Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / schemes / HMMERColourScheme.java

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index 2ba0898..ee6c873 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -8,7 +8,6 @@ import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
 import java.awt.Color;
-import java.util.List;
 import java.util.Map;
 
 /**
@@ -139,12 +138,9 @@ public class HMMERColourScheme extends ResidueColourScheme
   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    HiddenMarkovModel model = null;
-    List<SequenceI> seqs = sg.getHMMConsensusSequences();
-    if (!seqs.isEmpty())
-    {
-      model = seqs.get(0).getHMM();
-    }
+    SequenceI hmmSeq = sg.getHmmConsensus();
+    HiddenMarkovModel model = hmmSeq == null ? null : hmmSeq.getHMM();
+
     HMMERColourScheme colour = new HMMERColourScheme(model);
     return colour;
   }
@@ -161,10 +157,14 @@ public class HMMERColourScheme extends ResidueColourScheme
     return false;
   }
 
+  /**
+   * Answers true if the sequence collection has an HMM consensus sequence, else
+   * false
+   */
   @Override
   public boolean isApplicableTo(AnnotatedCollectionI ac)
   {
-    return !ac.getHMMConsensusSequences().isEmpty();
+    return ac.getHmmConsensus() != null;
   }
 
 }