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

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.seq.AbstractFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
      - org.biojava.bio.seq.MergeFeatureHolder (implements java.io.Serializable)
      - org.biojava.bio.seq.SimpleFeatureHolder (implements java.io.Serializable)
    - org.biojava.bio.seq.FeatureTypes.RepositoryImpl (implements org.biojava.bio.seq.FeatureTypes.Repository)
    - org.biojava.bio.seq.LazyFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
    - org.biojava.bio.seq.NewSimpleAssembly (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.seq.SimpleAssembly (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence)
  - org.biojava.bio.seq.ByLocationMinMaxComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.ByLocationMinMaxFeatureComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.DNATools
  - org.biojava.bio.seq.Feature.ByLocationComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.Feature.Template (implements java.lang.Cloneable, java.io.Serializable)
    - org.biojava.bio.seq.StrandedFeature.Template
      - org.biojava.bio.seq.ComponentFeature.Template
      - org.biojava.bio.seq.FramedFeature.Template
      - org.biojava.bio.seq.RemoteFeature.Template
  - org.biojava.bio.seq.FeatureFilter.And (implements org.biojava.bio.seq.FeatureFilter)
  - org.biojava.bio.seq.FeatureFilter.ByAncestor (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByAnnotationType (implements org.biojava.bio.seq.OptimizableFilter)
    - org.biojava.bio.seq.FeatureFilter.AnnotationContains
    - org.biojava.bio.seq.FeatureFilter.ByAnnotation
    - org.biojava.bio.seq.FeatureFilter.HasAnnotation
  - org.biojava.bio.seq.FeatureFilter.ByChild (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByClass (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByComponentName (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByDescendant (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByFeature (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByPairwiseScore (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByParent (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.BySequenceName (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.BySource (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByType (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ContainedByLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.FrameFilter (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.Not (implements org.biojava.bio.seq.FeatureFilter)
  - org.biojava.bio.seq.FeatureFilter.OnlyChildren (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.OnlyDescendants (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.Or (implements org.biojava.bio.seq.FeatureFilter)
  - org.biojava.bio.seq.FeatureFilter.OverlapsLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.StrandFilter (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureHolderUtils
  - org.biojava.bio.seq.FeatureTypes
  - org.biojava.bio.seq.FilterUtils
  - org.biojava.bio.seq.FilterUtils.DelegatingTransformer (implements org.biojava.bio.seq.FilterUtils.FilterTransformer)
  - org.biojava.bio.seq.FramedFeature.ReadingFrame (implements org.biojava.bio.seq.Frame, java.io.Serializable)
  - org.biojava.bio.seq.GeneticCodes
  - org.biojava.bio.seq.NucleotideTools
  - org.biojava.bio.seq.ProteinTools
  - org.biojava.bio.seq.RemoteFeature.Region
  - org.biojava.bio.seq.RNATools
  - org.biojava.bio.seq.SequenceTools
  - org.biojava.bio.seq.SimpleFeatureRealizer (implements org.biojava.bio.seq.FeatureRealizer, java.io.Serializable)
  - org.biojava.bio.seq.StrandedFeature.Strand (implements java.io.Serializable)
  - org.biojava.bio.seq.StrandParser
  - org.biojava.utils.Unchangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
    - org.biojava.bio.seq.impl.ViewSequence (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence, java.io.Serializable)
      - org.biojava.bio.seq.CircularView

## Interface Hierarchy

- org.biojava.utils.Changeable
  - org.biojava.bio.Annotatable
    - org.biojava.bio.seq.Feature (also extends org.biojava.bio.seq.FeatureHolder)
      - org.biojava.bio.seq.StrandedFeature
        - org.biojava.bio.seq.ComponentFeature
        - org.biojava.bio.seq.FramedFeature
        - org.biojava.bio.seq.RemoteFeature
    - org.biojava.bio.seq.FeatureTypes.Repository
    - org.biojava.bio.seq.FeatureTypes.Type
    - org.biojava.bio.seq.Sequence (also extends org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.SymbolList)
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
  - org.biojava.bio.seq.FeatureHolder
    - org.biojava.bio.seq.Feature (also extends org.biojava.bio.Annotatable)
      - org.biojava.bio.seq.StrandedFeature
        - org.biojava.bio.seq.ComponentFeature
        - org.biojava.bio.seq.FramedFeature
        - org.biojava.bio.seq.RemoteFeature
    - org.biojava.bio.seq.RealizingFeatureHolder
    - org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.symbol.SymbolList)
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
  - org.biojava.bio.symbol.SymbolList
    - org.biojava.bio.symbol.GappedSymbolList
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.seq.Sequence)
    - org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder)
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
- org.biojava.bio.seq.FeatureRealizer
- org.biojava.bio.seq.FilterUtils.FilterTransformer
- org.biojava.bio.seq.Frame
- org.biojava.bio.seq.RemoteFeature.Resolver
- org.biojava.bio.seq.SequenceAnnotator
- org.biojava.bio.seq.SequenceFactory
- org.biojava.bio.seq.SequenceIterator
- java.io.Serializable
  - org.biojava.bio.seq.FeatureFilter
    - org.biojava.bio.seq.OptimizableFilter

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