Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 123456]

►CAbstractAnnotationCollection
Cumms.core.annotation.AnnotationList< T extends Annotation >
Cumms.core.model.AlignmentModel
Cumms.core.model.JCSAlignmentModel
►Cbroad.core.sequence.AbstractFastaParser
Cbroad.core.sequence.FastaParser
Cbroad.core.sequence.FastaQualityParser
►CAbstractWindowScore
Cbroad.pda.seq.rap.SkellamScore
Cbroad.pda.geneexpression.agilent.AgilentArrayStats
Cbroad.pda.geneexpression.agilent.AgilentProbe
Cbroad.pda.geneexpression.agilent.AgilentToGCT
Cbroad.pda.geneexpression.agilent.AgilentUtils
Cjaligner.Alignment
Cumms.core.model.AlignmentModel.AlignmentCount
Cumms.core.model.JCSAlignmentModel.AlignmentCount
►Cbroad.pda.seq.segmentation.AlignmentDataModel
Cbroad.pda.seq.segmentation.GenericAlignmentDataModel
Cbroad.pda.seq.segmentation.AlignmentDataModelStats
Cbroad.core.multiplealignment.AlignmentExtractor
Cbroad.pda.seq.alignment.AlignmentUtils
Cbroad.core.motif.meme.AMEResultReader
Cumms.core.annotation.AnnotationCollection< T extends Annotation >
Cbroad.pda.countreads.AnnotationCounts
Cbroad.core.annotation.AnnotationFactoryFactory
Cumms.core.annotation.AnnotationFileReader
►Cbroad.core.annotation.AnnotationHandler
Cbroad.pda.datastructures.LocationAwareMatrix
Cbroad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
Cbroad.core.annotation.AnnotationReaderFactory
Cumms.core.utils.AnnotationUtils
Cbroad.core.annotation.AnnotationUtils
Cbroad.core.math.ANOVA
Cbroad.core.siphy.tools.conservation.AverageBranchLength
Cbroad.pda.differentialExpression.BatchNorm
Cbroad.core.siphy.tools.conservation.BatchSubmitEstimateExon
►Cbroad.pda.annotation.BEDFileParser
Cbroad.pda.annotation.GTFFileParser
Cumms.core.scripture.BuildScriptureCoordinateSpace
Cjaligner.Cell
Cbroad.pda.feature.genome.Chromosome
Cbroad.pda.differentialExpression.CisVsTrans
Cbroad.pda.geneexpression.agilent.ClassifyAgilentLincProbes
►CCloneable
►Cbroad.core.annotation.GenomicAnnotation
►Cbroad.core.annotation.BasicGenomicAnnotation
Cbroad.core.annotation.BED
Cbroad.core.annotation.GFF
Cbroad.core.annotation.RepeatMaskerAnnotation
►Cbroad.core.annotation.ShortBED
Cbroad.core.annotation.BEDGraph
Cbroad.pda.datastructures.Alignments
CJama.Matrix
Cbroad.pda.geneexpression.clustering.Cluster
►Cbroad.pda.geneexpression.clustering.ClusterDistanceFunction
Cbroad.pda.geneexpression.clustering.AbsolutePearsonFunction
Cbroad.pda.geneexpression.clustering.EuclideanDistance
Cbroad.pda.geneexpression.clustering.PearsonDistance
Cbroad.core.util.CLUtil
Cbroad.core.util.CollapseByIntersection
Cumms.esat.CollapsedGeneLengths
Cbroad.pda.geneexpression.agilent.CollapseProbesByMinPValue
Cbroad.pda.differentialExpression.CollapseProjections
►CCollectRnaSeqMetrics
Cbroad.pda.seq.rap.rna.CollectRnaSeqMetrics
Cbroad.core.math.CombinationGenerator
Cbroad.core.parser.CommandLineParser
Cjaligner.util.Commons
►CComparable
Cbroad.core.primer3.HairpinKmer
Cbroad.pda.seq.graph.Path
Cumms.core.alignment.FeatureSequenceAlignment.UnorderedGenePair
►Cumms.core.annotation.Annotation
►Cbroad.core.annotation.LightweightGenomicAnnotation
►Cbroad.core.annotation.BasicLightweightAnnotation
