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

Class BiomartMapping

java.lang.Object

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

public class BiomartMapping
extends Object

Mapping of the species to BioMart dataset.

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
BiomartMapping()	Constructor.

Method Summary

Modifier and Type	Method	Description
String	getDataset(String datasetName)	Returns the Ensembl dataset for the given assembly.
void	loadMapping(File ensemblFile)	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

BiomartMapping

public BiomartMapping()

Constructor.

Method Details

loadMapping

public void loadMapping(File ensemblFile)
                 throws IOException

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

Parameters:

ensemblFile - the Ensembl BioMart file

Throws:

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

getDataset

public String getDataset(String datasetName)

Returns the Ensembl dataset for the given assembly. Null if not found.

Parameters:

datasetName - the dataset name. E.g. 'hsapiens_gene_ensembl' or 'acomosus_eg_gene'.

Returns:

the Ensembl dataset version