X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=89d315c4ed7292cdfcf36cedacb4fe774bcc06f8;hb=02783b1d0f22e82e7854777646e39df0fc77de74;hp=c50330b93a5b0700def7f4988f8cdf8eeec38b5e;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index c50330b..89d315c 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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 
@@ -70,14 +70,14 @@ 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.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
     else
     {
@@ -137,8 +137,8 @@ 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);
             }
@@ -165,7 +165,7 @@ 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);
@@ -205,14 +205,14 @@ 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)
@@ -256,14 +256,14 @@ 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)
@@ -337,7 +337,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
   public void mouseMoved(MouseEvent evt)
   {
-    if (!av.hasHiddenColumns)
+    if (!av.hasHiddenColumns())
     {
       return;
     }
@@ -409,7 +409,7 @@ 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))
           {
@@ -473,7 +473,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       }
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       gg.setColor(Color.blue);
       int res;