Cbroad.core.annotation.BasicGenomicAnnotation
Cbroad.core.annotation.GenomicAnnotation
►Cumms.core.alignment.Alignment
►Cumms.core.alignment.AbstractPairedEndAlignment
Cumms.core.alignment.FragmentAlignment
Cumms.core.alignment.PairedReadAlignment
Cumms.core.alignment.SingleEndAlignment
►Cumms.core.annotation.AbstractAnnotation
►Cumms.core.annotation.BasicAnnotation
Cumms.core.alignment.AbstractPairedEndAlignment
Cumms.core.alignment.SingleEndAlignment
►Cumms.core.annotation.Gene
Cumms.core.feature.GeneWindow
Cumms.core.annotation.PSLRecord
Cumms.core.feature.GenomeWindow
►Cumms.core.feature.Window
Cumms.core.feature.GeneWindow
Cumms.core.feature.GenomeWindow
Cumms.core.annotation.CompoundInterval
Cumms.core.annotation.SingleInterval
►Cumms.core.model.score.CountScore
Cumms.core.model.score.BasicScanStatisticScore
Cumms.core.model.score.BinomialEnrichmentScore
Cumms.core.model.score.MultiScore
Cumms.core.model.score.NewRatioScore
Cumms.core.model.score.PoissonEnrichmentScore
Cumms.core.model.score.RatioScore
Cumms.core.model.score.ScanStatisticScore
Cumms.core.model.score.WindowAllScore
Cumms.core.model.score.EndInWindowCountScore
Cumms.core.model.score.StartInWindowCountScore
Cbroad.core.motif.misc.ComputeConservedMotifs
Cbroad.pda.geneexpression.clustering.ComputeCorrelationOfReplicates
Cbroad.pda.seq.chip.ComputeEnrichments
Cbroad.core.math.ComputeFDR
Cbroad.pda.geneexpression.ComputeHypergeomtricEnrichment
Cbroad.core.siphy.tools.conservation.ComputeKmersForRegion
Cbroad.core.siphy.tools.conservation.ComputeMaxPercentileOfElements
Cbroad.core.primer3.ComputeMIRScore
Cbroad.core.primer3.ComputeOriginalScore
Cbroad.core.siphy.tools.conservation.ComputePercentageOfKmers
Cumms.core.scripture.statistics.ConnectDisconnectedTranscripts
Cbroad.core.siphy.ConservationUtils
Cbroad.core.siphy.ConservedPWMScanner
Cbroad.pda.seq.segmentation.ContinuousDataAlignmentModel
Cbroad.pda.differentialExpression.ConvertToDiscreteMatrix
►Cumms.core.coordinatesystem.CoordinateSpace
Cumms.core.coordinatesystem.GenomicSpace
Cumms.core.coordinatesystem.MaskedGenomicSpace
Cumms.core.coordinatesystem.TranscriptInGenomicSpace
Cumms.core.coordinatesystem.TranscriptomeSpace
Cbroad.pda.geneexpression.agilent.CorrelationAgilentNanostring
Cbroad.pda.geneexpression.agilent.CorrelationBetweenReplicates
Cbroad.pda.geneexpression.clustering.CorrelationMatrix
Cbroad.pda.geneexpression.CountNums
Cbroad.core.primer3.CrossJunctionPCRDesigner
Cbroad.projection.gsa.DefineGeneSignatures
Cbroad.pda.seq.segmentation.DefineSourceAndSinkFromPairedEnds
Cbroad.pda.differentialExpression.DifferentialExpression
Cbroad.pda.differentialExpression.DifferentialScoring
Cjaligner.Directions
Cbroad.pda.feature.genome.DirectoryInstalledGenomeAssembly
Cbroad.core.math.Distribution
Cbroad.pda.seq.graph.ChromosomeWithBubblesJGraphT.EdgeSourceType
Cbroad.core.math.EmpiricalDistribution
Cbroad.pda.enrichment.EnrichmentMetric
Cbroad.pda.enrichment.EnrichmentUtils
Cumms.esat.ESAT
Cumms.esat.ESATDistanceCalculator
Cbroad.core.siphy.tools.conservation.EstimateOmegaPerExon
Cbroad.core.siphy.EvolutionaryModel
Cbroad.core.siphy.EvolutionaryModelParameters
