X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=e77134ecd9c32bade9b049cb0d7ae5e3ef2b3992;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=0c937dddc68958f2fd14d63dc0a9de94cbdecedd;hpb=40f08a931412edd1bc0e776033792fe3d4c0a5fa;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 0c937dd..e77134e 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.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.gui;
 
@@ -141,6 +140,10 @@ public class TreePanel extends GTreePanel
           if (tree == null)
           {
             System.out.println("tree is null");
+            // TODO: deal with case when a change event is received whilst a
+            // tree is still being calculated - should save reference for
+            // processing message later.
+            return;
           }
           if (evt.getNewValue() == null)
           {
@@ -361,12 +364,19 @@ public class TreePanel extends GTreePanel
       buffer.append("PID");
     }
 
-    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
             .getTopNode());
-    cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+    try {
+      cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
             tree.isHasRootDistance()));
+      Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("generating newick tree file",oom);
+      cap.dispose();
+    }
+
   }
 
   /**
@@ -493,6 +503,7 @@ public class TreePanel extends GTreePanel
 
   /**
    * sort the associated alignment view by the current tree.
+   * 
    * @param e
    */
   public void sortByTree_actionPerformed(ActionEvent e)
@@ -501,9 +512,8 @@ public class TreePanel extends GTreePanel
     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(av.getAlignment(), tree);
 
-    ap.alignFrame
-            .addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
-                    av.alignment));
+    ap.alignFrame.addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
+            av.alignment));
 
     ap.paintAlignment(true);
 
@@ -690,4 +700,75 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
+
+  /**
+   * change node labels to the annotation referred to by labelClass TODO:
+   * promote to a datamodel modification that can be undone TODO: make argument
+   * one case of a generic transformation function ie { undoStep = apply(Tree,
+   * TransformFunction)};
+   * 
+   * @param labelClass
+   */
+  public void changeNames(final String labelClass)
+  {
+    tree.applyToNodes(new NodeTransformI()
+    {
+
+      public void transform(BinaryNode node)
+      {
+        if (node instanceof SequenceNode
+                && !((SequenceNode) node).isPlaceholder()
+                && !((SequenceNode) node).isDummy())
+        {
+          String newname = null;
+          SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+          if (sq != null)
+          {
+            // search dbrefs, features and annotation
+            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq
+                    .getDBRef(), new String[]
+            { labelClass.toUpperCase() });
+            if (refs != null)
+            {
+              for (int i = 0; i < refs.length; i++)
+              {
+                if (newname == null)
+                {
+                  newname = new String(refs[i].getAccessionId());
+                }
+                else
+                {
+                  newname = newname + "; " + refs[i].getAccessionId();
+                }
+              }
+            }
+            if (newname == null)
+            {
+              SequenceFeature sf[] = sq.getSequenceFeatures();
+              for (int i = 0; sf != null && i < sf.length; i++)
+              {
+                if (sf[i].getType().equals(labelClass))
+                {
+                  if (newname == null)
+                  {
+                    newname = new String(sf[i].getDescription());
+                  }
+                  else
+                  {
+                    newname = newname + "; " + sf[i].getDescription();
+                  }
+                }
+              }
+            }
+          }
+          if (newname != null)
+          {
+            String oldname = ((SequenceNode) node).getName();
+            // TODO : save in the undo object for this modification.
+            ((SequenceNode) node).setName(newname);
+          }
+        }
+      }
+    });
+  }
 }