X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=c70f3c16cc9c767676da378cfc0192537f6bdec5;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=a4f65460e4985685a065631cfff70ba6631d1668;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index a4f6546..c70f3c1 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/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.
  * 
@@ -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
     {
@@ -137,7 +137,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           {
             av.hideColumns(res, res);
             if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av.alignment
+                    && 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;