progress reporting and cancel support on iterator

Extended the iterator reachable from the moleculesmanager to support cancel (it seems to work sometimes and sometimes not) and to also give some progress report and time estimate.
bioclipse · May 23, 2012 · 4a81e15 · 4a81e15
1 parent b5e16dc
commit 4a81e15
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Showing 2 changed files with 29 additions and 5 deletions.
diff --git a/...se.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/business/MoleculeTableManager.java b/...se.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/business/MoleculeTableManager.java
@@ -48,6 +48,7 @@
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.OperationCanceledException;
 import org.eclipse.core.runtime.SubMonitor;
 import org.openscience.cdk.Molecule;
@@ -82,7 +83,7 @@ public void createSDFIndex( IFile file,
                                 IProgressMonitor monitor ) {
 
         returner.completeReturn(
-                  new SDFIndexEditorModel(createIndex( file, monitor ) ) );
+                  new SDFIndexEditorModel(createIndex( file, monitor ), monitor ) );
 
     }
 
@@ -381,7 +382,7 @@ private SDFIndexEditorModel saveSDF(IMoleculesEditorModel model, IFile file,
                   SDFileIndex index=
                  createIndex( file, subMonitor.newChild( 1000 ) );
                   if(index!=null) {
-                      sdfModel = new SDFIndexEditorModel(index);
+                      sdfModel = new SDFIndexEditorModel(index, new NullProgressMonitor());
                   }else
                      throw new BioclipseException("Failed to create new index");
          } catch ( CoreException e1 ) {
@@ -499,7 +500,7 @@ public void calculatePropertiesFor( IFile file,
         }
 
         SDFileIndex index = createIndex( file, progress.newChild( 1000 ) );
-        SDFIndexEditorModel model = new SDFIndexEditorModel(index);
+        SDFIndexEditorModel model = new SDFIndexEditorModel(index, new NullProgressMonitor());
 
         IFile target = null;
         SubMonitor loopProgress = progress.newChild( 8000 );

diff --git a/...pse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/business/SDFIndexEditorModel.java b/...pse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/business/SDFIndexEditorModel.java
@@ -31,6 +31,7 @@
 import net.bioclipse.cdk.ui.views.IFileMoleculesEditorModel;
 import net.bioclipse.core.domain.IMolecule.Property;
 import net.bioclipse.core.util.LogUtils;
+import net.bioclipse.core.util.TimeCalculator;
 
 import org.apache.log4j.Logger;
 import org.eclipse.core.resources.IFile;
@@ -39,7 +40,10 @@
 import org.eclipse.core.runtime.IExtension;
 import org.eclipse.core.runtime.IExtensionPoint;
 import org.eclipse.core.runtime.IExtensionRegistry;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.OperationCanceledException;
 import org.eclipse.core.runtime.Platform;
+import org.eclipse.core.runtime.SubProgressMonitor;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
@@ -88,6 +92,8 @@ public class SDFIndexEditorModel implements IFileMoleculesEditorModel,
 
     private boolean dirty = false;
 
+    private IProgressMonitor monitor;
+
     private SDFIndexEditorModel() {
         molProps = new HashMap<Integer, Map<String,Object>>();
         propertyList = new HashMap<String, Class<?>>();
@@ -100,9 +106,10 @@ private SDFIndexEditorModel() {
         }
     }
 
-    public SDFIndexEditorModel(SDFileIndex input) {
+    public SDFIndexEditorModel(SDFileIndex input, IProgressMonitor monitor) {
         this();
         this.input = input;
+        this.monitor = monitor;
         if(getNumberOfMolecules()>0) getMoleculeAt( 0 );
     }
 
@@ -123,6 +130,9 @@ private void setDirty(boolean dirty) {
      */
     public synchronized ICDKMolecule getMoleculeAt( int index ) {
 
+        if (monitor.isCanceled()) {
+            throw new OperationCanceledException();
+        }
         ICDKMolecule mol = edited.get( index );
         if(mol == null) {
             if ( cache.containsKey( index ) )  {
@@ -318,13 +328,26 @@ public Iterator<ICDKMolecule> iterator() {
 
         return new Iterator<ICDKMolecule>() {
 
+            IProgressMonitor m = new SubProgressMonitor( 
+                                         monitor, IProgressMonitor.UNKNOWN );
             int pos = 0;
+            int size = getNumberOfMolecules();
+            long before = System.currentTimeMillis();
             public boolean hasNext() {
                 return pos < getNumberOfMolecules();
             }
 
             public ICDKMolecule next() {
-
+                if ( pos % (size/100) == 0 ) {
+                    synchronized ( monitor ) {
+                        if (monitor.isCanceled()) {
+                            throw new OperationCanceledException();
+                        }
+                    }
+                    monitor.subTask( "Read molecule " + pos + "/" + size+" ("
+                                     +TimeCalculator.generateTimeRemainEst( 
+                                           before, pos, size ) + ")" );
+                }
                 return getMoleculeAt( ++pos );
             }