2.5.1 release branding

[jalview.git] / src / jalview / gui / ScalePanel.java

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 33131d3..6bb3716 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -73,10 +72,13 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     if (av.hasHiddenColumns)
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(x);
+      x = av.getColumnSelection().adjustForHiddenColumns(x);
     }
-    else
+    
+    if (x >= av.alignment.getWidth())
     {
+      res = av.alignment.getWidth() - 1;
+    } else {
       res = x;
     }
 
@@ -170,7 +172,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       iVec = null;
       sg.setStartRes(res);
       sg.setEndRes(res);
-      av.setSelectionGroup(sg);
 
       if (evt.isShiftDown())
       {
@@ -183,7 +184,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         sg.setStartRes(min);
         sg.setEndRes(max);
       }
-
+      av.setSelectionGroup(sg);
     }
 
     ap.paintAlignment(false);
@@ -202,14 +203,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    if (res > av.alignment.getWidth())
+    if (av.hasHiddenColumns)
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (av.hasHiddenColumns)
+    if (res >= av.alignment.getWidth())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.alignment.getWidth() - 1;
     }
 
     if (!stretchingGroup)
@@ -258,7 +259,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (res > av.alignment.getWidth())
+    if (res >= av.alignment.getWidth())
     {
       res = av.alignment.getWidth() - 1;
     }
@@ -296,7 +297,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       int col;
       for (int i = min; i <= max; i++)
       {
-        col = av.getColumnSelection().adjustForHiddenColumns(i);
+        col = i; // av.getColumnSelection().adjustForHiddenColumns(i);
 
         if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
         {
@@ -399,6 +400,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
+    int s;
     if (cs != null)
     {
       gg.setColor(new Color(220, 0, 0));
@@ -408,7 +410,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         int sel = cs.columnAt(i);
         if (av.hasHiddenColumns)
         {
-          sel = cs.findColumnPosition(sel);
+          if (cs.isVisible(sel))
+          {
+            sel = cs.findColumnPosition(sel);
+          }
+          else
+          {
+            continue;
+          }
         }
 
         if ((sel >= startx) && (sel <= endx))