►CException
Cbroad.core.datastructures.IllegalTreeOperationException
Cbroad.core.hmm.BadModelException
Cbroad.core.motif.SearchException
Cbroad.core.primer3.Primer3Exception
Cbroad.core.siphy.UnableToFitException
Cjaligner.matrix.MatrixLoaderException
Cjaligner.util.SequenceParserException
Cumms.core.alignment.ChromosomeInconsistencyException
Cumms.core.exception.IncompleteMethodImplementationException
Cbroad.pda.geneexpression.ExpressionExperimentInfo
Cbroad.projection.gsa.ExtractGenes
Cbroad.core.sequence.Extractor
Cbroad.pda.geneexpression.agilent.ExtractSamplesAndLabel
Cbroad.pda.rnai.ExtractSequence
►CFactory
Cbroad.core.annotation.AnnotationFactory< T extends LightweightGenomicAnnotation >
Cumms.core.general.TabbedReader.Factory< T >
Cbroad.pda.seq.clip.FastaExtendPeaks
►Cbroad.core.sequence.FastaHandler
Cbroad.core.sequence.FastaQualityHandler
Cbroad.core.sequence.FastaQualityBinaryIO
Cbroad.core.sequence.FastaQualityIndex
Cbroad.core.sequence.FastaSequenceIO
Cbroad.pda.countreads.FastqLibraryStats
Cbroad.pda.seq.fastq.FastqSequence
Cbroad.pda.seq.fastq.FastqSplitterByBarcode
Cbroad.core.math.FDRDistribution
►Cbroad.core.annotation.Feature
Cbroad.core.annotation.GenomicAnnotation
Cumms.core.alignment.FeatureSequenceAlignment
Cbroad.pda.geneexpression.FilterGCT
Cbroad.pda.geneexpression.FilterGCTFile
Cbroad.pda.geneexpression.agilent.FilterMatrixByMinCutoff
Cbroad.pda.seq.chip.FindDiffrentialEnrichedRegions
Cbroad.pda.rap.misc.FindEnrichedDepletedRegions
Cbroad.pda.geneexpression.agilent.FindProbesForGeneSet
Cbroad.core.math.FisherCombinedProbabilityTest
Cbroad.core.siphy.Fit
Cbroad.pda.differentialExpression.FixedControlDifferentialExpression
Cbroad.pda.differentialExpression.FoldSignificance
►Cjaligner.formats.Format
Cjaligner.formats.CLUSTAL
Cjaligner.formats.FASTA
Cjaligner.formats.Pair
Cjaligner.formats.FormatFactory
Cbroad.pda.gene.functionalAnnotation
Cbroad.pda.differentialExpression.FWERDistribution
Cbroad.pda.seq.segmentation.GeneCounts
Cbroad.pda.geneexpression.geneExpUtils
Cbroad.core.datastructures.GenericRootedTree< T >
Cbroad.projection.gsa.GeneSetEnrichment
Cbroad.core.overlaputils.GeneSetIntersect
Cbroad.pda.gene.GeneTools
Cumms.core.coordinatesystem.TranscriptomeSpace.GeneTree
Cbroad.pda.seq.segmentation.GenomeWithGaps
Cbroad.pda.seq.segmentation.GenomeWithGaps2
Cbroad.core.annotation.GenomicAnnotationFilter< T extends LightweightGenomicAnnotation >
Cbroad.pda.seq.segmentation.GlobalSpliceFilter
Cbroad.pda.geneexpression.GlobalStats
Cbroad.core.util.GMTParser
Cbroad.pda.differentialExpression.GrabProbes
Cbroad.pda.geneexpression.GrabSpecificColumns
Cbroad.pda.differentialExpression.GSAProjection
Cbroad.projection.gsa.GSAScoring
Cbroad.projection.gsa.GsaUtils
Cbroad.pda.geneexpression.clustering.HierarchicalClustering
Cbroad.core.datastructures.Interval
Cbroad.core.datastructures.IntervalTree< V >
Cbroad.core.primer3.isPCRLike
►CIterable
Cumms.core.annotation.AnnotationList< T extends Annotation >
Cbroad.core.datastructures.JCSCache
Cbroad.pda.geneexpression.clustering.Kmeans
Cbroad.core.math.KSTest
Cbroad.pda.annotation.Locus
Cbroad.core.math.Loess
