jebl.evolution.io
Class PHYLIPExporter

java.lang.Object
  extended by jebl.evolution.io.PHYLIPExporter
All Implemented Interfaces:
AlignmentExporter, TreeExporter

public class PHYLIPExporter
extends java.lang.Object
implements AlignmentExporter, TreeExporter

Export alignment to Phylip format. Must be one of the most braindead format around. Try to output something that hopefuly any "Phylip supported" variant can read - up to 9 name chars, followed by a blank, followed by sequence on one line.

Version:
$Id: PHYLIPExporter.java 841 2007-11-11 21:36:42Z twobeers $
Author:
Joseph Heled

Constructor Summary
PHYLIPExporter(java.io.Writer writer)
           
 
Method Summary
 void exportAlignment(Alignment alignment)
          export one alignment.
 void exportTree(Tree tree)
          Export a single tree
 void exportTrees(java.util.Collection<? extends Tree> trees)
          Export a collection of trees
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PHYLIPExporter

public PHYLIPExporter(java.io.Writer writer)
Parameters:
writer - where export text goes
Method Detail

exportAlignment

public void exportAlignment(Alignment alignment)
                     throws java.io.IOException
Description copied from interface: AlignmentExporter
export one alignment.

Specified by:
exportAlignment in interface AlignmentExporter
Parameters:
alignment - to export
Throws:
java.io.IOException

exportTree

public void exportTree(Tree tree)
                throws java.io.IOException
Description copied from interface: TreeExporter
Export a single tree

Specified by:
exportTree in interface TreeExporter
Throws:
java.io.IOException

exportTrees

public void exportTrees(java.util.Collection<? extends Tree> trees)
                 throws java.io.IOException
Description copied from interface: TreeExporter
Export a collection of trees

Specified by:
exportTrees in interface TreeExporter
Throws:
java.io.IOException


http://code.google.com/p/jebl2/