X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=32283ce8654192f0c8eea61795782ec0e3f571c2;hb=629aab8cacd34324f5bd6aad568db5857fec8c81;hp=b3d7cda24aa4d1e132b5d53781a686280ec4326b;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index b3d7cda..32283ce 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -73,83 +73,95 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
         min = res;
         max = res;
 
-        if(reveal != null && SwingUtilities.isRightMouseButton(evt))
+        if (SwingUtilities.isRightMouseButton(evt))
+        {
+          JPopupMenu pop = new JPopupMenu();
+          if (reveal != null)
           {
-            JPopupMenu pop = new JPopupMenu();
             JMenuItem item = new JMenuItem("Reveal");
             item.addActionListener(new ActionListener()
             {
               public void actionPerformed(ActionEvent e)
               {
-                av.getColumnSelection().revealHiddenColumns(reveal[0], av);
+                av.showColumn(reveal[0]);
                 reveal = null;
                 ap.repaint();
-                if(ap.overviewPanel != null)
-                    ap.overviewPanel.updateOverviewImage();
+                if (ap.overviewPanel != null)
+                  ap.overviewPanel.updateOverviewImage();
               }
             });
             pop.add(item);
 
-            if(av.getColumnSelection().hiddenColumns.size()>1)
+            if (av.getColumnSelection().getHiddenColumns().size() > 1)
             {
               item = new JMenuItem("Reveal All");
               item.addActionListener(new ActionListener()
               {
                 public void actionPerformed(ActionEvent e)
                 {
-                  av.getColumnSelection().revealAllHiddenColumns(av);
+                  av.showAllHiddenColumns();
                   reveal = null;
                   ap.repaint();
-                  if(ap.overviewPanel != null)
+                  if (ap.overviewPanel != null)
                     ap.overviewPanel.updateOverviewImage();
                 }
               });
               pop.add(item);
             }
-
             pop.show(this, evt.getX(), evt.getY());
-
           }
-        else
-      if (av.getColumnSelection().contains(res))
-        {
-          if( SwingUtilities.isRightMouseButton(evt))
+          else if (av.getColumnSelection().contains(res))
           {
-            JPopupMenu pop = new JPopupMenu();
             JMenuItem item = new JMenuItem("Hide Columns");
             item.addActionListener(new ActionListener()
             {
               public void actionPerformed(ActionEvent e)
               {
-                av.getColumnSelection().hideColumns(res, av);
+                av.hideColumns(res, res);
+                if(av.getSelectionGroup()!=null
+                   && av.getSelectionGroup().getSize()==av.alignment.getHeight())
+                  av.setSelectionGroup(null);
+
                 ap.repaint();
-                if(ap.overviewPanel != null)
+                if (ap.overviewPanel != null)
                   ap.overviewPanel.updateOverviewImage();
               }
             });
             pop.add(item);
             pop.show(this, evt.getX(), evt.getY());
-
-          }
-          else
-          {
-            av.getColumnSelection().removeElement(res);
-            av.setSelectionGroup(null);
           }
         }
-        else
+        else // LEFT MOUSE TO SELECT
         {
-            av.getColumnSelection().addElement(res);
-            SequenceGroup sg = new SequenceGroup();
+          if (!evt.isControlDown() && !evt.isShiftDown())
+          {
+            av.getColumnSelection().clear();
+          }
+
+          av.getColumnSelection().addElement(res);
+          SequenceGroup sg = new SequenceGroup();
+          for (int i = 0; i < av.alignment.getSequences().size(); i++)
+          {
+            sg.addSequence(av.alignment.getSequenceAt(i), false);
+          }
+
+          sg.setStartRes(res);
+          sg.setEndRes(res);
+          av.setSelectionGroup(sg);
 
-            for (int i = 0; i < av.alignment.getSequences().size(); i++)
+          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++)
             {
-                sg.addSequence(av.alignment.getSequenceAt(i), false);
+                av.getColumnSelection().addElement(i);
             }
+            sg.setStartRes(min);
+            sg.setEndRes(max);
+          }
+
 
-            sg.setStartRes(res);
-            sg.setEndRes(res);
-            av.setSelectionGroup(sg);
         }
 
 
@@ -184,15 +196,16 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
 
         SequenceGroup sg = av.getSelectionGroup();
 
-        if (res > sg.getStartRes())
-        {
+        if(sg!=null){
+          if (res > sg.getStartRes())
+          {
             sg.setEndRes(res);
-        }
-        else if (res < sg.getStartRes())
-        {
+          }
+          else if (res < sg.getStartRes())
+          {
             sg.setStartRes(res);
+          }
         }
-
         stretchingGroup = false;
         ap.repaint();
     }
@@ -207,6 +220,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
         mouseDragging = true;
 
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+        if(res<0)
+          res = 0;
 
         if(av.hasHiddenColumns)
           res = av.getColumnSelection().adjustForHiddenColumns(res);
@@ -229,7 +244,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
 
 
 
-
         SequenceGroup sg = av.getSelectionGroup();
 
         if (sg != null)
@@ -401,20 +415,29 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
         {
           gg.setColor(Color.blue);
           int res;
-          for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+          if(av.getShowHiddenMarkers())
           {
-            res = av.getColumnSelection().findHiddenRegionPosition( i )-startx;
+            for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+                 i++)
+            {
 
-            gg.fillPolygon(new int[] { res*av.charWidth - av.charHeight/4,
-                                         res*av.charWidth + av.charHeight/4,
-                                         res*av.charWidth },
-                                new int[]
-                                {
-                                    y-av.charHeight/2 , y-av.charHeight/2 ,
-                                    y + 8
-                                }, 3);
+              res = av.getColumnSelection().findHiddenRegionPosition(i) -
+                  startx;
 
+              if(res < 0 || res > endx-scalestartx)
+                continue;
 
+              gg.fillPolygon(new int[]
+                             {res * av.charWidth - av.charHeight / 4,
+                             res * av.charWidth + av.charHeight / 4,
+                             res * av.charWidth},
+                             new int[]
+                             {
+                             y - av.charHeight / 2, y - av.charHeight / 2,
+                             y + 8
+              }, 3);
+
+            }
           }
 
           if (reveal != null && reveal[0] > startx && reveal[0] < endx)