Package com.compomics.util.experiment.biology.genes.ensembl

Class GeneMapping

java.lang.Object

com.compomics.util.experiment.biology.genes.ensembl.GeneMapping

public class GeneMapping
extends Object

Class for the handling of gene mappings.

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
GeneMapping()	Constructor.

Method Summary

Modifier and Type	Method	Description
String	getChromosome(String geneName)	Returns the chromosome for a given gene.
String	getEnsemblAccession(String geneName)	Returns the Ensembl accession for a given gene.
HashMap<String,String>	getGeneNameToAccession()	Returns the gene name to protein accession map.
HashMap<String,String>	getGeneNameToChromosome()	Returns the gene name to chromosome map.
void	importFromFile(File file, WaitingHandler waitingHandler)	Reads go mappings from a BioMart 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

GeneMapping

public GeneMapping()

Constructor.

Method Details

importFromFile

public void importFromFile(File file,
 WaitingHandler waitingHandler)
                    throws IOException

Reads go mappings from a BioMart file. The structure of the file should be Ensembl Accession Gene name Chromosome name. Previous mappings are silently overwritten.

Parameters:

file - the file containing the mapping

waitingHandler - a waiting handler allowing display of the progress and canceling of the process.

Throws:

IOException - if an exception occurs while reading the file

getChromosome

public String getChromosome(String geneName)

Returns the chromosome for a given gene.

Parameters:

geneName - the gene name

Returns:

the chromosome for a given gene

getEnsemblAccession

public String getEnsemblAccession(String geneName)

Returns the Ensembl accession for a given gene.

Parameters:

geneName - the gene name

Returns:

the Ensembl accession for a given gene

getGeneNameToChromosome

public HashMap<String,String> getGeneNameToChromosome()

Returns the gene name to chromosome map.

Returns:

the gene name to chromosome map

getGeneNameToAccession

public HashMap<String,String> getGeneNameToAccession()

Returns the gene name to protein accession map.

Returns:

the gene name to protein accession map