JAL-2629 add documentation to previous work

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 5cf07e2..479db4e 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -578,7 +578,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       {
         HiddenMarkovModel hmm = information.sequenceRef.getHMM();
 
-        ProfilesI info = AAFrequency.calculateInformation(hmm,
+        ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
                 (endRes + 1) - startRes, startRes, endRes + 1,
                 showHMMSequenceLogo, ignoreBelowBackground);
         _updateInformationRow(info, sequences.size());
@@ -681,6 +681,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     // ignoreGapsInConsensusCalculation);
   }
 
+  /**
+   * Recalculates the information content on the HMM annotation.
+   * 
+   * @param cnsns
+   * @param nseq
+   */
   private void _updateInformationRow(ProfilesI cnsns, long nseq)
   {
     if (information == null)