uk.ac.ebi.pridemod.controller.impl

Class UnimodDataAccessController

java.lang.Object

uk.ac.ebi.pridemod.controller.AbstractDataAccessController

uk.ac.ebi.pridemod.controller.impl.UnimodDataAccessController

All Implemented Interfaces:

DataAccessController

public class UnimodDataAccessController
extends AbstractDataAccessController

Class to retrieve all Modifications from Unimod database. All modifications are store in memory using the yperez.

Field Summary

Fields inherited from class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

ptmMap

Constructor Summary

Constructors

Constructor and Description
UnimodDataAccessController(InputStream xml)

Method Summary

Methods

Modifier and Type	Method and Description
PTM	getPTMbyAccession(String accession) We decided to put the UNIOMD: prefix in order to be compatible with the same PSI-MOD style and the mzIdentML.

Methods inherited from class uk.ac.ebi.pridemod.controller.AbstractDataAccessController

getPTMListByAvgDeltaMass, getPTMListByEqualName, getPTMListByMonoDeltaMass, getPTMListByPatternDescription, getPTMListByPatternName, getPTMListBySpecificity, getSource

Methods inherited from class java.lang.Object

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

Constructor Detail

UnimodDataAccessController

public UnimodDataAccessController(InputStream xml)

Method Detail

getPTMbyAccession

public PTM getPTMbyAccession(String accession)

We decided to put the UNIOMD: prefix in order to be compatible with the same PSI-MOD style and the mzIdentML.

Specified by:

getPTMbyAccession in interface DataAccessController

Overrides:

getPTMbyAccession in class AbstractDataAccessController

Parameters:

accession - an accession in a way of UNIMOD:(number) can be also a number in the case of a number we added the prefix UNIMOD at the beginning.

Returns: