X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=9245761638afd2dcb3319eeaf98848a69ea9977c;hb=dc4e35ab621a97c049f89ea9aa6d19737179139e;hp=046f1e6cda95f029b3156180e2e2bb94ab037006;hpb=eb5e0ce96aa9936a540b4d99a57cc2e5df3704f0;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 046f1e6..9245761 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -23,14 +23,11 @@ package jalview.datamodel;
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
 
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
-import java.util.Vector;
 
 /**
  * Collects a set contiguous ranges on a set of sequences
@@ -46,8 +43,6 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   Conservation conserve;
 
-  Vector aaFrequency;
-
   boolean displayBoxes = true;
 
   boolean displayText = true;
@@ -532,7 +527,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     boolean upd = false;
     try
     {
-      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+      ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
@@ -548,8 +543,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName,
-                ResidueProperties.propHash, 3, sequences, startRes,
+        Conservation c = new Conservation(groupName, sequences, startRes,
                 endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
@@ -605,9 +599,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public Hashtable[] consensusData = null;
+  public ProfilesI consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
+  private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
     {