jebl.evolution.io
Class NexusExporter

java.lang.Object
  jebl.evolution.io.NexusExporter

All Implemented Interfaces:

AlignmentExporter, SequenceExporter, TreeExporter

public class NexusExporter
extends Object
implements AlignmentExporter, SequenceExporter, TreeExporter

Export sequences and trees to Nexus format.

Author:

Joseph Heled

Field Summary

static String	treeNameAttributeKey
protected PrintWriter	writer

Constructor Summary

NexusExporter(Writer writer)

Method Summary

void	exportAlignment(Alignment alignment) exportAlignment.
void	exportMatrix(DistanceMatrix distanceMatrix)
void	exportSequences(Collection<? extends Sequence> sequences) export alignment.
void	exportTree(Tree tree) Export a single tree
void	exportTrees(Collection<? extends Tree> trees) export trees
void	exportTreesWithTranslation(Collection<? extends Tree> trees, Map<String,String> t)
static boolean	isGeneratedTreeName(String name)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

treeNameAttributeKey

public static String treeNameAttributeKey

writer

protected final PrintWriter writer

Constructor Detail

NexusExporter

public NexusExporter(Writer writer)

Parameters:

writer - where export text goes

Method Detail

exportAlignment

public void exportAlignment(Alignment alignment)
                     throws IOException

exportAlignment.

Specified by:

exportAlignment in interface AlignmentExporter

Throws:

IOException

exportSequences

public void exportSequences(Collection<? extends Sequence> sequences)
                     throws IOException,
                            IllegalArgumentException

export alignment.

Specified by:

exportSequences in interface SequenceExporter

Throws:

IOException

IllegalArgumentException

exportTree

public void exportTree(Tree tree)
                throws IOException

Export a single tree

Specified by:

exportTree in interface TreeExporter

Parameters:

tree -

Throws:

IOException

exportTrees

public void exportTrees(Collection<? extends Tree> trees)
                 throws IOException

export trees

Specified by:

exportTrees in interface TreeExporter

Throws:

IOException

exportTreesWithTranslation

public void exportTreesWithTranslation(Collection<? extends Tree> trees,
                                       Map<String,String> t)
                                throws IOException

Throws:

IOException

exportMatrix

public void exportMatrix(DistanceMatrix distanceMatrix)

isGeneratedTreeName

public static boolean isGeneratedTreeName(String name)