Hierarchy For All Packages

Package Hierarchies:

• demo,
• org.biojava.nbio.alignment,
• org.biojava.nbio.alignment.aaindex,
• org.biojava.nbio.alignment.io,
• org.biojava.nbio.alignment.routines,
• org.biojava.nbio.alignment.template

Class Hierarchy

• java.lang.Object
  • org.biojava.nbio.alignment.aaindex.AAindexFactory
  • org.biojava.nbio.alignment.aaindex.AAIndexFileParser
  • 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.routines.GuanUberbacher<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.routines.AlignerHelper
  • org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
  • org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.alignment.routines.AlignerHelper.Cut
  • org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
  • org.biojava.nbio.alignment.Alignments
  • org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.alignment.template.CallableProfileProfileAligner<S,C> (implements java.util.concurrent.Callable<V>)
  • demo.CookbookMSA
  • org.biojava.nbio.alignment.aaindex.DefaultAAIndexProvider (implements org.biojava.nbio.alignment.aaindex.AAIndexProvider)
  • demo.DemoAlignProteins
  • demo.DemoLoadSubstMax
  • 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.aaindex.ScaledSubstitutionMatrix (implements org.biojava.nbio.alignment.template.SubstitutionMatrix<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.io.StockholmFileAnnotation
  • org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
  • org.biojava.nbio.alignment.io.StockholmFileParser
  • org.biojava.nbio.alignment.io.StockholmStructure
  • org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
  • org.biojava.nbio.alignment.SubstitutionMatrixHelper
  • demo.TestDNANeedlemanWunsch

Interface Hierarchy

• org.biojava.nbio.alignment.aaindex.AAIndexProvider
• org.biojava.nbio.core.sequence.template.Accessioned
  • org.biojava.nbio.alignment.template.AlignedSequence<S,C>
    • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.core.sequence.template.Sequence<C> (also extends java.lang.Iterable<T>)
    • org.biojava.nbio.alignment.template.AlignedSequence<S,C>
      • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
• org.biojava.nbio.alignment.template.GapPenalty
• org.biojava.nbio.alignment.template.HierarchicalClusterer<S,C>
• java.lang.Iterable<T>
  • org.biojava.nbio.alignment.template.AlignedSequence<S,C>
    • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.alignment.template.MutableProfile<S,C>
    • org.biojava.nbio.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.alignment.template.ProfilePair<S,C>)
    • org.biojava.nbio.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.alignment.template.SequencePair<S,C>)
  • org.biojava.nbio.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>, org.biojava.nbio.alignment.template.ProfilePair<S,C>)
  • org.biojava.nbio.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>, org.biojava.nbio.alignment.template.SequencePair<S,C>)
  • org.biojava.nbio.alignment.template.Profile<S,C>
    • org.biojava.nbio.alignment.template.MutableProfile<S,C>
      • org.biojava.nbio.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.alignment.template.ProfilePair<S,C>)
      • org.biojava.nbio.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.alignment.template.SequencePair<S,C>)
    • org.biojava.nbio.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>, org.biojava.nbio.alignment.template.ProfilePair<S,C>)
    • org.biojava.nbio.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>, org.biojava.nbio.alignment.template.SequencePair<S,C>)
    • org.biojava.nbio.alignment.template.ProfilePair<S,C>
      • org.biojava.nbio.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>)
    • org.biojava.nbio.alignment.template.ProfileView<S,C>
    • org.biojava.nbio.alignment.template.SequencePair<S,C>
      • org.biojava.nbio.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>)
  • org.biojava.nbio.alignment.template.ProfilePair<S,C>
    • org.biojava.nbio.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>)
  • org.biojava.nbio.alignment.template.ProfileView<S,C>
  • org.biojava.nbio.core.sequence.template.Sequence<C> (also extends org.biojava.nbio.core.sequence.template.Accessioned)
    • org.biojava.nbio.alignment.template.AlignedSequence<S,C>
      • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.alignment.template.SequencePair<S,C>
    • org.biojava.nbio.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.alignment.template.MutableProfile<S,C>)
• org.biojava.nbio.alignment.template.Scorer
  • org.biojava.nbio.alignment.template.Aligner<S,C>
    • org.biojava.nbio.alignment.template.MatrixAligner<S,C>
    • org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
    • org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
    • org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
    • org.biojava.nbio.alignment.template.RescoreRefiner<S,C>
  • org.biojava.nbio.alignment.template.MatrixAligner<S,C>
  • org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>
  • org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>, org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
  • org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>
    • org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>
    • org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
  • org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>, org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
  • org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>, org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
  • org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>
    • org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
    • org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
  • org.biojava.nbio.alignment.template.RescoreRefiner<S,C>
• org.biojava.nbio.alignment.template.SubstitutionMatrix<C>
• javax.swing.tree.TreeNode
  • org.biojava.nbio.alignment.template.GuideTreeNode<S,C>

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
    • org.biojava.nbio.alignment.routines.AlignerHelper.Last
    • org.biojava.nbio.alignment.template.GapPenalty.Type
    • org.biojava.nbio.alignment.template.AlignedSequence.Step
    • org.biojava.nbio.alignment.template.Profile.StringFormat