIO , broad.pda.annotation.BEDFileParser , broad.pda.datastructures.LocationAwareMatrix , umms.core.annotation.Gene
• getOverlappingAnnotationList() : umms.core.annotation.AnnotationList< T extends Annotation >
• getOverlappingAnnotations() : umms.core.annotation.AbstractAnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getOverlappingGenes() : umms.core.scripture.BuildScriptureCoordinateSpace
• getOverlappingNodes() : broad.pda.seq.graph.Path
• getOverlappingReadCounts() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getOverlappingReadReplicateCounts() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getOverlappingReads() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getOverlappingRegion() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getOverlappingRegions() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getOverlappingSplicedReads() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getOverlappingVertices() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getOverlapWithRandomizedPositions() : broad.core.overlaputils.GeneSetIntersect
• getP() : broad.core.math.MannWhitneyPermutations , broad.core.math.Wilcox2Sample
• getPair1Parser() : broad.pda.seq.fastq.FastqSplitterByBarcode
• getPair2Parser() : broad.pda.seq.fastq.FastqSplitterByBarcode
• getPairedData() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getPairedEndEdges() : broad.pda.seq.graph.Path
• getPairedEndFile() : umms.core.readers.PairedEndReader
• getParameters() : broad.core.siphy.EvolutionaryModel , broad.core.util.CLUtil
• getParents() : umms.core.utils.AnnotationUtils
• getPaths() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.scripture.BuildScriptureCoordinateSpace , umms.core.scripture.OrientedChromosomeTranscriptGraph
• getPeak() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getPeakBedFileName() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• getPeakScores() : broad.pda.seq.rap.CollectAnnotationEnrichments
• getPercent3UTR() : umms.core.annotation.Gene
• getPercentCDS() : umms.core.annotation.Gene
• getPercentConsistent() : broad.pda.seq.graph.Path
• getPercentDuplicated() : broad.pda.countreads.FastqLibraryStats
• getPercentFeaturesWellAboveBackground() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getPercentGC() : broad.core.primer3.HairpinKmer
• getPercentIdentity() : jaligner.Alignment , umms.core.annotation.PSLRecord
• getPercentOfValuesBetween() : broad.core.math.EmpiricalDistribution
• getPercentOfValuesLargerThan() : broad.core.math.EmpiricalDistribution
• getPercentVariantsCovered() : broad.core.primer3.HairpinKmer
• getPermNum() : broad.pda.gene.NeighborsNullModel
• getPermutationMatrix() : broad.pda.differentialExpression.DifferentialExpression
• getPermutedAnnotations() : umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getPi() : broad.core.siphy.EvolutionaryModel
• getPIDToName() : broad.core.datastructures.MatrixWithHeaders
• getPivot() : Jama.LUDecomposition
• getPlateName() : broad.pda.geneexpression.ExpressionExperimentInfo
• getPoissonLambda() : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• getPosition() : broad.core.siphy.Fit
• getPositionAtCoordinate() : umms.core.annotation.CompoundInterval
• getPositionAtReferenceCoordinate() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• getPositionCountList() : umms.core.model.AlignmentModel
• getPositionCountMap() : umms.core.coordinatesystem.TranscriptomeSpace
• getPreferredFileExtension() : broad.core.multiplealignment.FastaMultipleAlignmentIO , broad.core.multiplealignment.MAFIO , broad.core.multiplealignment.MultipleAlignmentIO , broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO , broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO
• getPrimerPickingSummary() : broad.core.primer3.Primer3PrimerPickingResult
• getPrimers() : broad.core.primer3.Primer3PrimerPickingResult
• getPriorClosest() : broad.pda.datastructures.LocationAwareMatrix
• getProbability() : broad.core.math.EmpiricalDistribution , broad.core.motif.PositionWeightColumn
• getProbename() : broad.pda.geneexpression.agilent.AgilentProbe
• getProcessedSignal() : broad.pda.geneexpression.agilent.AgilentProbe
