com.compomics.util.experiment.biology.genes.go

Class GoDomains

java.lang.Object

com.compomics.util.experiment.biology.genes.go.GoDomains

public class GoDomains
extends Object

Class parsing go domains and storing them in a map.

Author:

Marc Vaudel, Harald Barsnes

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
GoDomains() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addDomain(String goAccession, String goDomain) Adds a go domain to the mapping.
String	getTermDomain(String goAccession) Returns the description of a GO term.
void	laodMappingFromFile(File file, WaitingHandler waitingHandler) Reads go mappings from a file.
void	saveMapping(File destinationFile) Saves the mapping to the given 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

GoDomains

public GoDomains()

Constructor.

Method Detail

laodMappingFromFile

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

Reads go mappings from a file. The structure of the file should go accession go name Previous mappings are silently overwritten.

Parameters:

file - the file containing the GO mapping

waitingHandler - a waiting handler allowing canceling of the process.

Throws:

IOException - if an exception occurs while reading the file

getTermDomain

public String getTermDomain(String goAccession)

Returns the description of a GO term.

Parameters:

goAccession - the accession number of the GO term of interest

Returns:

the first description found, null if not found

addDomain

public void addDomain(String goAccession,
                      String goDomain)

Adds a go domain to the mapping.

Parameters:

goAccession - the accession of the GO term

goDomain - the domain of the GO term

saveMapping

public void saveMapping(File destinationFile)
                 throws IOException

Saves the mapping to the given file.

Parameters:

destinationFile - the destination file

Throws:

IOException - exception thrown whenever an error occurred while writing the file