X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=1e38a6d00ec197ba359e48b0e8ce5899f5d3b2c4;hb=6ddf2d553aee329db44dd36b564211c3880563ec;hp=353accf324cfd95f26d2677f9db04f4778f6f285;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 353accf..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;
@@ -262,13 +267,13 @@ public class ClustalxColourScheme
       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))
-      {
-        currentColour = ResidueColour[i].c;
-      }
+      currentColour = ResidueColour[i].c;
     }
+  }
 
     if (i == 4)
     {