Package org.biojavax.bio.taxa.io

Class SimpleNCBITaxonomyLoader

java.lang.Object
org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
All Implemented Interfaces:
NCBITaxonomyLoader
public class SimpleNCBITaxonomyLoader extends Object implements NCBITaxonomyLoader
Loads NCBI taxon information from names.dmp and nodes.dmp, which are two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ . This simple implementation makes no attempt to process deletions or merges - it merely creates instances as it goes along, reusing any that may already exist.
Since:
1.5
Author:
Richard Holland

  • Constructor Details

  • Method Details

    • readNode

      public NCBITaxon readNode(BufferedReader nodes) throws IOException, ParseException
      Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
      Specified by:
      readNode in interface NCBITaxonomyLoader
      Parameters:
      nodes - something that reads the nodes.dmp file
      Returns:
      the next NCBITaxon object in the file, or null if the file has ended.
      Throws:
      IOException
      ParseException

    • findTaxon

      protected NCBITaxon findTaxon(Object[] theKeys)

    • readName

      public 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(); }
      Specified by:
      readName in interface NCBITaxonomyLoader
      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