- t -

• takeComplement() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• takeIntersection() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• takeUnion() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.Gene
• testGoodnessOfFit() : broad.core.math.EmpiricalDistribution
• times() : broad.core.datastructures.MatrixWithHeaders , Jama.Matrix
• timesEquals() : Jama.Matrix
• toArray() : jaligner.Sequence
• toBED() : broad.core.annotation.BED , broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.Gene
• toBEDGraph() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• toBEDwithBedScore() : umms.core.annotation.Gene
• toCigar() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• toCollection() : broad.core.datastructures.IntervalTree< V >
• toConsensus() : broad.core.motif.PositionWeightColumn
• toConstituentIntroformMap() : broad.pda.annotation.BEDFileParser
• toConstituentIsoformMap() : broad.pda.annotation.BEDFileParser
• toCufflinksGTF() : umms.core.annotation.Gene
• toCufflinksString() : broad.core.annotation.GFF
• toDBFromAscii() : broad.core.sequence.FastaQualityBinaryIO
• toDoubleArray() : broad.core.math.Statistics
• toDoubleArrayList() : broad.core.math.Statistics
• toFasta() : broad.pda.seq.fastq.FastqSequence
• toFastq() : broad.pda.seq.fastq.FastqSequence
• toFileName() : broad.pda.datastructures.Alignments
• toFilledInGene() : broad.pda.seq.graph.Path
• toGene() : broad.pda.seq.graph.Path
• toGTF() : umms.core.annotation.Gene
• toList() : broad.core.datastructures.IntervalTree< V > , umms.core.annotation.AnnotationList< T extends Annotation >
• toMap() : broad.core.datastructures.MatrixWithHeaders , broad.pda.annotation.BEDFileParser
• toMultipleAlignment() : broad.core.multiplealignment.MAFAlignment
• toNanostring() : broad.pda.rnai.RNAiGeneAnnotation
• toRefSeq() : umms.core.annotation.Gene
• toRNAi() : broad.pda.rnai.RNAiGeneAnnotation
• toSAM() : umms.core.annotation.Gene
• toSAMRecord() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• toShortBED() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• toShortString() : broad.core.annotation.BED , broad.core.annotation.ShortBED
• toString() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.BED , broad.core.annotation.GFF , broad.core.annotation.RepeatMaskerAnnotation , broad.core.annotation.ShortBED , broad.core.motif.PositionWeightColumn , broad.core.motif.SequenceMotif , broad.core.sequence.SequenceRegion , broad.core.siphy.EvolutionaryModelParameters , broad.pda.datastructures.Alignments , broad.pda.enrichment.EnrichmentMetric , broad.pda.gene.GeneWithIsoforms , broad.pda.geneexpression.clustering.Cluster , broad.pda.rnai.RNAiGeneAnnotation , broad.pda.seq.fastq.FastqSequence , broad.pda.seq.graph.Path , broad.pda.seq.rap.SkellamScore , jaligner.Alignment , jaligner.Sequence , Jama.Matrix , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.SingleEndAlignment , umms.core.annotation.Annotation.Strand , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval , umms.core.annotation.Gene , umms.core.annotation.SingleInterval , umms.core.model.score.AbstractListScore , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.CountScore , umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.ScanStatisticScore , umms.core.model.score.WindowAllScore
• toStringForWriting() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• toStringNum() : broad.pda.datastructures.Alignments
• toStringWithScores() : broad.pda.datastructures.Alignments
• toUCSC() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion , broad.pda.datastructures.Alignments , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.Gene
• toUniqueSortedList() : broad.core.math.Statistics
• toWIGString() : broad.core.annotation.BED , broad.core.annotation.ShortBED
• trace() : Jama.Matrix
• TracebackNode() : jaligner.TracebackNode
• track() : broad.core.annotation.AnnotationHandler , broad.pda.datastructures.LocationAwareMatrix
• TranscribedRegions() : broad.core.sequence.TranscribedRegions
• TranscribedSequenceComposition() : broad.core.sequence.TranscribedSequenceComposition
• TranscriptInGenomicSpace() : umms.core.coordinatesystem.TranscriptInGenomicSpace
• TranscriptomeSpace() : umms.core.coordinatesystem.TranscriptomeSpace
• transcriptsNullModel() : broad.pda.gene.transcriptsNullModel
• transcriptToGenomicPosition() : umms.core.annotation.Gene
• translocate() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• transpose() : Jama.Matrix
• TreeScaler() : broad.core.siphy.TreeScaler
• TreeScalerIO() : broad.core.siphy.TreeScalerIO
• trim() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• trimAbsolute() : umms.core.annotation.Gene
• trimBeginning() : broad.pda.seq.fastq.FastqSequence
• trimByInformationContent() : broad.core.motif.PositionWeightMatrix
• trimEndBases() : broad.pda.seq.fastq.FastqSequence
• trimEnds() : broad.pda.seq.fastq.FastqSequence
• trimFirstNBPs() : broad.pda.seq.fastq.FastqSequence
• trimGene() : umms.core.annotation.Gene
• trimGeneEnds() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• trimLinker() : broad.pda.seq.fastq.FastqSequence
• trimMaxContiguous() : broad.pda.seq.protection.SampleData , broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• trimPeak() : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• trimPolyA() : broad.pda.seq.fastq.FastqSequence
• trimStartBases() : broad.pda.seq.fastq.FastqSequence
• tScoresByRow() : broad.core.datastructures.MatrixWithHeaders
• tstat() : broad.core.math.Statistics