org.biojava.nbio.alignment Class Hierarchy

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.SimpleGapPenalty (implements org.biojava.nbio.alignment.template.GapPenalty, java.io.Serializable)

Enum Class Hierarchy

java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, 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

Hierarchy For Package org.biojava.nbio.alignment

Class Hierarchy

Enum Class Hierarchy