Package psidev.psi.mi.jami.xml.model.extension.xml300

Class XmlBioactiveEntity

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.xml.model.extension.xml300.XmlBioactiveEntity

All Implemented Interfaces:

FileSourceContext, BioactiveEntity, Interactor, Molecule, ExtendedPsiXmlInteractor

public class XmlBioactiveEntity
extends DefaultBioactiveEntity
implements ExtendedPsiXmlInteractor, FileSourceContext

Xml implementation of BioactiveEntity

Since:

24/07/13

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

Method Summary

Modifier and Type	Method	Description
int	getId()	Gets the value of the id property.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setId(int value)	setId.
void	setInteractorType(CvTerm interactorType)	Sets the interactor type of this bioactive entity.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
void	setSourceLocator(PsiXmlLocator sourceLocator)	Setter for the field sourceLocator.
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, 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, getPreferredIdentifier, getPreferredName, getShortName, getXrefs, setFullName, setOrganism, setShortName

Constructor Detail

XmlBioactiveEntity

public XmlBioactiveEntity(String name,
                          CvTerm type)

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueChebi - a String object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueChebi - a String object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueChebi - a String object.

XmlBioactiveEntity

public XmlBioactiveEntity(String name)

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

XmlBioactiveEntity

public XmlBioactiveEntity(String name,
                          String fullName)

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

XmlBioactiveEntity

public XmlBioactiveEntity(String name,
                          Organism organism)

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

XmlBioactiveEntity

public XmlBioactiveEntity(String name,
                          Xref uniqueId)

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

uniqueChebi - a String object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

organism - a Organism object.

uniqueChebi - a String object.

XmlBioactiveEntity

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

Constructor for XmlBioactiveEntity.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueChebi - a String object.

Method Detail

setInteractorType

public void setInteractorType(CvTerm interactorType)

Sets the interactor type of this bioactive entity. If the given interactorType is null, it sets the interactorType to 'bioactive entity'(MI:1100)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultBioactiveEntity

Parameters:

interactorType - : molecule type

getId

public int getId()

Gets the value of the id property.

Specified by:

getId in interface ExtendedPsiXmlInteractor

Returns:

a int.

setId

public void setId(int value)

setId.

Sets the value of the id property.

Specified by:

setId in interface ExtendedPsiXmlInteractor

Parameters:

value - a int.

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

setSourceLocator

public void setSourceLocator(PsiXmlLocator sourceLocator)

Setter for the field sourceLocator.

Parameters:

sourceLocator - a PsiXmlLocator object.

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