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 Summary

Constructors

Constructor and Description
SimpleNCBITaxonomyLoader()

Method Summary

Modifier and Type	Method and Description
protected NCBITaxon	findTaxon(Object[] theKeys)
NCBITaxon	readName(BufferedReader names) Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.
NCBITaxon	readNode(BufferedReader nodes) Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleNCBITaxonomyLoader

public SimpleNCBITaxonomyLoader()

Method Detail

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