Changeset 3131 for trunk/src/core/org/pathvisio/model/GpmlFormat2010a.java

Timestamp:

03/02/10 11:24:34 (6 months ago)

Author:

martijn

Message:

Convert embedded biopax from level 2 to level 3. Fixes #1129

Files:

• trunk/src/core/org/pathvisio/model/GpmlFormat2010a.java (modified) (2 diffs)

trunk/src/core/org/pathvisio/model/GpmlFormat2010a.java

@@ -28 +28 @@
 
 import org.bridgedb.DataSource;
+import org.jdom.Attribute;
 import org.jdom.Document;
 import org.jdom.Element;
@@ -788 +789 @@
         }
 
+        protected void mapBiopax(PathwayElement o, Element e) throws ConverterException
+        {
+                //this method clones all content,
+                //getContent will leave them attached to the parent, which we don't want
+                //We can safely remove them, since the JDOM element isn't used anymore after this method
+                Element root = new Element("RDF", GpmlFormat.RDF);
+                root.addNamespaceDeclaration(GpmlFormat.RDFS);
+                root.addNamespaceDeclaration(GpmlFormat.RDF);
+                root.addNamespaceDeclaration(GpmlFormat.OWL);
+                root.addNamespaceDeclaration(GpmlFormat.BIOPAX);
+                root.setAttribute(new Attribute("base", getGpmlNamespace().getURI() + "#", Namespace.XML_NAMESPACE));
+                //Element owl = new Element("Ontology", OWL);
+                //owl.setAttribute(new Attribute("about", "", RDF));
+                //Element imp = new Element("imports", OWL);
+                //imp.setAttribute(new Attribute("resource", BIOPAX.getURI(), RDF));
+                //owl.addContent(imp);
+                //root.addContent(owl);
+
+                root.addContent(e.cloneContent());
+                Document bp = new Document(root);
+
+                o.setBiopax(bp);
+        }
+
 }