JAL-2668 fix broken factory method for colour scheme

diff --git a/src/jalview/schemes/HMMERAlignmentColourScheme.java b/src/jalview/schemes/HMMERAlignmentColourScheme.java
index 8e7aef7..52ee6e5 100644 (file)
--- a/src/jalview/schemes/HMMERAlignmentColourScheme.java
+++ b/src/jalview/schemes/HMMERAlignmentColourScheme.java
@@ -10,6 +10,7 @@ import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -131,7 +132,9 @@ public class HMMERAlignmentColourScheme extends ResidueColourScheme
   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    return new HMMERAlignmentColourScheme(sg, hmm);
+    List<SequenceI> hmms = sg.getHMMConsensusSequences();
+    HiddenMarkovModel model = hmms.isEmpty() ? null : hmms.get(0).getHMM();
+    return new HMMERAlignmentColourScheme(sg, model);
   }
 
   @Override