• getPromoter() : umms.core.annotation.Gene
• getPromoters() : broad.pda.annotation.BEDFileParser
• getPVal() : broad.core.siphy.EvolutionaryModel
• getPValue() : broad.core.math.EmpiricalDistribution
• getPvalue() : broad.core.math.MannWhitney
• getPValue() : broad.pda.enrichment.EnrichmentMetric , umms.core.annotation.Gene
• getPvalue() : umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.CountScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore , umms.core.model.score.ScanStatisticScore
• getPValue2() : broad.core.math.EmpiricalDistribution
• getPWM() : broad.core.motif.meme.MemeMotif
• getPWMiterator() : broad.core.siphy.ConservedPWMScanner
• getQ() : Jama.QRDecomposition
• getQualityBases() : broad.core.sequence.FastaQualityBinaryIO
• getQuantileOfBins() : broad.core.math.EmpiricalDistribution
• getR() : Jama.QRDecomposition
• getRandomAnnotation() : umms.core.coordinatesystem.TranscriptomeSpace.GeneTree
• getRandomSets() : broad.pda.gene.transcriptsNullModel
• getRankedList() : broad.projection.gsa.GeneSetEnrichment
• getRateMatrix() : broad.core.siphy.EvolutionaryModel , broad.core.siphy.EvolutionaryModelParameters
• getRatio() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getRawDensity() : broad.core.math.EmpiricalDistribution
• getRead() : umms.core.model.AlignmentModel.AlignmentCount , umms.core.model.JCSAlignmentModel.AlignmentCount
• getRead1Trim3p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• getRead1Trim5p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• getRead2Trim3p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• getRead2Trim5p() : broad.pda.seq.fastq.FastqSplitterByBarcode
• getReadAlignmentBlocks() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getReadAlignments() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getReader() : broad.pda.samtools.SAMPairedEndFileReader
• getReadIterator() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getReadLength() : umms.core.alignment.SingleEndAlignment
• getReadMates() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getReadName() : broad.pda.samtools.FilterFastqReads , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getReads() : broad.core.datastructures.JCSCache
• getReadSequence() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getReadSizeDistribution() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getReadString() : umms.core.alignment.SingleEndAlignment.WrapSamRecord
• getRealEigenvalues() : Jama.EigenvalueDecomposition
• getReasonForUnsafe() : broad.pda.seq.alignment.StoredAlignmentStats
• getReducedRepresentation() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getReference() : broad.core.multiplealignment.MultipleAlignment
• getReferenceAnnotation() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getReferenceAnnotations() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getReferenceCoordinateAtPosition() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• getReferenceEnd() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• getReferenceId() : broad.core.multiplealignment.MultipleAlignment
• getReferenceName() : broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• getReferenceNames() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getReferenceStart() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• getReferenceTranscript() : broad.pda.annotation.Locus
• getRefseqGeneName() : broad.core.sequence.Sequence
• getRefseqRnaClassName() : broad.core.sequence.Sequence
• getRefseqSpeciesName() : broad.core.sequence.Sequence
• getRefSequenceCounts() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getRefSequenceLambda() : umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getRefSequenceLength() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getRefSequenceLengths() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel , umms.core.readers.PairedEndReader
• getRegion() : broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , broad.core.sequence.SequenceRegionWindow , broad.pda.feature.genome.Chromosome , broad.pda.rnai.RNAiGeneAnnotation , umms.core.coordinatesystem.TranscriptomeSpace.GeneTree
• getRegionDenominatorRPKM() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getRegionEnd() : broad.core.sequence.SequenceRegion
