Package 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, Harald Barsnes

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	EnsemblSpecies.EnsemblDivision	Enum of the different Ensembl divisions.

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
EnsemblSpecies()	Constructor.

Method Summary

Modifier and Type	Method	Description
String	getAssembly(String latinName)	Returns the Ensembl assembly corresponding to the given Latin name.
String	getCommonName(String latinName)	Returns the common name corresponding to the given Latin name.
EnsemblSpecies.EnsemblDivision	getDivision(String latinName)	Returns the division corresponding to the given Latin name.
HashSet<String>	getLatinNames()	Returns the Latin names in this map.
String	getTaxon(String latinName)	Returns the NCBI taxon corresponding to the given Latin 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

EnsemblSpecies

public EnsemblSpecies()

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.

getCommonName

public String getCommonName(String latinName)

Returns the common name corresponding to the given Latin name.

Parameters:

latinName - the Latin name, e.g. 'homo_sapiens'.

Returns:

the common name

getDivision

public EnsemblSpecies.EnsemblDivision getDivision(String latinName)

Returns the division corresponding to the given Latin name.

Parameters:

latinName - the Latin name, e.g. 'homo_sapiens'.

Returns:

the Ensembl division

getAssembly

public String getAssembly(String latinName)

Returns the Ensembl assembly corresponding to the given Latin name.

Parameters:

latinName - the Latin name, e.g. 'homo_sapiens'.

Returns:

the Ensembl assembly

getTaxon

public String getTaxon(String latinName)

Returns the NCBI taxon corresponding to the given Latin name.

Parameters:

latinName - the Latin name, e.g. 'homo_sapiens'.

Returns:

the NCBI taxon

getLatinNames

public HashSet<String> getLatinNames()

Returns the Latin names in this map.

Returns:

the Latin names in this map