All Classes

AbstractAlignmentBlock AbstractAlignmentSequence AbstractMAFMultipleAlignment AbstractStreamDataSource AbstractUnivariateStatistic AbstractWiggle Accumulator Alignment AlignmentAnnotation ALNParser AminoAcidMapping AnnotationEvent ArrayIterable ArrayIterator BAMreads BasicScore BasicShortRead BBCompressionUtils BBFileHeader BBFileReader BBTotalSummaryBlock BBZoomLevelFormat BBZoomLevelHeader BBZoomLevels BEDCodec BedFeature BedGraphParser BEDParser BEDTools BEDWrapper BigBedDataBlock BigBedIterator BigWigData BigWigDataBlock BigWigDataSource BigWigIterator BigWigSection BigWigSectionHeader BigWigSectionHeader.WigItemType BinaryBlob BinaryCodec BlastM8Parser BPTree BPTreeChildNode BPTreeChildNodeItem BPTreeHeader BPTreeLeafNode BPTreeLeafNodeItem BPTreeNode BroadSolexa BufferedByteWriter CachedURLSource CachingQueryReader ChangeEvent Cleaner Codec CompressionUtils Constants ConvertBAM2TDF DAS DAS.EntryPoint Data DataKey DataSource DataSource DataSourceFactory DataSourceFactory.Sources DensityEstimate Description DiskArrayWiggle DoubleArrayList DoublePile DSN DualPivotQuicksort EMBLParser EmptyIterator EmptyIterator Entry EntrySet EntrySetAnnotation Faidx FaidxData FaidxIndex FaixDataIterable FastaParser Feature Feature FeatureAnnotation FeatureEvent FeatureWrapper FileSource FindPeaksParser Flat3Map FloatArrayList FloatArrayWiggle GenbankParser GeneMarkParser GFF3Parser GFFCodec GFFWrapper Graph HashFunctions HashingStrategy IdentityHashingStrategy IndexedFastaDataSource IndexedFeatureFile IndexedMAF IndexedMAFDataSource IndexManager IntArrayList LazyAlignmentBlock LazyAlignmentSequence LineBlockCompressedInputStream ListIterable ListIterator LittleEndianInputStream Located LocatedListIterable LocatedListIterator Location Locator LocusScore LRUCache MafixFactory MAFMemoryMultipleAlignment MAFParser MapViewParser MaqSNPParser MemoryAlignmentBlock MemoryAlignmentSequence MemoryFeatureAnnotation MemoryListData MemoryReadSet MemorySequence MultiPile Pair64 Parser ParserTools Percentile Pile PileTools PileupCodec PileupWrapper PrimeFinder PTTParser Query ReadDetailPile ReadFailedException ReadGroup ReferenceSequence RPChromosomeRegion RPTree RPTreeChildNode RPTreeChildNodeItem RPTreeHeader RPTreeLeafNode RPTreeLeafNodeItem RPTreeNode RuntimeEOFException RuntimeIOException SAMDataSource SaveFailedException SeekableFileCachedHTTPStream SeekableStreamUtils Sequence SequenceTools SequenceTranslator ShortRead ShortReadTools SinglePile SIPHTParser SourceCache SSL Strand StringKey StringUtils SubSequence SWigCodec SWigWrapper SyntenicAnnotation SyntenicBlock SyntenicParser TabixLine TabixReader TabixWrapper TabixWriter TabixWriter.Conf TAdvancingIterator TBLParser TByteFunction TByteProcedure TCharFunction TCharProcedure TDFBedTile TDFData TDFDataset TDFDataset.DataType TDFDataSource TDFEntity TDFFixedTile TDFGroup TDFReader TDFTile TDFTile.Type TDFTools TDFUtils TDFVaryTile TDFWriter TDoubleCollection TDoubleFunction TDoubleIterator TDoubleProcedure TFloatCollection TFloatFunction TFloatIterator TFloatProcedure THash THashIterator THashMap THashPrimitiveIterator THashSet TileFactory TileManager TIntCollection TIntFloatHash TIntFloatHashMap TIntFloatIterator TIntFloatMap TIntFloatProcedure TIntFunction TIntHash TIntHashSet TIntIterator TIntProcedure TIntSet TIterator TLongCollection TLongDoubleHash TLongDoubleHashMap TLongDoubleIterator TLongDoubleMap TLongDoubleProcedure TLongFunction TLongHash TLongHashSet TLongIterator TLongProcedure TLongSet TObjectFunction TObjectHash TObjectHashIterator TObjectObjectProcedure TObjectProcedure ToObjectArrayProceedure TPrimitiveHash TPrimitiveIterator TransTermHPParser TRNAscanParser TroveArrayWiggle TShortCollection TShortFunction TShortIterator TShortProcedure Type UnsupportedException URLSource WiggleParser WigItem WindowFunction ZoomDataBlock ZoomDataRecord ZoomLevelIterator ZoomLevelIterator.EmptyIterator