Hierarchy For All Packages

Package Hierarchies:

gnu.trove, gnu.trove.function, gnu.trove.impl, gnu.trove.impl.hash, gnu.trove.iterator, gnu.trove.iterator.hash, gnu.trove.map, gnu.trove.map.hash, gnu.trove.procedure, gnu.trove.procedure.array, gnu.trove.set, gnu.trove.set.hash, gnu.trove.strategy, net.sf.jannot, net.sf.jannot.alignment, net.sf.jannot.alignment.maf, net.sf.jannot.alignment.mfa, net.sf.jannot.bigwig, net.sf.jannot.event, net.sf.jannot.exception, net.sf.jannot.indexing, net.sf.jannot.mafix, net.sf.jannot.parser, net.sf.jannot.parser.software, net.sf.jannot.picard, net.sf.jannot.pileup, net.sf.jannot.refseq, net.sf.jannot.shortread, net.sf.jannot.source, net.sf.jannot.source.cache, net.sf.jannot.source.das, net.sf.jannot.tabix, net.sf.jannot.tabix.codec, net.sf.jannot.tdf, net.sf.jannot.utils, net.sf.jannot.wiggle, org.apache.commons.collections.iterators, org.apache.commons.collections.map, org.apache.commons.math.stat, org.broad, org.broad.igv.bbfile, org.broad.igv.data, org.broad.igv.feature, org.broad.igv.tdf, org.broad.igv.tools, org.broad.igv.track, org.broad.igv.util, org.broad.igv.util.collections, org.broad.tools, org.broad.tribble

Class Hierarchy

• java.lang.Object
  • net.sf.jannot.alignment.maf.AbstractAlignmentBlock (implements java.lang.Comparable<T>, java.lang.Iterable<T>, net.sf.jannot.Located)
    • net.sf.jannot.alignment.maf.LazyAlignmentBlock
    • net.sf.jannot.alignment.maf.MemoryAlignmentBlock
  • net.sf.jannot.alignment.maf.AbstractAlignmentSequence
    • net.sf.jannot.alignment.maf.LazyAlignmentSequence
    • net.sf.jannot.alignment.maf.MemoryAlignmentSequence
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • net.sf.jannot.MemoryListData<T> (implements net.sf.jannot.Data<K>)
          • net.sf.jannot.alignment.mfa.AlignmentAnnotation (implements net.sf.jannot.Data<K>)
          • net.sf.jannot.MemoryFeatureAnnotation (implements net.sf.jannot.FeatureAnnotation)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • gnu.trove.map.hash.THashMap.EntryView
      • gnu.trove.map.hash.THashMap.KeyView
      • gnu.trove.map.hash.THashMap.ValueView
  • net.sf.jannot.alignment.maf.AbstractMAFMultipleAlignment (implements net.sf.jannot.Data<K>)
    • net.sf.jannot.mafix.IndexedMAF
    • net.sf.jannot.alignment.maf.MAFMemoryMultipleAlignment
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • java.util.LinkedHashMap<K,V> (implements java.util.Map<K,V>)
        • org.broad.LRUCache<K,V>
  • org.apache.commons.math.stat.AbstractUnivariateStatistic (implements java.io.Serializable)
    • org.apache.commons.math.stat.Percentile (implements java.io.Serializable)
  • net.sf.jannot.wiggle.AbstractWiggle (implements net.sf.jannot.wiggle.Graph, net.sf.jannot.wiggle.Query)
    • net.sf.jannot.wiggle.DiskArrayWiggle (implements java.lang.Iterable<T>)
    • net.sf.jannot.wiggle.FloatArrayWiggle
    • net.sf.jannot.wiggle.TroveArrayWiggle (implements java.lang.Iterable<T>)
  • org.broad.igv.tools.Accumulator
  • net.sf.jannot.alignment.mfa.Alignment (implements net.sf.jannot.Located)
  • net.sf.jannot.event.AnnotationEvent (implements net.sf.jannot.event.ChangeEvent)
  • net.sf.jannot.utils.ArrayIterable<T> (implements java.lang.Iterable<T>)
  • net.sf.jannot.utils.ArrayIterator<T> (implements java.util.Iterator<E>)
  • org.broad.igv.data.BasicScore (implements org.broad.igv.feature.LocusScore)