Cbroad.pda.geneexpression.agilent.MakeCLSFiles
Cbroad.pda.geneexpression.agilent.MakeCLSFromDescription
Cbroad.pda.differentialExpression.MakePositionalGeneSets
Cbroad.core.math.MannWhitney
Cbroad.core.math.MannWhitneyPermutations
Cbroad.core.hmm.MarkovModel< T >
Cbroad.core.hmm.MarkovState< T >
Cjaligner.Markups
CJama.util.Maths
Cbroad.core.math.MathUtil
Cjaligner.matrix.MatrixGenerator
►Cbroad.core.datastructures.MatrixWithHeaders
Cbroad.pda.datastructures.LocationAwareMatrix
Cbroad.core.datastructures.MatrixWithHeaderUtils
Cbroad.core.annotation.MaximumContiguousSubsequence
Cbroad.core.motif.meme.MemeMotif
Cbroad.core.motif.meme.MemeResultReader
Cbroad.pda.differentialExpression.MergeGSEAOutputIntoMatrix
►Cbroad.core.multiplealignment.MultipleAlignment
Cbroad.core.multiplealignment.MAFAlignment
Cbroad.core.multiplealignment.MultipleAlignmentFactory
►Cbroad.core.multiplealignment.MultipleAlignmentIO
Cbroad.core.multiplealignment.FastaMultipleAlignmentIO
Cbroad.core.multiplealignment.MAFIO
Cbroad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO
Cbroad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO
Cbroad.core.multiplealignment.MultipleAlignmentIOFactory
►Cbroad.pda.seq.protection.MultiSampleScanPeakCaller
Cbroad.pda.seq.protection.BatchedMultiSampleScanPeakCaller
Cjaligner.NeedlemanWunsch
Cjaligner.NeedlemanWunschGotoh
Cbroad.pda.gene.NeighborAnalysis
Cbroad.pda.gene.NeighborsNullModel
Cbroad.pda.geneexpression.PaGEJava
Cbroad.core.datastructures.Pair< T1 >
Cumms.core.alignment.PairedEndAlignmentFactory
Cumms.core.readers.PairedEndReader
Cumms.core.writers.PairedEndWriter
Cbroad.core.util.ParseGCTFile
Cbroad.pda.seq.chip.PeakFilter
Cbroad.core.math.PermutationDistribution
Cbroad.pda.differentialExpression.Permutations
Cbroad.core.siphy.PhastconsReader
Cbroad.pda.seq.clip.Pileup
Cbroad.core.motif.PositionWeightColumn
Cbroad.core.motif.PositionWeightMatrixIO
Cbroad.core.siphy.PositionWeightMatrixModel
Cbroad.pda.seq.segmentation.PrecomputeDataAlignmentStats
Cumms.core.general.Predicates
Cbroad.pda.geneexpression.PreprocessDataSet
Cbroad.core.primer3.Primer3PickingSummary
Cbroad.core.primer3.Primer3PrimerPickingResult
Cbroad.core.primer3.PrimerUtils
Cbroad.pda.geneexpression.agilent.analysis.ProcessDataset
Cbroad.pda.tools.PSLXToSAM
Cbroad.core.motif.PWMUtils
Cbroad.pda.geneexpression.agilent.QCAgilentResults
Cbroad.pda.geneexpression.clustering.RankOrder
Cbroad.pda.seq.rap.RAPPeakCaller
Cbroad.pda.seq.segmentation.ReadCountNormalizer
Cbroad.pda.seq.segmentation.ReadFilter< T >
Cbroad.pda.seq.protection.ReadSimulator
Cbroad.pda.seq.protection.ReadSimulator2
Cbroad.pda.seq.segmentation.utils.ReconstructionComparer
Cbroad.core.primer3.RestrictionEnzyme
Cbroad.pda.rnai.RNAiGeneAnnotation
Cbroad.pda.differentialExpression.RunAllGSEABatch
Cbroad.pda.differentialExpression.RunDifferentialExpression
Cbroad.pda.differentialExpression.RunGSEA
►CRuntimeException
Cbroad.core.error.ParseException
Cumms.core.coordinatesystem.AnnotationOutOfBoundsException
Cumms.core.coordinatesystem.PermutationNotFoundException
Cumms.core.exception.RuntimeIOException
Cbroad.pda.differentialExpression.RunTimeSeries
Cbroad.pda.samtools.SAMFragmentWriter
