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

Class CharactersBlock

java.lang.Object

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

org.biojavax.bio.phylo.io.nexus.CharactersBlock

All Implemented Interfaces:

NexusBlock, NexusObject

Direct Known Subclasses:

DataBlock

public class CharactersBlock
extends NexusBlock.Abstract

Represents 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.NexusBlock

NexusBlock.Abstract

Field Summary

Fields

Modifier and Type	Field	Description
static String	CHARACTERS_BLOCK	A constant representing the name of Characters blocks.

Constructor Summary

Constructors

Modifier	Constructor	Description
	CharactersBlock()	Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name.
protected	CharactersBlock(String replacementLabel)	For the DATA block subclass.

Method Summary

Modifier and Type	Method	Description
void	addCharLabel(String charLabel)
void	addCharState(String charState)
void	addCharStateKeyword(String charState, String keyword)
void	addComment(NexusComment comment)	Adds a comment.
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)
boolean	containsCharLabel(String charLabel)
boolean	containsTaxLabel(String taxLabel)	Checks to see if we contain the given TAXLABEL.
Set	getAllCharStates()
List	getCharLabels()
String	getCharStateLabel(String charState)
List	getCharStateLabelKeywords(String charState)
List	getComments()	Returns all comments.
String	getDataType()
int	getDimensionsNChar()	Get the NCHAR value.
int	getDimensionsNTax()	Get the NTAX value.
int	getEliminateEnd()
int	getEliminateStart()
Map	getEquates()
String	getGap()
List	getItems()
String	getMatchChar()
List	getMatrixData(String taxa)
Collection	getMatrixLabels()
String	getMissing()
List	getStateLabels(String state)
String	getStatesFormat()
List	getSymbols()
List	getTaxLabels()	Get the TAXLABEL values added so far.
boolean	isInterleaved()
boolean	isLabels()
boolean	isRespectCase()
boolean	isTokens()
boolean	isTransposed()
void	removeAllItems()
void	removeAllSymbols()
void	removeCharLabel(String charLabel)
void	removeCharState(String charState)
void	removeComment(NexusComment comment)	Removes a comment.
void	removeEquate(String symbol)
void	removeItem(String item)
void	removeState(String state)
void	removeSymbol(String symbol)
void	removeTaxLabel(String taxLabel)	Removes the given TAXLABEL.
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 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

CHARACTERS_BLOCK

public static final String CHARACTERS_BLOCK

A constant representing the name of Characters blocks.

See Also:

Constant Field Values

Constructor Detail

CharactersBlock

public CharactersBlock()

Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name.

CharactersBlock

protected CharactersBlock(String replacementLabel)

For the DATA block subclass.

Parameters:

replacementLabel - the different label to use.

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.

setDimensionsNChar

public void setDimensionsNChar(int dimensionsNChar)

Set the NCHAR value.

Parameters:

dimensionsNChar - the NCHAR value.

getDimensionsNChar

public int getDimensionsNChar()

Get the NCHAR value.

Returns:

the NCHAR value.

setDataType

public void setDataType(String dataType)

getDataType

public String getDataType()

setRespectCase

public void setRespectCase(boolean respectCase)

isRespectCase

public boolean isRespectCase()

setMissing

public void setMissing(String missing)

getMissing

public String getMissing()

setGap

public void setGap(String gap)

getGap

public String getGap()

addSymbol

public void addSymbol(String symbol)

removeSymbol

public void removeSymbol(String symbol)

removeAllSymbols

public void removeAllSymbols()

getSymbols

public List getSymbols()

addEquate

public void addEquate(String symbol,
                      List symbols)

removeEquate

public void removeEquate(String symbol)

getEquates

public Map getEquates()

setMatchChar

public void setMatchChar(String matchChar)

getMatchChar

public String getMatchChar()

setLabels

public void setLabels(boolean labels)

isLabels

public boolean isLabels()

setTransposed

public void setTransposed(boolean transposed)

isTransposed

public boolean isTransposed()

setInterleaved

public void setInterleaved(boolean interleaved)

isInterleaved

public boolean isInterleaved()

addItem

public void addItem(String item)

removeItem

public void removeItem(String item)

removeAllItems

public void removeAllItems()

getItems

public List getItems()

setStatesFormat

public void setStatesFormat(String statesFormat)

getStatesFormat

public String getStatesFormat()

setTokens

public void setTokens(boolean tokens)

isTokens

public boolean isTokens()

setEliminateStart

public void setEliminateStart(int eliminateStart)

getEliminateStart

public int getEliminateStart()

setEliminateEnd

public void setEliminateEnd(int eliminateEnd)

getEliminateEnd

public int getEliminateEnd()

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.

addCharState

public void addCharState(String charState)

setCharStateLabel

public void setCharStateLabel(String charState,
                              String label)

addCharStateKeyword

public void addCharStateKeyword(String charState,
                                String keyword)

getCharStateLabel

public String getCharStateLabel(String charState)

getCharStateLabelKeywords

public List getCharStateLabelKeywords(String charState)

removeCharState

public void removeCharState(String charState)

getAllCharStates

public Set getAllCharStates()

addCharLabel

public void addCharLabel(String charLabel)

removeCharLabel

public void removeCharLabel(String charLabel)

containsCharLabel

public boolean containsCharLabel(String charLabel)

getCharLabels

public List getCharLabels()

addState

public void addState(String state)

addStateLabel

public void addStateLabel(String state,
                          String label)

getStateLabels

public List getStateLabels(String state)

removeState

public void removeState(String state)

addMatrixEntry

public void addMatrixEntry(String taxa)

appendMatrixData

public void appendMatrixData(String taxa,
                             Object data)

getMatrixData

public List getMatrixData(String taxa)

getMatrixLabels

public Collection getMatrixLabels()

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.