Class NexusPhylogeniesParser

Method Details

• getName

  public String getName()

  Specified by:

  getName in interface PhylogenyParser

• hasNext

  public final boolean hasNext()

  Specified by:

  hasNext in interface IteratingPhylogenyParser

• next

  public final Phylogeny next() throws NHXFormatException, IOException

  Specified by:

  next in interface IteratingPhylogenyParser

  Throws:

  NHXFormatException

  IOException

• parse

  public final Phylogeny[] parse() throws IOException

  Specified by:

  parse in interface PhylogenyParser

  Throws:

  IOException

• reset

  public final void reset() throws FileNotFoundException, IOException

  Specified by:

  reset in interface IteratingPhylogenyParser

  Throws:

  FileNotFoundException

  IOException

• setIgnoreQuotes

  public final void setIgnoreQuotes(boolean ignore_quotes_in_nh_data)

• setReplaceUnderscores

  public final void setReplaceUnderscores(boolean replace_underscores)

• setSource

  public final void setSource(Object nexus_source) throws PhylogenyParserException, IOException

  Specified by:

  setSource in interface IteratingPhylogenyParser

  Specified by:

  setSource in interface PhylogenyParser

  Throws:

  PhylogenyParserException

  IOException

• setTaxonomyExtraction

  public final void setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)