X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=da47a8981783b8a68c62eeb1c31b14cbdd49cb44;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=ee4d7c23722c2660524c9ce16bca8ab3e9c207ac;hpb=88d5ff9b60bc7c99a427c2d6fc9d04823e185d68;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index ee4d7c2..da47a89 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;
@@ -529,24 +524,26 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     // TODO: try harder to detect changes in state in order to minimise
     // recalculation effort
+    boolean upd = false;
     try
     {
-      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+      ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
         _updateConsensusRow(cnsns, sequences.size());
+        upd = true;
       }
       if (cs != null)
       {
         cs.setConsensus(cnsns);
+        upd = true;
       }
 
       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);
@@ -561,6 +558,8 @@ public class SequenceGroup implements AnnotatedCollectionI
             cs.setConservation(c);
           }
         }
+        // eager update - will cause a refresh of overview regardless
+        upd = true;
       }
       if (cs != null && !defer)
       {
@@ -570,14 +569,14 @@ public class SequenceGroup implements AnnotatedCollectionI
       }
       else
       {
-        return false;
+        return upd;
       }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
-    return false;
+    return upd;
   }
 
   private void _updateConservationRow(Conservation c)
@@ -600,9 +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)
     {
@@ -1062,7 +1061,8 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   /**
    * 
-   * @return automatically calculated consensus row
+   * @return automatically calculated consensus row note: the row is a stub if a
+   *         consensus calculation has not yet been performed on the group
    */
   public AlignmentAnnotation getConsensus()
   {
@@ -1269,10 +1269,14 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    if (calcId == null)
+    {
+      return aa;
+    }
     for (AlignmentAnnotation a : getAlignmentAnnotation())
     {
-      if (a.getCalcId() == calcId)
+      if (calcId.equals(a.getCalcId()))
       {
         aa.add(a);
       }