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 taxonomy.

Author:

Marc Vaudel

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
UniprotTaxonomy() Constructor.

Method Summary

Modifier and Type	Method and Description
void	downloadMapping(String name) Downloads the mapping for the given species name from UniProt and saves it to the mapping file.
static void	downloadTaxonomyFile(File destinationFile) Downloads the UniProt taxonomy mapping to the given file.
String	getCommonName(Integer id) Returns the common name corresponding to the given NCBI taxon.
Integer	getId(String name, boolean query) Returns the NCBI taxon corresponding to the given species name.
String	getLatinName(Integer id) Returns the Latin name corresponding to the given NCBI taxon.
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 Detail

SEPARATOR

public static final String SEPARATOR

The separator used to separate line contents.

See Also:

Constant Field Values

Constructor Detail

UniprotTaxonomy

public UniprotTaxonomy()

Constructor.

Method Detail

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.

downloadMapping

public void downloadMapping(String name)
                     throws MalformedURLException,
                            org.apache.commons.httpclient.URIException,
                            IOException

Downloads the mapping for the given species name from UniProt and saves it to the mapping file.

Parameters:

name - the name of the species to query

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

getId

public Integer getId(String name,
                     boolean query)
              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

query - boolean indicating whether UniProt should be queried if the species is not found

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

downloadTaxonomyFile

public static void downloadTaxonomyFile(File destinationFile)
                                 throws IOException

Downloads the UniProt taxonomy mapping to the given file.

Parameters:

destinationFile - the file where to write the taxonomy file

Throws:

IOException - Exception thrown whenever an error occurred while reading or writing data.