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

Class EnsemblSpecies

java.lang.Object

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

public class EnsemblSpecies
extends Object

Mapping of the Ensembl species.

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
EnsemblSpecies() Constructor.

Method Summary

Modifier and Type	Method and Description
String	getAssembly(Integer id) Returns the Ensembl assembly corresponding to the given NCBI taxon.
String	getCommonName(Integer id) Returns the common name corresponding to the given NCBI taxon.
String	getScientificName(Integer id) Returns the scientific name corresponding to the given NCBI taxon.
HashSet<Integer>	getTaxons() Returns the taxons in this map.
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

EnsemblSpecies

public EnsemblSpecies()

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.

getScientificName

public String getScientificName(Integer id)

Returns the scientific name corresponding to the given NCBI taxon.

Parameters:

id - the NCBI taxon

Returns:

the scientific 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

getAssembly

public String getAssembly(Integer id)

Returns the Ensembl assembly corresponding to the given NCBI taxon.

Parameters:

id - the NCBI taxon

Returns:

the Ensembl assembly

getTaxons

public HashSet<Integer> getTaxons()

Returns the taxons in this map.

Returns:

the taxons in this map