Start of creating the objects Archaeopteryx needs

[jalview.git] / src / jalview / ext / archaeopteryx / ArchaeopteryxInit.java

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
index 4381a83..04147ce 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
@@ -1,24 +1,23 @@
-/*******************************************************************************
+/*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) 2017 The Jalview Authors
- *
+ * 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.
- *   
+ *  
  * 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.ext.archaeopteryx;
 
 import jalview.analysis.TreeModel;
@@ -63,7 +62,6 @@ public class ArchaeopteryxInit
       writer = new PrintWriter(newickFile);
       writer.println(newickOutput);
 
-      // System.out.println(writer.checkError());
       writer.close();
 
       String[] commandLineArgs = { "-open", newickFile.getCanonicalPath() };
@@ -118,11 +116,6 @@ public class ArchaeopteryxInit
     NewickFile newickTree = new NewickFile(tree.getTopNode(),
             tree.hasBootstrap(), tree.hasDistances(),
             tree.hasRootDistance());
-      /*     System.out.println(newickTree.print(tree.hasBootstrap(),
-             tree.hasDistances(), tree.hasRootDistance()));
-      
-           System.out.println(newickTree.print(newickTree.hasBootstrap(),
-             newickTree.hasDistances(), newickTree.hasRootDistance()));*/
 
     return newickTree;
   }