From e2399fe0a610faf5dee11a68a8643c34e3ef2490 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 11 Jan 2016 12:37:52 +0000
Subject: [PATCH] JAL-1989 additional ways to 'mirror' show/hide columns in
 split frame

---
 src/jalview/appletgui/AlignFrame.java |   13 +++
 src/jalview/appletgui/ScalePanel.java |  185 +++++++++++++++++++--------------
 src/jalview/gui/AlignFrame.java       |    5 +
 src/jalview/gui/ScalePanel.java       |  179 +++++++++++++++++--------------
 4 files changed, 224 insertions(+), 158 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index cd679fc..b7e7899 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -759,6 +759,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         viewport.showAllHiddenColumns();
       }
+      viewport.sendSelection();
     }
   }
 
@@ -1080,11 +1081,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == invertSequenceMenuItem)
     {
       invertSequenceMenuItem_actionPerformed();
+      // uncomment to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == invertColSel)
     {
       viewport.invertColumnSelection();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == remove2LeftMenuItem)
     {
@@ -1118,27 +1122,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.showAllHiddenColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showSeqs)
     {
       viewport.showAllHiddenSeqs();
       alignPanel.paintAlignment(true);
+      // uncomment if we want to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == hideColumns)
     {
       viewport.hideSelectedColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == hideSequences
             && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
       alignPanel.paintAlignment(true);
+      // uncomment if we want to slave sequence selections in split frame
+      // viewport.sendSelection();
     }
     else if (source == hideAllButSelection)
     {
       toggleHiddenRegions(false, false);
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == hideAllSelection)
     {
@@ -1147,12 +1158,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.hideAllSelectedSeqs();
       viewport.hideSelectedColumns();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showAllHidden)
     {
       viewport.showAllHiddenColumns();
       viewport.showAllHiddenSeqs();
       alignPanel.paintAlignment(true);
+      viewport.sendSelection();
     }
     else if (source == showGroupConsensus)
     {
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index cd50f3f..3c6a4f1 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -89,112 +89,137 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     max = res;
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      PopupMenu pop = new PopupMenu();
-      if (reveal != null)
+      rightMouseButtonPressed(evt, res);
+    }
+    else
+    {
+      leftMouseButtonPressed(evt, res);
+    }
+  }
+
+  /**
+   * Handles left mouse button pressed (selection / clear selections)
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void leftMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    if (!evt.isControlDown() && !evt.isShiftDown())
+    {
+      av.getColumnSelection().clear();
+    }
+
+    av.getColumnSelection().addElement(res);
+    SequenceGroup sg = new SequenceGroup();
+    for (int i = 0; i < av.getAlignment().getSequences().size(); i++)
+    {
+      sg.addSequence(av.getAlignment().getSequenceAt(i), false);
+    }
+
+    sg.setStartRes(res);
+    sg.setEndRes(res);
+    av.setSelectionGroup(sg);
+
+    if (evt.isShiftDown())
+    {
+      int min = Math.min(av.getColumnSelection().getMin(), res);
+      int max = Math.max(av.getColumnSelection().getMax(), res);
+      for (int i = min; i < max; i++)
       {
-        MenuItem item = new MenuItem(
-                MessageManager.getString("label.reveal"));
-        item.addActionListener(new ActionListener()
-        {
-          @Override
-          public void actionPerformed(ActionEvent e)
-          {
-            av.showColumn(reveal[0]);
-            reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
-          }
-        });
-        pop.add(item);
+        av.getColumnSelection().addElement(i);
+      }
+      sg.setStartRes(min);
+      sg.setEndRes(max);
+    }
+    ap.paintAlignment(true);
+    av.sendSelection();
+  }
 
