X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FScalePanel.java;h=8fe6e30f00520a27833720b26aca0b023e4d4305;hb=c634b124bf5ee7ef6935959c451fb4debfc4fa5d;hp=1f256fea9cd6d41332dcf4fde025dac0484e9d29;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 1f256fe..8fe6e30 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -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);
     }
@@ -122,7 +122,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
           {
             av.hideColumns(res, res);
             if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av.alignment
+                    && 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;