From 7182b83bcc2d48f6335ac0ca16528607cee81408 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 27 May 2016 15:24:15 +0100
Subject: [PATCH] JAL-1989 tightened up use of flag for 'column selection
 changed'

---
 src/jalview/appletgui/SeqPanel.java          |    1 -
 src/jalview/gui/ScalePanel.java              |   35 +++++++++++++++-----------
 src/jalview/gui/SeqPanel.java                |    1 -
 src/jalview/viewmodel/AlignmentViewport.java |   10 +++++---
 4 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 479b746..a4dad4b 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1964,7 +1964,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
             av);
     av.setColumnSelection(cs);
-    av.isColSelChanged(true);
 
     ap.scalePanelHolder.repaint();
     ap.repaint();
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index f2cbf33..2165b2c 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -43,17 +43,14 @@ import javax.swing.JPopupMenu;
 import javax.swing.ToolTipManager;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * The panel containing the sequence ruler (when not in wrapped mode), and
+ * supports a range of mouse operations to select, hide or reveal columns.
  */
 public class ScalePanel extends JPanel implements MouseMotionListener,
         MouseListener
 {
   protected int offy = 4;
 
-  /** DOCUMENT ME!! */
   public int width;
 
   protected AlignViewport av;
@@ -62,13 +59,26 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
   boolean stretchingGroup = false;
 
-  int min; // used by mouseDragged to see if user
+  /*
+   * min, max hold the extent of a mouse drag action
+   */
+  int min;
 
-  int max; // used by mouseDragged to see if user
+  int max;
 
   boolean mouseDragging = false;
 
-  // wants to delete columns
+  /*
+   * holds a hidden column range when the mouse is over an adjacent column
+   */
+  int[] reveal;
+
+  /**
+   * Constructor
+   * 
+   * @param av
+   * @param ap
+   */
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
     this.av = av;
@@ -393,6 +403,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   @Override
   public void mouseMoved(MouseEvent evt)
   {
+    this.setToolTipText(null);
+    reveal = null;
     if (!av.hasHiddenColumns())
     {
       return;
@@ -402,7 +414,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
-    reveal = null;
     if (av.getColumnSelection().getHiddenColumns() != null)
     {
       for (int[] region : av.getColumnSelection().getHiddenColumns())
@@ -415,17 +426,11 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
                   .getString("label.reveal_hidden_columns"));
           break;
         }
-        else
-        {
-          this.setToolTipText(null);
-        }
       }
     }
     repaint();
   }
 
-  int[] reveal;
-
   /**
    * DOCUMENT ME!
    * 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3fbb809..bd4b234 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -2061,7 +2061,6 @@ public class SeqPanel extends JPanel implements MouseListener,
     ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
             av);
     av.setColumnSelection(cs);
-    av.isColSelChanged(true);
 
     PaintRefresher.Refresh(this, av.getSequenceSetId());
 
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index fbd1622..c16fdce 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1078,6 +1078,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       updateHiddenColumns();
     }
+    isColSelChanged(true);
   }
 
   /**
@@ -1206,8 +1207,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isColSelChanged(boolean b)
   {
-    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
-            .hashCode();
+    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
     if (hc != -1 && hc != colselhash)
     {
       if (b)
@@ -1308,7 +1308,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
-
+    isColSelChanged(true);
   }
 
   public void hideColumns(int start, int end)
@@ -1321,17 +1321,19 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       colSel.hideColumns(start, end);
     }
+    isColSelChanged(true);
   }
 
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-
+    isColSelChanged(true);
   }
 
   public void showAllHiddenColumns()
   {
     colSel.revealAllHiddenColumns();
+    isColSelChanged(true);
   }
 
   // common hide/show seq stuff
-- 
1.7.10.2