  • org.broad.igv.bbfile.BBCompressionUtils
  • org.broad.igv.bbfile.BBFileHeader
  • org.broad.igv.bbfile.BBFileReader
  • org.broad.igv.bbfile.BBTotalSummaryBlock
  • org.broad.igv.bbfile.BBZoomLevelFormat
  • org.broad.igv.bbfile.BBZoomLevelHeader
  • org.broad.igv.bbfile.BBZoomLevels
  • org.broad.igv.bbfile.BedFeature
  • net.sf.jannot.parser.BEDTools
  • org.broad.igv.bbfile.BigBedDataBlock
  • org.broad.igv.bbfile.BigBedIterator (implements java.util.Iterator<E>)
  • net.sf.jannot.bigwig.BigWigData (implements net.sf.jannot.Data<K>)
  • org.broad.igv.bbfile.BigWigDataBlock
  • org.broad.igv.bbfile.BigWigIterator (implements java.util.Iterator<E>)
  • org.broad.igv.bbfile.BigWigSection
  • org.broad.igv.bbfile.BigWigSectionHeader
  • net.sf.jannot.picard.BinaryBlob
  • net.sf.jannot.tabix.BinaryCodec
  • org.broad.igv.bbfile.BPTree
  • org.broad.igv.bbfile.BPTreeChildNode (implements org.broad.igv.bbfile.BPTreeNode)
  • org.broad.igv.bbfile.BPTreeChildNodeItem
  • org.broad.igv.bbfile.BPTreeHeader
  • org.broad.igv.bbfile.BPTreeLeafNode (implements org.broad.igv.bbfile.BPTreeNode)
  • org.broad.igv.bbfile.BPTreeLeafNodeItem
  • org.broad.igv.tdf.BufferedByteWriter
  • net.sf.jannot.shortread.CachingQueryReader
  • net.sf.jannot.shortread.CachingQueryReader.TiledIterator (implements net.sf.samtools.util.CloseableIterator<T>)
  • net.sf.jannot.Cleaner
  • net.sf.jannot.tabix.codec.Codec<T> (implements java.lang.Iterable<T>)
    • net.sf.jannot.tabix.codec.BEDCodec
    • net.sf.jannot.tabix.codec.GFFCodec
    • net.sf.jannot.tabix.codec.PileupCodec
    • net.sf.jannot.tabix.codec.SWigCodec
  • org.broad.igv.util.CompressionUtils
  • gnu.trove.impl.Constants
  • org.broad.tools.ConvertBAM2TDF
  • net.sf.jannot.source.das.DAS.EntryPoint
  • net.sf.jannot.source.DataSource (implements java.lang.Comparable<T>)
    • net.sf.jannot.source.AbstractStreamDataSource
      • net.sf.jannot.source.FileSource
      • net.sf.jannot.source.URLSource
        • net.sf.jannot.source.cache.CachedURLSource
    • net.sf.jannot.bigwig.BigWigDataSource
    • net.sf.jannot.source.das.DAS
    • net.sf.jannot.source.IndexedFastaDataSource
    • net.sf.jannot.tabix.IndexedFeatureFile
    • net.sf.jannot.source.IndexedMAFDataSource
    • net.sf.jannot.source.SAMDataSource
    • net.sf.jannot.tdf.TDFDataSource
  • net.sf.jannot.source.DataSourceFactory
  • net.sf.jannot.Description
  • org.broad.igv.util.collections.DoubleArrayList
  • net.sf.jannot.source.das.DSN
  • gnu.trove.impl.DualPivotQuicksort
  • net.sf.jannot.shortread.EmptyIterator<T> (implements net.sf.samtools.util.CloseableIterator<T>)
  • org.apache.commons.collections.iterators.EmptyIterator
  • net.sf.jannot.Entry (implements java.lang.Comparable<T>, java.lang.Iterable<T>)
  • net.sf.jannot.EntrySet (implements java.lang.Iterable<T>)
  • net.sf.jannot.EntrySetAnnotation<T> (implements java.lang.Iterable<T>)
    • net.sf.jannot.SyntenicAnnotation
  • net.sf.jannot.indexing.Faidx
  • net.sf.jannot.refseq.FaidxIndex
  • net.sf.jannot.refseq.FaixDataIterable (implements java.lang.Iterable<T>)
  • net.sf.jannot.Feature (implements java.lang.Comparable<T>, net.sf.jannot.Located)
  • net.sf.jannot.event.FeatureEvent (implements net.sf.jannot.event.ChangeEvent)
  • org.apache.commons.collections.map.Flat3Map<K,V> (implements java.util.Map<K,V>)
