From f2046fb81157088cd140dc1e49487af2410cce87 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 13 Nov 2017 19:19:10 +0000
Subject: [PATCH] JAL-2805 deleted old Aptx class for loading just Newick
 files

---
 .../ext/archaeopteryx/ArchaeopteryxNewickInit.java |  123 --------------------
 1 file changed, 123 deletions(-)
 delete mode 100644 src/jalview/ext/archaeopteryx/ArchaeopteryxNewickInit.java

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxNewickInit.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxNewickInit.java
deleted file mode 100644
index eb4af6f..0000000
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxNewickInit.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
- * 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.
- *  
- * 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;
-import jalview.io.NewickFile;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.PrintWriter;
-
-import org.forester.archaeopteryx.Archaeopteryx;
-
-public class ArchaeopteryxNewickInit
-{
-  private String filePath = "/tmp/jalviewtree.nwk";
-
-  private TreeModel tree;
-
-  private NewickFile newickTree;
-
-  public ArchaeopteryxNewickInit(TreeModel jalviewTreeModel)
-  {
-    this.tree = jalviewTreeModel;
-    this.newickTree = treeToNewick(tree);
-  }
-
-  public ArchaeopteryxNewickInit(NewickFile newickTreeModel)
-  {
-    this.newickTree = newickTreeModel;
-  }
-
-  public void startArchaeopteryx()
-  {
-    String newickOutput = newickTree.print(newickTree.hasBootstrap(),
-            newickTree.hasDistances(), newickTree.hasRootDistance());
-
-    File newickFile = new File(filePath);
-    PrintWriter writer;
-
-    try
-    {
-      writer = new PrintWriter(newickFile);
-      writer.println(newickOutput);
-
-      writer.close();
-
-      String[] commandLineArgs = { "-open", newickFile.getCanonicalPath() };
-      Archaeopteryx.main(commandLineArgs);
-
-    } catch (FileNotFoundException e)
-    {
-      // TODO Auto-generated catch block
-      e.printStackTrace();
-    } catch (IOException e)
-    {
-      // TODO Auto-generated catch block
-      e.printStackTrace();
-    }
-
-
-  }
-
-
-  public String getFilePath()
-  {
-    return filePath;
-  }
-
-  public void setFilePath(String newFilePath)
-  {
-    this.filePath = newFilePath;
-  }
-
-  public TreeModel getTree()
-  {
-    return tree;
-  }
-
-  public void setTree(TreeModel newTree)
-  {
-    this.tree = newTree;
-  }
-
-  public NewickFile getNewickTree()
-  {
-    return newickTree;
-  }
-
-  public void setNewickTree(NewickFile newNewickTree)
-  {
-    this.newickTree = newNewickTree;
-  }
-
-  public static NewickFile treeToNewick(TreeModel tree)
-  {
-    NewickFile newickTree = new NewickFile(tree.getTopNode(),
-            tree.hasBootstrap(), tree.hasDistances(),
-            tree.hasRootDistance());
-
-    return newickTree;
-  }
-
-}
\ No newline at end of file
-- 
1.7.10.2