X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=9bd092e6be7f96f9a56370ee33bfd210e685e22d;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=7f4bebeae89016568d89bbe635c565f09fc6a1fe;hpb=0bdaa0deb6ee514912d2ed730e19f618bc44cb69;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 7f4bebe..9bd092e 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -44,8 +44,9 @@ public class PIDColourScheme
       s = String.valueOf(res -= ('a' - 'A'));
     }
 
-    if (consensus == null ||
-        j >= consensus.length)
+    if (consensus == null
+        || j >= consensus.length
+        || consensus[j]==null)
     {
       return Color.white;
     }
@@ -55,7 +56,7 @@ public class PIDColourScheme
       return Color.white;
     }
 
-    currentColour = Color.white;
+    Color currentColour = Color.white;
 
     double sc = 0;
 
@@ -82,7 +83,7 @@ public class PIDColourScheme
       }
 
     if(conservationColouring)
-         applyConservation(j);
+      currentColour = applyConservation(currentColour, j);
 
     return currentColour;
   }