## Hierarchy For Package org.biojava.bio.search

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.search.SequenceDBSearchHit (implements org.biojava.bio.Annotatable, org.biojava.bio.search.SeqSimilaritySearchHit)
    - org.biojava.bio.search.SequenceDBSearchResult (implements org.biojava.bio.Annotatable, org.biojava.bio.search.SeqSimilaritySearchResult)
    - org.biojava.bio.search.SequenceDBSearchSubHit (implements org.biojava.bio.search.SeqSimilaritySearchSubHit)
    - org.biojava.bio.search.SimpleSeqSimilaritySearchHit (implements org.biojava.bio.search.SeqSimilaritySearchHit)
    - org.biojava.bio.search.SimpleSeqSimilaritySearchResult (implements org.biojava.bio.search.SeqSimilaritySearchResult)
    - org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit (implements org.biojava.bio.search.SeqSimilaritySearchSubHit)
  - org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter (implements org.biojava.bio.search.BlastLikeSearchFilter)
    - org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
    - org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
    - org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
    - org.biojava.bio.search.BlastLikeSearchFilter.Not
  - org.biojava.bio.search.BlastLikeSearchFilter.And
  - org.biojava.bio.search.BlastLikeSearchFilter.Or
  - org.biojava.bio.search.FilteringContentHandler.FilterVisitor (implements org.biojava.utils.walker.Visitor)
  - org.biojava.bio.search.FilterTest.Equals (implements org.biojava.bio.search.FilterTest)
  - org.biojava.bio.search.FilterTest.FindRegex
  - org.biojava.bio.search.FilterTest.GreaterThan (implements org.biojava.bio.search.FilterTest)
  - org.biojava.bio.search.FilterTest.LessThan (implements org.biojava.bio.search.FilterTest)
  - org.biojava.bio.search.FilterTest.MatchRegex
  - org.biojava.bio.search.KnuthMorrisPrattSearch
  - org.biojava.bio.search.MaxMismatchMatcher (implements org.biojava.bio.search.BioMatcher)
  - org.biojava.bio.search.MaxMismatchPattern (implements org.biojava.bio.search.BioPattern)
  - org.biojava.bio.search.SearchContentAdapter (implements org.biojava.bio.search.SearchContentHandler)
    - org.biojava.bio.search.FilteringContentHandler (implements org.biojava.bio.search.BlastLikeSearchFilter.Node)
  - org.biojava.bio.search.SearchContentFilter (implements org.biojava.bio.search.SearchContentHandler)
  - org.biojava.bio.search.SearchContentHandlerDebugger (implements org.biojava.bio.search.SearchContentHandler)
  - org.biojava.bio.search.SeqContentPattern (implements org.biojava.bio.search.BioPattern)
  - org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator (implements java.util.Comparator<T>)

## Interface Hierarchy

- org.biojava.bio.search.BioMatcher
- org.biojava.bio.search.BioPattern
- org.biojava.bio.search.BlastLikeSearchFilter.Node
- org.biojava.utils.Changeable
  - org.biojava.bio.Annotatable
    - org.biojava.bio.search.SeqSimilaritySearchHit
    - org.biojava.bio.search.SeqSimilaritySearchResult
    - org.biojava.bio.search.SeqSimilaritySearchSubHit
- org.biojava.bio.search.FilterTest
- org.biojava.bio.search.SearchContentHandler
  - org.biojava.bio.search.SearchBuilder
- org.biojava.bio.search.SeqSimilaritySearcher
- java.io.Serializable
  - org.biojava.bio.search.BlastLikeSearchFilter