Jalview 2.6 source licence

[jalview.git] / src / jalview / io / vamsas / Tree.java

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 1866336..2a62df4 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.io.vamsas;
 
@@ -98,8 +97,10 @@ public class Tree extends DatastoreItem
     tree = (uk.ac.vamsas.objects.core.Tree) vobj;
     doSync();
   }
-  
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
    */
   public void addFromDocument()
@@ -127,16 +128,20 @@ public class Tree extends DatastoreItem
     }
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.io.vamsas.DatastoreItem#conflict()
    */
   public void conflict()
   {
     Cache.log
-    .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
+            .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.io.vamsas.DatastoreItem#update()
    */
   public void updateToDoc()
@@ -150,38 +155,32 @@ 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.");
     }
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
    */
   public void updateFromDoc()
   {
-    // should probably just open a new tree panel in the same place as the old one
+    // should probably just open a new tree panel in the same place as the old
+    // one
     // TODO: Tree.updateFromDoc
     /*
-    TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
-    
-    // make a new tree
-    Object[] idata = recoverInputData(tree.getProvenance());
-    try
-    {
-      if (idata != null && idata[0] != null)
-      {
-        inputData = (AlignmentView) idata[0];
-      }
-      ntree = getNtree();
-      title = tree.getNewick(0).getTitle();
-      if (title == null || title.length() == 0)
-      {
-        title = tree.getTitle(); // hack!!!!
-      }
-    } catch (Exception e)
-    {
-      Cache.log.warn("Problems parsing treefile '"
-              + tree.getNewick(0).getContent() + "'", e);
-    }*/
+     * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
+     * 
+     * // make a new tree Object[] idata =
+     * recoverInputData(tree.getProvenance()); try { if (idata != null &&
+     * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
+     * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
+     * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
+     * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
+     * tree.getNewick(0).getContent() + "'", e); }
+     */
     log.debug("Update the local tree in jalview from the document.");
 
     if (isModifiable(tree.getModifiable()))
@@ -294,7 +293,7 @@ public class Tree extends DatastoreItem
    * Update jalview newick representation with TreeNode map
    * 
    * @param tp
-   *                the treepanel that this tree is bound to.
+   *          the treepanel that this tree is bound to.
    */
   public void UpdateSequenceTreeMap(TreePanel tp)
   {
@@ -439,7 +438,7 @@ public class Tree extends DatastoreItem
    * 
    * @param nodespec
    * @param leaves
-   *                as returned from NJTree.findLeaves( .., ..) ..
+   *          as returned from NJTree.findLeaves( .., ..) ..
    * @return
    */
   private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,