Class TaxaBlock

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String TAXA_BLOCK
      A constant representing the name of Taxa blocks.
    • Constructor Summary

      Constructors 
      Constructor Description
      TaxaBlock()
      Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name.
    • Constructor Detail

      • TaxaBlock

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