  • org.broad.igv.util.collections.FloatArrayList
  • gnu.trove.impl.HashFunctions
  • gnu.trove.strategy.IdentityHashingStrategy<K> (implements gnu.trove.strategy.HashingStrategy<T>)
  • net.sf.jannot.source.IndexManager
  • java.io.InputStream (implements java.io.Closeable)
    • net.sf.samtools.util.BlockCompressedInputStream
      • net.sf.jannot.picard.LineBlockCompressedInputStream
    • java.io.FilterInputStream
      • org.broad.tribble.LittleEndianInputStream
    • net.sf.samtools.util.SeekableStream
      • net.sf.samtools.util.SeekableHTTPStream
        • net.sf.jannot.picard.SeekableFileCachedHTTPStream
  • org.broad.igv.util.collections.IntArrayList
  • net.sf.jannot.ListIterable<T> (implements java.lang.Iterable<T>)
  • net.sf.jannot.ListIterator<T> (implements java.util.Iterator<E>)
  • net.sf.jannot.LocatedListIterable<T> (implements java.lang.Iterable<T>)
  • net.sf.jannot.LocatedListIterator<T> (implements java.util.Iterator<E>)
  • net.sf.jannot.Location (implements java.lang.Comparable<T>)
  • net.sf.jannot.source.Locator
  • net.sf.jannot.mafix.MafixFactory
  • net.sf.jannot.tabix.Pair64 (implements java.lang.Comparable<T>)
  • net.sf.jannot.parser.Parser
    • net.sf.jannot.parser.ALNParser
    • net.sf.jannot.parser.BedGraphParser
    • net.sf.jannot.parser.BEDParser
    • net.sf.jannot.parser.software.BlastM8Parser
    • net.sf.jannot.parser.software.BroadSolexa
    • net.sf.jannot.parser.EMBLParser
    • net.sf.jannot.parser.FastaParser
    • net.sf.jannot.parser.software.FindPeaksParser
    • net.sf.jannot.parser.GenbankParser
    • net.sf.jannot.parser.software.GeneMarkParser
    • net.sf.jannot.parser.GFF3Parser
    • net.sf.jannot.parser.MAFParser
    • net.sf.jannot.parser.software.MapViewParser
    • net.sf.jannot.parser.software.MaqSNPParser
    • net.sf.jannot.parser.PTTParser
    • net.sf.jannot.parser.software.SIPHTParser
    • net.sf.jannot.parser.SyntenicParser
    • net.sf.jannot.parser.TBLParser
    • net.sf.jannot.parser.software.TransTermHPParser
    • net.sf.jannot.parser.software.TRNAscanParser
    • net.sf.jannot.parser.WiggleParser
  • net.sf.jannot.parser.ParserTools
  • net.sf.jannot.pileup.PileTools
  • gnu.trove.impl.PrimeFinder
  • net.sf.jannot.shortread.ReadGroup (implements net.sf.jannot.Data<K>)
    • net.sf.jannot.shortread.BAMreads (implements java.lang.Iterable<T>)
    • net.sf.jannot.shortread.MemoryReadSet
  • org.broad.igv.bbfile.RPChromosomeRegion
    • org.broad.igv.bbfile.RPTreeLeafNodeItem
  • org.broad.igv.bbfile.RPTree
  • org.broad.igv.bbfile.RPTreeChildNode (implements org.broad.igv.bbfile.RPTreeNode)
  • org.broad.igv.bbfile.RPTreeChildNodeItem
  • org.broad.igv.bbfile.RPTreeHeader
  • org.broad.igv.bbfile.RPTreeLeafNode (implements org.broad.igv.bbfile.RPTreeNode)
  • org.broad.tribble.SeekableStreamUtils
  • net.sf.jannot.refseq.Sequence (implements net.sf.jannot.Data<K>)
    • net.sf.jannot.refseq.FaidxData
    • net.sf.jannot.refseq.MemorySequence
      • net.sf.jannot.alignment.ReferenceSequence
    • net.sf.jannot.refseq.SubSequence
  • net.sf.jannot.utils.SequenceTools
  • net.sf.jannot.alignment.maf.SequenceTranslator
  • net.sf.jannot.shortread.ShortRead (implements java.lang.Comparable<T>)
    • net.sf.jannot.shortread.BasicShortRead
  • net.sf.jannot.shortread.ShortReadTools
  • net.sf.jannot.pileup.SinglePile (implements net.sf.jannot.Located, net.sf.jannot.pileup.Pile)
    • net.sf.jannot.pileup.DoublePile
      • net.sf.jannot.pileup.MultiPile
      • net.sf.jannot.pileup.ReadDetailPile
  • net.sf.jannot.source.cache.SourceCache
  • net.sf.jannot.source.SSL
  • net.sf.jannot.StringKey (implements net.sf.jannot.DataKey)
  • org.broad.igv.util.StringUtils
  • net.sf.jannot.SyntenicBlock
  • net.sf.jannot.tabix.TabixLine
  • net.sf.jannot.tabix.TabixReader
    • net.sf.jannot.tabix.TabixWriter
  • net.sf.jannot.tabix.TabixReader.Iterator
  • net.sf.jannot.tabix.TabixReader.TIndex
  • net.sf.jannot.tabix.TabixReader.TIntv
  • net.sf.jannot.tabix.TabixReader.TPair64 (implements java.lang.Comparable<T>)
  • net.sf.jannot.tabix.TabixWrapper<T> (implements net.sf.jannot.Data<K>, net.sf.jannot.DensityEstimate)
    • net.sf.jannot.tabix.FeatureWrapper (implements net.sf.jannot.FeatureAnnotation)
      • net.sf.jannot.tabix.BEDWrapper
      • net.sf.jannot.tabix.GFFWrapper
    • net.sf.jannot.tabix.PileupWrapper
    • net.sf.jannot.tabix.SWigWrapper
  • net.sf.jannot.tabix.TabixWriter.Conf
  • org.broad.igv.tdf.TDFBedTile (implements org.broad.igv.tdf.TDFTile)
  • net.sf.jannot.tdf.TDFData (implements net.sf.jannot.Data<K>)
  • org.broad.igv.tdf.TDFEntity
    • org.broad.igv.tdf.TDFDataset
    • org.broad.igv.tdf.TDFGroup
  • org.broad.igv.tdf.TDFFixedTile (implements org.broad.igv.tdf.TDFTile)
  • org.broad.igv.tdf.TDFReader
  • org.broad.tools.TDFTools
  • org.broad.igv.tdf.TDFUtils
  • org.broad.igv.tdf.TDFVaryTile (implements org.broad.igv.tdf.TDFTile)
  • org.broad.igv.tdf.TDFWriter
  • gnu.trove.impl.hash.THash (implements java.io.Externalizable)
    • gnu.trove.impl.hash.TObjectHash<T>
      • gnu.trove.map.hash.THashMap<K,V> (implements java.io.Externalizable, java.util.Map<K,V>)
      • gnu.trove.set.hash.THashSet<E> (implements java.io.Externalizable, java.lang.Iterable<T>, java.util.Set<E>)
    • gnu.trove.impl.hash.TPrimitiveHash
      • gnu.trove.impl.hash.TIntFloatHash
        • gnu.trove.map.hash.TIntFloatHashMap (implements java.io.Externalizable, gnu.trove.map.TIntFloatMap)
      • gnu.trove.impl.hash.TIntHash
        • gnu.trove.set.hash.TIntHashSet (implements java.io.Externalizable, gnu.trove.set.TIntSet)
      • gnu.trove.impl.hash.TLongDoubleHash
        • gnu.trove.map.hash.TLongDoubleHashMap (implements java.io.Externalizable, gnu.trove.map.TLongDoubleMap)
      • gnu.trove.impl.hash.TLongHash
        • gnu.trove.set.hash.TLongHashSet (implements java.io.Externalizable, gnu.trove.set.TLongSet)
  • gnu.trove.impl.hash.THashIterator<V> (implements java.util.Iterator<E>, gnu.trove.iterator.TIterator)
    • gnu.trove.iterator.hash.TObjectHashIterator<E>
  • gnu.trove.impl.hash.THashPrimitiveIterator (implements gnu.trove.iterator.TPrimitiveIterator)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • net.sf.jannot.exception.ReadFailedException
      • java.lang.RuntimeException
        • net.sf.jannot.tabix.RuntimeEOFException
        • net.sf.jannot.tabix.RuntimeIOException
        • net.sf.jannot.parser.UnsupportedException
      • net.sf.jannot.exception.SaveFailedException
  • org.broad.igv.tdf.TileFactory
  • org.broad.igv.tdf.TileManager
  • gnu.trove.map.hash.TIntFloatHashMap.TKeyView (implements gnu.trove.set.TIntSet)