-        if (av.getColumnSelection().hasManyHiddenColumns())
+  /**
+   * Handles right mouse button press. If pressed in a selected column, opens
+   * context menu for 'Hide Columns'. If pressed on a hidden columns marker,
+   * opens context menu for 'Reveal / Reveal All'. Else does nothing.
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void rightMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    PopupMenu pop = new PopupMenu();
+    if (reveal != null)
+    {
+      MenuItem item = new MenuItem(
+              MessageManager.getString("label.reveal"));
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          item = new MenuItem(MessageManager.getString("action.reveal_all"));
-          item.addActionListener(new ActionListener()
+          av.showColumn(reveal[0]);
+          reveal = null;
+          ap.paintAlignment(true);
+          if (ap.overviewPanel != null)
           {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              av.showAllHiddenColumns();
-              reveal = null;
-              ap.paintAlignment(true);
-              if (ap.overviewPanel != null)
-              {
-                ap.overviewPanel.updateOverviewImage();
-              }
-            }
-          });
-          pop.add(item);
+            ap.overviewPanel.updateOverviewImage();
+          }
+          av.sendSelection();
         }
-        this.add(pop);
-        pop.show(this, evt.getX(), evt.getY());
-      }
-      else if (av.getColumnSelection().contains(res))
+      });
+      pop.add(item);
+
+      if (av.getColumnSelection().hasManyHiddenColumns())
       {
-        MenuItem item = new MenuItem(
-                MessageManager.getString("label.hide_columns"));
+        item = new MenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
         {
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            av.hideColumns(res, res);
-            if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av
-                            .getAlignment().getHeight())
-            {
-              av.setSelectionGroup(null);
-            }
-
+            av.showAllHiddenColumns();
+            reveal = null;
             ap.paintAlignment(true);
             if (ap.overviewPanel != null)
             {
               ap.overviewPanel.updateOverviewImage();
             }
+            av.sendSelection();
           }
         });
         pop.add(item);
-        this.add(pop);
-        pop.show(this, evt.getX(), evt.getY());
       }
+      this.add(pop);
+      pop.show(this, evt.getX(), evt.getY());
     }
-    else
-    // LEFT MOUSE TO SELECT
+    else if (av.getColumnSelection().contains(res))
     {
-      if (!evt.isControlDown() && !evt.isShiftDown())
-      {
-        av.getColumnSelection().clear();
-      }
-
-      av.getColumnSelection().addElement(res);
-      SequenceGroup sg = new SequenceGroup();
-      for (int i = 0; i < av.getAlignment().getSequences().size(); i++)
-      {
-        sg.addSequence(av.getAlignment().getSequenceAt(i), false);
-      }
-
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      av.setSelectionGroup(sg);
-
-      if (evt.isShiftDown())
+      MenuItem item = new MenuItem(
+              MessageManager.getString("label.hide_columns"));
+      item.addActionListener(new ActionListener()
       {
-        int min = Math.min(av.getColumnSelection().getMin(), res);
-        int max = Math.max(av.getColumnSelection().getMax(), res);
-        for (int i = min; i < max; i++)
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          av.getColumnSelection().addElement(i);
+          av.hideColumns(res, res);
+          if (av.getSelectionGroup() != null
+                  && av.getSelectionGroup().getSize() == av
+                          .getAlignment().getHeight())
+          {
+            av.setSelectionGroup(null);
+          }
+
+          ap.paintAlignment(true);
+          if (ap.overviewPanel != null)
+          {
+            ap.overviewPanel.updateOverviewImage();
+          }
+          av.sendSelection();
         }
-        sg.setStartRes(min);
-        sg.setEndRes(max);
-      }
+      });
+      pop.add(item);
+      this.add(pop);
+      pop.show(this, evt.getX(), evt.getY());
     }
-
-    ap.paintAlignment(true);
-    av.sendSelection();
   }
 
   @Override
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8aae64f..c615f6c 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2966,6 +2966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.showAllHiddenColumns();
     repaint();
+    viewport.sendSelection();
   }
 
   @Override
@@ -3056,6 +3057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
     toggleHiddenRegions(false, false);
+    viewport.sendSelection();
   }
 
