X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=a2ffff574e4f111fff4aa819c1f9608836ed0d11;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=774fc950b9becff80bf92d46caef7bf8275dcda2;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 774fc95..a2ffff5 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.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 
@@ -21,6 +21,7 @@ import java.awt.*;
 import java.util.Hashtable;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
 
 /**
  * Looks at the information computed from an RNA Stockholm format file on the
@@ -56,40 +57,60 @@ public class RNAHelicesColour extends ResidueColourScheme
    */
   public RNAHelicesColour(AlignmentAnnotation annotation)
   {
+    super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
+    refresh();
+  }
 
-    // Figure out number of helices
-    // Length of rnasecstr is the number of pairs of positions that base pair
-    // with each other in the secondary structure
-    for (int x = 0; x < this.annotation._rnasecstr.length; x++)
+  private long lastrefresh = -1;
+
+  public void refresh()
+  {
+    if ((annotation._rnasecstr == null
+    		|| lastrefresh != annotation._rnasecstr.hashCode())
+            && annotation.isValidStruc())
     {
+      annotation.getRNAStruc();
+      lastrefresh = annotation._rnasecstr.hashCode();
+      numHelix = 0;
+      positionsToHelix = new Hashtable();
+
+      // Figure out number of helices
+      // Length of rnasecstr is the number of pairs of positions that base pair
+      // with each other in the secondary structure
+      for (int x = 0; x < this.annotation._rnasecstr.length; x++)
+      {
 
-      /*
-       * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
-       * this.annotation._rnasecstr[x].getBegin());
-       */
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+        /*
+         * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+         * this.annotation._rnasecstr[x].getBegin());
+         */
+        // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
 
-      positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
-              this.annotation._rnasecstr[x].getFeatureGroup());
-      positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
-              this.annotation._rnasecstr[x].getFeatureGroup());
+        positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
+                this.annotation._rnasecstr[x].getFeatureGroup());
+        positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
+                this.annotation._rnasecstr[x].getFeatureGroup());
 
-      if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
-      {
-        numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
-                .getFeatureGroup());
-      }
+        if (Integer.parseInt(this.annotation._rnasecstr[x]
+                .getFeatureGroup()) > numHelix)
+        {
+          numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
+                  .getFeatureGroup());
+        }
 
-    }
+      }
 
-    // Generate random colors and store
-    for (int j = 0; j <= numHelix; j++)
-    {
-      helixcolorhash.put(Integer.toString(j), jalview.util.ColorUtils
-              .generateRandomColor(Color.white));
+      // Generate random colors and store
+      for (int j = 0; j <= numHelix; j++)
+      {
+        if (!helixcolorhash.containsKey(Integer.toString(j)))
+        {
+          helixcolorhash.put(Integer.toString(j),
+                  jalview.util.ColorUtils.generateRandomColor(Color.white));
+        }
+      }
     }
-
   }
 
   /**
@@ -101,6 +122,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return color in RGB
    */
+  @Override
   public Color findColour(char c)
   {
     return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
@@ -118,8 +140,10 @@ 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;
     String currentHelix = null;
     currentHelix = (String) positionsToHelix.get(j);