• getRegionLength() : 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
• getRegionNumeratorRPKM() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getRegionRatio() : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• getRegions() : broad.core.sequence.Sequence , broad.pda.feature.genome.Chromosome , broad.pda.seq.rap.GenomeCommandLineProgram
• getRegionSet() : broad.pda.seq.rap.GenomeCommandLineProgram
• getRegionsMap() : broad.pda.seq.rap.GenomeCommandLineProgram
• getRegionStart() : broad.core.sequence.SequenceRegion
• getRegionTotal() : umms.core.model.score.CountScore
• getRelationship() : broad.core.datastructures.Interval
• getRelativeGenomeLength() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.segmentation.GenomeWithGaps2
• getRelativePositions() : broad.core.primer3.HairpinKmer
• getRelativeWindow() : broad.pda.seq.segmentation.GenomeWithGaps2
• getRepeatClass() : broad.core.annotation.RepeatMaskerAnnotation
• getRepeatFamily() : broad.core.annotation.RepeatMaskerAnnotation
• getRepeatFile() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getRepeatName() : broad.core.annotation.RepeatMaskerAnnotation
• getREST() : broad.pda.geneexpression.ScoreDiffGenes
• getResults() : broad.pda.differentialExpression.RunDifferentialExpression
• getReverseStrand() : umms.core.annotation.Annotation.Strand
• getReverseTargets() : umms.core.alignment.SmatchLike
• getRgb() : broad.core.annotation.BED
• getRight() : broad.pda.geneexpression.clustering.Cluster
• getRightHighInfoStart() : broad.core.motif.PositionWeightMatrix
• getRightNeighbor() : broad.pda.gene.NeighborAnalysis
• getRoot() : broad.core.datastructures.GenericRootedTree< T >
• getRow() : broad.core.datastructures.MatrixWithHeaders , jaligner.Cell , Jama.Matrix
• getRowAnnotations() : broad.pda.datastructures.LocationAwareMatrix
• getRowDescriptions() : broad.core.datastructures.MatrixWithHeaders
• getRowDimension() : Jama.Matrix
• getRowLocationMap() : broad.pda.datastructures.LocationAwareMatrix
• getRowName() : broad.core.datastructures.MatrixWithHeaders
• getRowNames() : broad.core.datastructures.MatrixWithHeaders
• getRownum() : broad.pda.geneexpression.agilent.AgilentProbe
• getRowPackedCopy() : Jama.Matrix
• getRowPosition() : broad.pda.datastructures.LocationAwareMatrix
• getRowTree() : broad.pda.datastructures.LocationAwareMatrix
• getRPK() : umms.core.model.score.CountScore
• getRPKM() : broad.pda.seq.segmentation.GeneScore , umms.core.annotation.Gene , umms.core.model.score.CountScore
• getRPKMConstant() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.segmentation.AlignmentDataModelStats
• getRS8Score() : broad.core.primer3.HairpinKmer
• getS() : Jama.SingularValueDecomposition
• getSAMEnd() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• getSamHeader() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getSampleCoordSpace() : umms.core.model.score.MultiScore
• getSampleCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore , umms.core.model.score.PoissonEnrichmentScore
• getSampleLambda() : umms.core.model.score.PoissonEnrichmentScore
• getSampleName() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• getSampleRegionCount() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.MultiScore
• getSampleRegionTotal() : umms.core.model.score.PoissonEnrichmentScore
• getSampleTotal() : umms.core.model.score.PoissonEnrichmentScore
• getSampleType() : broad.pda.geneexpression.ExpressionExperimentInfo
• getSAMRecordIterator() : broad.pda.samtools.SAMPairedEndFileReader
• getSAMStart() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• getSamString() : broad.pda.samtools.SAMFragmentWriter
• getSAMString() : umms.core.annotation.Gene
• getSaturationSignalValue() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getScaledWindows() : broad.core.siphy.TreeScalerIO
• getScanDistribution() : broad.core.math.PermutationDistribution
• getScanPvalFragmentEndsMaxPositionAllRegionsBam() : broad.pda.seq.clip.Pileup
• getScanPvalFragmentEndsMaxPositionBam() : broad.pda.seq.clip.Pileup
• getScanPvalsFragmentEndPileupsAllRegionsWig() : broad.pda.seq.clip.Pileup
