owltools.gaf.io
Class XgmmlWriter

java.lang.Object
  extended by owltools.gaf.io.AbstractXmlWriter
      extended by owltools.gaf.io.XgmmlWriter

public class XgmmlWriter
extends AbstractXmlWriter

Generates Xgmml for import into Cytoscape


Constructor Summary
XgmmlWriter()
           
 
Method Summary
 String getId(String in)
           
 void write(OutputStream stream, OWLGraphWrapper graph, List<GafDocument> gafs)
          Write a pseudo RDF XML for the given ontology and gene annotations.
 
Methods inherited from class owltools.gaf.io.AbstractXmlWriter
createWriter
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

XgmmlWriter

public XgmmlWriter()
Method Detail

write

public void write(OutputStream stream,
                  OWLGraphWrapper graph,
                  List<GafDocument> gafs)
           throws IOException
Write a pseudo RDF XML for the given ontology and gene annotations.

Parameters:
stream -
graph - the ontology
gafs - (optional) list of gaf documents or null
Throws:
IOException

getId

public String getId(String in)


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