com.hfg.bio.taxonomy.uniprot

Class UniprotSpecies

java.lang.Object

com.hfg.bio.taxonomy.uniprot.UniprotSpecies

public class UniprotSpecies
extends Object

Species class for Uniprot codes. Uses the speclist.txt provided with Uniprot to map the species codes that are a part of the locus name (Ex: 'HUMAN' in the locus 'TNF_HUMAN').

Method Summary

Modifier and Type	Method and Description
static UniprotSpecies	getByCode(String inValue) Retrieves the UniprotSpecies for the specified species code (Ex: 'HUMAN' from the locus 'TNF_HUMAN').
static UniprotSpecies	getByLocus(String inValue) Retrieves the UniprotSpecies for the specified loucs (Ex: 'TNF_HUMAN').
String	getCommonName()
char	getKingdomCode()
String	getScientificName()
String	getSpeciesCode()
String	getSynonym()
Integer	getTaxonId() Returns the taxon id.
static void	setSpeciesListFile(File inValue) Used to load a newer version of the speclist.txt file.

Methods inherited from class java.lang.Object

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

Method Detail

setSpeciesListFile

public static void setSpeciesListFile(File inValue)

Used to load a newer version of the speclist.txt file. The file may be gzip compressed. File found at ftp://www.expasy.ch/databases/uniprot/knowledgebase/docs/speclist.txt

Parameters:

inValue - the file to use as the source of Uniprot species data

getByLocus

public static UniprotSpecies getByLocus(String inValue)

Retrieves the UniprotSpecies for the specified loucs (Ex: 'TNF_HUMAN').

Parameters:

inValue - the Uniprot locus name for the species object to return

Returns:

the species object corresponding to the specified Uniprot locus.

getByCode

public static UniprotSpecies getByCode(String inValue)

Retrieves the UniprotSpecies for the specified species code (Ex: 'HUMAN' from the locus 'TNF_HUMAN').

Parameters:

inValue - the Uniprot code for the species object to return

Returns:

the species object corresponding to the specified Uniprot code.

getSpeciesCode

public String getSpeciesCode()

getKingdomCode

public char getKingdomCode()

getTaxonId

public Integer getTaxonId()

Returns the taxon id. The value is equal to the NCBI taxon id.

Returns:

the taxon id

getScientificName

public String getScientificName()

getCommonName

public String getCommonName()

getSynonym

public String getSynonym()