X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=9bd092e6be7f96f9a56370ee33bfd210e685e22d;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=e09745a0c315399fcfbac91a366b1daf9cd6683f;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e09745a..9bd092e 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -44,13 +44,19 @@ public class PIDColourScheme
       s = String.valueOf(res -= ('a' - 'A'));
     }
 
+    if (consensus == null
+        || j >= consensus.length
+        || consensus[j]==null)
+    {
+      return Color.white;
+    }
 
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
       return Color.white;
     }
 
-    currentColour = Color.white;
+    Color currentColour = Color.white;
 
     double sc = 0;
 
@@ -77,7 +83,7 @@ public class PIDColourScheme
       }
 
     if(conservationColouring)
-         applyConservation(j);
+      currentColour = applyConservation(currentColour, j);
 
     return currentColour;
   }