jebl.evolution.io
Class NexusExporter

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

public class NexusExporter
extends java.lang.Object
implements AlignmentExporter, SequenceExporter, TreeExporter

Export sequences and trees to Nexus format.

Version:
$Id: NexusExporter.java 1060 2010-06-01 08:52:55Z rambaut $
Author:
Andrew Rambaut, Alexei Drummond, Joseph Heled

Field Summary
static java.lang.String[] exportExcludeKeys
           
static int MAX_ROW_LENGTH
           
static java.lang.String treeNameAttributeKey
           
 
Constructor Summary
NexusExporter(java.io.Writer writer)
           
NexusExporter(java.io.Writer writer, boolean writeMetaComments)
           
NexusExporter(java.io.Writer writer, boolean writeMetaComments, boolean interleave)
           
 
Method Summary
 void exportAlignment(Alignment alignment)
          exportAlignment.
 void exportMatrix(DistanceMatrix distanceMatrix)
           
 void exportSequences(java.util.Collection<? extends Sequence> sequences)
          export alignment.
 void exportTree(Tree tree)
          Export a single tree
 void exportTrees(java.util.Collection<? extends Tree> trees)
          Export a collection of trees
 void exportTreesWithTranslation(java.util.Collection<? extends Tree> trees, java.util.Map<java.lang.String,java.lang.String> t)
           
static boolean isGeneratedTreeName(java.lang.String name)
           
static double roundDouble(double value, int decimalPlace)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

treeNameAttributeKey

public static final java.lang.String treeNameAttributeKey
See Also:
Constant Field Values

exportExcludeKeys

public static final java.lang.String[] exportExcludeKeys

MAX_ROW_LENGTH

public static final int MAX_ROW_LENGTH
See Also:
Constant Field Values
Constructor Detail

NexusExporter

public NexusExporter(java.io.Writer writer)

NexusExporter

public NexusExporter(java.io.Writer writer,
                     boolean writeMetaComments)
Parameters:
writer - where export text goes

NexusExporter

public NexusExporter(java.io.Writer writer,
                     boolean writeMetaComments,
                     boolean interleave)
Parameters:
writer - where export text goes
Method Detail

exportAlignment

public void exportAlignment(Alignment alignment)
                     throws java.io.IOException
exportAlignment.

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

exportSequences

public void exportSequences(java.util.Collection<? extends Sequence> sequences)
                     throws java.io.IOException,
                            java.lang.IllegalArgumentException
export alignment.

Specified by:
exportSequences in interface SequenceExporter
Throws:
java.io.IOException
java.lang.IllegalArgumentException

exportTree

public void exportTree(Tree tree)
                throws java.io.IOException
Export a single tree

Specified by:
exportTree in interface TreeExporter
Parameters:
tree -
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

exportTreesWithTranslation

public void exportTreesWithTranslation(java.util.Collection<? extends Tree> trees,
                                       java.util.Map<java.lang.String,java.lang.String> t)
                                throws java.io.IOException
Throws:
java.io.IOException

exportMatrix

public void exportMatrix(DistanceMatrix distanceMatrix)

roundDouble

public static double roundDouble(double value,
                                 int decimalPlace)

isGeneratedTreeName

public static boolean isGeneratedTreeName(java.lang.String name)


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