X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=4c20873c4a62a690dda22d31636ece89670ca1a4;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=addf00f4e02549b301862a5534eccc8bfe801690;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index addf00f..4c20873 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -86,8 +86,7 @@ public class ClustalxColourScheme
         }
         else
         {
-          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +
-              "")).intValue();
+          res =  ResidueProperties.aaIndex[seq.charAt(i)];
         }
 
         cons2[i][res]++;
@@ -248,37 +247,43 @@ public class ClustalxColourScheme
 
   public Color findColour(String s, int j)
   {
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    Color currentColour;
+
+
+    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(s, j)))
     {
       return Color.white;
     }
 
-    int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
+    int i = ResidueProperties.aaIndex[s.charAt(0)];
 
-    Color c = Color.white;
+    currentColour = Color.white;
 
     if (i > 19)
     {
-      return c;
+      return currentColour;
     }
 
-    for (int k = 0; k < ResidueColour[i].conses.length; k++)
+  for (int k = 0; k < ResidueColour[i].conses.length; k++)
+  {
+    if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
     {
-      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
-      {
-        c = ResidueColour[i].c;
-      }
+      currentColour = ResidueColour[i].c;
     }
+  }
 
     if (i == 4)
     {
       if (conses[27].isConserved(cons2, j, size))
       {
-        c = (Color) colhash.get("PINK");
+        currentColour = (Color) colhash.get("PINK");
       }
     }
 
-    return c;
+    if(conservationColouring)
+      currentColour = applyConservation(currentColour, j);
+
+    return currentColour;
   }
 }