org.expasy.mzjava.proteomics.mol.modification.unimod

Class UnimodModificationResolver

java.lang.Object

org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver

All Implemented Interfaces:

ModificationResolver

Direct Known Subclasses:

ProteinPilotModificationResolver

public class UnimodModificationResolver
extends Object
implements ModificationResolver

A Modification that converts Strings to modifications. The modifications are retrieved from Unimod. This function can be customised by overriding the Modification that is unimod stores for a name by using the (String name, Modification modification). Or by specifying a translation from a name to a unimod name.

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
UnimodModificationResolver()

Method Summary

Methods

Modifier and Type	Method and Description
void	clearOverrides()
void	clearTranslations()
void	putOverrideUnimod(String name, Modification modification) Override the modification that the name is mapped to in Unimod.
void	putTranslate(String name, String unimodName) Add a translation for the name.
com.google.common.base.Optional<Modification>	resolve(String input) Create or fetch a modification for input

Methods inherited from class java.lang.Object

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

Constructor Detail

UnimodModificationResolver

public UnimodModificationResolver()

Method Detail

resolve

public com.google.common.base.Optional<Modification> resolve(String input)

Description copied from interface: ModificationResolver

Create or fetch a modification for input

Specified by:

resolve in interface ModificationResolver

Parameters:

input - the input

Returns:

Optional containing the modification if the input can be resolved, Optional.absent if not

putOverrideUnimod

public void putOverrideUnimod(String name,
                     Modification modification)

Override the modification that the name is mapped to in Unimod.

Parameters:

name - the modification name

modification - the modification to return

clearOverrides

public void clearOverrides()

putTranslate

public void putTranslate(String name,
                String unimodName)

Add a translation for the name.

Parameters:

name - the name to translate

unimodName - the unimod name that the name translates to

clearTranslations

public void clearTranslations()