JAL-3117 raise AlignFrame or SplitFrame when Overview clicked

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4a18067..604e813 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -38,6 +38,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
 import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyAdapter;
@@ -412,7 +413,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
     {
-      this.overviewMenuItem_actionPerformed(null);
+      this.overviewMenuItem_actionPerformed();
     }
 
     addKeyListener();
@@ -479,7 +480,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
 
                   ap.updateLayout();
-                  ap.setSelected(true);
+                  ap.setSelected(true, true);
                   ap.alignFrame.setMenusForViewport();
 
                 }
@@ -3423,13 +3424,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Opens a new Overview window for the current alignment view, unless one is
+   * open already, in which case does nothing.
    */
   @Override
-  public void overviewMenuItem_actionPerformed(ActionEvent e)
+  public void overviewMenuItem_actionPerformed()
   {
     if (alignPanel.overviewPanel != null)
     {
@@ -3460,24 +3459,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       frame.addKeyListener(getKeyListeners()[0]);
     }
-    
-    /*
-     * bring alignment panel to front when Overview gets focus
-     * (even after New View / eXpand / Gather!)
-     */
+
     final AlignmentPanel ap = alignPanel;
     frame.addFocusListener(new FocusAdapter()
     {
       @Override
       public void focusGained(FocusEvent e)
       {
+        /*
+         * bring alignment panel to front when Overview gets focus
+         * (AlignFrame, or SplitFrame if alignment is in a split frame)
+         */
+        ap.setSelected(true, true);
+        
+        /*
+         * restore focus to the Overview
+         * (temporarily removing the focus listener)
+         */
+        FocusListener me = frame.getFocusListeners()[0];
+        frame.removeFocusListener(me);
         try
         {
-          ap.alignFrame.setSelected(true);
-          ap.alignFrame.setIcon(false);
-          ap.alignFrame.setDisplayedView(ap);
+          frame.setSelected(true);
         } catch (PropertyVetoException e1)
         {
+        } finally
+        {
+          /*
+           * restore the listener _after_ setSelected has run
+           */
+          SwingUtilities.invokeLater(new Runnable()
+          {
+            @Override
+            public void run()
+            {
+              frame.addFocusListener(me);
+            }
+          });
         }
       }
     });

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 45e4b95..c2d94dc 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,29 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.ImageExporter.ImageWriterI;
-import jalview.io.HTMLOutput;
-import jalview.jbgui.GAlignmentPanel;
-import jalview.math.AlignmentDimension;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Container;
@@ -60,6 +37,7 @@ import java.awt.print.Printable;
 import java.awt.print.PrinterException;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
@@ -67,6 +45,30 @@ import java.util.List;
 
 import javax.swing.SwingUtilities;
 
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * DOCUMENT ME!
  * 
@@ -122,7 +124,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
-//     setBackground(Color.white);  // BH 2019
+    // setBackground(Color.white); // BH 2019
     alignFrame = af;
     this.av = av;
     setSeqPanel(new SeqPanel(av, this));
@@ -471,8 +473,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
-                + 1);
+        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -572,7 +573,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension e = idPanel.getSize();
     alabels.setSize(new Dimension(e.width, annotationHeight));
 
-
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -1020,8 +1020,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq - 1);
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
+            startRes, endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
@@ -1065,8 +1065,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @throws PrinterException
    */
-  public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
-          Graphics g) throws PrinterException
+  public int printWrappedAlignment(int pageWidth, int pageHeight,
+          int pageNumber, Graphics g) throws PrinterException
   {
     getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
             getHeight());
@@ -1118,8 +1118,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     g.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
-            totalHeight, 0);
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
+            pageWidth - idWidth, totalHeight, 0);
 
     if ((pageNumber * pageHeight) < totalHeight)
     {
@@ -1284,13 +1284,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(column) + "");
+              triplet = ResidueProperties.nucleotideName
+                      .get(seq.getCharAt(column) + "");
             }
             else
             {
-              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
-                      + "");
+              triplet = ResidueProperties.aa2Triplet
+                      .get(seq.getCharAt(column) + "");
             }
 
