/*
 * 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;
  }

}