Package psidev.psi.mi.jami.tab.extension

Class MitabNucleicAcid

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.DefaultNucleicAcid

psidev.psi.mi.jami.tab.extension.MitabNucleicAcid

All Implemented Interfaces:

FileSourceContext, Interactor, Molecule, NucleicAcid, Polymer

public class MitabNucleicAcid
extends DefaultNucleicAcid
implements FileSourceContext

Mitab extension for NucleicAcid It will contain a FileSourceLocator

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.NucleicAcid

NULCEIC_ACID, NULCEIC_ACID_MI

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

POLYMER, POLYMER_MI

Constructor Summary

Constructors

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

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.DefaultNucleicAcid

clearPropertiesLinkedToIdentifiers, getDdbjEmblGenbank, getPreferredIdentifier, getRefseq, initialiseIdentifiers, processAddedIdentifiersEvent, processRemovedIdentifierEvent, setDdbjEmblGenbank, setInteractorType, setRefseq

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, getPreferredName, getShortName, getXrefs, initialiseAliases, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, 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, getPreferredName, getShortName, getXrefs, setFullName, setOrganism, setShortName

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

getSequence, setSequence

Constructor Detail

MitabNucleicAcid

public MitabNucleicAcid(String name,
                        CvTerm type)

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

MitabNucleicAcid

public MitabNucleicAcid(String name)

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

MitabNucleicAcid

public MitabNucleicAcid(String name,
                        String fullName)

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

MitabNucleicAcid

public MitabNucleicAcid(String name,
                        Organism organism)

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

organism - a Organism object.

MitabNucleicAcid

public MitabNucleicAcid(String name,
                        Xref uniqueId)

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

uniqueId - a Xref object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

MitabNucleicAcid

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

Constructor for MitabNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism 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 DefaultNucleicAcid

Returns:

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