Package com.compomics.util.experiment.biology.taxonomy.mappings

Class UniprotTaxonomy

java.lang.Object

com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy

public class UniprotTaxonomy
extends Object

Mapping of the UniProt species taken from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static final String	SEPARATOR	The separator used to separate line contents.

Constructor Summary

Constructors

Constructor	Description
UniprotTaxonomy()	Constructor.

Method Summary

Modifier and Type	Method	Description
String	getCommonName(Integer id)	Returns the common name corresponding to the given NCBI taxon.
Integer	getId(String name)	Returns the NCBI taxon corresponding to the given species name.
String	getLatinName(Integer id)	Returns the Latin name corresponding to the given NCBI taxon.
String	getSynonym(String scientificName)	Returns the synonym corresponding to the scientific name.
void	loadMapping(File speciesFile)	Loads the species mapping from a file.

Methods inherited from class java.lang.Object

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

Field Details

SEPARATOR

public static final String SEPARATOR

The separator used to separate line contents.

See Also:

• Constant Field Values

Constructor Details

UniprotTaxonomy

public UniprotTaxonomy()

Constructor.

Method Details

loadMapping

public void loadMapping(File speciesFile)
                 throws IOException

Loads the species mapping from a file. Previous mapping will be overwritten.

Parameters:

speciesFile - the species file

Throws:

IOException - exception thrown whenever an error occurred while reading the file.

getId

public Integer getId(String name)
              throws MalformedURLException,
org.apache.commons.httpclient.URIException,
IOException

Returns the NCBI taxon corresponding to the given species name. Null if not found.

Parameters:

name - the species name

Returns:

the taxon

Throws:

MalformedURLException - exception thrown whenever the query URL is malformed

org.apache.commons.httpclient.URIException - exception thrown whenever an error occurred while downloading the mapping

IOException - exception thrown whenever an error occurred while downloading the mapping

getLatinName

public String getLatinName(Integer id)

Returns the Latin name corresponding to the given NCBI taxon.

Parameters:

id - the NCBI taxon

Returns:

the Latin name

getCommonName

public String getCommonName(Integer id)

Returns the common name corresponding to the given NCBI taxon.

Parameters:

id - the NCBI taxon

Returns:

the common name

getSynonym

public String getSynonym(String scientificName)

Returns the synonym corresponding to the scientific name. E.g. 'Ajellomyces capsulatus (strain H143)' returns 'Histoplasma capsulatum'.

Parameters:

scientificName - the scientific name

Returns:

the synonym