Interface NCBITaxonomyLoader

  • All Known Implementing Classes:
    SimpleNCBITaxonomyLoader

    public interface NCBITaxonomyLoader
    Implementors are able to load taxonomy files and generate sets of NCBITaxon objects that represent them. Taxon objects should be generated using RichObjectFactory.
    Since:
    1.5
    Author:
    Richard Holland
    • Method Detail

      • readName

        NCBITaxon readName​(BufferedReader names)
                    throws IOException,
                           ParseException
        Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already. Note that this does not clear out existing names from the taxon, it only adds them. Use the code snippet below if you want to clear out the names first: for (Iterator i = taxon.getNameClasses().iterator(); i.hasNext(); ) { taxon.getNames((String)i.next()).clear(); }
        Parameters:
        names - something that reads the names.dmp file
        Returns:
        the NCBITaxon object corresponding to the next entry in the file, or null if the file has ended.
        Throws:
        IOException
        ParseException