Class DistancesBlock

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.

• setTriangle

  public void setTriangle(String triangle)

• setDiagonal

  public void setDiagonal(boolean diagonal)

• isDiagonal

  public boolean isDiagonal()

• setLabels

  public void setLabels(boolean labels)

• isLabels

  public boolean isLabels()

• setMissing

  public void setMissing(String missing)

• getMissing

  public String getMissing()

• setInterleaved

  public void setInterleaved(boolean interleaved)

• isInterleaved

  public boolean isInterleaved()

• 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.

• 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.