From eac3f8019fe37f2c84784adef3a7db56598c5cb8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 28 Aug 2017 13:51:42 +0100
Subject: [PATCH] JAL-2608 close any Overview when alignment view is closed

---
 src/jalview/appletgui/AlignFrame.java    |   10 ++++++----
 src/jalview/appletgui/OverviewPanel.java |    4 ++++
 src/jalview/gui/AlignmentPanel.java      |    7 +++++++
 src/jalview/gui/OverviewPanel.java       |   17 ++++++++++++++++-
 4 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b48dec9..7d82dd7 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1590,10 +1590,12 @@ 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();
   }
@@ -1725,7 +1727,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       EditCommand editCommand = (EditCommand) command;
       al = editCommand.getAlignment();
-      Vector comps = (Vector) PaintRefresher.components
+      Vector comps = PaintRefresher.components
               .get(viewport.getSequenceSetId());
       for (int i = 0; i < comps.size(); i++)
       {
@@ -2485,7 +2487,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
             newaf.alignPanel.av.getSequenceSetId());
 
-    Vector comps = (Vector) PaintRefresher.components
+    Vector comps = PaintRefresher.components
             .get(viewport.getSequenceSetId());
     int viewSize = -1;
     for (int i = 0; i < comps.size(); i++)
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index be552c0..3ee3c1d 100755
--- 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;
@@ -325,6 +326,9 @@ 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/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 922e481..b6bd4af 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1625,6 +1625,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (annotationPanel != null)
     {
       annotationPanel.dispose();
+      annotationPanel = null;
     }
 
     if (av != null)
@@ -1654,9 +1655,15 @@ 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 28de801..7cbe8b7 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -38,8 +38,10 @@ 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;
@@ -316,7 +318,20 @@ public class OverviewPanel extends JPanel
   {
     try
     {
-      av.getRanges().removePropertyChangeListener(this);
+      if (av != null)
+      {
+        av.getRanges().removePropertyChangeListener(this);
+      }
+
+      /*
+       * 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
     {
       av = null;
-- 
1.7.10.2