From dda31e19407a907dcab8180c2ffc7fd4f193df28 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 25 Mar 2016 15:33:38 +0000
Subject: [PATCH] =?utf8?q?JAL-2034=20JAL-1421=20use=20ArrayLists,=20and=20ma?=
 =?utf8?q?ke=20=E2=80=98selection=E2=80=99=20group=20an=20ScGroup?=
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---
 src/jalview/datamodel/AlignmentView.java |   59 ++++++++++++++++++++++++------
 1 file changed, 47 insertions(+), 12 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 756a116..fa72e80 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -26,7 +26,6 @@ import jalview.util.ShiftList;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 /**
  * Transient object compactly representing a 'view' of an alignment - with
@@ -69,13 +68,51 @@ public class AlignmentView
    */
   private class ScGroup
   {
-    public Vector seqs;
+    public List<SeqCigar> seqs;
 
     public SequenceGroup sg;
 
     ScGroup()
     {
-      seqs = new Vector();
+      seqs = new ArrayList<SeqCigar>();
+    }
+
+    /**
+     * @param seq
+     * @return true if seq was not a member before and was added to group
+     */
+    public boolean add(SeqCigar seq)
+    {
+      if (!seq.isMemberOf(this))
+      {
+        seqs.add(seq);
+        seq.setGroupMembership(this);
+        return true;
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    /**
+     * 
+     * @param seq
+     * @return true if seq was a member and was removed from group
+     */
+    public boolean remove(SeqCigar seq)
+    {
+      if (seq.removeGroupMembership(this))
+      {
+        seqs.remove(seq);
+        return true;
+      }
+      return false;
+    }
+
+    public int size()
+    {
+      return seqs.size();
     }
   }
 
@@ -83,7 +120,7 @@ public class AlignmentView
    * vector of selected seqCigars. This vector is also referenced by each
    * seqCigar contained in it.
    */
-  private Vector selected;
+  private ScGroup selected;
 
   /**
    * Construct an alignmentView from a live jalview alignment view. Note -
@@ -124,7 +161,7 @@ public class AlignmentView
     if (selection != null && selection.getSize() > 0)
     {
       List<SequenceI> sel = selection.getSequences(null);
-      this.selected = new Vector();
+      this.selected = new ScGroup();
       selseqs = selection
               .getSequencesInOrder(alignment, selectedRegionOnly);
     }
@@ -194,8 +231,7 @@ public class AlignmentView
         if (selection != null && selection.getSize() > 0
                 && !selectedRegionOnly)
         {
-          sequences[csi].setGroupMembership(selected);
-          selected.addElement(sequences[csi]);
+          selected.add(sequences[csi]);
         }
         if (seqsets != null)
         {
@@ -203,9 +239,8 @@ public class AlignmentView
           {
             if ((seqsets.get(sg)).contains(selseqs[i]))
             {
-              sequences[csi].setGroupMembership(sgrps[sg]);
               sgrps[sg].sg.deleteSequence(selseqs[i], false);
-              sgrps[sg].seqs.addElement(sequences[csi]);
+              sgrps[sg].add(sequences[csi]);
               if (!addedgps[sg])
               {
                 if (scGroups == null)
@@ -1073,10 +1108,10 @@ public class AlignmentView
                 + sgr.sg.getEndRes());
         for (int s = 0; s < sgr.seqs.size(); s++)
         {
-          if (!((SeqCigar) sgr.seqs.elementAt(s)).isMemberOf(sgr))
+          // JBPnote this should be a unit test for ScGroup
+          if (!sgr.seqs.get(s).isMemberOf(sgr))
           {
-            os.println("** WARNING: sequence "
-                    + ((SeqCigar) sgr.seqs.elementAt(s)).toString()
+            os.println("** WARNING: sequence " + sgr.seqs.get(s).toString()
                     + " is not marked as member of group.");
           }
         }
-- 
1.7.10.2