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

Package Hierarchies:
  All Packages

## Class Hierarchy

- class java.lang.Object
  - class org.biojava.bio.seq.io.AbstractGenEmblFileFormer
    - class org.biojava.bio.seq.io.EmblFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
    - class org.biojava.bio.seq.io.GenbankFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
      - class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
    - class org.biojava.bio.seq.io.SwissprotFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
  - class org.biojava.bio.seq.io.AlignIOConstants
  - class org.biojava.bio.seq.io.ChunkedSymbolListBuilder
  - class org.biojava.bio.seq.io.ChunkedSymbolListFactory
  - class org.biojava.bio.seq.io.EmblLikeFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.seq.io.EmblLikeLocationParser
  - class org.biojava.bio.seq.io.EmblProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.io.FastaAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.io.FastaFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.seq.io.FeatureTableParser
  - class org.biojava.bio.seq.io.GAMEFormat (implements org.biojava.bio.seq.io.SequenceFormat)
  - class org.biojava.bio.seq.io.GenbankFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.seq.io.GenbankProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.io.MSFAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - class org.biojava.bio.seq.io.OrganismParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.io.SeqAlignReadWrite
  - class org.biojava.bio.seq.io.SeqIOAdapter (implements org.biojava.bio.seq.io.SeqIOListener)
  - class org.biojava.bio.seq.io.SeqIOConstants
  - class org.biojava.bio.seq.io.SeqIOFilter (implements org.biojava.bio.seq.io.SeqIOListener)
  - class org.biojava.bio.seq.io.SeqIOTools
  - class org.biojava.bio.seq.io.SequenceBuilderBase (implements org.biojava.bio.seq.io.SequenceBuilder)
    - class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
    - class org.biojava.bio.seq.io.SimpleAssemblyBuilder
    - class org.biojava.bio.seq.io.SimpleSequenceBuilder
    - class org.biojava.bio.seq.io.SmartSequenceBuilder
  - class org.biojava.bio.seq.io.SequenceBuilderFilter (implements org.biojava.bio.seq.io.SequenceBuilder)
    - class org.biojava.bio.seq.io.EmblProcessor (implements org.biojava.utils.ParseErrorSource)
    - class org.biojava.bio.seq.io.FastaDescriptionLineParser
    - class org.biojava.bio.seq.io.GenbankProcessor (implements org.biojava.utils.ParseErrorSource)
      - class org.biojava.bio.seq.io.ProteinRefSeqProcessor
    - class org.biojava.bio.seq.io.OrganismParser
    - class org.biojava.bio.seq.io.SwissprotProcessor (implements org.biojava.utils.ParseErrorSource)
  - class org.biojava.bio.seq.io.StreamReader (implements org.biojava.utils.ParseErrorListener, org.biojava.bio.seq.SequenceIterator)
  - class org.biojava.bio.seq.io.StreamWriter
  - class org.biojava.bio.seq.io.SwissprotProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.io.SymbolListCharSequence (implements java.lang.CharSequence)
  - class org.biojava.bio.seq.io.SymbolTokenization.TokenType
  - class java.lang.Throwable (implements java.io.Serializable)
    - class java.lang.Exception
      - class org.biojava.utils.NestedException
        - class org.biojava.bio.BioException
          - class org.biojava.bio.seq.io.ParseException
  - class org.biojava.utils.Unchangeable (implements org.biojava.utils.Changeable)
    - class org.biojava.bio.seq.io.CharacterTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
    - class org.biojava.bio.seq.io.WordTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
      - class org.biojava.bio.seq.io.CrossProductTokenization
      - class org.biojava.bio.seq.io.DoubleTokenization
      - class org.biojava.bio.seq.io.IntegerTokenization
      - class org.biojava.bio.seq.io.NameTokenization

## Interface Hierarchy

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