JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 16f822f..4cfa45b 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,26 +1,31 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 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.
- * 
+ *  
  * 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/>.
+ * 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;
 
 /**
  * Looks at the information computed from an RNA Stockholm format file on the
@@ -56,15 +61,44 @@ public class RNAHelicesColour extends ResidueColourScheme
    */
   public RNAHelicesColour(AlignmentAnnotation annotation)
   {
+    super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
     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 (lastrefresh != annotation._rnasecstr.hashCode() && annotation.isValidStruc())
+    
+    if (annotation!=null && ((annotation._rnasecstr == null
+               || lastrefresh != annotation._rnasecstr.hashCode())
+            && annotation.isValidStruc()))
     {
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
@@ -118,6 +152,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return color in RGB
    */
+  @Override
   public Color findColour(char c)
   {
     return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
@@ -135,7 +170,8 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return Color in RGB
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     refresh();
     Color currentColour = Color.white;