From 3ad26765f3e72cc506df226ac026034c9b20ce5d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 27 Feb 2018 15:56:53 +0000
Subject: [PATCH] JAL-2668 fix broken factory method for colour scheme

---
 src/jalview/schemes/HMMERAlignmentColourScheme.java |    5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/jalview/schemes/HMMERAlignmentColourScheme.java b/src/jalview/schemes/HMMERAlignmentColourScheme.java
index 8e7aef7..52ee6e5 100644
--- 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
-- 
1.7.10.2