Interface SeqIOListener

All Known Subinterfaces:
RichSeqIOListener, RichSequenceBuilder, SeqFileFormer, SequenceBuilder
All Known Implementing Classes:
DebuggingRichSeqIOListener, EmblFileFormer, EmblProcessor, FastaDescriptionLineParser, GenbankFileFormer, GenbankProcessor, OrganismParser, ProteinRefSeqFileFormer, ProteinRefSeqProcessor, RichSeqIOAdapter, SeqIOAdapter, SeqIOFilter, SequenceBuilderBase, SequenceBuilderFilter, SequenceDBSequenceBuilder, SimpleAssemblyBuilder, SimpleRichSequenceBuilder, SimpleSequenceBuilder, SmartSequenceBuilder, SwissprotFileFormer, SwissprotProcessor

public interface SeqIOListener
Notification interface for objects which listen to a sequence stream parser. More functionality is offered by the RichSeqIOListener.
Since:
1.1
Author:
Thomas Down, Matthew Pocock
See Also:
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Notify the listener of a feature property.
    void
    Notify the listener of a sequence-wide property.
    void
    addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)
    Notify the listener of symbol data.
    void
    Mark the end of data associated with one specific feature.
    void
    Notify the listener that processing of the sequence is complete.
    void
    Notify the listener that the current sequence is generally known by a particular name.
    void
    Notify the listener of a URI identifying the current sequence.
    void
    Notify the listener that a new feature object is starting.
    void
    Start the processing of a sequence.
  • Method Details

    • startSequence

      Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.
      Throws:
      ParseException
    • endSequence

      Notify the listener that processing of the sequence is complete.
      Throws:
      ParseException
    • setName

      void setName(String name) throws ParseException
      Notify the listener that the current sequence is generally known by a particular name.
      Parameters:
      name - the String that should be returned by getName for the sequence being parsed
      Throws:
      ParseException
    • setURI

      void setURI(String uri) throws ParseException
      Notify the listener of a URI identifying the current sequence.
      Throws:
      ParseException
    • addSymbols

      void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException
      Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception
      Parameters:
      alpha - The alphabet of the symbol data
      syms - An array containing symbols
      start - The start offset of valid data within the array
      length - The number of valid symbols in the array
      Throws:
      IllegalAlphabetException - if we can't cope with this alphabet.
    • addSequenceProperty

      void addSequenceProperty(Object key, Object value) throws ParseException
      Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.
      Throws:
      ParseException
    • startFeature

      Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.
      Throws:
      ParseException
    • endFeature

      void endFeature() throws ParseException
      Mark the end of data associated with one specific feature.
      Throws:
      ParseException
    • addFeatureProperty

      void addFeatureProperty(Object key, Object value) throws ParseException
      Notify the listener of a feature property.
      Throws:
      ParseException