Class CharactersBlock

Method Details

• 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.