• getScanPvalsFragmentEndPileupsWig() : broad.pda.seq.clip.Pileup
• getScanPvalue() : broad.core.math.PermutationDistribution , broad.pda.seq.segmentation.GeneScore , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.ScanStatisticScore
• getScore() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.Feature , broad.core.annotation.LightweightGenomicAnnotation , broad.core.multiplealignment.MultipleAlignment , broad.core.sequence.SequenceRegion , broad.core.sequence.SequenceRegionWindow , broad.pda.datastructures.Alignments , broad.pda.geneexpression.clustering.Cluster , broad.pda.seq.graph.Path , broad.pda.seq.rap.SkellamScore , jaligner.Alignment , jaligner.Cell , jaligner.matrix.Matrix , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.model.score.AbstractListScore , umms.core.model.score.CountScore , umms.core.model.score.EndInWindowCountScore , umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.StartInWindowCountScore , umms.core.model.score.SumScore , umms.core.model.score.WindowAllScore , umms.core.model.score.WindowScore
• getScoredExons() : broad.pda.gene.GeneWithIsoforms
• getScorePerAlignmentFromCache() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getScores() : broad.pda.datastructures.Alignments , jaligner.matrix.Matrix , umms.core.model.score.AbstractListScore , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.ScanStatisticScore
• getScoreSum() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getScoreWithNoTerminalGaps() : jaligner.Alignment
• getSecondGene() : umms.core.alignment.FeatureSequenceAlignment.UnorderedGenePair
• getSecondMate() : umms.core.alignment.AbstractPairedEndAlignment
• getSentinel() : broad.core.datastructures.IntervalTree< V >
• getSequence() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion , broad.pda.datastructures.Alignments , broad.pda.feature.genome.Chromosome , broad.pda.rnai.RNAiGeneAnnotation , broad.pda.seq.fastq.FastqSequence , jaligner.Sequence , umms.core.annotation.Gene
• getSequence1() : jaligner.Alignment
• getSequence2() : jaligner.Alignment
• getSequenceAnnotationMap() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getSequenceBases() : broad.core.sequence.Sequence
• getSequenceBuilder() : broad.core.sequence.Sequence
• getSequenceDir() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getSequenceForGene() : broad.pda.rnai.ExtractSequence
• getSequenceName() : broad.core.annotation.GFF
• getSequenceNames() : broad.core.sequence.FastaSequenceIO , broad.pda.samtools.SAMPairedEndFileReader , umms.core.readers.PairedEndReader
• getSequenceObject() : umms.core.annotation.Gene
• getSequences() : broad.pda.seq.fastq.FastqParser
• getSequenceUnoriented() : broad.pda.rnai.ExtractSequence
• getSetIsoforms() : broad.pda.annotation.Locus
• getShortArm() : broad.pda.feature.genome.Chromosome
• getShuffledPositions() : broad.pda.seq.clip.Pileup
• getShuffledPositionsAllRegions() : broad.pda.seq.clip.Pileup
• getSignificantGeneSets() : broad.pda.geneexpression.PaGEJava
• getSilhouette() : broad.pda.geneexpression.clustering.Kmeans
• getSimilarity() : jaligner.Alignment
• getSingleReadsSkipped() : broad.pda.samtools.PairedEndReadIterator
• getSingleSampleScanPeaks() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• getSingularValues() : Jama.SingularValueDecomposition
• getSinkVertices() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.scripture.OrientedChromosomeTranscriptGraph
• getSites() : broad.core.motif.meme.MemeMotif
• getSize() : broad.core.sequence.SequenceRegion , broad.pda.seq.graph.Path , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.Gene , umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace , umms.core.feature.GeneWindow
• getSizesFromSAM() : broad.pda.seq.alignment.AlignmentUtils
• getSkellamPvalue() : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• getSkellamPValue() : broad.pda.seq.rap.SkellamScore , umms.core.model.score.WindowAllScore
• getSlider() : broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion , broad.core.sequence.WindowSlider
• getSoftmaskedRegions() : broad.core.sequence.Sequence
• getSortedAndUniqueExons() : umms.core.annotation.Gene
• getSortedNodes() : broad.pda.seq.graph.Path
