X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=40b2cac6f5af4ed3cc762493d48049e21cdd4208;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=e06c9689caa0a68d51237b7a7d983bd2a0108041;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index e06c968..40b2cac 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -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);
     }
@@ -160,8 +160,8 @@ public class SliderPanel extends GSliderPanel
 
     if (!conservationSlider.isVisible())
     {
-      Desktop.addInternalFrame(conservationSlider, conservationSlider
-              .getTitle(), 420, 90, false);
+      Desktop.addInternalFrame(conservationSlider,
+              conservationSlider.getTitle(), 420, 90, false);
       conservationSlider
               .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
               {
@@ -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