Class TaxaBlock

All Implemented Interfaces:
NexusBlock, NexusObject

public class TaxaBlock extends NexusBlock.Abstract
Represents Nexus taxa blocks.
Since:
1.6
Author:
Richard Holland, Tobias Thierer, Jim Balhoff
  • Field Details

  • Constructor Details

    • TaxaBlock

      public TaxaBlock()
      Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name.
  • 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.
    • 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.
    • 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.