• getSource() : broad.core.annotation.GFF
• getSourceAnnotations() : umms.core.feature.GeneWindow , umms.core.feature.GenomeWindow , umms.core.feature.Window
• getSourceVertices() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.scripture.OrientedChromosomeTranscriptGraph
• getSpan() : umms.core.annotation.CompoundInterval
• getSpikeInDetectionLimit() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getSpliceConnections() : broad.core.sequence.SequenceRegion , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• getSplicedCount() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• getSplicedReadExons() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getSplicedReads() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getSpliceJunctionCoordinates() : umms.core.annotation.Gene
• getSpliceJunctionCoordinatesTree() : umms.core.annotation.Gene
• getSpliceWeight() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.graph.Path
• getSpliceWeightFactor() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getStandardDeviation() : broad.core.math.EmpiricalDistribution , umms.core.model.score.AbstractListScore
• getStart() : broad.core.annotation.LightweightGenomicAnnotation , broad.core.datastructures.Interval , broad.core.sequence.SequenceRegion , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.graph.Path , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• getStart1() : jaligner.Alignment
• getStart2() : jaligner.Alignment
• getStartCodon() : umms.core.annotation.Gene
• getStartVertex() : broad.pda.seq.graph.Path
• getState() : broad.core.hmm.MarkovModel< T >
• getStates() : broad.core.hmm.MarkovModel< T >
• getStateTransitionMatrix() : broad.core.hmm.MarkovModel< T >
• getStatistic() : broad.pda.enrichment.EnrichmentMetric
• getStepSize() : broad.pda.seq.protection.SampleData
• getStrand() : broad.core.annotation.GFF , broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.model.AlignmentModel
• getString() : umms.core.annotation.Gene
• getStringArg() : broad.core.parser.CommandLineParser
• getStringArray() : broad.core.parser.StringParser
• getStringListArg() : broad.core.parser.CommandLineParser
• getSubAlignment() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• getSubAnnotationFromEnd() : umms.esat.ESAT , umms.esat.ESATDistanceCalculator
• getSubAnnotationFromStart() : umms.esat.ESAT , umms.esat.ESATDistanceCalculator
• getSubAnnotationMidpointWithinAnnotation() : umms.core.utils.AnnotationUtils
• getSubclusters() : broad.pda.geneexpression.clustering.Cluster
• getSubmethod() : broad.pda.enrichment.EnrichmentMetric
• getSubSequence() : broad.core.sequence.Sequence
• getSubsequence() : broad.core.sequence.Sequence
• getSubSequence() : broad.core.sequence.Sequence
• getSubsequence() : broad.core.sequence.Sequence
• getSubSequence() : broad.core.sequence.Sequence
• getSum() : broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , umms.core.model.score.AbstractListScore
• getSummary() : jaligner.Alignment
• getSymbol() : broad.pda.feature.genome.Chromosome
• getTermGenes() : broad.pda.gene.functionalAnnotation
• getTestStatistic() : broad.core.math.FisherCombinedProbabilityTest
• getTestStatisticMatrix() : broad.pda.differentialExpression.DifferentialExpression
• getThickEnd() : broad.core.annotation.BED
• getThickStart() : broad.core.annotation.BED
• getThreePrimeBases() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion
• getTimePoint() : broad.pda.geneexpression.ExpressionExperimentInfo
• getTokens() : broad.core.parser.StringParser
• getTotal() : broad.core.math.CombinationGenerator , umms.core.model.score.CountScore
• getTotalCoverage() : umms.core.annotation.AbstractAnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationCollection< T extends Annotation >
• getTotalDistanceFromNode() : broad.core.siphy.TreeScaler
• getTotalInSources() : broad.core.siphy.TreeScalerIO
• getTotalNumberOffeatures() : broad.pda.geneexpression.agilent.AgilentArrayStats
• getTotalNumberOfMappedReads() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getTotalNumberOfMappedStrandedReads() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getTotalNumberOfReads() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• getTotalNumberOfStrandedReads() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• getTotalObservations() : broad.core.math.EmpiricalDistribution
