Jalview 2.6 source licence

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

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 4dfb8c8..d2ed1d9 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 (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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;
 
@@ -64,7 +63,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mousePressed(MouseEvent evt)
   {
@@ -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())
       {
@@ -183,17 +184,18 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         sg.setStartRes(min);
         sg.setEndRes(max);
       }
-
+      av.setSelectionGroup(sg);
     }
 
     ap.paintAlignment(false);
+    av.sendSelection();
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent evt)
   {
@@ -201,14 +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)
@@ -233,13 +235,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     }
     stretchingGroup = false;
     ap.paintAlignment(false);
+    av.sendSelection();
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseDragged(MouseEvent evt)
   {
@@ -256,7 +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;
     }
@@ -294,7 +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()))
         {
@@ -370,7 +373,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -397,23 +400,33 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
-    gg.setColor(new Color(220, 0, 0));
-
-    for (int i = 0; i < cs.size(); i++)
+    int s;
+    if (cs != null)
     {
-      int sel = cs.columnAt(i);
-      if (av.hasHiddenColumns)
-      {
-        sel = av.getColumnSelection().findColumnPosition(sel);
-      }
+      gg.setColor(new Color(220, 0, 0));
 
-      if ((sel >= startx) && (sel <= endx))
+      for (int i = 0; i < cs.size(); i++)
       {
-        gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
-                getHeight());
+        int sel = cs.columnAt(i);
+        if (av.hasHiddenColumns)
+        {
+          if (cs.isVisible(sel))
+          {
+            sel = cs.findColumnPosition(sel);
+          }
+          else
+          {
+            continue;
+          }
+        }
+
+        if ((sel >= startx) && (sel <= endx))
+        {
+          gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
+                  getHeight());
+        }
       }
     }
-
     // Draw the scale numbers
     gg.setColor(Color.black);