Constructor Detail

• NexusPhylogeniesParser

  public NexusPhylogeniesParser()

Method Detail

• getName

  public java.lang.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,
                              java.io.IOException

  Specified by:

  next in interface IteratingPhylogenyParser

  Throws:

  NHXFormatException

  java.io.IOException

• parse

  public final Phylogeny[] parse()
                          throws java.io.IOException

  Specified by:

  parse in interface PhylogenyParser

  Throws:

  java.io.IOException

• reset

  public final void reset()
                   throws java.io.FileNotFoundException,
                          java.io.IOException

  Specified by:

  reset in interface IteratingPhylogenyParser

  Throws:

  java.io.FileNotFoundException

  java.io.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(java.lang.Object nexus_source)
                       throws PhylogenyParserException,
                              java.io.IOException

  Specified by:

  setSource in interface IteratingPhylogenyParser

  Specified by:

  setSource in interface PhylogenyParser

  Throws:

  PhylogenyParserException

  java.io.IOException

• setTaxonomyExtraction

  public final void setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)