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

Class MitabBioactiveEntity

java.lang.Object

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

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

psidev.psi.mi.jami.model.impl.DefaultBioactiveEntity

psidev.psi.mi.jami.tab.extension.MitabBioactiveEntity

All Implemented Interfaces:

FileSourceContext, BioactiveEntity, Interactor, Molecule

public class MitabBioactiveEntity
extends DefaultBioactiveEntity
implements FileSourceContext

Mitab extension for BioactiveEntity. It contains a file sourceLocator

Since:

11/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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

BIOACTIVE_ENTITY, BIOACTIVE_ENTITY_MI, POLYSACCHARIDE, POLYSACCHARIDE_MI, SMALL_MOLECULE, SMALL_MOLECULE_MI

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

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Constructor Summary

Constructors

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

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.DefaultBioactiveEntity

clearPropertiesLinkedToChecksums, clearPropertiesLinkedToIdentifiers, getChebi, getPreferredIdentifier, getSmile, getStandardInchi, getStandardInchiKey, initialiseChecksums, initialiseIdentifiers, processAddedChecksumEvent, processAddedIdentifierEvent, processRemovedChecksumEvent, processRemovedIdentifierEvent, setChebi, setInteractorType, setSmile, setStandardInchi, setStandardInchiKey

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, 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

Constructor Detail

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            CvTerm type)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            String fullName,
                            CvTerm type,
                            String uniqueChebi)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueChebi - a String object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            CvTerm type,
                            Organism organism,
                            String uniqueChebi)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueChebi - a String object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            String fullName,
                            CvTerm type,
                            Organism organism,
                            String uniqueChebi)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueChebi - a String object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            String fullName)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            Organism organism)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            Xref uniqueId)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

uniqueId - a Xref object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

MitabBioactiveEntity

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

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            String fullName,
                            String uniqueChebi)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

uniqueChebi - a String object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            Organism organism,
                            String uniqueChebi)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

uniqueChebi - a String object.

MitabBioactiveEntity

public MitabBioactiveEntity(String name,
                            String fullName,
                            Organism organism,
                            String uniqueChebi)

Constructor for MitabBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueChebi - a String 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 DefaultBioactiveEntity

Returns:

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