X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=64b1d19916f248855d43abfff7ba9015fdf4a9af;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=eca0b4c88b9ed16bdea371c851649060a4629d4c;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index eca0b4c..64b1d19 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.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.
  * 
@@ -51,14 +51,11 @@ public class AnnotationColourChooser extends JPanel
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
       oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg:ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         if (sg.cs != null)
         {
           oldgroupColours.put(sg, sg.cs);
@@ -91,7 +88,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
 
-    if (av.alignment.getAlignmentAnnotation() == null)
+    if (av.getAlignment().getAlignmentAnnotation() == null)
     {
       return;
     }
@@ -113,9 +110,9 @@ public class AnnotationColourChooser extends JPanel
     adjusting = true;
     Vector list = new Vector();
     int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
     {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
+      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
       if (!list.contains(label))
         list.addElement(label);
       else
@@ -378,7 +375,7 @@ public class AnnotationColourChooser extends JPanel
       return;
     }
 
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
             .getSelectedIndex()];
 
     int aboveThreshold = -1;
@@ -450,14 +447,11 @@ public class AnnotationColourChooser extends JPanel
 
     av.setGlobalColourScheme(acg);
 
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      
+      for (SequenceGroup sg:ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
-
         if (sg.cs == null)
         {
           continue;
@@ -508,13 +502,11 @@ public class AnnotationColourChooser extends JPanel
   void reset()
   {
     av.setGlobalColourScheme(oldcs);
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      
+      for (SequenceGroup sg:ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }