X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=25b65b339152cccee91ddd0d62eb2c66750d6b04;hb=4ea6a00274e0a209a7dbec074f04a21ec1a80b28;hp=e575b91dc058277b63fce6e632ade28bfad0ab1a;hpb=44f6e9fd1e6df7c78950ef2c778e86add4ec498e;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e575b91..25b65b3 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * 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 
@@ -15,11 +15,13 @@
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-package jalview.gui;
+package jalview.schemes;
 
 import java.util.*;
 import java.awt.event.*;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
@@ -33,9 +35,9 @@ import jalview.schemes.*;
 public class RNAHelicesColourChooser
 {
 
-  AlignViewport av;
+  AlignViewportI av;
 
-  AlignmentPanel ap;
+  AlignmentViewPanel ap;
 
   ColourSchemeI oldcs;
 
@@ -45,17 +47,15 @@ public class RNAHelicesColourChooser
 
   boolean adjusting = false;
 
-  public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
+  public RNAHelicesColourChooser(AlignViewportI av,
+          final AlignmentViewPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
       oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg : ap.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         if (sg.cs != null)
         {
           oldgroupColours.put(sg, sg.cs);
@@ -107,12 +107,8 @@ public class RNAHelicesColourChooser
 
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg : ap.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
-
         if (sg.cs == null)
         {
           continue;
@@ -131,11 +127,8 @@ public class RNAHelicesColourChooser
     av.setGlobalColourScheme(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg : ap.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }