Package com.compomics.util.pride

Class PtmToPrideMap

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.pride.PtmToPrideMap

All Implemented Interfaces:

Serializable

public class PtmToPrideMap
extends ExperimentObject

Map linking user modification names to Unimod CV terms.

Author:

Marc Vaudel, Harald Barsnes

See Also:

• Serialized Form

Field Summary

Fields

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

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
PtmToPrideMap()	Constructor.

Method Summary

Modifier and Type	Method	Description
CvTerm	getCVTerm(String ptmName)	Returns the CV term corresponding to the given PTM name.
static CvTerm	getDefaultCVTerm(String ptmName)	Deprecated. use the getCvTerm method for the PTM instead
static PtmToPrideMap	loadPtmToPrideMap(SearchParameters searchParameters)	Deprecated. the CV term is now part of the PTM object
void	putCVTerm(String modName, CvTerm cvTerm)	Puts a new mapping in the map.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

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

Field Details

fileName

public static final String fileName

The name of the file to save.

See Also:

• Constant Field Values

Constructor Details

PtmToPrideMap

public PtmToPrideMap()

Constructor.

Method Details

getCVTerm

public CvTerm getCVTerm(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(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(String ptmName)

Deprecated.

use the getCvTerm method for the PTM instead

Returns the default cvTerm of a modification when it exists.

Parameters:

ptmName - the PTM name according to the XML file, null if no mapping is found

Returns:

a default CV term

loadPtmToPrideMap

public static PtmToPrideMap loadPtmToPrideMap(SearchParameters searchParameters)
                                       throws FileNotFoundException,
IOException,
ClassNotFoundException

Deprecated.

the CV term is now part of the PTM object

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:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

ClassNotFoundException - if a ClassNotFoundException occurs