JAL-2629 moved HMM storage location to placeholder sequence

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

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index 09092a6..c9e081f 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -1,6 +1,5 @@
 package jalview.schemes;
 
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceCollectionI;
@@ -106,35 +105,19 @@ public class HMMERColourScheme extends ResidueColourScheme
   public void alignmentChanged(AnnotatedCollectionI collection,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    AlignmentAnnotation[] annArr = collection.getAlignmentAnnotation();
-    for (AlignmentAnnotation ann : annArr)
-    {
-      if (ann.label.indexOf("Information Content") > -1)
-      {
-        hmm = ann.getHMM();
-      }
-    }
-
+    SequenceI seq = collection.getSequences().get(0);
+    hmm = seq.getHMM();
   }
 
+
+
   @Override
   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     HiddenMarkovModel markov = null;
-    AlignmentAnnotation[] annArr = sg.getAlignmentAnnotation();
-    for (AlignmentAnnotation ann : annArr)
-    {
-      if (ann.label.indexOf("Information Content") > -1)
-      {
-        markov = ann.getHMM();
-      }
-    }
-    
-    
-    
-    
-
+    SequenceI seq = sg.getSequences().get(0);
+    markov = seq.getHMM();
     HMMERColourScheme colour = new HMMERColourScheme(markov);
     return colour;