X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=15a1455c446cb5aa77501507279a88ad48d8e6a8;hb=5d2e589a842cf831e4fdeff6b8ed7e7ce6729fd5;hp=e513e594a62614f5e352dfd05bca2d3a64ac4a35;hpb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e513e59..15a1455 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -11,10 +11,9 @@ public class Alignment implements AlignmentI
 
   protected Vector      sequences;
   protected Vector      groups = new Vector();
-  protected ArrayList   superGroup = new ArrayList();
+  protected Vector   superGroup = new Vector();
   protected char        gapCharacter = '-';
   public AlignmentAnnotation [] annotations;
-  public Conservation conservation;
 
   public boolean featuresAdded = false;
 
@@ -322,18 +321,19 @@ public class Alignment implements AlignmentI
   public SequenceGroup [] findAllGroups(SequenceI s)
   {
 
-    ArrayList temp = new ArrayList();
+    Vector temp = new Vector();
 
     for (int i = 0; i < this.groups.size();i++)
     {
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 
       if (sg.sequences.contains(s))
-       temp.add(sg);
+       temp.addElement(sg);
     }
 
     SequenceGroup [] ret = new SequenceGroup[temp.size()];
-    temp.toArray( ret );
+    for(int i=0; i<temp.size(); i++)
+      ret[i] = (SequenceGroup)temp.elementAt(i);
 
     return ret;
 
@@ -358,19 +358,19 @@ public class Alignment implements AlignmentI
 
   public void addSuperGroup(SuperGroup sg)
   {
-    superGroup.add(sg);
+    superGroup.addElement(sg);
   }
 
   public void removeSuperGroup(SuperGroup sg)
   {
-    superGroup.remove(sg);
+    superGroup.removeElement(sg);
   }
 
   public SuperGroup     getSuperGroup(SequenceGroup sg)
   {
     for (int i = 0; i < this.superGroup.size(); i++)
     {
-      SuperGroup temp = (SuperGroup) superGroup.get(i);
+      SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
       if (temp.sequenceGroups.contains(sg))
         return temp;
     }
@@ -385,8 +385,8 @@ public class Alignment implements AlignmentI
 
   public void deleteAllGroups()
   {
-    groups.clear();
-    superGroup.clear();
+    groups.removeAllElements();
+    superGroup.removeAllElements();
    int i=0;
     while (i < sequences.size()) {
      SequenceI s = getSequenceAt(i);