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