Hierarchy For Package org.biojava.nbio.alignment

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • org.biojava.nbio.alignment.template.AbstractScorer (implements org.biojava.nbio.alignment.template.Scorer)
    • org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C> (implements org.biojava.nbio.alignment.template.MatrixAligner<S,C>)
      • org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C>)
        • org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>
          • org.biojava.nbio.alignment.NeedlemanWunsch<S,C>
        • org.biojava.nbio.alignment.SmithWaterman<S,C>
      • org.biojava.nbio.alignment.template.AbstractProfileProfileAligner<S,C> (implements org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C>)
        • org.biojava.nbio.alignment.SimpleProfileProfileAligner<S,C>
    • org.biojava.nbio.alignment.FractionalIdentityScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
      • org.biojava.nbio.alignment.FractionalIdentityInProfileScorer<S,C> (implements org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>)
    • org.biojava.nbio.alignment.FractionalSimilarityScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
      • org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer<S,C> (implements org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>)
    • org.biojava.nbio.alignment.StandardRescoreRefiner<S,C> (implements org.biojava.nbio.alignment.template.RescoreRefiner<S,C>)
    • org.biojava.nbio.alignment.SubstitutionMatrixScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
  • org.biojava.nbio.alignment.Alignments
  • org.biojava.nbio.alignment.GuideTree<S,C> (implements java.lang.Iterable<T>)
  • org.biojava.nbio.alignment.GuideTree.Node (implements org.biojava.nbio.alignment.template.GuideTreeNode<S,C>)
  • org.biojava.nbio.alignment.SimpleAlignedSequence<S,C> (implements org.biojava.nbio.alignment.template.AlignedSequence<S,C>)
  • org.biojava.nbio.alignment.SimpleGapPenalty (implements org.biojava.nbio.alignment.template.GapPenalty)
  • org.biojava.nbio.alignment.SimpleProfile<S,C> (implements org.biojava.nbio.alignment.template.Profile<S,C>)
    • org.biojava.nbio.alignment.SimpleProfilePair<S,C> (implements org.biojava.nbio.alignment.template.ProfilePair<S,C>)
    • org.biojava.nbio.alignment.SimpleSequencePair<S,C> (implements org.biojava.nbio.alignment.template.SequencePair<S,C>)
  • org.biojava.nbio.alignment.SimpleSubstitutionMatrix<C> (implements org.biojava.nbio.alignment.template.SubstitutionMatrix<C>)
  • org.biojava.nbio.alignment.SubstitutionMatrixHelper

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
    • org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
    • org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
    • org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
    • org.biojava.nbio.alignment.Alignments.RefinerType