X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=43febb451c8c4e6f2194c07591bf469b414e5317;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=5fdd0c9c6cdf6d5448b0df96f5ef4f018783810a;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 5fdd0c9..43febb4 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,29 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io.vamsas;
 
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 import jalview.analysis.NJTree;
-import jalview.analysis.SequenceIdMatcher;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -32,7 +33,6 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.TreePanel;
 import jalview.io.NewickFile;
@@ -103,6 +103,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
    */
+  @Override
   public void addFromDocument()
   {
     tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
@@ -133,6 +134,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#conflict()
    */
+  @Override
   public void conflict()
   {
     Cache.log
@@ -144,6 +146,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#update()
    */
+  @Override
   public void updateToDoc()
   {
     if (isModifiable(tree.getModifiable()))
@@ -164,6 +167,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
    */
+  @Override
   public void updateFromDoc()
   {
     // should probably just open a new tree panel in the same place as the old
@@ -264,20 +268,22 @@ public class Tree extends DatastoreItem
     SeqCigar[] tseqs = new SeqCigar[sequences.length];
     System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
     Vector alsq = new Vector();
-    Enumeration as = jal.getSequences().elements();
-    while (as.hasMoreElements())
+    List<SequenceI> jalsqs;
+    synchronized (jalsqs = jal.getSequences())
     {
-      SequenceI asq = (SequenceI) as.nextElement();
-      for (int t = 0; t < sequences.length; t++)
+      for (SequenceI asq : jalsqs)
       {
-        if (tseqs[t] != null
-                && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
-                        .getDatasetSequence()))
-        // && tseqs[t].getStart()>=asq.getStart() &&
-        // tseqs[t].getEnd()<=asq.getEnd())
+        for (int t = 0; t < sequences.length; t++)
         {
-          tseqs[t] = null;
-          alsq.add(asq);
+          if (tseqs[t] != null
+                  && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
+                          .getDatasetSequence()))
+          // && tseqs[t].getStart()>=asq.getStart() &&
+          // tseqs[t].getEnd()<=asq.getEnd())
+          {
+            tseqs[t] = null;
+            alsq.add(asq);
+          }
         }
       }
     }
@@ -475,6 +481,7 @@ public class Tree extends DatastoreItem
    * add jalview object to vamsas document
    * 
    */
+  @Override
   public void addToDocument()
   {
     tree = new uk.ac.vamsas.objects.core.Tree();