X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=9245761638afd2dcb3319eeaf98848a69ea9977c;hb=dc4e35ab621a97c049f89ea9aa6d19737179139e;hp=a92eadeffc92f989c3eb1ae2118cba906afb8664;hpb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index a92eade..9245761 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -527,7 +527,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     boolean upd = false;
     try
     {
-      Profile[] cnsns = AAFrequency.calculate(sequences, startRes,
+      ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
@@ -543,8 +543,8 @@ public class SequenceGroup implements AnnotatedCollectionI
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName, 3, sequences,
-                startRes, endRes + 1);
+        Conservation c = new Conservation(groupName, sequences, startRes,
+                endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
         if (conservation != null)
@@ -599,9 +599,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public Profile[] consensusData = null;
+  public ProfilesI consensusData = null;
 
-  private void _updateConsensusRow(Profile[] cnsns, long nseq)
+  private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
     {