Class SeqIOFilter

  • All Implemented Interfaces:
    SeqIOListener

    public class SeqIOFilter
    extends java.lang.Object
    implements SeqIOListener
    Base-class for listeners that pass filtered events onto another listener.
    Since:
    1.1
    Author:
    Matthew Pocock
    See Also:
    RichSeqIOAdapter
    • Constructor Summary

      Constructors 
      Constructor Description
      SeqIOFilter​(SeqIOListener delegate)
      Create a new SeqIOFilter that will forward events on to another listener.
    • Method Summary

      All Methods Instance Methods Concrete 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.
      SeqIOListener getDelegate()
      Retrieve the delegate that is wrapped.
      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.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • SeqIOFilter

        public SeqIOFilter​(SeqIOListener delegate)
        Create a new SeqIOFilter that will forward events on to another listener.
        Parameters:
        delegate - the SeqIOListener to wrap
    • Method Detail

      • getDelegate

        public SeqIOListener getDelegate()
        Retrieve the delegate that is wrapped.
        Returns:
        the SeqIOListener delegate
      • setName

        public void setName​(java.lang.String name)
                     throws ParseException
        Description copied from interface: SeqIOListener
        Notify the listener that the current sequence is generally known by a particular name.
        Specified by:
        setName in interface SeqIOListener
        Parameters:
        name - the String that should be returned by getName for the sequence being parsed
        Throws:
        ParseException
      • addSymbols

        public void addSymbols​(Alphabet alpha,
                               Symbol[] syms,
                               int start,
                               int length)
                        throws IllegalAlphabetException
        Description copied from interface: SeqIOListener
        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
        Specified by:
        addSymbols in interface SeqIOListener
        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

        public void addSequenceProperty​(java.lang.Object key,
                                        java.lang.Object value)
                                 throws ParseException
        Description copied from interface: SeqIOListener
        Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.
        Specified by:
        addSequenceProperty in interface SeqIOListener
        Throws:
        ParseException
      • startFeature

        public void startFeature​(Feature.Template templ)
                          throws ParseException
        Description copied from interface: SeqIOListener
        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.
        Specified by:
        startFeature in interface SeqIOListener
        Throws:
        ParseException