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

- i -

• ic() : broad.core.motif.PositionWeightMatrix
• IDENTITY : jaligner.Markups
• identity() : Jama.Matrix
• IGNORE_STRAND : broad.pda.seq.rap.DistanceToBED
• IllegalTreeOperationException() : broad.core.datastructures.IllegalTreeOperationException
• INCLUDE_DUPLICATES : broad.pda.samtools.PairedEndTDF
• IncompleteMethodImplementationException() : umms.core.exception.IncompleteMethodImplementationException
• IncrementScoreIfOverlap() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.pda.annotation.BEDFileParser
• INF : broad.core.sequence.SequenceRegion
• init() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.motif.PositionWeightColumn , broad.pda.seq.segmentation.AlignmentDataModelStats
• initColIndexMaps() : broad.core.datastructures.MatrixWithHeaders
• initFromGene() : umms.core.annotation.Gene
• initFromIGVMatrix() : broad.pda.datastructures.LocationAwareMatrix
• initFromNanostring() : broad.core.datastructures.MatrixWithHeaders
• initFromReader() : broad.core.datastructures.MatrixWithHeaders
• initFromRegularMatrix() : broad.core.datastructures.MatrixWithHeaders
• initGCTFromReader() : broad.core.datastructures.MatrixWithHeaders
• initializeFilterRejectWriters() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• initNameIndexMaps() : broad.core.datastructures.MatrixWithHeaders
• initRegion() : umms.core.model.score.WindowProcessor< S extends WindowScore >.AbstractProcessor< S extends WindowScore > , umms.core.model.score.WindowProcessor< S extends WindowScore >
• initRowDescrIndexMaps() : broad.core.datastructures.MatrixWithHeaders
• initRowIndexMaps() : broad.core.datastructures.MatrixWithHeaders
• INNER_LENGTH : broad.pda.seq.rap.PlotAggregateRegions
• inOrientedDegree() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• INPUT : broad.pda.samtools.FilterPairedReadsByMAQ , broad.pda.samtools.PairedEndTDF , broad.pda.samtools.TrimFastqReads , broad.pda.seq.rap.CalculateCoverageStats , broad.pda.seq.rap.CollectAnnotationEnrichments , broad.pda.seq.rap.CountProbes , broad.pda.seq.rap.ShuffleBAM , broad.pda.seq.rap.ShuffleBED , broad.pda.seq.rap.UnmarkDuplicates
• INPUT_1 : broad.pda.samtools.FilterFastqReads
• INPUT_2 : broad.pda.samtools.FilterFastqReads
• inReversedOrientation() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• insert() : broad.pda.feature.genome.Chromosome , broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• INTER_VERTICAL_SPACING : broad.core.annotation.BasicGenomicAnnotationReader
• intersect() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.annotation.BasicLightweightAnnotation , broad.core.sequence.SequenceRegion , broad.pda.annotation.BEDFileParser , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval , umms.core.annotation.SingleInterval
• IntersectBlocks() : broad.core.annotation.BED
• intersectGeneSets() : broad.pda.gene.GeneTools
• introduceGaps() : broad.core.multiplealignment.MultipleAlignment
• inverse() : Jama.Matrix
• invert() : broad.pda.feature.genome.Chromosome , broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• IS_ADJACENT_AND_EMPTY : broad.core.datastructures.Interval
• IS_LEFT_OVERHANGING_OVERLAPPER : broad.core.datastructures.Interval
• IS_RIGHT_OVERHANGING_OVERLAPPER : broad.core.datastructures.Interval
• IS_STRICTLY_GREATER : broad.core.datastructures.Interval
• IS_STRICTLY_LESS : broad.core.datastructures.Interval
• IS_SUBSET : broad.core.datastructures.Interval
• IS_SUPERSET : broad.core.datastructures.Interval
• isAddToReadName() : broad.pda.seq.fastq.FastqSplitterByBarcode
• isAdjacent() : broad.core.datastructures.Interval
• isAlignmentPaired() : broad.pda.seq.alignment.StoredAlignmentStats
• isAtEnd() : broad.pda.seq.fastq.FastqSplitterByBarcode
• isAutosome() : broad.pda.feature.genome.Chromosome
• isChimera() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• isCodingGene() : umms.core.annotation.Gene
• isColumnNonTrivial() : broad.core.datastructures.MatrixWithHeaders
• isComplete() : umms.core.alignment.AlignmentPair
• isControl() : broad.pda.geneexpression.ExpressionExperimentInfo
