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

Interface CharactersBlockListener

All Superinterfaces:

NexusBlockListener

All Known Subinterfaces:

DataBlockListener

All Known Implementing Classes:

CharactersBlockBuilder, DataBlockBuilder

public interface CharactersBlockListener
extends NexusBlockListener

Listens to events that represent Nexus characters blocks.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Method Summary

Modifier and Type	Method	Description
void	addCharLabel(java.lang.String charLabel)
void	addCharState(java.lang.String charState)
void	addCharStateKeyword(java.lang.String charState, java.lang.String keyword)
void	addEquate(java.lang.String symbol, java.util.List symbols)
void	addItem(java.lang.String item)
void	addMatrixEntry(java.lang.String taxa)
void	addState(java.lang.String state)
void	addStateLabel(java.lang.String state, java.lang.String label)
void	addSymbol(java.lang.String symbol)
void	addTaxLabel(java.lang.String taxLabel)	Add a TAXLABEL.
void	appendMatrixData(java.lang.String taxa, java.lang.Object data)
void	setCharStateLabel(java.lang.String charState, java.lang.String label)
void	setDataType(java.lang.String dataType)
void	setDimensionsNChar(int dimensionsNChar)	Set the NCHAR value.
void	setDimensionsNTax(int dimensionsNTax)	Set the NTAX value.
void	setEliminateEnd(int eliminateEnd)
void	setEliminateStart(int eliminateStart)
void	setGap(java.lang.String gap)
void	setInterleaved(boolean interleaved)
void	setLabels(boolean labels)
void	setMatchChar(java.lang.String matchChar)
void	setMissing(java.lang.String missing)
void	setRespectCase(boolean respectCase)
void	setStatesFormat(java.lang.String statesFormat)
void	setTokens(boolean tokens)
void	setTransposed(boolean transposed)

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.

setDataType

void setDataType(java.lang.String dataType)

setRespectCase

void setRespectCase(boolean respectCase)

setMissing

void setMissing(java.lang.String missing)

setGap

void setGap(java.lang.String gap)

addSymbol

void addSymbol(java.lang.String symbol)

addEquate

void addEquate(java.lang.String symbol,
               java.util.List symbols)

setMatchChar

void setMatchChar(java.lang.String matchChar)

setLabels

void setLabels(boolean labels)

setTransposed

void setTransposed(boolean transposed)

setInterleaved

void setInterleaved(boolean interleaved)

addItem

void addItem(java.lang.String item)

setStatesFormat

void setStatesFormat(java.lang.String statesFormat)

setTokens

void setTokens(boolean tokens)

setEliminateStart

void setEliminateStart(int eliminateStart)

setEliminateEnd

void setEliminateEnd(int eliminateEnd)

addTaxLabel

void addTaxLabel(java.lang.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.

addCharState

void addCharState(java.lang.String charState)

setCharStateLabel

void setCharStateLabel(java.lang.String charState,
                       java.lang.String label)

addCharStateKeyword

void addCharStateKeyword(java.lang.String charState,
                         java.lang.String keyword)

addCharLabel

void addCharLabel(java.lang.String charLabel)

addState

void addState(java.lang.String state)

addStateLabel

void addStateLabel(java.lang.String state,
                   java.lang.String label)

addMatrixEntry

void addMatrixEntry(java.lang.String taxa)

appendMatrixData

void appendMatrixData(java.lang.String taxa,
                      java.lang.Object data)