org.biojavax.bio.phylo.io.nexus

Interface DistancesBlockListener

All Superinterfaces:

NexusBlockListener

All Known Implementing Classes:

DistancesBlockBuilder

public interface DistancesBlockListener
extends NexusBlockListener

Listens to events that represent Nexus distances blocks.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Method Summary

Modifier and Type	Method and Description
void	addMatrixEntry(String taxa)
void	addTaxLabel(String taxLabel) Add a TAXLABEL.
void	appendMatrixData(String taxa, Object data)
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)

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

beginComment, commentText, endBlock, endComment, endTokenGroup, startBlock

Method Detail

setDimensionsNTax

void setDimensionsNTax(int dimensionsNTax)

Set the NTAX value.

Parameters:

dimensionsNTax - the NTAX value.

setDimensionsNChar

void setDimensionsNChar(int dimensionsNChar)

Set the NCHAR value.

Parameters:

dimensionsNChar - the NCHAR value.

setTriangle

void setTriangle(String triangle)

setDiagonal

void setDiagonal(boolean diagonal)

setLabels

void setLabels(boolean labels)

setMissing

void setMissing(String missing)

setInterleaved

void setInterleaved(boolean interleaved)

addTaxLabel

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.

addMatrixEntry

void addMatrixEntry(String taxa)

appendMatrixData

void appendMatrixData(String taxa,
                      Object data)