Interface SeqIOListener

    • Method Detail

      • setName

        void setName​(String name)
              throws ParseException
        Notify the listener that the current sequence is generally known by a particular name.
        name - the String that should be returned by getName for the sequence being parsed
      • 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
        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
        IllegalAlphabetException - if we can't cope with this alphabet.
      • 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.