## 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
`static 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(String replacementLabel)` For the DATA block subclass.

Method Summary
`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.