             if (triplet == null)
@@ -1307,7 +1307,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\"")
                         .append((idWidth + column * av.getCharWidth()))
                         .append(",").append(sy).append(",")
-                        .append((idWidth + (column + 1) * av.getCharWidth()))
+                        .append((idWidth
+                                + (column + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
                         .append(seqPos).append(" ").append(triplet);
@@ -1333,7 +1334,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             }
             if (!Comparison.isGap(seq.getCharAt(column)))
             {
-              List<SequenceFeature> features = seq.findFeatures(column, column);
+              List<SequenceFeature> features = seq.findFeatures(column,
+                      column);
               for (SequenceFeature sf : features)
               {
                 if (sf.isContactFeature())
@@ -1522,29 +1524,40 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Make/Unmake this alignment panel the current input focus
+   * Make/Unmake this alignment panel the current input focus, optionally
+   * restoring it if iconised
    * 
-   * @param b
+   * @param sel
+   * @param deIconify
    */
-  public void setSelected(boolean b)
+  public void setSelected(boolean sel, boolean deIconify)
   {
     try
     {
-      if (alignFrame.getSplitViewContainer() != null)
+      SplitContainerI splitFrame = alignFrame.getSplitViewContainer();
+      if (splitFrame != null)
       {
         /*
          * bring enclosing SplitFrame to front first if there is one
          */
-        ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
+        ((SplitFrame) splitFrame).setSelected(sel);
+        if (sel && deIconify)
+        {
+          ((SplitFrame) splitFrame).setIcon(false);
+        }
       }
-      alignFrame.setSelected(b);
-    } catch (Exception ex)
-    {
-    }
+      alignFrame.setSelected(sel);
 
-    if (b)
+      if (sel)
+      {
+        if (deIconify)
+        {
+          alignFrame.setIcon(false);
+        }
+        alignFrame.setDisplayedView(this);
+      }
+    } catch (PropertyVetoException e)
     {
-      alignFrame.setDisplayedView(this);
     }
   }
 

diff --git a/src/jalview/gui/ViewSelectionMenu.java b/src/jalview/gui/ViewSelectionMenu.java
index a1529fc..d7909ac 100644 (file)
--- a/src/jalview/gui/ViewSelectionMenu.java
+++ b/src/jalview/gui/ViewSelectionMenu.java
@@ -20,9 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.util.MessageManager;
-
 import java.awt.Component;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -38,6 +35,9 @@ import javax.swing.JMenuItem;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.util.MessageManager;
+
 /**
  * this is an implementation of an abstract Jalview GUI class that provides a
  * dialog/menu which allows the user to select/deselect specific views from a
@@ -268,7 +268,7 @@ public class ViewSelectionMenu extends JMenu
         {
           try
           {
-            ap.setSelected(false);
+            ap.setSelected(false, false);
           } catch (Exception ex)
           {
           }
@@ -279,7 +279,7 @@ public class ViewSelectionMenu extends JMenu
         {
           try
           {
-            ap.setSelected(true);
+            ap.setSelected(true, false);
           } catch (Exception ex)
           {
           }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6685c67..125dcb3 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,18 +20,6 @@
  */
 package jalview.jbgui;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.GeneticCodeI;
-import jalview.analysis.GeneticCodes;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.io.FileFormats;
-import jalview.schemes.ResidueColourScheme;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
@@ -61,6 +49,18 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 @SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
@@ -687,7 +687,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        overviewMenuItem_actionPerformed(e);
+        overviewMenuItem_actionPerformed();
       }
     });
 
@@ -2313,7 +2313,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void overviewMenuItem_actionPerformed(ActionEvent e)
+  protected void overviewMenuItem_actionPerformed()
   {
   }
 

diff --git a/test/jalview/gui/FreeUpMemoryTest.java b/test/jalview/gui/FreeUpMemoryTest.java
index 3a5a9e4..956ba5c 100644 (file)
--- a/test/jalview/gui/FreeUpMemoryTest.java
+++ b/test/jalview/gui/FreeUpMemoryTest.java
@@ -204,7 +204,7 @@ public class FreeUpMemoryTest
     /*
      * open an Overview window
      */
-    af.overviewMenuItem_actionPerformed(null);
+    af.overviewMenuItem_actionPerformed();
     assertNotNull(af.alignPanel.overviewPanel);
 
     /*