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

Class DistancesBlockBuilder

java.lang.Object

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

org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder

All Implemented Interfaces:

DistancesBlockListener, NexusBlockBuilder, NexusBlockListener

public class DistancesBlockBuilder
extends NexusBlockBuilder.Abstract
implements DistancesBlockListener

Builds 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.NexusBlockBuilder

NexusBlockBuilder.Abstract

Constructor Summary

Constructors

Constructor	Description
DistancesBlockBuilder()

Method Summary

Modifier and Type	Method	Description
protected void	addComment(NexusComment comment)	Tell the builder to add the given comment at the current location.
void	addMatrixEntry(String taxa)
void	addTaxLabel(String taxLabel)	Add a TAXLABEL.
void	appendMatrixData(String taxa, Object data)
void	endBlock()	Notifies the parser that a block is ending.
void	endTokenGroup()	Closing a line (semi-colon encountered).
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 NexusBlock	startBlockObject()	Tell the builder to start a new block object.

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

beginComment, commentText, endComment, getBlockName, getNexusBlock, startBlock

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener

beginComment, commentText, endComment, startBlock

Constructor Detail

DistancesBlockBuilder

public DistancesBlockBuilder()

Method Detail

addComment

protected void addComment(NexusComment comment)

Description copied from class: NexusBlockBuilder.Abstract

Tell the builder to add the given comment at the current location.

Specified by:

addComment in class NexusBlockBuilder.Abstract

Parameters:

comment - the comment to add.

startBlockObject

protected NexusBlock startBlockObject()

Description copied from class: NexusBlockBuilder.Abstract

Tell the builder to start a new block object.

Specified by:

startBlockObject in class NexusBlockBuilder.Abstract

endBlock

public void endBlock()

Description copied from interface: NexusBlockListener

Notifies the parser that a block is ending.

Specified by:

endBlock in interface NexusBlockListener

endTokenGroup

public void endTokenGroup()

Description copied from interface: NexusBlockListener

Closing a line (semi-colon encountered). This indicates that anything received after it is on the next logical line of the block.

Specified by:

endTokenGroup in interface NexusBlockListener

addMatrixEntry

public void addMatrixEntry(String taxa)

Specified by:

addMatrixEntry in interface DistancesBlockListener

addTaxLabel

public void addTaxLabel(String taxLabel)
                 throws ParseException

Description copied from interface: DistancesBlockListener

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

Specified by:

addTaxLabel in interface DistancesBlockListener

Parameters:

taxLabel - the label to add.

Throws:

ParseException - if the label cannot be added.

appendMatrixData

public void appendMatrixData(String taxa,
                             Object data)

Specified by:

appendMatrixData in interface DistancesBlockListener

setDimensionsNChar

public void setDimensionsNChar(int dimensionsNChar)

Description copied from interface: DistancesBlockListener

Set the NCHAR value.

Specified by:

setDimensionsNChar in interface DistancesBlockListener

Parameters:

dimensionsNChar - the NCHAR value.

setDimensionsNTax

public void setDimensionsNTax(int dimensionsNTax)

Description copied from interface: DistancesBlockListener

Set the NTAX value.

Specified by:

setDimensionsNTax in interface DistancesBlockListener

Parameters:

dimensionsNTax - the NTAX value.

setInterleaved

public void setInterleaved(boolean interleaved)

Specified by:

setInterleaved in interface DistancesBlockListener

setLabels

public void setLabels(boolean labels)

Specified by:

setLabels in interface DistancesBlockListener

setMissing

public void setMissing(String missing)

Specified by:

setMissing in interface DistancesBlockListener

setDiagonal

public void setDiagonal(boolean diagonal)

Specified by:

setDiagonal in interface DistancesBlockListener

setTriangle

public void setTriangle(String triangle)

Specified by:

setTriangle in interface DistancesBlockListener