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

Class EnsemblGenomesSpecies

java.lang.Object

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

public class EnsemblGenomesSpecies
extends Object

This class provides information about the species mapping in Ensembl Genomes (Bacteria, Fungi, Metazoa, Plants, Protists).

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	EnsemblGenomesSpecies.EnsemblGenomeDivision Enum of the different Ensembl genome divisions.

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
EnsemblGenomesSpecies() Constructor.

Method Summary

Modifier and Type	Method and Description
String	getAssembly(Integer taxon) Returns the Ensembl assembly corresponding to the given NCBI taxon.
EnsemblGenomesSpecies.EnsemblGenomeDivision	getDivision(Integer taxon) Returns the division corresponding to the given NCBI taxon.
String	getName(Integer taxon) Returns the 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

EnsemblGenomesSpecies

public EnsemblGenomesSpecies()

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.

getName

public String getName(Integer taxon)

Returns the name corresponding to the given NCBI taxon.

Parameters:

taxon - the NCBI taxon

Returns:

the name

getDivision

public EnsemblGenomesSpecies.EnsemblGenomeDivision getDivision(Integer taxon)

Returns the division corresponding to the given NCBI taxon.

Parameters:

taxon - the NCBI taxon

Returns:

the division

getAssembly

public String getAssembly(Integer taxon)

Returns the Ensembl assembly corresponding to the given NCBI taxon.

Parameters:

taxon - the NCBI taxon

Returns:

the Ensembl assembly

getTaxons

public HashSet<Integer> getTaxons()

Returns the taxons in this map.

Returns:

the taxons in this map