X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FScalePanel.java;h=baa41658a94e5784969940ad3168300786594fcc;hb=a923c0fa51ce22d052ac06f54b006c57385cc8e0;hp=1f256fea9cd6d41332dcf4fde025dac0484e9d29;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 1f256fe..baa4165 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 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 
@@ -60,7 +60,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
     final int res;
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(x);
     }
@@ -122,8 +122,8 @@ public class ScalePanel extends Panel 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);
             }
@@ -150,9 +150,9 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
       av.getColumnSelection().addElement(res);
       SequenceGroup sg = new SequenceGroup();
-      for (int i = 0; i < av.alignment.getSequences().size(); i++)
+      for (int i = 0; i < av.getAlignment().getSequences().size(); i++)
       {
-        sg.addSequence(av.alignment.getSequenceAt(i), false);
+        sg.addSequence(av.getAlignment().getSequenceAt(i), false);
       }
 
       sg.setStartRes(res);
@@ -182,12 +182,12 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
     int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    if (res > av.alignment.getWidth())
+    if (res > av.getAlignment().getWidth())
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
@@ -225,14 +225,14 @@ public class ScalePanel extends Panel 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)
@@ -307,7 +307,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
   public void mouseMoved(MouseEvent evt)
   {
-    if (!av.hasHiddenColumns)
+    if (!av.hasHiddenColumns())
     {
       return;
     }
@@ -360,7 +360,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     for (int i = 0; i < cs.size(); i++)
     {
       int sel = cs.columnAt(i);
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         sel = av.getColumnSelection().findColumnPosition(sel);
       }
@@ -417,7 +417,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       }
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       gg.setColor(Color.blue);
       int res;