Class AGAVEHandler

All Implemented Interfaces:
AGAVECallbackItf, StAXContentHandler

public class AGAVEHandler extends StAXFeatureHandler implements AGAVECallbackItf
Handles the root AGAVE element modified for agave format
Author:
Hanning Ni Doubletwist Inc
  • Constructor Details

  • Method Details

    • 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

      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(String nsURI, String localName, String qName, Attributes attrs, DelegationManager dm) throws SAXException
      Throws:
      SAXException