JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 7cbca66..57fcba5 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,27 +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 ($$Version-Rel$$)
+ * 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.awt.*;
 import java.util.Hashtable;
+import java.util.Map;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 /**
@@ -63,13 +68,43 @@ public class RNAHelicesColour extends ResidueColourScheme
     refresh();
   }
 
+  public RNAHelicesColour(AnnotatedCollectionI alignment)
+  {
+    super(ResidueProperties.nucleotideIndex);
+    alignmentChanged(alignment, null);
+  }
+
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+
+    // This loop will find the first rna structure annotation by which to colour
+    // the sequences.
+    AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+    for (int i = 0; i < annotations.length; i++)
+    {
+
+      // is this a sensible way of determining type of annotation?
+      if (annotations[i].getRNAStruc() != null)
+      {
+        annotation = annotations[i];
+        break;
+      }
+    }
+
+    refresh();
+
+  }
+
   private long lastrefresh = -1;
 
   public void refresh()
   {
-    if ((annotation._rnasecstr == null
-               || lastrefresh != annotation._rnasecstr.hashCode())
-            && annotation.isValidStruc())
+
+    if (annotation != null
+            && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
+                    .hashCode()) && annotation.isValidStruc()))
     {
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();