Class Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | W

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

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | W