Merge branch 'bug/JAL-2691_nomultimermapping' into documentation/JAL-2675_release2102b1

[jalview.git] / src / jalview / gui / OverviewPanel.java

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 5fbefb5..3c94f26 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.OverviewDimensions;
@@ -51,8 +52,8 @@ import javax.swing.SwingUtilities;
  * @author $author$
  * @version $Revision$
  */
-public class OverviewPanel extends JPanel implements Runnable,
-        ViewportListenerI
+public class OverviewPanel extends JPanel
+        implements Runnable, ViewportListenerI
 {
   private OverviewDimensions od;
 
@@ -79,9 +80,20 @@ public class OverviewPanel extends JPanel implements Runnable,
     this.av = alPanel.av;
     this.ap = alPanel;
 
-    od = new OverviewDimensionsShowHidden(av.getRanges(),
-            (av.isShowAnnotation() && av
-                    .getAlignmentConservationAnnotation() != null));
+    showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+            true);
+    if (showHidden)
+    {
+      od = new OverviewDimensionsShowHidden(av.getRanges(),
+            (av.isShowAnnotation()
+                    && av.getAlignmentConservationAnnotation() != null));
+    }
+    else
+    {
+      od = new OverviewDimensionsHideHidden(av.getRanges(),
+              (av.isShowAnnotation()
+                      && av.getAlignmentConservationAnnotation() != null));
+    }
 
     setSize(od.getWidth(), od.getHeight());
 
@@ -110,22 +122,22 @@ public class OverviewPanel extends JPanel implements Runnable,
       @Override
       public void mouseDragged(MouseEvent evt)
       {
-        if (!SwingUtilities.isRightMouseButton(evt)
-                && !av.getWrapAlignment())
+        if (!SwingUtilities.isRightMouseButton(evt))
         {
           if (draggingBox)
           {
-            od.adjustViewportFromMouse(evt.getX(),
-                    evt.getY(), av.getAlignment().getHiddenSequences(),
+            // set the mouse position as a fixed point in the box
+            // and drag relative to that position
+            od.adjustViewportFromMouse(evt.getX(), evt.getY(),
+                    av.getAlignment().getHiddenSequences(),
                     av.getAlignment().getHiddenColumns());
           }
           else
           {
-            od.updateViewportFromMouse(evt.getX(), evt.getY(), av
-                  .getAlignment().getHiddenSequences(), av.getAlignment()
-                  .getHiddenColumns());
+            od.updateViewportFromMouse(evt.getX(), evt.getY(),
+                    av.getAlignment().getHiddenSequences(),
+                    av.getAlignment().getHiddenColumns());
           }
-
         }
       }
 
@@ -157,7 +169,7 @@ public class OverviewPanel extends JPanel implements Runnable,
             showPopupMenu(evt);
           }
         }
-        else if (!av.getWrapAlignment())
+        else
         {
           if (!od.isPositionInBox(evt.getX(), evt.getY()))
           {
@@ -195,11 +207,8 @@ public class OverviewPanel extends JPanel implements Runnable,
           showPopupMenu(evt);
         }
       }
-
-
     });
 
-
     updateOverviewImage();
   }
 
@@ -237,15 +246,15 @@ public class OverviewPanel extends JPanel implements Runnable,
     {
       showHidden = false;
       od = new OverviewDimensionsHideHidden(av.getRanges(),
-              (av.isShowAnnotation() && av
-                      .getAlignmentConservationAnnotation() != null));
+              (av.isShowAnnotation()
+                      && av.getAlignmentConservationAnnotation() != null));
     }
     else
     {
       showHidden = true;
       od = new OverviewDimensionsShowHidden(av.getRanges(),
-              (av.isShowAnnotation() && av
-                      .getAlignmentConservationAnnotation() != null));
+              (av.isShowAnnotation()
+                      && av.getAlignmentConservationAnnotation() != null));
     }
     oviewCanvas.resetOviewDims(od);
     updateOverviewImage();
@@ -257,12 +266,20 @@ public class OverviewPanel extends JPanel implements Runnable,
    */
   public void updateOverviewImage()
   {
+    if (oviewCanvas == null)
+    {
+      /*
+       * panel has been disposed
+       */
+      return;
+    }
+
     if ((getWidth() > 0) && (getHeight() > 0))
     {
       od.setWidth(getWidth());
       od.setHeight(getHeight());
     }
-    
+
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
     if (oviewCanvas.restartDraw())
@@ -273,16 +290,15 @@ public class OverviewPanel extends JPanel implements Runnable,
     Thread thread = new Thread(this);
     thread.start();
     repaint();
-
   }
 
   @Override
   public void run()
   {
     oviewCanvas.draw(av.isShowSequenceFeatures(),
-            (av.isShowAnnotation() && av
-                    .getAlignmentConservationAnnotation() != null), ap
-                    .getSeqPanel().seqCanvas.getFeatureRenderer());
+            (av.isShowAnnotation()
+                    && av.getAlignmentConservationAnnotation() != null),
+            ap.getSeqPanel().seqCanvas.getFeatureRenderer());
     setBoxPosition();
   }
 
@@ -293,8 +309,8 @@ public class OverviewPanel extends JPanel implements Runnable,
    */
   private void setBoxPosition()
   {
-    od.setBoxPosition(av.getAlignment().getHiddenSequences(), av
-            .getAlignment().getHiddenColumns());
+    od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+            av.getAlignment().getHiddenColumns());
     repaint();
   }
 
@@ -303,4 +319,21 @@ public class OverviewPanel extends JPanel implements Runnable,
   {
     setBoxPosition();
   }
+
+  /**
+   * Removes this object as a property change listener, and nulls references
+   */
+  protected void dispose()
+  {
+    try
+    {
+      av.getRanges().removePropertyChangeListener(this);
+    } finally
+    {
+      av = null;
+      oviewCanvas = null;
+      ap = null;
+      od = null;
+    }
+  }
 }