►Cbroad.pda.seq.protection.SampleData
Cbroad.pda.seq.protection.GenomeSpaceSampleData
►Cbroad.pda.seq.clip.SampleData
Cbroad.pda.seq.clip.GenomeSpaceSampleData
Cbroad.core.siphy.ScaledWindowParserListener
Cbroad.core.math.ScanStatistics
Cbroad.pda.geneexpression.ScoreDiffGenes
Cbroad.core.motif.misc.ScoreMotifInstances
►Cbroad.core.sequence.Sequence
Cbroad.core.sequence.SequenceRegion
►Cbroad.core.motif.SequenceMotif
Cbroad.core.motif.SequenceMotifCluster
Cjaligner.util.SequenceParser
Cbroad.core.sequence.SequenceRegionWindow
Cbroad.core.sequence.SequenceUtils
►CSerializable
CJama.CholeskyDecomposition
CJama.EigenvalueDecomposition
CJama.LUDecomposition
CJama.Matrix
CJama.QRDecomposition
CJama.SingularValueDecomposition
Cumms.core.alignment.AbstractPairedEndAlignment
Cumms.core.alignment.SingleEndAlignment
Cumms.core.alignment.SingleEndAlignment.WrapSamRecord
Cumms.core.annotation.BasicAnnotation
Cumms.core.annotation.CompoundInterval
Cumms.core.annotation.SingleInterval
Cumms.core.alignment.SmatchLike
Cumms.core.alignment.SmithWatermanAlignment
Cjaligner.SmithWatermanGotoh
Cbroad.pda.seq.fastq.SplitAndTrimIndex
Cbroad.pda.differentialExpression.SplitByName
Cbroad.pda.seq.fastq.SplitFastqByIndex
Cbroad.core.siphy.tools.conservation.SplitFile
Cbroad.core.siphy.StationaryDistributionIO
Cbroad.core.math.Statistics
Cbroad.pda.seq.alignment.StoredAlignmentStats
Cumms.core.annotation.Annotation.Strand
Cbroad.core.parser.StringParser
Cumms.core.general.TabbedReader
Cjaligner.TracebackNode
Cbroad.core.sequence.TranscribedRegions
Cbroad.core.sequence.TranscribedSequenceComposition
Cbroad.pda.gene.transcriptsNullModel
Cbroad.core.siphy.TreeScaler
Cbroad.core.siphy.TreeScalerIO
Cbroad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
►Cbroad.core.annotation.TwoSubjectAnnotation
Cbroad.core.annotation.BasicTwoSubjectAnnotation
Cbroad.core.math.UnfairDie
Cbroad.core.math.Wilcox2Sample
Cumms.core.model.score.WindowProcessor< S extends WindowScore >
►Cumms.core.model.score.WindowScore
►Cumms.core.model.score.WindowScore.AbstractWindowScore
►Cumms.core.model.score.AbstractListScore
Cumms.core.model.score.CoverageScore
Cumms.core.model.score.LengthScore
Cumms.core.model.score.SumScore
Cumms.core.model.score.CountScore
Cumms.core.model.score.EndInWindowCountScore
Cumms.core.model.score.StartInWindowCountScore
Cbroad.pda.seq.protection.WindowScores
►CAlignmentQueryReader
Cbroad.pda.samtools.SAMPairedEndFileReader
►CAnnotation
Cbroad.core.sequence.SequenceRegion
►CAnnotationCollection
Cumms.core.annotation.AbstractAnnotationCollection< T extends Annotation >
►CAnnotationReader
Cbroad.core.annotation.BasicAnnotationReader
Cbroad.core.annotation.BasicGenomicAnnotationReader
Cbroad.core.annotation.BEDGraphReader
Cbroad.core.annotation.BEDReader
Cbroad.core.annotation.GFFReader
Cbroad.core.annotation.RepeatMaskerAnnotationReader
Cbroad.core.annotation.ShortBEDReader
Cbroad.pda.datastructures.AlignmentsReader
►CArrayList
Cbroad.core.motif.PositionWeightMatrix
►CBasicAnnotation
Cbroad.core.annotation.BasicLightweightAnnotation
►CCloseableIterator
Cbroad.core.datastructures.JCSCache.JCSNodeIterator
