src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.TreeModel;
   4 import jalview.io.NewickFile;
   5
   6 import java.io.File;
   7 import java.io.FileNotFoundException;
   8 import java.io.IOException;
   9 import java.io.PrintWriter;
  10
  11 import org.forester.archaeopteryx.Archaeopteryx;
  12
  13 public class ArchaeopteryxInit
  14 {
  15   private String filePath = "/tmp/jalviewtree.nwk";
  16
  17   private TreeModel tree;
  18
  19   private NewickFile newickTree;
  20
  21   public ArchaeopteryxInit(TreeModel jalviewTreeModel)
  22   {
  23     this.tree = jalviewTreeModel;
  24     this.newickTree = treeToNewick(tree);
  25   }
  26
  27   public ArchaeopteryxInit(NewickFile newickTreeModel)
  28   {
  29     this.newickTree = newickTreeModel;
  30   }
  31
  32   public void startArchaeopteryx()
  33   {
  34     String newickOutput = newickTree.print(newickTree.hasBootstrap(),
  35             newickTree.hasDistances(), newickTree.hasRootDistance());
  36
  37     File newickFile = new File(filePath);
  38     PrintWriter writer;
  39
  40     try
  41     {
  42       writer = new PrintWriter(newickFile);
  43       writer.println(newickOutput);
  44
  45       // System.out.println(writer.checkError());
  46       writer.close();
  47
  48       String[] commandLineArgs = { "-open", newickFile.getCanonicalPath() };
  49       Archaeopteryx.main(commandLineArgs);
  50
  51     } catch (FileNotFoundException e)
  52     {
  53       // TODO Auto-generated catch block
  54       e.printStackTrace();
  55     } catch (IOException e)
  56     {
  57       // TODO Auto-generated catch block
  58       e.printStackTrace();
  59     }
  60
  61
  62   }
  63
  64
  65   public String getFilePath()
  66   {
  67     return filePath;
  68   }
  69
  70   public void setFilePath(String newFilePath)
  71   {
  72     this.filePath = newFilePath;
  73   }
  74
  75   public TreeModel getTree()
  76   {
  77     return tree;
  78   }
  79
  80   public void setTree(TreeModel newTree)
  81   {
  82     this.tree = newTree;
  83   }
  84
  85   public NewickFile getNewickTree()
  86   {
  87     return newickTree;
  88   }
  89
  90   public void setNewickTree(NewickFile newNewickTree)
  91   {
  92     this.newickTree = newNewickTree;
  93   }
  94
  95   public static NewickFile treeToNewick(TreeModel tree)
  96   {
  97     NewickFile newickTree = new NewickFile(tree.getTopNode(),
  98             tree.hasBootstrap(), tree.hasDistances(),
  99             tree.hasRootDistance());
 100       /*     System.out.println(newickTree.print(tree.hasBootstrap(),
 101              tree.hasDistances(), tree.hasRootDistance()));
 102
 103            System.out.println(newickTree.print(newickTree.hasBootstrap(),
 104              newickTree.hasDistances(), newickTree.hasRootDistance()));*/
 105
 106     return newickTree;
 107   }
 108
 109 }