Hierarchy For Package org.biojava.nbio.alignment.template

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.template.AbstractProfileProfileAligner<S,C> (implements org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C>)
  • 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>)

Interface Hierarchy

• org.biojava.nbio.alignment.template.GapPenalty
• org.biojava.nbio.alignment.template.HierarchicalClusterer<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.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.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>)
• 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.template.GapPenalty.Type