Merge remote-tracking branch 'origin/develop' into bug/JAL-2282

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 98fd8f2..ca90003 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -22,7 +22,6 @@ package jalview.datamodel;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
@@ -528,7 +527,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     boolean upd = false;
     try
     {
-      Profile[] cnsns = AAFrequency.calculate(sequences, startRes,
+      ProfileI[] cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
@@ -544,8 +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)
@@ -600,9 +599,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public Profile[] consensusData = null;
+  public ProfileI[] consensusData = null;
 
-  private void _updateConsensusRow(Profile[] cnsns, long nseq)
+  private void _updateConsensusRow(ProfileI[] cnsns, long nseq)
   {
     if (consensus == null)
     {