X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTextColourChooser.java;h=9a0e1b7be9e1c1653d4225ac11d55438c24fe797;hb=02e9934037787599aefda03a6af9b7501e867dc3;hp=bec682384b3dc8921e7de46aede4e94a287f0e93;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index bec6823..9a0e1b7 100644
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.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 
@@ -17,8 +17,6 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
@@ -137,7 +135,7 @@ public class TextColourChooser
     if (sg == null)
     {
       ap.av.textColour = col;
-      if (ap.av.colourAppliesToAllGroups)
+      if (ap.av.getColourAppliesToAllGroups())
       {
         setGroupTextColour();
       }
@@ -155,7 +153,7 @@ public class TextColourChooser
     if (sg == null)
     {
       ap.av.textColour2 = col;
-      if (ap.av.colourAppliesToAllGroups)
+      if (ap.av.getColourAppliesToAllGroups())
       {
         setGroupTextColour();
       }
@@ -173,7 +171,7 @@ public class TextColourChooser
     if (sg == null)
     {
       ap.av.thresholdTextColour = value;
-      if (ap.av.colourAppliesToAllGroups)
+      if (ap.av.getColourAppliesToAllGroups())
       {
         setGroupTextColour();
       }
@@ -188,16 +186,13 @@ public class TextColourChooser
 
   void setGroupTextColour()
   {
-    if (ap.av.alignment.getGroups() == null)
+    if (ap.av.getAlignment().getGroups() == null)
     {
       return;
     }
 
-    Vector groups = ap.av.alignment.getGroups();
-
-    for (int i = 0; i < groups.size(); i++)
+    for (SequenceGroup sg : ap.av.getAlignment().getGroups())
     {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
       sg.textColour = ap.av.textColour;
       sg.textColour2 = ap.av.textColour2;
       sg.thresholdTextColour = ap.av.thresholdTextColour;