Merge branch 'JAL-1139_proguard' into develop

[jalview.git] / src / jalview / schemes / RNAHelicesColourChooser.java

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e58099d..cef7eb6 100644 (file)
--- 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 
@@ -47,17 +47,15 @@ public class RNAHelicesColourChooser
 
   boolean adjusting = false;
 
-  public RNAHelicesColourChooser(AlignViewportI av, final AlignmentViewPanel ap)
+  public RNAHelicesColourChooser(AlignViewportI av,
+          final AlignmentViewPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
       oldgroupColours = new Hashtable();
-      Vector allGroups = ap.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);
@@ -99,22 +97,34 @@ public class RNAHelicesColourChooser
       return;
     }
 
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
+    // This loop will find the first rna structure annotation by which to colour
+    //  the sequences.
+    AlignmentAnnotation[] annotations = av.getAlignment().getAlignmentAnnotation();
+    for (int i = 0; i < annotations.length; i++) {
+       
+       // is this a sensible way of determining type of annotation?
+       if (annotations[i].getRNAStruc() != null) { 
+               currentAnnotation = annotations[i];
+               break;
+       }
+    }
+    if (currentAnnotation == null)   
+    {
+       System.err.println("Jalview is about to try and colour by RNAHelices even"
+                       + " though there are no RNA secondary structure annotations present!");
+       currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
+    }
+    
     RNAHelicesColour rhc = null;
 
     rhc = new RNAHelicesColour(currentAnnotation);
-   
+
     av.setGlobalColourScheme(rhc);
 
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.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;
@@ -133,11 +143,8 @@ public class RNAHelicesColourChooser
     av.setGlobalColourScheme(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.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);
       }
     }