Hierarchy For All Packages

Package Hierarchies:

jbil.common, jbil.rv, jbil.sequence, jbil.sequence.test, jbil.util

Class Hierarchy

• java.lang.Object
  • jbil.common.AbstractAlgorithm (implements jbil.common.Algorithm)
    • jbil.sequence.GibbsMotifSiteSampler
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • jbil.sequence.Alphabet
        • jbil.sequence.DNAAlphabet
        • jbil.sequence.ExtendedDNAAlphabet
  • jbil.sequence.AbstractFixedLengthSequenceModel (implements jbil.sequence.FixedLengthSequenceModel)
    • jbil.sequence.MarkovFixedLengthSequenceModel
    • jbil.sequence.UniformFixedLengthSequenceModel
  • jbil.sequence.AlphabetRegistry
  • jbil.util.ArrayPrinter
  • jbil.util.ArrayUtilities
  • jbil.util.BooleanArrayUtilities
  • jbil.sequence.CharSymbol (implements jbil.sequence.Symbol)
    • jbil.sequence.AtomicCharSymbol (implements jbil.sequence.AtomicSymbol)
    • jbil.sequence.HighOrderCharSymbol (implements jbil.sequence.HighOrderSymbol)
  • umontreal.iro.lecuyer.probdist.DiscreteDistributionInt (implements umontreal.iro.lecuyer.probdist.Distribution)
    • jbil.rv.IntIntervalDist
  • jbil.sequence.test.GibbsMotifSiteSamplerTest
  • jbil.sequence.test.MarkovMotifPvalueTest
  • jbil.common.Pair<E,F>
  • jbil.util.RandomManager
  • umontreal.iro.lecuyer.rng.RandomStreamBase (implements umontreal.iro.lecuyer.rng.CloneableRandomStream, java.io.Serializable)
    • jbil.util.JDKRandomStream
  • jbil.util.RandomUtilities
  • umontreal.iro.lecuyer.randvar.RandomVariateGen
    • umontreal.iro.lecuyer.randvar.RandomVariateGenInt
      • jbil.rv.IntIntervalGen
  • jbil.sequence.Sequence
    • jbil.sequence.ByteArraySequence
    • jbil.sequence.SymbolArraySequence
  • jbil.sequence.SequenceFactory
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • jbil.common.BadInputException
        • jbil.sequence.InvalidSymbolException
  • jbil.sequence.Trie (implements jbil.sequence.KMerCounter)
    • jbil.sequence.FactorTrie
  • jbil.sequence.TrieForest (implements jbil.sequence.KMerCounter)

Interface Hierarchy

• jbil.common.Algorithm
• jbil.sequence.KMerCounter
• jbil.sequence.SequenceModel
  • jbil.sequence.FixedLengthSequenceModel
• jbil.sequence.Symbol
  • jbil.sequence.AtomicSymbol
  • jbil.sequence.HighOrderSymbol