X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=b1b3c5ae261a8d34820f5335cbc0359fa80f6279;hb=7d123b6259738869c16529b8c28cfd8931da4205;hp=e58099d4590b93fdab82f0e5a10aeefd6a7c966d;hpb=887c53273a44cff58d64ee094d9e76bb2f90265b;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e58099d..b1b3c5a 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,29 +1,33 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * 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.
- * 
+ * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-import java.util.*;
-import java.awt.event.*;
-
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+
+import java.awt.event.ActionEvent;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * Helps generate the colors for RNA secondary structure. Future: add option to
@@ -47,17 +51,15 @@ 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);
@@ -76,13 +78,21 @@ public class RNAHelicesColourChooser
     adjusting = true;
     Vector list = new Vector();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns != null)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label + "_" + (index++));
+      for (int i = 0; i < anns.length; i++)
+      {
+        String label = anns[i].label;
+        if (!list.contains(label))
+        {
+          list.addElement(label);
+        }
+        else
+        {
+          list.addElement(label + "_" + (index++));
+        }
+      }
     }
 
     adjusting = false;
@@ -98,34 +108,13 @@ public class RNAHelicesColourChooser
     {
       return;
     }
-
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
     RNAHelicesColour rhc = null;
 
-    rhc = new RNAHelicesColour(currentAnnotation);
-   
-    av.setGlobalColourScheme(rhc);
+    rhc = new RNAHelicesColour(av.getAlignment());
 
-    if (av.getAlignment().getGroups() != null)
-    {
-      Vector allGroups = ap.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        sg.cs = new RNAHelicesColour(currentAnnotation);
-
-      }
-    }
+    av.setGlobalColourScheme(rhc);
 
-    ap.paintAlignment(false);
+    ap.paintAlignment(true);
   }
 
   void reset()
@@ -133,11 +122,8 @@ 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);
       }
     }