uk.ac.ebi.pridemod.controller

Class AbstractDataAccessController

java.lang.Object

uk.ac.ebi.pridemod.controller.AbstractDataAccessController

All Implemented Interfaces:

DataAccessController

Direct Known Subclasses:

PRIDEModDataAccessController, PSIModDataAccessController, UnimodDataAccessController

public class AbstractDataAccessController
extends Object
implements DataAccessController

yperez

Field Summary

Fields

Modifier and Type	Field and Description
Map<Comparable,PTM>	ptmMap

Constructor Summary

Constructors

Constructor and Description
AbstractDataAccessController(InputStream inputStream) Default constructor for Controllers

Method Summary

Methods

Modifier and Type	Method and Description
PTM	getPTMbyAccession(String accession) Return the PTM with an specific accession.
List<PTM>	getPTMListByAvgDeltaMass(Double delta) Get List PTMs by Average Delta Mass
List<PTM>	getPTMListByEqualName(String name) Return all PTMs with the same name.
List<PTM>	getPTMListByMonoDeltaMass(Double delta) Get List of PTMs by Monoisotopic delta mass
List<PTM>	getPTMListByPatternDescription(String descriptionPattern) Description pattern to found PTMs with the pattern
List<PTM>	getPTMListByPatternName(String namePattern) Return the ptm with an specific pattern in the name
List<PTM>	getPTMListBySpecificity(Specificity specificity) Specificity to filter all the identifications in the
InputStream	getSource()

Methods inherited from class java.lang.Object

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

Field Detail

ptmMap

public Map<Comparable,PTM> ptmMap

Constructor Detail

AbstractDataAccessController

public AbstractDataAccessController(InputStream inputStream)

Default constructor for Controllers

Method Detail

getSource

public InputStream getSource()

Specified by:

getSource in interface DataAccessController

getPTMbyAccession

public PTM getPTMbyAccession(String accession)

Return the PTM with an specific accession.

Specified by:

getPTMbyAccession in interface DataAccessController

Parameters:

accession -

Returns:

getPTMListByPatternName

public List<PTM> getPTMListByPatternName(String namePattern)

Return the ptm with an specific pattern in the name

Specified by:

getPTMListByPatternName in interface DataAccessController

Parameters:

namePattern -

Returns:

getPTMListBySpecificity

public List<PTM> getPTMListBySpecificity(Specificity specificity)

Description copied from interface: DataAccessController

Specificity to filter all the identifications in the

Specified by:

getPTMListBySpecificity in interface DataAccessController

Returns:

getPTMListByPatternDescription

public List<PTM> getPTMListByPatternDescription(String descriptionPattern)

Description copied from interface: DataAccessController

Description pattern to found PTMs with the pattern

Specified by:

getPTMListByPatternDescription in interface DataAccessController

Returns:

getPTMListByEqualName

public List<PTM> getPTMListByEqualName(String name)

Description copied from interface: DataAccessController

Return all PTMs with the same name. In case of PSI-Mod modifications different mofifications can have the same name.

Specified by:

getPTMListByEqualName in interface DataAccessController

Returns:

getPTMListByMonoDeltaMass

public List<PTM> getPTMListByMonoDeltaMass(Double delta)

Description copied from interface: DataAccessController

Get List of PTMs by Monoisotopic delta mass

Specified by:

getPTMListByMonoDeltaMass in interface DataAccessController

Returns:

getPTMListByAvgDeltaMass

public List<PTM> getPTMListByAvgDeltaMass(Double delta)

Description copied from interface: DataAccessController

Get List PTMs by Average Delta Mass

Specified by:

getPTMListByAvgDeltaMass in interface DataAccessController

Returns: