X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=1e38a6d00ec197ba359e48b0e8ce5899f5d3b2c4;hb=91c5d2144a780716e755e99882acffe46b40f18f;hp=addf00f4e02549b301862a5534eccc8bfe801690;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index addf00f..1e38a6d 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -248,6 +248,11 @@ public class ClustalxColourScheme
 
   public Color findColour(String s, int j)
   {
+
+    if(cons2.length<=j)
+      return currentColour;
+
+
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
       return Color.white;
@@ -255,30 +260,33 @@ public class ClustalxColourScheme
 
     int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
 
-    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)
+         applyConservation(j);
+
+    return currentColour;
   }
 }