JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 45c374d..5a09a34 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,30 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.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
@@ -79,9 +81,13 @@ public class RNAHelicesColourChooser
     {
       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
       if (!list.contains(label))
+      {
         list.addElement(label);
+      }
       else
+      {
         list.addElement(label + "_" + (index++));
+      }
     }
 
     adjusting = false;
@@ -97,46 +103,13 @@ public class RNAHelicesColourChooser
     {
       return;
     }
-
-    // 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);
+    rhc = new RNAHelicesColour(av.getAlignment());
 
     av.setGlobalColourScheme(rhc);
 
-    if (av.getAlignment().getGroups() != null)
-    {
-      for (SequenceGroup sg : ap.getAlignment().getGroups())
-      {
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        sg.cs = new RNAHelicesColour(currentAnnotation);
-
-      }
-    }
-
-    ap.paintAlignment(false);
+    ap.paintAlignment(true);
   }
 
   void reset()