X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=1575a6a5d8a7a1f87f1138cca08995bc8c48cf31;hb=04011072920c5e2587a8d549869ee47e28ad7d81;hp=66f180be4c72186c75934d0e2cb817a4dd865b8f;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 66f180b..1575a6a 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -53,24 +53,27 @@ public class PIDColourScheme
 
     double sc = 0;
 
-    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
-        consensus[j].contains(s))
-    {
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
+    if(consensus.length<=j)
+      return Color.white;
 
-      if (!jalview.util.Comparison.isGap( res ))
+      if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
+          consensus[j].contains(s))
       {
-        for (int i = 0; i < thresholds.length; i++)
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+
+        if (!jalview.util.Comparison.isGap(res))
         {
-          if (sc > thresholds[i])
+          for (int i = 0; i < thresholds.length; i++)
           {
-            currentColour = pidColours[i];
+            if (sc > thresholds[i])
+            {
+              currentColour = pidColours[i];
 
-            break;
+              break;
+            }
           }
         }
       }
-    }
 
     if(conservationColouring)
          applyConservation(j);