X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;fp=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=ccc69c286b29259be84f278ddac2fd1bbab00b61;hp=5f63ca99405702dc1e7d46dfb7debcce956fdcc2;hb=08fa75428822ee384d35eb67b1e23e33e83d8d9d;hpb=86cc86e5815d20b058456c0bf09b979546acde6e

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 5f63ca9..ccc69c2 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -22,6 +22,7 @@ package jalview.schemes;
 
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 
@@ -66,19 +67,22 @@ public class PIDColourScheme extends ResidueColourScheme
       return Color.white;
     }
 
-    if (consensus[j].getMaxCount() > 0) //!= -1)
-            //&& consensus[j].contains(String.valueOf(c)))
+    /*
+     * test whether this is the consensus (or joint consensus) residue
+     */
+    boolean matchesConsensus = consensus[j].getModalResidue().contains(
+            String.valueOf(c));
+    if (matchesConsensus)
     {
       sc = consensus[j].getPercentageIdentity(ignoreGaps);
 
-      if (!jalview.util.Comparison.isGap(c))
+      if (!Comparison.isGap(c))
       {
         for (int i = 0; i < thresholds.length; i++)
         {
           if (sc > thresholds[i])
           {
             currentColour = pidColours[i];
-
             break;
           }
         }