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

- h -

• HairpinKmer() : broad.core.primer3.HairpinKmer
• hamming() : broad.core.math.Statistics
• HAS_GREATER_PART : broad.core.datastructures.Interval
• HAS_LESSER_PART : broad.core.datastructures.Interval
• HAS_OVERLAPPING_PART : broad.core.datastructures.Interval
• hasAnnotationThatContains() : umms.core.annotation.AnnotationList< T extends Annotation >
• hasAnnotationThatOverlaps() : umms.core.annotation.AnnotationList< T extends Annotation >
• hasAnOverlappingGene() : umms.core.scripture.BuildScriptureCoordinateSpace
• hasBooleanFlag() : broad.core.parser.CommandLineParser
• hasCDS() : umms.core.annotation.Gene
• hasChromosome() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• hasColumn() : broad.core.datastructures.MatrixWithHeaders
• hasDataForChromosome() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• hasDoubleFlag() : broad.core.parser.CommandLineParser
• hasEntries() : umms.core.alignment.AlignmentPair
• hasFloatFlag() : broad.core.parser.CommandLineParser
• hashCode() : broad.core.annotation.BasicLightweightAnnotation , broad.core.datastructures.Pair< T1 > , broad.core.motif.SequenceMotif , broad.pda.seq.clip.SampleData , broad.pda.seq.graph.Path , broad.pda.seq.protection.SampleData , umms.core.alignment.FeatureSequenceAlignment.UnorderedGenePair , umms.core.alignment.FragmentAlignment , umms.core.alignment.PairedReadAlignment , umms.core.annotation.Gene , umms.core.model.score.CountScore , umms.core.readFilters.SplicedReadFilter
• hasIndel() : umms.core.alignment.AbstractPairedEndAlignment , umms.core.alignment.Alignment , umms.core.alignment.SingleEndAlignment
• hasIndex() : broad.pda.samtools.SAMPairedEndFileReader , umms.core.readers.PairedEndReader
• hasIntFlag() : broad.core.parser.CommandLineParser
• hasMore() : broad.core.math.CombinationGenerator , broad.pda.seq.fastq.FastqSplitterByBarcode
• hasNanostringProbeClasses() : broad.core.datastructures.MatrixWithHeaders
• hasNext() : broad.core.datastructures.IntervalTree< V >.FwdIterator , broad.core.datastructures.IntervalTree< V >.OverlapIterator , broad.core.datastructures.IntervalTree< V >.RevIterator , broad.core.datastructures.JCSCache.JCSNodeIterator , broad.core.datastructures.ReversibleIterator< E > , broad.core.sequence.WindowSlider , broad.pda.samtools.PairedEndReadIterator , broad.pda.samtools.WrappedIterator , broad.pda.seq.fastq.FastqParser , broad.pda.seq.segmentation.GenomeWithGaps , broad.pda.seq.segmentation.WrappedIGVIterator , umms.core.coordinatesystem.ShuffledIterator< T extends Annotation > , umms.core.general.CloseableFilterIterator< T > , umms.core.model.AlignmentModel.FilteredIterator , umms.core.model.AlignmentModel.NodeIterator , umms.core.model.AlignmentModel.WrapAlignmentCountIterator , umms.core.model.JCSAlignmentModel.FilteredIterator , umms.core.model.JCSAlignmentModel.NodeIterator , umms.core.model.JCSAlignmentModel.WrapAlignmentCountIterator , umms.core.model.score.WindowScoreIterator< T extends WindowScore >
• hasNextExon() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• hasOrientation() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• hasOverlapping3PUTR() : broad.pda.gene.GeneWithIsoforms
• hasOverlapping5PUTR() : broad.pda.gene.GeneWithIsoforms
• hasRow() : broad.core.datastructures.MatrixWithHeaders
• hasStringFlag() : broad.core.parser.CommandLineParser
• hasSubClusters() : broad.pda.geneexpression.clustering.Cluster
• hasValue1() : broad.core.datastructures.Pair< T1 >
• hasValue2() : broad.core.datastructures.Pair< T1 >
• HierarchicalClustering() : broad.pda.geneexpression.clustering.HierarchicalClustering
• hochbergPvalueAdjust() : broad.core.math.Statistics
• hypergeometric() : broad.core.math.Statistics
• hypot() : broad.core.math.MathUtil , Jama.util.Maths