Package org.biojavax.bio.phylo.io.nexus

Class DistancesBlock

java.lang.Object

org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract

org.biojavax.bio.phylo.io.nexus.DistancesBlock

All Implemented Interfaces:

NexusBlock, NexusObject

public class DistancesBlock
extends NexusBlock.Abstract

Represents Nexus distances blocks.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlock

NexusBlock.Abstract

Field Summary

Fields

Modifier and Type	Field	Description
static String	DISTANCES_BLOCK	A constant representing the name of Distances blocks.

Constructor Summary

Constructors

Constructor	Description
DistancesBlock()	Delegates to NexusBlock.Abstract constructor using DistancesBlock.DISTANCES_BLOCK as the name.

Method Summary

Modifier and Type	Method	Description
void	addComment(NexusComment comment)	Adds a comment.
void	addMatrixEntry(String taxa)
void	addTaxLabel(String taxLabel)	Add a TAXLABEL.
void	appendMatrixData(String taxa, Object data)
boolean	containsTaxLabel(String taxLabel)	Checks to see if we contain the given TAXLABEL.
List	getComments()	Returns all comments.
int	getDimensionsNChar()	Get the NCHAR value.
int	getDimensionsNTax()	Get the NTAX value.
List	getMatrixData(String taxa)
Collection	getMatrixLabels()
String	getMissing()
List	getTaxLabels()	Get the TAXLABEL values added so far.
boolean	isDiagonal()
boolean	isInterleaved()
boolean	isLabels()
void	removeComment(NexusComment comment)	Removes a comment.
void	removeTaxLabel(String taxLabel)	Removes the given TAXLABEL.
void	setDiagonal(boolean diagonal)
void	setDimensionsNChar(int dimensionsNChar)	Set the NCHAR value.
void	setDimensionsNTax(int dimensionsNTax)	Set the NTAX value.
void	setInterleaved(boolean interleaved)
void	setLabels(boolean labels)
void	setMissing(String missing)
void	setTriangle(String triangle)
protected void	writeBlockContents(Writer writer)	Implement this to write out block contents, not including the BEGIN and END tags.

Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract

getBlockName, writeObject, writeToken

Methods inherited from class java.lang.Object

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

Field Detail

DISTANCES_BLOCK

public static final String DISTANCES_BLOCK

A constant representing the name of Distances blocks.

See Also:

Constant Field Values

Constructor Detail

DistancesBlock

public DistancesBlock()

Delegates to NexusBlock.Abstract constructor using DistancesBlock.DISTANCES_BLOCK as the name.

Method Detail

setDimensionsNTax

public void setDimensionsNTax(int dimensionsNTax)

Set the NTAX value.

Parameters:

dimensionsNTax - the NTAX value.

getDimensionsNTax

public int getDimensionsNTax()

Get the NTAX value.

Returns:

the NTAX value.

setDimensionsNChar

public void setDimensionsNChar(int dimensionsNChar)

Set the NCHAR value.

Parameters:

dimensionsNChar - the NCHAR value.

getDimensionsNChar

public int getDimensionsNChar()

Get the NCHAR value.

Returns:

the NCHAR value.

setTriangle

public void setTriangle(String triangle)

setDiagonal

public void setDiagonal(boolean diagonal)

isDiagonal

public boolean isDiagonal()

setLabels

public void setLabels(boolean labels)

isLabels

public boolean isLabels()

setMissing

public void setMissing(String missing)

getMissing

public String getMissing()

setInterleaved

public void setInterleaved(boolean interleaved)

isInterleaved

public boolean isInterleaved()

addTaxLabel

public void addTaxLabel(String taxLabel)
                 throws ParseException

Add a TAXLABEL. If it already exists, or is a number that refers to an index position that already exists, an exception is thrown.

Parameters:

taxLabel - the label to add.

Throws:

ParseException - if the label cannot be added.

removeTaxLabel

public void removeTaxLabel(String taxLabel)

Removes the given TAXLABEL.

Parameters:

taxLabel - the label to remove.

containsTaxLabel

public boolean containsTaxLabel(String taxLabel)

Checks to see if we contain the given TAXLABEL.

Parameters:

taxLabel - the label to check for.

Returns:

true if we already contain it.

getTaxLabels

public List getTaxLabels()

Get the TAXLABEL values added so far.

Returns:

this labels so far.

addMatrixEntry

public void addMatrixEntry(String taxa)

appendMatrixData

public void appendMatrixData(String taxa,
                             Object data)

getMatrixData

public List getMatrixData(String taxa)

getMatrixLabels

public Collection getMatrixLabels()

addComment

public void addComment(NexusComment comment)

Adds a comment.

Parameters:

comment - the comment to add.

removeComment

public void removeComment(NexusComment comment)

Removes a comment.

Parameters:

comment - the comment to remove.

getComments

public List getComments()

Returns all comments.

Returns:

all the selected comments.

writeBlockContents

protected void writeBlockContents(Writer writer)
                           throws IOException

Description copied from class: NexusBlock.Abstract

Implement this to write out block contents, not including the BEGIN and END tags.

Specified by:

writeBlockContents in class NexusBlock.Abstract

Parameters:

writer - the writer to write to.

Throws:

IOException - if writing failed.