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

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.AbstractAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
      - org.biojava.bio.seq.io.ReferenceAnnotation
  - org.biojava.bio.seq.io.AlignIOConstants
  - org.biojava.bio.seq.io.ChunkedSymbolListFactory
  - org.biojava.bio.seq.io.EmblFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
  - org.biojava.bio.seq.io.EmblLikeFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - org.biojava.bio.seq.io.EmblLikeLocationParser
  - org.biojava.bio.seq.io.EmblProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.EmblReferenceComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.io.FastaAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.FastaFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - org.biojava.bio.seq.io.FeatureTableParser
  - org.biojava.bio.seq.io.GAMEFormat (implements org.biojava.bio.seq.io.SequenceFormat)
  - org.biojava.bio.seq.io.GenbankFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
    - org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  - org.biojava.bio.seq.io.GenbankFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
    - org.biojava.bio.seq.io.GenbankXmlFormat
    - org.biojava.bio.seq.io.GenpeptFormat
  - org.biojava.bio.seq.io.GenbankProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.GenEmblFeatureComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.io.GenEmblPropertyComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.io.MSFAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - org.biojava.bio.seq.io.OrganismParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.SeqIOAdapter (implements org.biojava.bio.seq.io.SeqIOListener)
  - org.biojava.bio.seq.io.SeqIOConstants
  - org.biojava.bio.seq.io.SeqIOEventEmitter
  - org.biojava.bio.seq.io.SeqIOFilter (implements org.biojava.bio.seq.io.SeqIOListener)
  - org.biojava.bio.seq.io.SeqIOTools
  - org.biojava.bio.seq.io.SequenceBuilderBase (implements org.biojava.bio.seq.io.SequenceBuilder)
    - org.biojava.bio.seq.io.SequenceDBSequenceBuilder
    - org.biojava.bio.seq.io.SimpleAssemblyBuilder
    - org.biojava.bio.seq.io.SimpleSequenceBuilder
    - org.biojava.bio.seq.io.SmartSequenceBuilder
  - org.biojava.bio.seq.io.SequenceBuilderFilter (implements org.biojava.bio.seq.io.SequenceBuilder)
    - org.biojava.bio.seq.io.EmblProcessor (implements org.biojava.utils.ParseErrorSource)
    - org.biojava.bio.seq.io.FastaDescriptionLineParser
    - org.biojava.bio.seq.io.GenbankProcessor (implements org.biojava.utils.ParseErrorSource)
      - org.biojava.bio.seq.io.ProteinRefSeqProcessor
    - org.biojava.bio.seq.io.OrganismParser
    - org.biojava.bio.seq.io.SwissprotProcessor (implements org.biojava.utils.ParseErrorSource)
  - org.biojava.bio.seq.io.StreamReader (implements org.biojava.utils.ParseErrorListener, org.biojava.bio.seq.SequenceIterator)
  - org.biojava.bio.seq.io.StreamWriter
  - org.biojava.bio.seq.io.SwissprotFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
  - org.biojava.bio.seq.io.SwissprotProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.SymbolListCharSequence (implements java.lang.CharSequence)
  - org.biojava.bio.seq.io.SymbolTokenization.TokenType
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - org.biojava.bio.BioException
        - org.biojava.bio.seq.io.ParseException
  - org.biojava.utils.Unchangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.seq.io.AlternateTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
    - org.biojava.bio.seq.io.CharacterTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
    - org.biojava.bio.seq.io.WordTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
      - org.biojava.bio.seq.io.CrossProductTokenization
      - org.biojava.bio.seq.io.DoubleTokenization
      - org.biojava.bio.seq.io.IntegerTokenization
      - org.biojava.bio.seq.io.NameTokenization
      - org.biojava.bio.seq.io.SubIntegerTokenization

## Interface Hierarchy

- org.biojava.bio.seq.io.AlignmentFormat
- org.biojava.utils.Changeable
  - org.biojava.bio.Annotatable
    - org.biojava.bio.seq.io.SymbolTokenization
- org.biojava.bio.seq.io.SeqIOListener
  - org.biojava.bio.seq.io.SeqFileFormer
  - org.biojava.bio.seq.io.SequenceBuilder
- org.biojava.bio.seq.io.SequenceBuilderFactory
- org.biojava.bio.seq.io.SequenceFormat
- org.biojava.bio.seq.io.StreamParser
- org.biojava.bio.seq.io.SymbolReader

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