X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=f6b7c5e16e31cd3da8f34f14597aa751cb071c90;hb=8b1e1c7cf7bcf6499dad546699c85d8d52e6d86c;hp=c9abb0e40c5940f69d4368342643f2dbc64e4a8a;hpb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index c9abb0e..f6b7c5e 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -22,7 +22,8 @@ package jalview.schemes;
 
 import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
@@ -54,7 +55,7 @@ public class ResidueColourScheme implements ColourSchemeI
   /*
    * Consensus data indexed by column
    */
-  Profile[] consensus;
+  ProfilesI consensus;
 
   /*
    * Conservation string as a char array 
@@ -182,19 +183,20 @@ public class ResidueColourScheme implements ColourSchemeI
       residue -= ('a' - 'A');
     }
 
-    if (consensus == null || consensus.length < column
-            || consensus[column] == null)
+    if (consensus == null)
     {
       return false;
     }
 
+    ProfileI profile = consensus.get(column);
+
     /*
      * test whether this is the consensus (or joint consensus) residue
      */
-    if (consensus[column].getModalResidue().contains(
-            String.valueOf(residue)))
+    if (profile != null
+            && profile.getModalResidue().contains(String.valueOf(residue)))
     {
-      if (consensus[column].getPercentageIdentity(ignoreGaps) >= threshold)
+      if (profile.getPercentageIdentity(ignoreGaps) >= threshold)
       {
         return true;
       }
@@ -234,7 +236,7 @@ public class ResidueColourScheme implements ColourSchemeI
    *          DOCUMENT ME!
    */
   @Override
-  public void setConsensus(Profile[] consensus)
+  public void setConsensus(ProfilesI consensus)
   {
     if (consensus == null)
     {