• getTotalReads() : broad.pda.countreads.FastqLibraryStats , broad.pda.seq.segmentation.AlignmentDataModelStats
• getTrackInfo() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• getTranscribedBase() : broad.core.sequence.TranscribedRegions
• getTranscribedBaseAtBeginningPosition() : broad.core.sequence.TranscribedSequenceComposition
• getTranscriptLength() : umms.core.annotation.Gene
• getTranscriptName() : broad.pda.rnai.RNAiGeneAnnotation
• getTranscriptomeSpace() : broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram , umms.core.coordinatesystem.TranscriptomeSpace
• getTranscripts() : broad.core.primer3.HairpinKmer
• getTranscriptSequence() : broad.pda.rnai.RNAiGeneAnnotation
• getTree() : broad.core.siphy.EvolutionaryModel , broad.core.siphy.EvolutionaryModelParameters
• getType() : jaligner.Sequence
• getU() : Jama.LUDecomposition , Jama.SingularValueDecomposition
• getUn() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getUngappedReferenceIslands() : broad.core.multiplealignment.MultipleAlignment
• getUngappedSequenceReferenceIslands() : broad.core.multiplealignment.MultipleAlignment
• getUngappedSize() : broad.pda.feature.genome.Chromosome
• getUniqueNeighbors() : broad.pda.gene.NeighborsNullModel
• getUniqueRepeatClasses() : broad.core.annotation.RepeatMaskerAnnotationReader
• getUniqueRepeatFamilies() : broad.core.annotation.RepeatMaskerAnnotationReader
• getUniqueRepeatNames() : broad.core.annotation.RepeatMaskerAnnotationReader
• getUnmaskedLength() : umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace
• getUnqComaptibleBetweenAny2Sets() : broad.pda.annotation.Locus
• getUnqComaptibleBetweenSubsets() : broad.pda.annotation.Locus
• getUserDirectory() : jaligner.util.Commons
• getUtr3Counts() : broad.pda.seq.segmentation.GeneCounts
• getUtr5Counts() : broad.pda.seq.segmentation.GeneCounts
• getV() : Jama.EigenvalueDecomposition , Jama.SingularValueDecomposition
• getValidOutgoingEdges() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• getValue1() : broad.core.datastructures.Pair< T1 >
• getValue2() : broad.core.datastructures.Pair< T1 >
• getValues() : broad.core.annotation.GFF , broad.core.datastructures.MatrixWithHeaders
• getVectorEncodedSequence() : broad.core.sequence.Sequence
• getWeight() : broad.core.motif.PositionWeightColumn , broad.pda.seq.graph.Path , broad.pda.seq.segmentation.GenericAlignmentDataModel , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• getWidth() : broad.core.motif.meme.MemeMotif
• getWidths() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• getWindowCount() : broad.pda.seq.protection.SampleData
• getWindowIterator() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• getWindowLength() : umms.core.model.score.BasicScanStatisticScore
• getWindowProcessor() : broad.pda.seq.rap.GenomeScoringProgram , broad.pda.seq.rap.rna.TranscriptomeScoringProgram
• getWindows() : umms.core.annotation.Gene , umms.core.feature.GeneWindow , umms.core.feature.GenomeWindow , umms.core.feature.Window
• getWindowScoreIterator() : broad.pda.seq.rap.SlideAndCalculate
• getWindowScores() : broad.pda.seq.protection.SampleData
• getWindowSize() : broad.pda.seq.protection.SampleData
• getX() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• getZ() : broad.core.math.MannWhitney , broad.core.math.Wilcox2Sample
• getZscore() : broad.core.math.EmpiricalDistribution
• GFF() : broad.core.annotation.GFF
• gffFactory : broad.core.annotation.AnnotationFactoryFactory
• GFFReader() : broad.core.annotation.GFFReader
• GlobalSpliceFilter() : broad.pda.seq.segmentation.GlobalSpliceFilter
• GlobalStats() : broad.pda.geneexpression.GlobalStats
• gotWindowScoresFromFile() : broad.pda.seq.protection.SampleData
• GrabProbes() : broad.pda.differentialExpression.GrabProbes
• GSAProjection() : broad.pda.differentialExpression.GSAProjection
• GSAScoring() : broad.projection.gsa.GSAScoring
• GTFFileParser() : broad.pda.annotation.GTFFileParser
• GTFWrite() : broad.pda.annotation.GTFFileParser