update

uk/ac/sanger/artemis/components/ValidateViewer.java

+/* ValidateViewer
+ *
+ * created: 2013
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2013 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
 package uk.ac.sanger.artemis.components;
 
 import java.awt.event.ActionEvent;
@@ -5,12 +28,10 @@ import java.awt.event.ActionListener;
 
 import javax.swing.JButton;
 
-import uk.ac.sanger.artemis.EntryChangeEvent;
 import uk.ac.sanger.artemis.EntryGroup;
 import uk.ac.sanger.artemis.EntryGroupChangeEvent;
 import uk.ac.sanger.artemis.EntryGroupChangeListener;
-import uk.ac.sanger.artemis.FeatureChangeEvent;
-import uk.ac.sanger.artemis.FeatureChangeListener;
+import uk.ac.sanger.artemis.Feature;
 import uk.ac.sanger.artemis.FeatureVector;
 import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
@@ -35,36 +56,27 @@ class ValidateViewer extends FileViewer implements EntryGroupChangeListener
 
     update(features);
     setVisible(true);
-    
-    
+
     final JButton fixButton = new JButton("Auto-Fix");
     fixButton.addActionListener(new ActionListener() 
     {
       public void actionPerformed(ActionEvent e) 
       {
-        //entryGrp.getActionController().startAction();
-        for(int i=0; i<features.size(); i++)
+        try
         {
-          if(features.elementAt(i).getEmblFeature() instanceof GFFStreamFeature)
-          {
-            fixBoundary((GFFStreamFeature)features.elementAt(i).getEmblFeature());
-          }
+          entryGrp.getActionController().startAction();
+          for(int i=0; i<features.size(); i++)
+            fixBoundary(features.elementAt(i));
+        }
+        finally
+        {
+          //update(features);
+          entryGrp.getActionController().endAction();
         }
-        
-        //entryGrp.entryChanged(new EntryChangeEvent());
-        //entryGrp.getActionController().endAction();
       }
     });
     button_panel.add(fixButton);
-
-    entryGrp.addFeatureChangeListener(new FeatureChangeListener(){
-      public void featureChanged(FeatureChangeEvent event)
-      {
-        System.out.println("HEREREE");
-        update(features);
-      }
-    });
-    
+ 
     entryGrp.addEntryGroupChangeListener(new EntryGroupChangeListener(){
       public void entryGroupChanged(EntryGroupChangeEvent event)
       {
@@ -87,14 +99,18 @@ class ValidateViewer extends FileViewer implements EntryGroupChangeListener
       gffTest.featureValidate(features.elementAt(i).getEmblFeature(), this);
   }
   
-  private void fixBoundary(final GFFStreamFeature gffFeature)
+  private void fixBoundary(final Feature feature)
   {
+    if( ! (feature.getEmblFeature() instanceof GFFStreamFeature) )
+      return;
+    
+    final GFFStreamFeature gffFeature = (GFFStreamFeature) feature.getEmblFeature();
     final ChadoCanonicalGene gene = gffFeature.getChadoGene();
     if(gene != null && !gene.getGene().isReadOnly() && GeneUtils.isBoundaryOK(gene) > 0)
     {
-      System.out.println(GeneUtils.getUniqueName(gffFeature));
+      //updatedFeatures.add(feature);
       
-      GeneUtils.checkGeneBoundary(gene);
+      GeneUtils.checkGeneBoundary(gene, false);
     }
   }