X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=268fece143a705abf7a29062fea12f2aa618c333;hb=4fcca76a6c1460d492469ace09a728925b733bfe;hp=f3cde9d555c0504fda1a00e607c248495d2352fb;hpb=1660a4fe03b8dda74b008ae4de2d804f8044a463;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index f3cde9d..268fece 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 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.appletgui;
 
@@ -54,17 +53,17 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
    * Creates a new TreePanel object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqVector
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pwtype
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public TreePanel(AlignViewport av, String type, String pwtype)
   {
@@ -84,15 +83,15 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
    * Creates a new TreePanel object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqVector
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pwtype
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public TreePanel(AlignViewport av, String type, String pwtype,
           NewickFile newtree)
@@ -215,14 +214,20 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       treeCanvas.setTree(tree);
       if (newtree != null)
       {
-        // Set default view, paying lip service to any overriding tree view parameter settings
-        boolean showDist = newtree.HasDistances() && av.applet.getDefaultParameter("showTreeDistances", newtree.HasDistances());
-        boolean showBoots = newtree.HasBootstrap() && av.applet.getDefaultParameter("showTreeBootstraps", newtree.HasBootstrap());
+        // Set default view, paying lip service to any overriding tree view
+        // parameter settings
+        boolean showDist = newtree.HasDistances()
+                && av.applet.getDefaultParameter("showTreeDistances",
+                        newtree.HasDistances());
+        boolean showBoots = newtree.HasBootstrap()
+                && av.applet.getDefaultParameter("showTreeBootstraps",
+                        newtree.HasBootstrap());
         distanceMenu.setState(showDist);
         bootstrapMenu.setState(showBoots);
         treeCanvas.setShowBootstrap(showBoots);
         treeCanvas.setShowDistances(showDist);
-        treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter("showUnlinkedTreeNodes", false));
+        treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
+                "showUnlinkedTreeNodes", false));
       }
 
       treeCanvas.repaint();
@@ -275,8 +280,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
 
   public void newickOutput_actionPerformed()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-            .getTopNode());
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(
+            tree.getTopNode());
     String output = fout.print(false, true);
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);