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

Class GoMapping

java.lang.Object

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

public class GoMapping
extends Object

Class parsing BioMart protein go mappings and storing them in maps.

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
GoMapping() Constructor.

Method Summary

Modifier and Type	Method and Description
HashSet<String>	getGoAccessions(String proteinAccession) Returns the GO accessions linked to a given protein accession.
HashMap<String,String>	getGoNamesMap() Returns the GO accession to name map.
HashMap<String,HashSet<String>>	getGoToProteinMap() Returns the GO to protein accession map.
HashSet<String>	getProteinAccessions(String goTermAccession) Returns the protein accessions linked to a given GO term.
HashMap<String,HashSet<String>>	getProteinToGoMap() Returns the protein to GO accession map.
ArrayList<String>	getSortedTermNames() Returns a sorted list of all GO Terms names linked to proteins in the proteinToGoMap.
String	getTermAccession(String goName) Returns the accession of a GO term.
String	getTermName(String goAccession) Returns the name of a GO term.
void	loadMappingsFromFile(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 Detail

SEPARATOR

public static final String SEPARATOR

The separator used to separate line contents.

See Also:

Constant Field Values

Constructor Detail

GoMapping

public GoMapping()

Constructor.

Method Detail

loadMappingsFromFile

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

Reads go mappings from a BioMart file. The structure of the file should be protein accession 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

getGoAccessions

public HashSet<String> getGoAccessions(String proteinAccession)

Returns the GO accessions linked to a given protein accession. Null if not found.

Parameters:

proteinAccession - the accession of the protein of interest

Returns:

a list of GO accession numbers, an empty list if no mapping is found

getProteinAccessions

public HashSet<String> getProteinAccessions(String goTermAccession)

Returns the protein accessions linked to a given GO term. Null if not found.

Parameters:

goTermAccession - the accession of the GO term

Returns:

a list of GO accession numbers, an empty list if no mapping is found

getTermName

public String getTermName(String goAccession)

Returns the name of a GO term.

Parameters:

goAccession - the accession number of the GO term of interest

Returns:

the name, null if not found

getTermAccession

public String getTermAccession(String goName)

Returns the accession of a GO term.

Parameters:

goName - the name of the GO term of interest

Returns:

the accession, null if not found

getGoNamesMap

public HashMap<String,String> getGoNamesMap()

Returns the GO accession to name map.

Returns:

the GO accession to name map

getProteinToGoMap

public HashMap<String,HashSet<String>> getProteinToGoMap()

Returns the protein to GO accession map.

Returns:

the protein to GO accession map

getGoToProteinMap

public HashMap<String,HashSet<String>> getGoToProteinMap()

Returns the GO to protein accession map.

Returns:

the GO to protein accession map

getSortedTermNames

public ArrayList<String> getSortedTermNames()

Returns a sorted list of all GO Terms names linked to proteins in the proteinToGoMap.

Returns:

a sorted list of all GO Terms names