• isControlProbe() : broad.pda.geneexpression.agilent.AgilentProbe
• isDiagonal() : Jama.Matrix
• isDirect() : broad.core.annotation.BasicTwoSubjectAnnotation , broad.core.annotation.TwoSubjectAnnotation
• isDuplicate() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• isEmpty() : broad.core.datastructures.IntervalTree< V > , broad.core.datastructures.Pair< T1 > , broad.core.motif.PositionWeightMatrix , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , broad.pda.annotation.BEDFileParser
• isEnough() : broad.core.annotation.GenomicAnnotationFilter< T extends LightweightGenomicAnnotation >
• IsExactOverlappingIsoform() : broad.pda.gene.GeneWithIsoforms
• isExpressed() : broad.pda.seq.clip.GenomeSpaceSampleData , broad.pda.seq.clip.SampleData , broad.pda.seq.protection.GenomeSpaceSampleData , broad.pda.seq.protection.MultiSampleScanPeakCaller , broad.pda.seq.protection.SampleData
• isExpressedInAllControlSamples() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• isFlagged() : broad.pda.geneexpression.agilent.AgilentProbe
• isFlankedBy() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion
• isForwardStrand() : broad.core.sequence.Sequence
• isFullRank() : Jama.QRDecomposition
• isFullyComaptible() : broad.pda.annotation.Locus
• isFullyCompatible() : umms.core.annotation.Gene
• isGap() : broad.core.sequence.Sequence , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• isGenomicSpace() : broad.pda.seq.rap.GenomeCommandLineProgram
• isInAllGaps() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• isInExon() : umms.core.annotation.Gene
• isJnlp() : jaligner.util.Commons
• isMapped() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• isNegativeStrand() : broad.core.sequence.SequenceRegion , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.Gene
• isNegativeStranded() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• isNonsingular() : Jama.LUDecomposition
• isoformMapContains() : umms.core.scripture.BuildScriptureCoordinateSpace
• isOverlapCompatible() : broad.pda.annotation.BEDFileParser
• isPaired() : broad.pda.seq.fastq.FastqSplitterByBarcode , broad.pda.seq.segmentation.AlignmentDataModelStats , umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• isPairedEndFormat() : umms.core.readers.PairedEndReader
• isPartialPolyA() : broad.pda.seq.fastq.FastqSequence
• isPCRLike() : broad.core.primer3.isPCRLike
• isPolyA() : broad.pda.seq.fastq.FastqSequence
• isPositiveStranded() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• isProbeFound() : broad.pda.geneexpression.agilent.AgilentProbe
• isProbeNonUniform() : broad.pda.geneexpression.agilent.AgilentProbe
• isProbePopulationOutlier() : broad.pda.geneexpression.agilent.AgilentProbe
• isProbeWellAboveBackground() : broad.pda.geneexpression.agilent.AgilentProbe
• isProperPair() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• isRefGapped() : broad.core.multiplealignment.MultipleAlignment
• isSafeToLoad() : broad.pda.seq.alignment.StoredAlignmentStats
• isSaturated() : broad.pda.geneexpression.agilent.AgilentProbe
• isSexChromosome() : broad.pda.feature.genome.Chromosome
• isSpanningGap() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• isSPD() : Jama.CholeskyDecomposition
• isStopCodon() : umms.core.annotation.Gene
• isStranded() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• isSymmetric() : Jama.Matrix
• isTerminiCoverageBias() : broad.pda.annotation.Locus
• isToComplex() : broad.pda.seq.graph.Path
• isUnoriented() : broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• isValid() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• isValidWindow() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• iterator() : broad.core.datastructures.IntervalTree< V > , broad.pda.samtools.SAMPairedEndFileReader , broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , umms.core.annotation.AnnotationCollection< T extends Annotation > , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel , umms.core.readers.PairedEndReader
• itr : umms.core.coordinatesystem.ShuffledIterator< T extends Annotation >