  • gnu.trove.map.hash.TIntFloatHashMap.TValueView (implements gnu.trove.TFloatCollection)
  • gnu.trove.map.hash.TLongDoubleHashMap.TKeyView (implements gnu.trove.set.TLongSet)
  • gnu.trove.map.hash.TLongDoubleHashMap.TValueView (implements gnu.trove.TDoubleCollection)
  • gnu.trove.procedure.array.ToObjectArrayProceedure<T> (implements gnu.trove.procedure.TObjectProcedure<T>)
  • net.sf.jannot.Type (implements net.sf.jannot.DataKey)
  • org.broad.igv.bbfile.WigItem
  • org.broad.igv.bbfile.ZoomDataBlock
  • org.broad.igv.bbfile.ZoomDataRecord
  • org.broad.igv.bbfile.ZoomLevelIterator
    • org.broad.igv.bbfile.ZoomLevelIterator.EmptyIterator

Interface Hierarchy

• org.broad.igv.bbfile.BPTreeNode
• net.sf.jannot.event.ChangeEvent
• java.lang.Comparable<T>
  • net.sf.jannot.DataKey
• net.sf.jannot.Data<K>
  • net.sf.jannot.FeatureAnnotation (also extends net.sf.jannot.DensityEstimate)
  • net.sf.jannot.wiggle.Graph
• org.broad.igv.data.DataSource
• net.sf.jannot.DensityEstimate
  • net.sf.jannot.FeatureAnnotation (also extends net.sf.jannot.Data<K>)
• org.broad.tribble.Feature
  • org.broad.igv.feature.LocusScore
• net.sf.jannot.Located
• net.sf.jannot.pileup.Pile
• net.sf.jannot.wiggle.Query
• org.broad.igv.bbfile.RPTreeNode
• java.io.Serializable
  • gnu.trove.strategy.HashingStrategy<T>
  • gnu.trove.TDoubleCollection
  • gnu.trove.TFloatCollection
  • gnu.trove.TIntCollection
    • gnu.trove.set.TIntSet (also extends java.io.Serializable)
  • gnu.trove.map.TIntFloatMap
  • gnu.trove.set.TIntSet (also extends gnu.trove.TIntCollection)
  • gnu.trove.TLongCollection
    • gnu.trove.set.TLongSet (also extends java.io.Serializable)
  • gnu.trove.map.TLongDoubleMap
  • gnu.trove.set.TLongSet (also extends gnu.trove.TLongCollection)
  • gnu.trove.TShortCollection
• gnu.trove.function.TByteFunction
• gnu.trove.procedure.TByteProcedure
• gnu.trove.function.TCharFunction
• gnu.trove.procedure.TCharProcedure
• org.broad.igv.tdf.TDFTile
• gnu.trove.function.TDoubleFunction
• gnu.trove.procedure.TDoubleProcedure
• gnu.trove.function.TFloatFunction
• gnu.trove.procedure.TFloatProcedure
• gnu.trove.procedure.TIntFloatProcedure
• gnu.trove.function.TIntFunction
• gnu.trove.procedure.TIntProcedure
• gnu.trove.iterator.TIterator
  • gnu.trove.iterator.TAdvancingIterator
    • gnu.trove.iterator.TIntFloatIterator
    • gnu.trove.iterator.TLongDoubleIterator
  • gnu.trove.iterator.TDoubleIterator
  • gnu.trove.iterator.TFloatIterator
  • gnu.trove.iterator.TIntFloatIterator
  • gnu.trove.iterator.TIntIterator
  • gnu.trove.iterator.TLongDoubleIterator
  • gnu.trove.iterator.TLongIterator
  • gnu.trove.iterator.TPrimitiveIterator
  • gnu.trove.iterator.TShortIterator
• gnu.trove.procedure.TLongDoubleProcedure
• gnu.trove.function.TLongFunction
• gnu.trove.procedure.TLongProcedure
• gnu.trove.function.TObjectFunction<T,R>
• gnu.trove.procedure.TObjectObjectProcedure<K,V>
• gnu.trove.procedure.TObjectProcedure<T>
• gnu.trove.function.TShortFunction
• gnu.trove.procedure.TShortProcedure

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • net.sf.jannot.AminoAcidMapping
    • net.sf.jannot.Strand
    • net.sf.jannot.source.DataSourceFactory.Sources
    • org.broad.igv.bbfile.BigWigSectionHeader.WigItemType
    • org.broad.igv.tdf.TDFDataset.DataType
    • org.broad.igv.tdf.TDFTile.Type
    • org.broad.igv.track.WindowFunction