Return list<ICDKMolecule> and enforce 1 conformation when coordinate …

…selected.
bioclipse · Aug 30, 2011 · 2fd77bf · 2fd77bf
1 parent 0fe377e
commit 2fd77bf
Show file tree

Hide file tree

Showing 2 changed files with 50 additions and 19 deletions.
diff --git a/...ins/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/BalloonManager.java b/...ins/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/BalloonManager.java
@@ -26,13 +26,15 @@
 import net.bioclipse.core.ResourcePathTransformer;
 import net.bioclipse.core.business.BioclipseException;
 import net.bioclipse.core.domain.IMolecule;
+import net.bioclipse.managers.business.IBioclipseManager;
 import net.bioclipse.ui.business.Activator;
 import net.bioclipse.ui.business.IUIManager;
 
 import org.apache.log4j.Logger;
 import org.eclipse.core.resources.IContainer;
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.Platform;
 import org.eclipse.core.runtime.content.IContentDescription;
 import org.eclipse.core.runtime.content.IContentType;
@@ -48,7 +50,7 @@
  * 
  * @author ola
  */
-public class BalloonManager implements IBalloonManager {
+public class BalloonManager implements IBioclipseManager {
 
     private static final Logger logger 
         = Logger.getLogger( BalloonManager.class );
@@ -74,37 +76,52 @@ public String generate3Dcoordinates( String inputfile )
 
 
 
-    public List<IMolecule> generateMultiple3Dcoordinates(
-                                                    List<IMolecule> molecules )
+    public List<ICDKMolecule> generateMultiple3Dcoordinates(
+                                                    List<IMolecule> molecules, IProgressMonitor monitor )
                                                     throws BioclipseException {
 
-        return generateMultiple3Dconformations( molecules, 1 );
+        return generateMultiple3Dconformations( molecules, 1, monitor );
     }
 
 
-    public List<IMolecule> generateMultiple3Dconformations(
+    public List<ICDKMolecule> generateMultiple3Dconformations(
                                                      List<IMolecule> molecules,
-                                                     int numConf )
+                                                     int numConf, IProgressMonitor monitor )
                                                      throws BioclipseException {
 
-        List<IMolecule> retlist=new ArrayList<IMolecule>();
+        List<ICDKMolecule> retlist=new ArrayList<ICDKMolecule>();
+        monitor.beginTask("Balloon conformation generation", molecules.size());
 
+        int i=0;
         for (IMolecule mol : molecules){
-            List<ICDKMolecule> conformations = generate3Dconformations( mol, 
-                                                                      numConf );
-            if (numConf==1)
-                retlist.add( conformations.get( 0 ));
-            else
-                retlist.addAll( conformations);
+        	i++;
+
+        	List<ICDKMolecule> conformations;
+			try {
+				conformations = generate3Dconformations( mol,numConf );
+
+				//We only enforce one conformation for target conf 1
+	            if (numConf==1)
+	                retlist.add( conformations.get( 0 ));
+	            else
+	                retlist.addAll( conformations);
+			} catch (BioclipseException e) {
+				logger.error("Balloon failed on mol " + i + ". Reason: " + e.getMessage());
+			}
+            monitor.worked(1);
+            if (i%5==0)
+            	monitor.subTask("Processed: " + i + "/" + molecules.size() +" molecules");
         }
+
+        monitor.done();
 
        return retlist;
    }
 
     /**
      * Generate 3D conf for a single molecule
      */
-    public IMolecule generate3Dcoordinates( IMolecule molecule ) 
+    public ICDKMolecule generate3Dcoordinates( IMolecule molecule ) 
                   throws BioclipseException {
 
        return generate3Dconformations( molecule, 1 ).get( 0 );

diff --git a/...ns/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/IBalloonManager.java b/...ns/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/IBalloonManager.java
@@ -12,6 +12,8 @@
 
 import java.util.List;
 
+import org.eclipse.core.runtime.IProgressMonitor;
+
 import net.bioclipse.cdk.domain.ICDKMolecule;
 import net.bioclipse.core.PublishedClass;
 import net.bioclipse.core.PublishedMethod;
@@ -144,7 +146,7 @@ String generate3Dconformations( String inputfile,
                      methodSummary = "Return a new molecule with 3D " +
                      		"coordinates generated by Balloon.")
     @Recorded
-    public IMolecule generate3Dcoordinates( IMolecule molecule ) 
+    public ICDKMolecule generate3Dcoordinates( IMolecule molecule ) 
     throws BioclipseException;
 
     @PublishedMethod(
@@ -161,20 +163,32 @@ public List<ICDKMolecule> generate3Dconformations( IMolecule molecule, int numCo
                      methodSummary = "Return a list of molecules with 3D " +
                         "coordinates generated by Balloon.")
     @Recorded
-    public List<IMolecule> generateMultiple3Dcoordinates( 
+    public List<ICDKMolecule> generateMultiple3Dcoordinates( 
                                                      List<IMolecule> molecules ) 
-    throws BioclipseException;
+                                                     throws BioclipseException;
+
+    public List<ICDKMolecule> generateMultiple3Dcoordinates( 
+    												List<IMolecule> molecules, 
+    												IProgressMonitor monitor ) 
+    												throws BioclipseException;
 
+
     @PublishedMethod(
                      params = "List<IMolecule> molecules, int numConf",
                      methodSummary = "Return a list of molecule with the " +
                      		"selected " +
                         "number of target 3D " +
                         "conformations generated by Balloon.")
     @Recorded
-    public List<IMolecule> generateMultiple3Dconformations( 
+    public List<ICDKMolecule> generateMultiple3Dconformations( 
                                                       List<IMolecule> molecules, 
                                                       int numConf) 
-    throws BioclipseException;
+                                                      throws BioclipseException;
+
+    public List<ICDKMolecule> generateMultiple3Dconformations( 
+    												   List<IMolecule> molecules, 
+    												   int numConf,
+    												   IProgressMonitor monitor) 
+    												   throws BioclipseException;
 
 }