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

java.lang.Object
  extended by org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
      extended by 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
static java.lang.String CHARACTERS_BLOCK
          A constant representing the name of Characters blocks.
 
Constructor Summary
  CharactersBlock()
          Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name.
protected CharactersBlock(java.lang.String replacementLabel)
          For the DATA block subclass.
 
Method Summary
 void addCharLabel(java.lang.String charLabel)
           
 void addCharState(java.lang.String charState)
           
 void addCharStateKeyword(java.lang.String charState, java.lang.String keyword)
           
 void addComment(NexusComment comment)
          Adds a comment.
 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)
           
 boolean containsCharLabel(java.lang.String charLabel)
           
 boolean containsTaxLabel(java.lang.String taxLabel)
          Checks to see if we contain the given TAXLABEL.
 java.util.Set getAllCharStates()
           
 java.util.List getCharLabels()
           
 java.lang.String getCharStateLabel(java.lang.String charState)
           
 java.util.List getCharStateLabelKeywords(java.lang.String charState)
           
 java.util.List getComments()
          Returns all comments.
 java.lang.String getDataType()
           
 int getDimensionsNChar()
          Get the NCHAR value.
 int getDimensionsNTax()
          Get the NTAX value.
 int getEliminateEnd()
           
 int getEliminateStart()
           
 java.util.Map getEquates()
           
 java.lang.String getGap()
           
 java.util.List getItems()
           
 java.lang.String getMatchChar()
           
 java.util.List getMatrixData(java.lang.String taxa)
           
 java.lang.String getMissing()
           
 java.util.List getStateLabels(java.lang.String state)
           
 java.lang.String getStatesFormat()
           
 java.util.List getSymbols()
           
 java.util.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(java.lang.String charLabel)
           
 void removeCharState(java.lang.String charState)
           
 void removeComment(NexusComment comment)
          Removes a comment.
 void removeEquate(java.lang.String symbol)
           
 void removeItem(java.lang.String item)
           
 void removeState(java.lang.String state)
           
 void removeSymbol(java.lang.String symbol)
           
 void removeTaxLabel(java.lang.String taxLabel)
          Removes the given TAXLABEL.
 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)
           
protected  void writeBlockContents(java.io.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 java.lang.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(java.lang.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(java.lang.String dataType)

getDataType

public java.lang.String getDataType()

setRespectCase

public void setRespectCase(boolean respectCase)

isRespectCase

public boolean isRespectCase()

setMissing

public void setMissing(java.lang.String missing)

getMissing

public java.lang.String getMissing()

setGap

public void setGap(java.lang.String gap)

getGap

public java.lang.String getGap()

addSymbol

public void addSymbol(java.lang.String symbol)

removeSymbol

public void removeSymbol(java.lang.String symbol)

removeAllSymbols

public void removeAllSymbols()

getSymbols

public java.util.List getSymbols()

addEquate

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

removeEquate

public void removeEquate(java.lang.String symbol)

getEquates

public java.util.Map getEquates()

setMatchChar

public void setMatchChar(java.lang.String matchChar)

getMatchChar

public java.lang.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(java.lang.String item)

removeItem

public void removeItem(java.lang.String item)

removeAllItems

public void removeAllItems()

getItems

public java.util.List getItems()

setStatesFormat

public void setStatesFormat(java.lang.String statesFormat)

getStatesFormat

public java.lang.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(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.

removeTaxLabel

public void removeTaxLabel(java.lang.String taxLabel)
Removes the given TAXLABEL.

Parameters:
taxLabel - the label to remove.

containsTaxLabel

public boolean containsTaxLabel(java.lang.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 java.util.List getTaxLabels()
Get the TAXLABEL values added so far.

Returns:
this labels so far.

addCharState

public void addCharState(java.lang.String charState)

setCharStateLabel

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

addCharStateKeyword

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

getCharStateLabel

public java.lang.String getCharStateLabel(java.lang.String charState)

getCharStateLabelKeywords

public java.util.List getCharStateLabelKeywords(java.lang.String charState)

removeCharState

public void removeCharState(java.lang.String charState)

getAllCharStates

public java.util.Set getAllCharStates()

addCharLabel

public void addCharLabel(java.lang.String charLabel)

removeCharLabel

public void removeCharLabel(java.lang.String charLabel)

containsCharLabel

public boolean containsCharLabel(java.lang.String charLabel)

getCharLabels

public java.util.List getCharLabels()

addState

public void addState(java.lang.String state)

addStateLabel

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

getStateLabels

public java.util.List getStateLabels(java.lang.String state)

removeState

public void removeState(java.lang.String state)

addMatrixEntry

public void addMatrixEntry(java.lang.String taxa)

appendMatrixData

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

getMatrixData

public java.util.List getMatrixData(java.lang.String taxa)

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 java.util.List getComments()
Returns all comments.

Returns:
all the selected comments.

writeBlockContents

protected void writeBlockContents(java.io.Writer writer)
                           throws java.io.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:
java.io.IOException - if writing failed.