Cbroad.pda.samtools.PairedEndReadIterator
Cbroad.pda.samtools.WrappedIterator
Cbroad.pda.seq.segmentation.WrappedIGVIterator
Cumms.core.coordinatesystem.ShuffledIterator< T extends Annotation >
Cumms.core.general.CloseableFilterIterator< T >
Cumms.core.model.AlignmentModel.FilteredIterator
Cumms.core.model.AlignmentModel.NodeIterator
Cumms.core.model.AlignmentModel.WrapAlignmentCountIterator
Cumms.core.model.JCSAlignmentModel.FilteredIterator
Cumms.core.model.JCSAlignmentModel.NodeIterator
Cumms.core.model.JCSAlignmentModel.WrapAlignmentCountIterator
Cumms.core.model.score.WindowScoreIterator< T extends WindowScore >
►CClusterable
Cbroad.core.motif.PositionWeightMatrix
►CCommandLineProgram
Cbroad.pda.samtools.FilterFastqReads
Cbroad.pda.samtools.FilterPairedReadsByMAQ
Cbroad.pda.samtools.PairedEndTDF
Cbroad.pda.samtools.TrimFastqReads
Cbroad.pda.seq.rap.CalculateCoverageStats
Cbroad.pda.seq.rap.CountProbes
Cbroad.pda.seq.rap.DistanceToBED
►Cbroad.pda.seq.rap.GenomeCommandLineProgram
Cbroad.pda.seq.rap.BuildRatioNullDistribution
Cbroad.pda.seq.rap.CollectAnnotationEnrichments
Cbroad.pda.seq.rap.GCContent
►Cbroad.pda.seq.rap.GenomeScoringProgram
Cbroad.pda.seq.rap.CountReads
Cbroad.pda.seq.rap.PlotAggregateRegions
Cbroad.pda.seq.rap.SlideAndCalculate
Cbroad.pda.seq.rap.SlideAndCount
Cbroad.pda.seq.rap.RatioPermutationPeakCaller
►Cbroad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
►Cbroad.pda.seq.rap.rna.TranscriptomeScoringProgram
Cbroad.pda.seq.rap.rna.CountReads
Cbroad.pda.seq.rap.ShuffleBAM
Cbroad.pda.seq.rap.ShuffleBED
Cbroad.pda.seq.rap.SkellamKLPeakCaller
Cbroad.pda.seq.rap.UnmarkDuplicates
►CComparator
Cbroad.core.util.ChromosomeStringComparator
Cjaligner.matrix.MatricesCompartor
►CDefaultDirectedGraph
Cbroad.pda.seq.graph.ChromosomeWithBubblesJGraphT
►CDefaultDirectedWeightedGraph
Cumms.core.scripture.OrientedChromosomeTranscriptGraph
►CGene
Cbroad.pda.gene.GeneWithIsoforms
Cbroad.pda.seq.segmentation.GeneScore
►CGraphPath
Cbroad.pda.seq.graph.Path
►CIterator
Cbroad.core.datastructures.IntervalTree< V >.FwdIterator
Cbroad.core.datastructures.IntervalTree< V >.OverlapIterator
Cbroad.core.datastructures.IntervalTree< V >.RevIterator
Cbroad.core.datastructures.ReversibleIterator< E >
Cbroad.core.sequence.WindowSlider
Cbroad.pda.seq.fastq.FastqParser
►CMarkovModel
Cbroad.core.siphy.PiHMM
►CPair
Cumms.core.alignment.AlignmentPair
►CPredicate
Cnextgen.core.readFilters.GenomicSpanFilter
Cnextgen.core.readFilters.PairedAndProperFilter
Cnextgen.core.readFilters.ReadsToReconstructFilter
Cumms.core.annotation.filter.FullyContainedFilter
Cumms.core.annotation.filter.OverlapFilter
Cumms.core.readFilters.MappingQualityFilter
Cumms.core.readFilters.PairedEndFilter
Cumms.core.readFilters.PCRDuplicateFilter
Cumms.core.readFilters.ReadEndsInFilter
Cumms.core.readFilters.ReadStartsInFilter
Cumms.core.readFilters.SameOrientationFilter
Cumms.core.readFilters.SplicedReadFilter
Cumms.core.readFilters.UniqueMappedReadsFilter
►CSerializable
Cjaligner.matrix.Matrix
Cjaligner.Sequence
►CWindowProcessor
Cumms.core.model.score.WindowProcessor< S extends WindowScore >.AbstractProcessor< S extends WindowScore >