X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=5d14534afe6d7fcc896c45ae9492fc4828eebe0e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=64daf1f28424758973004c5569c39311704b6a20;hpb=ca3387f2bb9cd5b39ff89949ce3698af505f05fc;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 64daf1f..5d14534 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -70,15 +71,17 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
     final int res;
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       x = av.getColumnSelection().adjustForHiddenColumns(x);
     }
 
-    if (x >= av.alignment.getWidth())
+    if (x >= av.getAlignment().getWidth())
+    {
+      res = av.getAlignment().getWidth() - 1;
+    }
+    else
     {
-      res = av.alignment.getWidth() - 1;
-    } else {
       res = x;
     }
 
@@ -135,8 +138,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           {
             av.hideColumns(res, res);
             if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av.alignment
-                            .getHeight())
+                    && av.getSelectionGroup().getSize() == av
+                            .getAlignment().getHeight())
             {
               av.setSelectionGroup(null);
             }
@@ -163,7 +166,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       av.getColumnSelection().addElement(res);
       SequenceGroup sg = new SequenceGroup();
       // try to be as quick as possible
-      SequenceI[] iVec = av.alignment.getSequencesArray();
+      SequenceI[] iVec = av.getAlignment().getSequencesArray();
       for (int i = 0; i < iVec.length; i++)
       {
         sg.addSequence(iVec[i], false);
@@ -203,14 +206,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (res >= av.alignment.getWidth())
+    if (res >= av.getAlignment().getWidth())
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
 
     if (!stretchingGroup)
@@ -254,14 +257,14 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       res = 0;
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
 
-    if (res >= av.alignment.getWidth())
+    if (res >= av.getAlignment().getWidth())
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
 
     if (res < min)
@@ -335,7 +338,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
   public void mouseMoved(MouseEvent evt)
   {
-    if (!av.hasHiddenColumns)
+    if (!av.hasHiddenColumns())
     {
       return;
     }
@@ -353,8 +356,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       {
         reveal = region;
         ToolTipManager.sharedInstance().registerComponent(this);
-        this
-                .setToolTipText("Reveal Hidden Columns with Right Mouse Button");
+        this.setToolTipText("Reveal Hidden Columns with Right Mouse Button");
         break;
       }
       else
@@ -408,7 +410,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       for (int i = 0; i < cs.size(); i++)
       {
         int sel = cs.columnAt(i);
-        if (av.hasHiddenColumns)
+        if (av.hasHiddenColumns())
         {
           if (cs.isVisible(sel))
           {
@@ -455,26 +457,24 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
         }
 
-        gg
-                .drawLine(
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + 2,
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + (fm.getDescent() * 2));
+        gg.drawLine(
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + 2,
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + (fm.getDescent() * 2));
 
       }
       else
       {
-        gg
-                .drawLine(
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + fm.getDescent(),
-                        (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                        y + (fm.getDescent() * 2));
+        gg.drawLine(
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + fm.getDescent(),
+                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                y + (fm.getDescent() * 2));
       }
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       gg.setColor(Color.blue);
       int res;