Class SequenceBuilderBase

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      void addFeatureProperty​(java.lang.Object key, java.lang.Object value)
      Add an annotation-bundle entry to the feature.
      protected void addProperty​(Annotation ann, java.lang.Object key, java.lang.Object value)  
      void addSequenceProperty​(java.lang.Object key, java.lang.Object value)
      Add an annotation-bundle entry to the sequence.
      abstract void addSymbols​(Alphabet alpha, Symbol[] syms, int pos, int len)
      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.
      Sequence makeSequence()
      Return the Sequence object which has been constructed by this builder.
      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
    • Method Detail

      • startSequence

        public void startSequence()
        Description copied from interface: SeqIOListener
        Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.
        Specified by:
        startSequence in interface SeqIOListener
      • setName

        public void setName​(java.lang.String name)
        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
      • setURI

        public void setURI​(java.lang.String uri)
        Description copied from interface: SeqIOListener
        Notify the listener of a URI identifying the current sequence.
        Specified by:
        setURI in interface SeqIOListener
      • addSymbols

        public abstract void addSymbols​(Alphabet alpha,
                                        Symbol[] syms,
                                        int pos,
                                        int len)
                                 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
        pos - The start offset of valid data within the array
        len - 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)
        Add an annotation-bundle entry to the sequence. If the annotation key isn't currently defined, the value is added directly. Otherwise:
        • If the current value implements the Collection interface, the new value is added to that collection.
        • Otherwise, the current value is replaced by a List object containing the old value then the new value in that order.
        Specified by:
        addSequenceProperty in interface SeqIOListener
      • startFeature

        public void startFeature​(Feature.Template templ)
        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
      • addFeatureProperty

        public void addFeatureProperty​(java.lang.Object key,
                                       java.lang.Object value)
                                throws ParseException
        Add an annotation-bundle entry to the feature. If the annotation key isn't currently defined, the value is added directly. Otherwise:
        • If the current value implements the Collection interface, the new value is added to that collection.
        • Otherwise, the current value is replaced by a List object containing the old value then the new value in that order.
        Specified by:
        addFeatureProperty in interface SeqIOListener
        Throws:
        ParseException
      • addProperty

        protected void addProperty​(Annotation ann,
                                   java.lang.Object key,
                                   java.lang.Object value)