From e7ddb4e421ed93f92b6a94f13f11c6f5677e2a0b Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 28 Oct 2011 15:43:40 +0100
Subject: [PATCH] (JAL-889) ensure latest version of RNA pairlist is used to
 generate helical colouring

---
 src/jalview/schemes/RNAHelicesColour.java |   68 ++++++++++++++++++-----------
 1 file changed, 43 insertions(+), 25 deletions(-)

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 774fc95..16f822f 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -57,39 +57,56 @@ public class RNAHelicesColour extends ResidueColourScheme
   public RNAHelicesColour(AlignmentAnnotation annotation)
   {
     this.annotation = annotation;
+    refresh();
+  }
+
+  private long lastrefresh = -1;
 
-    // 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++)
+  public void refresh()
+  {
+    if (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));
+        }
+      }
     }
-
   }
 
   /**
@@ -120,6 +137,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    */
   public Color findColour(char c, int j)
   {
+    refresh();
     Color currentColour = Color.white;
     String currentHelix = null;
     currentHelix = (String) positionsToHelix.get(j);
-- 
1.7.10.2