Changeset 3131

Timestamp:

03/02/10 11:24:34 (5 months ago)

Author:

martijn

Message:

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

Location:

trunk/src/core/org/pathvisio/model

Files:

• GpmlFormat.java (modified) (1 diff)
• GpmlFormat200X.java (modified) (2 diffs)
• GpmlFormat2010a.java (modified) (2 diffs)
• GpmlFormatAbstract.java (modified) (1 diff)

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

@@ -48 +48 @@
         public static final Namespace RDF = Namespace.getNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
         public static final Namespace RDFS = Namespace.getNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
-        public static final Namespace BIOPAX = Namespace.getNamespace("bp", "http://www.biopax.org/release/biopax-level2.owl#");
+        public static final Namespace BIOPAX = Namespace.getNamespace("bp", "http://www.biopax.org/release/biopax-level3.owl#");
         public static final Namespace OWL = Namespace.getNamespace("owl", "http://www.w3.org/2002/07/owl#");
 

trunk/src/core/org/pathvisio/model/GpmlFormat200X.java

@@ -23 +23 @@
 
 import org.bridgedb.DataSource;
+import org.jdom.Attribute;
+import org.jdom.Document;
 import org.jdom.Element;
 import org.jdom.Namespace;
@@ -479 +481 @@
         }
 
+        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);
+
+                updateBiopaxNamespace(root);
+                o.setBiopax(bp);
+        }
+
+        private static final Namespace BP_LEV2 = Namespace.getNamespace("bp", "http://www.biopax.org/release/biopax-level2.owl#");
+        
+        /**
+         * Convert the namespace of biopax element from old level2 to new level3.
+         * Starting from GpmlFormat2010a, we only support level 3.
+         * <p>
+         * We ignore all other differences between level 2 and level 3 here. For
+         * PublicationXref, it doesn't matter.
+         */
+        private void updateBiopaxNamespace(Element e)
+        {
+                if (e.getNamespace().equals(BP_LEV2))
+                {
+                        e.setNamespace(GpmlFormat.BIOPAX);
+                }
+                for (Object f : e.getChildren())
+                {
+                        updateBiopaxNamespace((Element)f);
+                }
+        }
+        
 }

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);
+        }
+
 }

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

@@ -447 +447 @@
                 mapMappInfoDataVariable(o, e);
         }
-
-        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", nsGPML.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);
-        }
-
+        
         protected void updateBiopax(PathwayElement o, Element e) throws ConverterException
         {