X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=d7e452a962f5fd9ffa77c6fd08f2d9e0e8200507;hb=f3df97a8d39f8124610d661f8c141677f73d86b0;hp=ed3fc527bcc95b34ba003d903ff6e01a467e5a5a;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index ed3fc52..d7e452a 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.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 
@@ -133,7 +133,7 @@ public class SliderPanel extends GSliderPanel
     conservationSlider.setTitle("Conservation Colour Increment  (" + source
             + ")");
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       sp.setAllGroupsCheckEnabled(true);
     }
@@ -209,7 +209,7 @@ public class SliderPanel extends GSliderPanel
 
     PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       pid.setAllGroupsCheckEnabled(true);
     }
@@ -266,12 +266,12 @@ public class SliderPanel extends GSliderPanel
     }
 
     ColourSchemeI toChange = null;
-    Vector allGroups = null;
+    List<SequenceGroup> allGroups = null;
     int groupIndex = 0;
 
     if (allGroupsCheck.isSelected())
     {
-      allGroups = ap.av.alignment.getGroups();
+      allGroups = ap.av.getAlignment().getGroups();
       groupIndex = allGroups.size() - 1;
     }
     else