Class AGAVEHandler

    • Constructor Detail

      • AGAVEHandler

        public AGAVEHandler()
    • Method Detail

      • reportSequence

        public void reportSequence​(Sequence sequence)
        Specified by:
        reportSequence in interface AGAVECallbackItf
        Parameters:
        sequence - from sub-tag <bio_sequence>/<contig>/<chromosome>
         bio_sequence --> SimpleSequence
         contig   --> SimpleAssembly
                  --> SimpleSequence( if only one sequence )
         chromosome -> SimpleAssembly
                    -> SimpleSequence( if only one sequence)
         
      • getSequences

        public java.util.Iterator getSequences()
        get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)
      • startElementHandler

        public void startElementHandler​(java.lang.String nsURI,
                                        java.lang.String localName,
                                        java.lang.String qName,
                                        org.xml.sax.Attributes attrs,
                                        DelegationManager dm)
                                 throws org.xml.sax.SAXException
        Throws:
        org.xml.sax.SAXException