jebl.evolution.io

Class PHYLIPExporter

java.lang.Object

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

Constructors

Constructor and Description
PHYLIPExporter(java.io.Writer writer)

Method Summary

Methods

Modifier and Type	Method and Description
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