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

Class CharactersBlockBuilder

java.lang.Object

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

org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder

All Implemented Interfaces:

CharactersBlockListener, NexusBlockBuilder, NexusBlockListener

Direct Known Subclasses:

DataBlockBuilder

public class CharactersBlockBuilder
extends NexusBlockBuilder.Abstract
implements CharactersBlockListener

Builds Nexus characters 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
CharactersBlockBuilder()

Method Summary

Modifier and Type	Method	Description
void	addCharLabel(String charLabel)
void	addCharState(String charState)
void	addCharStateKeyword(String charState, String keyword)
protected void	addComment(NexusComment comment)	Tell the builder to add the given comment at the current location.
void	addEquate(String symbol, List symbols)
void	addItem(String item)
void	addMatrixEntry(String taxa)
void	addState(String state)
void	addStateLabel(String state, String label)
void	addSymbol(String symbol)
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).
protected CharactersBlock	makeNewBlock()
protected void	resetStatus()	Allowed to be called by DATA subclass.
void	setCharStateLabel(String charState, String label)
void	setDataType(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(String gap)
void	setInterleaved(boolean interleaved)
void	setLabels(boolean labels)
void	setMatchChar(String matchChar)
void	setMissing(String missing)
void	setRespectCase(boolean respectCase)
void	setStatesFormat(String statesFormat)
void	setTokens(boolean tokens)
void	setTransposed(boolean transposed)
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

CharactersBlockBuilder

public CharactersBlockBuilder()

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.

makeNewBlock

protected CharactersBlock makeNewBlock()

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

resetStatus

protected void resetStatus()

Allowed to be called by DATA subclass.

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

addCharLabel

public void addCharLabel(String charLabel)

Specified by:

addCharLabel in interface CharactersBlockListener

addCharState

public void addCharState(String charState)

Specified by:

addCharState in interface CharactersBlockListener

addCharStateKeyword

public void addCharStateKeyword(String charState,
                                String keyword)

Specified by:

addCharStateKeyword in interface CharactersBlockListener

addEquate

public void addEquate(String symbol,
                      List symbols)

Specified by:

addEquate in interface CharactersBlockListener

addItem

public void addItem(String item)

Specified by:

addItem in interface CharactersBlockListener

addMatrixEntry

public void addMatrixEntry(String taxa)

Specified by:

addMatrixEntry in interface CharactersBlockListener

addState

public void addState(String state)

Specified by:

addState in interface CharactersBlockListener

addStateLabel

public void addStateLabel(String state,
                          String label)

Specified by:

addStateLabel in interface CharactersBlockListener

addSymbol

public void addSymbol(String symbol)

Specified by:

addSymbol in interface CharactersBlockListener

addTaxLabel

public void addTaxLabel(String taxLabel)
                 throws ParseException

Description copied from interface: CharactersBlockListener

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 CharactersBlockListener

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 CharactersBlockListener

setCharStateLabel

public void setCharStateLabel(String charState,
                              String label)

Specified by:

setCharStateLabel in interface CharactersBlockListener

setDataType

public void setDataType(String dataType)

Specified by:

setDataType in interface CharactersBlockListener

setDimensionsNChar

public void setDimensionsNChar(int dimensionsNChar)

Description copied from interface: CharactersBlockListener

Set the NCHAR value.

Specified by:

setDimensionsNChar in interface CharactersBlockListener

Parameters:

dimensionsNChar - the NCHAR value.

setDimensionsNTax

public void setDimensionsNTax(int dimensionsNTax)

Description copied from interface: CharactersBlockListener

Set the NTAX value.

Specified by:

setDimensionsNTax in interface CharactersBlockListener

Parameters:

dimensionsNTax - the NTAX value.

setEliminateEnd

public void setEliminateEnd(int eliminateEnd)

Specified by:

setEliminateEnd in interface CharactersBlockListener

setEliminateStart

public void setEliminateStart(int eliminateStart)

Specified by:

setEliminateStart in interface CharactersBlockListener

setGap

public void setGap(String gap)

Specified by:

setGap in interface CharactersBlockListener

setInterleaved

public void setInterleaved(boolean interleaved)

Specified by:

setInterleaved in interface CharactersBlockListener

setLabels

public void setLabels(boolean labels)

Specified by:

setLabels in interface CharactersBlockListener

setMatchChar

public void setMatchChar(String matchChar)

Specified by:

setMatchChar in interface CharactersBlockListener

setMissing

public void setMissing(String missing)

Specified by:

setMissing in interface CharactersBlockListener

setRespectCase

public void setRespectCase(boolean respectCase)

Specified by:

setRespectCase in interface CharactersBlockListener

setStatesFormat

public void setStatesFormat(String statesFormat)

Specified by:

setStatesFormat in interface CharactersBlockListener

setTokens

public void setTokens(boolean tokens)

Specified by:

setTokens in interface CharactersBlockListener

setTransposed

public void setTransposed(boolean transposed)

Specified by:

setTransposed in interface CharactersBlockListener