When a reaction references a molecule which is unknown - automaticall…

…y create one with that Id. This happens when the set of molecules is defined after the reaction. This commit resolve the test in error 'CML2Test. testBug2697568' Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Aug 5, 2013 · a6c96d8 · a6c96d8
1 parent ac5a3e7
commit a6c96d8
Showing 1 changed file with 19 additions and 6 deletions.
diff --git a/src/main/org/openscience/cdk/io/cml/CMLReactionModule.java b/src/main/org/openscience/cdk/io/cml/CMLReactionModule.java
@@ -115,18 +115,31 @@ public void startElement(CMLStack xpath, String uri, String local, String raw, A
             }
 //            	cdo.setObjectProperty("Agent", "id", id);
         } else if ("molecule".equals(local)) {
-            // do nothing for now
+            // clear existing molecule data
             super.newMolecule();
             String id = atts.getValue("id");
-            if(id != null) {
-//                cdo.setObjectProperty(objectType, "id", id);
-                currentMolecule.setID(id);
-            }else{
+            if (id != null) {
+                // check for existing molecule of that id
+                IAtomContainer existing = getMoleculeFromID(currentMoleculeSet, id);
+                if (existing != null) {
+                    currentMolecule = existing;
+                } else {
+                    currentMolecule.setID(id);
+                }
+            } else {
             	String ref = atts.getValue("ref");
                 if(ref != null){
                 	IAtomContainer atomC = getMoleculeFromID(currentMoleculeSet, ref);
+
+                    // if there was no molecule create a new one for the reference. this
+                    // happens when the reaction is defined before the molecule set
+                    if (atomC == null) {
+                        atomC = currentChemFile.getBuilder().newInstance(IAtomContainer.class);
+                        atomC.setID(ref);
+                        currentMoleculeSet.addAtomContainer(atomC);
+                    }
+
                 	super.currentMolecule = atomC;
-//                    currentMolecule.setID(ref);
                 }
             }            
         } else {