Package psidev.psi.mi.jami.crosslink.extension

Class CsvProtein

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultInteractor

psidev.psi.mi.jami.model.impl.DefaultMolecule

psidev.psi.mi.jami.model.impl.DefaultPolymer

psidev.psi.mi.jami.model.impl.DefaultProtein

psidev.psi.mi.jami.crosslink.extension.CsvProtein

All Implemented Interfaces:

FileSourceContext, Interactor, Molecule, Polymer, Protein

public class CsvProtein
extends DefaultProtein
implements FileSourceContext

Crosslink CSV extension of Protein. It contains a FileSourceContext

Since:

11/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.Interactor

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Fields inherited from interface psidev.psi.mi.jami.model.Polymer

POLYMER, POLYMER_MI

Fields inherited from interface psidev.psi.mi.jami.model.Protein

PEPTIDE, PEPTIDE_MI, PROTEIN, PROTEIN_MI

Constructor Summary

Constructors

Constructor	Description
CsvProtein(String name)	Constructor for CsvProtein.
CsvProtein(String name, String fullName)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, CvTerm type)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, CvTerm type, Organism organism)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, Organism organism)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, CvTerm type)	Constructor for CsvProtein.
CsvProtein(String name, CvTerm type, Organism organism)	Constructor for CsvProtein.
CsvProtein(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, CvTerm type, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, Organism organism)	Constructor for CsvProtein.
CsvProtein(String name, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, Xref uniqueId)	Constructor for CsvProtein.

Method Summary

Modifier and Type	Method	Description
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultProtein

clearPropertiesLinkedToAliases, clearPropertiesLinkedToChecksums, clearPropertiesLinkedToIdentifiers, getGeneName, getPreferredIdentifier, getPreferredName, getRefseq, getRogid, getUniprotkb, initialiseAliases, initialiseChecksums, initialiseIdentifiers, processAddedAliasEvent, processAddedChecksumEvent, processAddedIdentifierEvent, processRemovedAliasEvent, processRemovedChecksumEvent, processRemovedIdentifierEvent, setGeneName, setInteractorType, setRefseq, setRogid, setUniprotkb

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultPolymer

getSequence, setSequence

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultInteractor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getShortName, getXrefs, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksumsWith, initialiseIdentifiersWith, initialiseXrefs, initialiseXrefsWith, setFullName, setOrganism, setShortName

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.model.Interactor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getShortName, getXrefs, setFullName, setOrganism, setShortName

Methods inherited from interface psidev.psi.mi.jami.model.Polymer

getSequence, setSequence

Constructor Detail

CsvProtein

public CsvProtein(String name,
                  CvTerm type)

Constructor for CsvProtein.

Parameters:

name - a String object.

type - a CvTerm object.

CsvProtein

public CsvProtein(String name,
                  String fullName,
                  CvTerm type)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

CsvProtein

public CsvProtein(String name,
                  CvTerm type,
                  Organism organism)

Constructor for CsvProtein.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

CsvProtein

public CsvProtein(String name,
                  String fullName,
                  CvTerm type,
                  Organism organism)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

CsvProtein

public CsvProtein(String name,
                  CvTerm type,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

CsvProtein

public CsvProtein(String name,
                  String fullName,
                  CvTerm type,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

CsvProtein

public CsvProtein(String name,
                  CvTerm type,
                  Organism organism,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

CsvProtein

public CsvProtein(String name,
                  String fullName,
                  CvTerm type,
                  Organism organism,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

CsvProtein

public CsvProtein(String name)

Constructor for CsvProtein.

Parameters:

name - a String object.

CsvProtein

public CsvProtein(String name,
                  String fullName)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

CsvProtein

public CsvProtein(String name,
                  Organism organism)

Constructor for CsvProtein.

Parameters:

name - a String object.

organism - a Organism object.

CsvProtein

public CsvProtein(String name,
                  String fullName,
                  Organism organism)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

CsvProtein

public CsvProtein(String name,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

uniqueId - a Xref object.

CsvProtein

public CsvProtein(String name,
                  String fullName,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

CsvProtein

public CsvProtein(String name,
                  Organism organism,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

CsvProtein

public CsvProtein(String name,
                  String fullName,
                  Organism organism,
                  Xref uniqueId)

Constructor for CsvProtein.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultProtein

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties