com.compomics.util.pride

Class PtmToPrideMap

java.lang.Object

com.compomics.util.pride.PtmToPrideMap

All Implemented Interfaces:

java.io.Serializable

public class PtmToPrideMap
extends java.lang.Object
implements java.io.Serializable

Map linking user modification names to PSI-MOD CV terms.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	fileName The name of the file to save.

Constructor Summary

Constructors

Constructor and Description
PtmToPrideMap() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
CvTerm	getCVTerm(java.lang.String ptmName) Returns the CV term corresponding to the given PTM name.
static CvTerm	getDefaultCVTerm(java.lang.String ptmName) Returns the default cvTerm of a modification when it exists.
static PtmToPrideMap	loadPtmToPrideMap(SearchParameters searchParameters) Loads the PRIDE to PTM map from the user folder or creates a new one if the file is not present.
void	putCVTerm(java.lang.String modName, CvTerm cvTerm) Puts a new mapping in the map.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

fileName

public static final java.lang.String fileName

The name of the file to save.

See Also:

Constant Field Values

Constructor Detail

PtmToPrideMap

public PtmToPrideMap()

Constructor.

Method Detail

getCVTerm

public CvTerm getCVTerm(java.lang.String ptmName)

Returns the CV term corresponding to the given PTM name. Null if not found.

Parameters:

ptmName - the PTM name

Returns:

the corresponding CV term

putCVTerm

public void putCVTerm(java.lang.String modName,
             CvTerm cvTerm)

Puts a new mapping in the map. If the modification name is already loaded it will be silently overwritten.

Parameters:

modName - the modification name

cvTerm - the corresponding cvTerm

getDefaultCVTerm

public static CvTerm getDefaultCVTerm(java.lang.String ptmName)

Returns the default cvTerm of a modification when it exists.

Parameters:

ptmName - the PTM Name according to the XML file

Returns:

a default CV term

loadPtmToPrideMap

public static PtmToPrideMap loadPtmToPrideMap(SearchParameters searchParameters)
                                       throws java.io.FileNotFoundException,
                                              java.io.IOException,
                                              java.lang.ClassNotFoundException

Loads the PRIDE to PTM map from the user folder or creates a new one if the file is not present. Loads a default mapping if a PTM is not mapped.

Parameters:

searchParameters - the search parameters

Returns:

the PRIDE to PTM map

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException