Removed duplicated cloning, now only down in DSMAnager.runTest(..)

bioclipse · Sep 7, 2012 · 83fdd99 · 83fdd99
1 parent ec3c2e3
commit 83fdd99
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Showing 2 changed files with 56 additions and 34 deletions.
diff --git a/plugins/net.bioclipse.ds.ui/src/net/bioclipse/ds/ui/views/DSView.java b/plugins/net.bioclipse.ds.ui/src/net/bioclipse/ds/ui/views/DSView.java
@@ -826,25 +826,26 @@ private void doRunAllTests() {
 
                     //Start by cloning the molecule. This is to avoid threading 
                     //issues in CDK.
-                    try {
-                        IAtomContainer clonedAC=(IAtomContainer) mol
-                                                    .getAtomContainer().clone();
-
-                        ICDKMolecule clonedMol=new CDKMolecule(clonedAC);
-
-                        preprocessClonedMol(clonedMol);
+//                    try {
+//                        IAtomContainer clonedAC=(IAtomContainer) mol
+//                                                    .getAtomContainer().clone();
+//                        
+//                        ICDKMolecule clonedMol=new CDKMolecule(clonedAC);
+//                        
+//                        preprocessClonedMol(clonedMol);
 
                         logger.debug( "== Testrun: " + tr.getTest().getName() + " started" );
                         tr.setStatus( TestRun.RUNNING );
-                        tr.setMolecule( clonedMol );
+                        tr.setMolecule( mol );
                         viewer.refresh(tr);
                         viewer.setExpandedState( tr, true );
 
-                        runTestAsJobs( clonedMol, ds, tr , mol); 
+                        runTestAsJobs( mol, ds, tr , mol); 
 
-                    } catch ( CloneNotSupportedException e ) {
-                        LogUtils.handleException( e, logger, Activator.PLUGIN_ID);
-                    }
+//                    } 
+//                    catch ( CloneNotSupportedException e ) {
+//                        LogUtils.handleException( e, logger, Activator.PLUGIN_ID);
+//                    }
 
                 }
             }

diff --git a/plugins/net.bioclipse.ds/src/net/bioclipse/ds/business/DSManager.java b/plugins/net.bioclipse.ds/src/net/bioclipse/ds/business/DSManager.java
@@ -165,10 +165,28 @@ public void runTest( String testID, IMolecule mol,
 			IProgressMonitor monitor) 
 	throws BioclipseException{
 
+		ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
+
+
 		IDSTest test = getTest( testID );
 		List<? extends ITestResult> ret=null;
 		try{
-			ret = test.runWarningTest( mol, monitor);
+
+			//Preprocess the molecule
+			ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
+
+			//Clone the mol
+			IAtomContainer clonedAC=null;
+			try {
+				clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
+			} catch (CloneNotSupportedException e) {
+				logger.error("Could not clone mol: " + cdkmol);
+				return;
+			}
+
+			ICDKMolecule clonedMol=new CDKMolecule(clonedAC);
+			ret = test.runWarningTest( clonedMol, monitor);
+
 		}catch (Exception e){
 			//in case of error...
 			LogUtils.debugTrace(logger, e);
@@ -211,38 +229,41 @@ public void runEndpoint( String endpointID, IMolecule mol,
 		//Get manager interface, we want to use the AOP
 		IDSManager ds = Activator.getDefault().getJavaManager();
 		Map<String,BioclipseJob<List<ITestResult>>> jobs = new HashMap<String, BioclipseJob<List<ITestResult>>>();
-		ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
 
-		//Preprocess the molecule
-		ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
 
-		try {
-			cdkmol = cdk.removeExplicitHydrogens(cdkmol);
-			cdkmol=cdk.perceiveAromaticity(cdkmol);
-			cdkmol=cdk.addImplicitHydrogens(cdkmol);
-		} catch (InvocationTargetException e1) {
-			throw new BioclipseException("Could not preprocess molecule: " + e1.getMessage());
-		} 
+		//This is done in abstractDSTest + ds.runTest
+
+//		ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
+//		//Preprocess the molecule
+//		ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
+//
+//		try {
+//			cdkmol = cdk.removeExplicitHydrogens(cdkmol);
+//			cdkmol=cdk.perceiveAromaticity(cdkmol);
+//			cdkmol=cdk.addImplicitHydrogens(cdkmol);
+//		} catch (InvocationTargetException e1) {
+//			throw new BioclipseException("Could not preprocess molecule: " + e1.getMessage());
+//		} 
 
 
 		//Loop over all tests in this endpoint and run them
 		for (IDSTest test : getEndpoint( endpointID ).getTests()){
 
-			//Clone the mol
-			IAtomContainer clonedAC=null;
-			try {
-				clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
-			} catch (CloneNotSupportedException e) {
-				//Should not happen
-				logger.error("Could not clone mol: " + cdkmol);
-				continue;
-			}
-			ICDKMolecule clonedMol=new CDKMolecule(clonedAC);
+//			//Clone the mol
+//			IAtomContainer clonedAC=null;
+//			try {
+//				clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
+//			} catch (CloneNotSupportedException e) {
+//				//Should not happen
+//				logger.error("Could not clone mol: " + cdkmol);
+//				continue;
+//			}
+//			ICDKMolecule clonedMol=new CDKMolecule(clonedAC);
 
 
 			//Start up a job with the test
 			BioclipseJob<List<ITestResult>> job = 
-				ds.runTest( test.getId(), clonedMol, 
+				ds.runTest( test.getId(), mol, 
 						new BioclipseJobUpdateHook<List<ITestResult>>(test.getName()));
 			jobs.put(test.getId(),job);
 			job.schedule();