Interface SeqIOListener

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void addFeatureProperty​(java.lang.Object key, java.lang.Object value)
      Notify the listener of a feature property.
      void addSequenceProperty​(java.lang.Object key, java.lang.Object value)
      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 endFeature()
      Mark the end of data associated with one specific feature.
      void endSequence()
      Notify the listener that processing of the sequence is complete.
      void setName​(java.lang.String name)
      Notify the listener that the current sequence is generally known by a particular name.
      void setURI​(java.lang.String uri)
      Notify the listener of a URI identifying the current sequence.
      void startFeature​(Feature.Template templ)
      Notify the listener that a new feature object is starting.
      void startSequence()
      Start the processing of a sequence.
    • Method Detail

      • startSequence

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

        void endSequence()
                  throws ParseException
        Notify the listener that processing of the sequence is complete.
        Throws:
        ParseException
      • setName

        void setName​(java.lang.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​(java.lang.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​(java.lang.Object key,
                                 java.lang.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

        void startFeature​(Feature.Template templ)
                   throws ParseException
        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
      • addFeatureProperty

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