   /*
@@ -3073,6 +3075,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   /*
@@ -3088,6 +3091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.showAllHiddenColumns();
     viewport.showAllHiddenSeqs();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
@@ -3095,6 +3099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 10963b6..b2c9a12 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -109,66 +109,56 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     if (SwingUtilities.isRightMouseButton(evt))
     {
-      JPopupMenu pop = new JPopupMenu();
-      if (reveal != null)
+      rightMouseButtonPressed(evt, res);
+    }
+    else
+    {
+      leftMouseButtonPressed(evt, res);
+    }
+  }
+
+  /**
+   * Handles right mouse button press. If pressed in a selected column, opens
+   * context menu for 'Hide Columns'. If pressed on a hidden columns marker,
+   * opens context menu for 'Reveal / Reveal All'. Else does nothing.
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void rightMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    JPopupMenu pop = new JPopupMenu();
+    if (reveal != null)
+    {
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("label.reveal"));
+      item.addActionListener(new ActionListener()
       {
-        JMenuItem item = new JMenuItem(
-                MessageManager.getString("label.reveal"));
-        item.addActionListener(new ActionListener()
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          @Override
-          public void actionPerformed(ActionEvent e)
+          av.showColumn(reveal[0]);
+          reveal = null;
+          ap.paintAlignment(true);
+          if (ap.overviewPanel != null)
           {
-            av.showColumn(reveal[0]);
-            reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
+            ap.overviewPanel.updateOverviewImage();
           }
-        });
-        pop.add(item);
-
-        if (av.getColumnSelection().hasHiddenColumns())
-        {
-          item = new JMenuItem(
-                  MessageManager.getString("action.reveal_all"));
-          item.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              av.showAllHiddenColumns();
-              reveal = null;
-              ap.paintAlignment(true);
-              if (ap.overviewPanel != null)
-              {
-                ap.overviewPanel.updateOverviewImage();
-              }
-            }
-          });
-          pop.add(item);
+          av.sendSelection();
         }
-        pop.show(this, evt.getX(), evt.getY());
-      }
-      else if (av.getColumnSelection().contains(res))
+      });
+      pop.add(item);
+
+      if (av.getColumnSelection().hasHiddenColumns())
       {
-        JMenuItem item = new JMenuItem(
-                MessageManager.getString("label.hide_columns"));
+        item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
         {
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            av.hideColumns(res, res);
-            if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av
-                            .getAlignment().getHeight())
-            {
-              av.setSelectionGroup(null);
-            }
-
+            av.showAllHiddenColumns();
+            reveal = null;
             ap.paintAlignment(true);
             if (ap.overviewPanel != null)
             {
@@ -178,44 +168,77 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           }
         });
         pop.add(item);
-        pop.show(this, evt.getX(), evt.getY());
       }
+      pop.show(this, evt.getX(), evt.getY());
     }
-    else
-    // LEFT MOUSE TO SELECT
+    else if (av.getColumnSelection().contains(res))
     {
-      if (!evt.isControlDown() && !evt.isShiftDown())
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("label.hide_columns"));
+      item.addActionListener(new ActionListener()
       {
-        av.getColumnSelection().clear();
-      }
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.hideColumns(res, res);
+          if (av.getSelectionGroup() != null
+                  && av.getSelectionGroup().getSize() == av.getAlignment()
+                          .getHeight())
+          {
+            av.setSelectionGroup(null);
+          }
 
-      av.getColumnSelection().addElement(res);
-      SequenceGroup sg = new SequenceGroup();
-      // try to be as quick as possible
-      SequenceI[] iVec = av.getAlignment().getSequencesArray();
-      for (int i = 0; i < iVec.length; i++)
-      {
-        sg.addSequence(iVec[i], false);
-        iVec[i] = null;
-      }
-      iVec = null;
-      sg.setStartRes(res);
-      sg.setEndRes(res);
+          ap.paintAlignment(true);
+          if (ap.overviewPanel != null)
+          {
+            ap.overviewPanel.updateOverviewImage();
+          }
+          av.sendSelection();
+        }
+      });
+      pop.add(item);
+      pop.show(this, evt.getX(), evt.getY());
+    }
+  }
 
-      if (evt.isShiftDown())
+  /**
+   * Handles left mouse button press
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void leftMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    if (!evt.isControlDown() && !evt.isShiftDown())
+    {
+      av.getColumnSelection().clear();
+    }
+
+    av.getColumnSelection().addElement(res);
+    SequenceGroup sg = new SequenceGroup();
+    // try to be as quick as possible
+    SequenceI[] iVec = av.getAlignment().getSequencesArray();
+    for (int i = 0; i < iVec.length; i++)
+    {
+      sg.addSequence(iVec[i], false);
+      iVec[i] = null;
+    }
+    iVec = null;
+    sg.setStartRes(res);
+    sg.setEndRes(res);
+
+    if (evt.isShiftDown())
+    {
+      int min = Math.min(av.getColumnSelection().getMin(), res);
+      int max = Math.max(av.getColumnSelection().getMax(), res);
+      for (int i = min; i < max; i++)
       {
-        int min = Math.min(av.getColumnSelection().getMin(), res);
-        int max = Math.max(av.getColumnSelection().getMax(), res);
-        for (int i = min; i < max; i++)
-        {
-          av.getColumnSelection().addElement(i);
-        }
-        sg.setStartRes(min);
-        sg.setEndRes(max);
+        av.getColumnSelection().addElement(i);
       }
-      av.setSelectionGroup(sg);
+      sg.setStartRes(min);
+      sg.setEndRes(max);
     }
-
+    av.setSelectionGroup(sg);
     ap.paintAlignment(false);
     av.sendSelection();
   }
-- 
1.7.10.2