Merge branch 'releases/Release_2_10_2b1_Branch' of http://source.jalview.org/git...

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 74c2112..51d7a84 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.renderer.OverviewRenderer;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -52,8 +53,8 @@ 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;
 
@@ -82,9 +83,20 @@ 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));
+    }
 
     setLayout(new BorderLayout());
     progressPanel = new ProgressPanel(OverviewRenderer.UPDATE,
@@ -140,15 +152,15 @@ public class OverviewPanel extends JPanel implements Runnable,
           {
             // 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(),
+            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());
           }
         }
       }
@@ -183,11 +195,12 @@ public class OverviewPanel extends JPanel implements Runnable,
         }
         else
         {
+          // don't do anything if the mouse press is in the overview's box
+          // (wait to see if it's a drag instead)
+          // otherwise update the viewport
           if (!od.isPositionInBox(evt.getX(), evt.getY()))
           {
-            // don't do anything if the mouse press is in the overview's box
-            // (wait to see if it's a drag instead)
-            // otherwise update the viewport
+            draggingBox = false;
             od.updateViewportFromMouse(evt.getX(), evt.getY(),
                     av.getAlignment().getHiddenSequences(),
                     av.getAlignment().getHiddenColumns());
@@ -203,15 +216,6 @@ public class OverviewPanel extends JPanel implements Runnable,
       }
 
       @Override
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (draggingBox)
-        {
-          draggingBox = false;
-        }
-      }
-
-      @Override
       public void mouseClicked(MouseEvent evt)
       {
         if (SwingUtilities.isRightMouseButton(evt))
@@ -256,15 +260,15 @@ 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();
@@ -308,11 +312,14 @@ public class OverviewPanel extends JPanel implements Runnable,
   @Override
   public void run()
   {
-    oviewCanvas.draw(av.isShowSequenceFeatures(),
-            (av.isShowAnnotation() && av
-                    .getAlignmentConservationAnnotation() != null), ap
-                    .getSeqPanel().seqCanvas.getFeatureRenderer());
-    setBoxPosition();
+    if (oviewCanvas != null)
+    {
+      oviewCanvas.draw(av.isShowSequenceFeatures(),
+              (av.isShowAnnotation()
+                      && av.getAlignmentConservationAnnotation() != null),
+              ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+      setBoxPosition();
+    }
   }
 
   /**
@@ -322,9 +329,12 @@ public class OverviewPanel extends JPanel implements Runnable,
    */
   private void setBoxPosition()
   {
-    od.setBoxPosition(av.getAlignment().getHiddenSequences(), av
-            .getAlignment().getHiddenColumns());
-    repaint();
+    if (od != null)
+    {
+      od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+              av.getAlignment().getHiddenColumns());
+      repaint();
+    }
   }
 
   @Override
@@ -341,6 +351,7 @@ public class OverviewPanel extends JPanel implements Runnable,
     try
     {
       av.getRanges().removePropertyChangeListener(this);
+      oviewCanvas.dispose();
     } finally
     {
       progressPanel = null;