X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=0bf40960b357075a97f049efdffba08195418c5f;hb=73204ed7001df8ec4fc431934333bb3cfc6c90f3;hp=0545839e1deb9d39608e38901860f174f5ddfb72;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 0545839..0bf4096 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,29 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- * 
+ * 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/>.
+ * 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.Vector;
-
 import jalview.analysis.NJTree;
-import jalview.analysis.SequenceIdMatcher;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -32,11 +29,17 @@ 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;
 import jalview.io.VamsasAppDatastore;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.Entry;
@@ -103,6 +106,7 @@ 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 +137,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#conflict()
    */
+  @Override
   public void conflict()
   {
     Cache.log
@@ -144,6 +149,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#update()
    */
+  @Override
   public void updateToDoc()
   {
     if (isModifiable(tree.getModifiable()))
@@ -155,8 +161,7 @@ public class Tree extends DatastoreItem
     else
     {
       // handle conflict
-      log
-              .info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
+      log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
     }
   }
 
@@ -165,6 +170,7 @@ 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
@@ -220,8 +226,8 @@ public class Tree extends DatastoreItem
       // or just correctly resolve the tree's seqData to the correct alignment
       // in
       // the document.
-      Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
-              .getTree().seqData.getSequences()));
+      Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
+              tp.getTree().seqData.getSequences()));
       Object[] alsqs = new Object[alsqrefs.size()];
       alsqrefs.copyInto(alsqs);
       vInput.setObjRef(alsqs);
@@ -265,20 +271,22 @@ 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);
+          }
         }
       }
     }
@@ -347,9 +355,7 @@ public class Tree extends DatastoreItem
         else
         {
           leaf.setPlaceholder(true);
-          leaf
-                  .setElement(new Sequence(leaf.getName(),
-                          "THISISAPLACEHLDER"));
+          leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
         }
       }
     }
@@ -416,8 +422,7 @@ public class Tree extends DatastoreItem
       tnv.copyInto(tn);
       return tn;
     }
-    return new Treenode[]
-    {};
+    return new Treenode[] {};
   }
 
   private String makeNodeSpec(Hashtable nodespecs,
@@ -478,6 +483,7 @@ public class Tree extends DatastoreItem
    * add jalview object to vamsas document
    * 
    */
+  @Override
   public void addToDocument()
   {
     tree = new uk.ac.vamsas.objects.core.Tree();
@@ -504,7 +510,7 @@ public class Tree extends DatastoreItem
    */
   public Object[] recoverInputData(Provenance tp)
   {
-    AlignViewport javport = null;
+    AlignmentViewport javport = null;
     jalview.datamodel.AlignmentI jal = null;
     jalview.datamodel.CigarArray view = null;
     for (int pe = 0; pe < tp.getEntryCount(); pe++)
@@ -589,8 +595,7 @@ public class Tree extends DatastoreItem
           // off by
           // one for to
         }
-        return new Object[]
-        { new AlignmentView(view), jal };
+        return new Object[] { new AlignmentView(view), jal };
       }
     }
     Cache.log
@@ -598,7 +603,7 @@ public class Tree extends DatastoreItem
     return null;
   }
 
-  private AlignViewport getViewport(Vobject v_parent)
+  private AlignmentViewport getViewport(Vobject v_parent)
   {
     if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
     {