Merge branch 'features/JAL-2608closeOverview' into develop

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 676d3cf..b8f3a30 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1603,10 +1603,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       System.exit(0);
     }
-    else
+
+    viewport = null;
+    if (alignPanel != null && alignPanel.overviewPanel != null)
     {
+      alignPanel.overviewPanel.dispose();
     }
-    viewport = null;
     alignPanel = null;
     this.dispose();
   }

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 0256055..8ce597d 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -31,6 +31,7 @@ import java.awt.BorderLayout;
 import java.awt.CheckboxMenuItem;
 import java.awt.Cursor;
 import java.awt.Dimension;
+import java.awt.Frame;
 import java.awt.Panel;
 import java.awt.PopupMenu;
 import java.awt.event.ComponentAdapter;
@@ -322,6 +323,9 @@ public class OverviewPanel extends Panel implements Runnable,
     try
     {
       av.getRanges().removePropertyChangeListener(this);
+      Frame parent = (Frame) getParent();
+      parent.dispose();
+      parent.setVisible(false);
     } finally
     {
       av = null;

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 32507fe..fe99187 100755 (executable)
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -24,8 +24,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Component;
-import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
@@ -78,13 +78,14 @@ public class PaintRefresher
       return;
     }
 
-    for (String id : components.keySet())
+    Iterator<String> it = components.keySet().iterator();
+    while (it.hasNext())
     {
-      Vector<Component> comps = components.get(id);
+      Vector<Component> comps = components.get(it.next());
       comps.removeElement(comp);
-      if (comps.size() == 0)
+      if (comps.isEmpty())
       {
-        components.remove(id);
+        it.remove();
       }
     }
   }
@@ -110,10 +111,10 @@ public class PaintRefresher
       return;
     }
 
-    Enumeration<Component> e = comps.elements();
-    while (e.hasMoreElements())
+    Iterator<Component> it = comps.iterator();
+    while (it.hasNext())
     {
-      comp = e.nextElement();
+      comp = it.next();
 
       if (comp == source)
       {
@@ -122,7 +123,7 @@ public class PaintRefresher
 
       if (!comp.isValid())
       {
-        comps.removeElement(comp);
+        it.remove();
       }
       else if (validateSequences && comp instanceof AlignmentPanel
               && source instanceof AlignmentPanel)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b2c4809..07c65fe 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1604,6 +1604,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (annotationPanel != null)
     {
       annotationPanel.dispose();
+      annotationPanel = null;
     }
 
     if (av != null)
@@ -1633,9 +1634,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void closeChildFrames()
   {
+    if (overviewPanel != null)
+    {
+      overviewPanel.dispose();
+      overviewPanel = null;
+    }
     if (calculationDialog != null)
     {
       calculationDialog.closeFrame();
+      calculationDialog = null;
     }
   }
 

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 51d7a84..9ddb751 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -40,8 +40,10 @@ import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseMotionAdapter;
 import java.beans.PropertyChangeEvent;
+import java.beans.PropertyVetoException;
 
 import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
@@ -350,8 +352,22 @@ public class OverviewPanel extends JPanel
   {
     try
     {
-      av.getRanges().removePropertyChangeListener(this);
+      if (av != null)
+      {
+        av.getRanges().removePropertyChangeListener(this);
+      }
+
       oviewCanvas.dispose();
+
+      /*
+       * close the parent frame (which also removes it from the
+       * Desktop Windows menu)
+       */
+      ((JInternalFrame) SwingUtilities.getAncestorOfClass(
+              JInternalFrame.class, (this))).setClosed(true);
+    } catch (PropertyVetoException e)
+    {
+      // ignore
     } finally
     {
       progressPanel = null;

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index d731e70..ced5544 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -26,9 +26,9 @@ import jalview.datamodel.SequenceI;
 import java.awt.Component;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
-import java.util.Map.Entry;
 
 /**
  * Route datamodel/view update events for a sequence set to any display
@@ -74,26 +74,21 @@ public class PaintRefresher
    */
   public static void RemoveComponent(Component comp)
   {
-    List<String> emptied = new ArrayList<String>();
-    for (Entry<String, List<Component>> registered : components.entrySet())
+    if (components == null)
     {
-      String id = registered.getKey();
-      List<Component> comps = components.get(id);
+      return;
+    }
+
+    Iterator<String> it = components.keySet().iterator();
+    while (it.hasNext())
+    {
+      List<Component> comps = components.get(it.next());
       comps.remove(comp);
       if (comps.isEmpty())
       {
-        emptied.add(id);
+        it.remove();
       }
     }
-
-    /*
-     * Remove now empty ids after the above (to avoid
-     * ConcurrentModificationException).
-     */
-    for (String id : emptied)
-    {
-      components.remove(id);
-    }
   }
 
   public static void Refresh(Component source, String id)