org.biojavax.bio.phylo.io.nexus

Class TaxaBlock

java.lang.Object

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

org.biojavax.bio.phylo.io.nexus.TaxaBlock

All Implemented Interfaces:

NexusBlock, NexusObject

public class TaxaBlock
extends NexusBlock.Abstract

Represents Nexus taxa 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 and Description
static String	TAXA_BLOCK A constant representing the name of Taxa blocks.

Constructor Summary

Constructors

Constructor and Description
TaxaBlock() Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name.

Method Summary

Modifier and Type	Method and Description
void	addComment(NexusComment comment) Adds a comment.
void	addTaxLabel(String taxLabel) Add a TAXLABEL.
boolean	containsTaxLabel(String taxLabel) Checks to see if we contain the given TAXLABEL.
List	getComments() Returns all comments.
int	getDimensionsNTax() Get the NTAX value.
List	getTaxLabels() Get the TAXLABEL values added so far.
void	removeComment(NexusComment comment) Removes a comment.
void	removeTaxLabel(String taxLabel) Removes the given TAXLABEL.
void	setDimensionsNTax(int dimensionsNTax) Set the NTAX value.
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

TAXA_BLOCK

public static final String TAXA_BLOCK

A constant representing the name of Taxa blocks.

See Also:

Constant Field Values

Constructor Detail

TaxaBlock

public TaxaBlock()

Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_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.

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.

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.