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

Class AbstractBaseXmlInteractor

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.AbstractBaseXmlInteractor

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Interactor, ExtendedPsiXmlInteractor

Direct Known Subclasses:

AbstractXmlInteractor, AbstractXmlInteractor, AbstractXmlInteractor

public abstract class AbstractBaseXmlInteractor
extends Object
implements Interactor, FileSourceContext, com.sun.xml.bind.Locatable, ExtendedPsiXmlInteractor

The Xml implementation of Interactor

Since:

23/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper

Field Summary

Fields

Modifier and Type	Field	Description
protected Locator	locator

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

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected abstract void	createDefaultInteractorType()	createDefaultInteractorType.
Collection<Alias>	getAliases()	getAliases.
Collection<Annotation>	getAnnotations()	getAnnotations.
Collection<Checksum>	getChecksums()	getChecksums.
String	getFullName()	getFullName.
int	getId()	Gets the value of the id property.
Collection<Xref>	getIdentifiers()	getIdentifiers.
CvTerm	getInteractorType()	Gets the value of the interactorType property.
protected AbstractNamesContainer	getNamesContainer()	Getter for the field namesContainer.
Organism	getOrganism()	Getter for the field organism.
Xref	getPreferredIdentifier()	getPreferredIdentifier.
String	getPreferredName()	getPreferredName.
String	getSequence()	getSequence.
String	getShortName()	getShortName.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
Collection<Xref>	getXrefs()	getXrefs.
protected abstract void	initialiseAnnotationWrapper()	initialiseAnnotationWrapper.
protected abstract void	initialiseNamesContainer()	initialiseNamesContainer.
protected abstract void	initialiseXrefContainer()	initialiseXrefContainer.
void	setFullName(String name)	Sets the full name of the interactor
void	setId(int value)	setId.
void	setInteractorType(CvTerm interactorType)	Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)
void	setJAXBAttributeWrapper(AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper wrapper)	Gets the value of the attributeList property.
void	setJAXBInteractorType(CvTerm interactorType)	setJAXBInteractorType.
void	setJAXBNames(AbstractNamesContainer value)	Sets the value of the names property.
void	setJAXBOrganism(Organism organism)	setJAXBOrganism.
void	setNamesContainer(AbstractNamesContainer namesContainer)
void	setOrganism(Organism organism)	Sets the source organism of this interactor
void	setSequence(String value)	Sets the value of the sequence property.
void	setShortName(String name)	Sets the short name of an interactor
void	setSourceLocation(PsiXmlLocator sourceLocator)	setSourceLocation.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
void	setXrefContainer(IInteractorXrefContainer xrefContainer)
Locator	sourceLocation()
String	toString()	toString

Methods inherited from class java.lang.Object

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

Field Detail

locator

protected Locator locator

Constructor Detail

AbstractBaseXmlInteractor

public AbstractBaseXmlInteractor()

Constructor for AbstractBaseXmlInteractor.

AbstractBaseXmlInteractor

public AbstractBaseXmlInteractor(String name,
                                 CvTerm type)

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

AbstractBaseXmlInteractor

public AbstractBaseXmlInteractor(String name)

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

AbstractBaseXmlInteractor

public AbstractBaseXmlInteractor(String name,
                                 String fullName)

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

AbstractBaseXmlInteractor

public AbstractBaseXmlInteractor(String name,
                                 Organism organism)

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

organism - a Organism object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

AbstractBaseXmlInteractor

public AbstractBaseXmlInteractor(String name,
                                 Xref uniqueId)

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

uniqueId - a Xref object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

AbstractBaseXmlInteractor

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

Constructor for AbstractBaseXmlInteractor.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

getInteractorType

public CvTerm getInteractorType()

Gets the value of the interactorType property.

Specified by:

getInteractorType in interface Interactor

Returns:

a CvTerm object.

setInteractorType

public void setInteractorType(CvTerm interactorType)

Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)

Specified by:

setInteractorType in interface Interactor

Parameters:

interactorType - : molecule type

getOrganism

public Organism getOrganism()

Getter for the field organism.

Specified by:

getOrganism in interface Interactor

Returns:

a Organism object.

setOrganism

public void setOrganism(Organism organism)

Sets the source organism of this interactor

Specified by:

setOrganism in interface Interactor

Parameters:

organism - : source organism

getShortName

public String getShortName()

getShortName.

Specified by:

getShortName in interface Interactor

Returns:

a String object.

setShortName

public void setShortName(String name)

Sets the short name of an interactor

Specified by:

setShortName in interface Interactor

Parameters:

name - : short name

getFullName

public String getFullName()

getFullName.

Specified by:

getFullName in interface Interactor

Returns:

a String object.

setFullName

public void setFullName(String name)

Sets the full name of the interactor

Specified by:

setFullName in interface Interactor

Parameters:

name - : full name

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers.

Specified by:

getIdentifiers in interface Interactor

Returns:

a Collection object.

setNamesContainer

public void setNamesContainer(AbstractNamesContainer namesContainer)

setXrefContainer

public void setXrefContainer(IInteractorXrefContainer xrefContainer)

initialiseXrefContainer

protected abstract void initialiseXrefContainer()

initialiseXrefContainer.

initialiseNamesContainer

protected abstract void initialiseNamesContainer()

initialiseNamesContainer.

getPreferredIdentifier

public Xref getPreferredIdentifier()

getPreferredIdentifier.

Specified by:

getPreferredIdentifier in interface Interactor

Returns:

the first identifier in the list of identifiers or null if the list is empty

getPreferredName

public String getPreferredName()

getPreferredName.

Specified by:

getPreferredName in interface Interactor

Returns:

preferred name

getChecksums

public Collection<Checksum> getChecksums()

getChecksums.

Specified by:

getChecksums in interface Interactor

Returns:

a Collection object.

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface Interactor

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Interactor

Returns:

a Collection object.

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface Interactor

Returns:

a Collection object.

setJAXBNames

public void setJAXBNames(AbstractNamesContainer value)

Sets the value of the names property.

Parameters:

value - allowed object is AbstractNamesContainer

setJAXBInteractorType

public void setJAXBInteractorType(CvTerm interactorType)

setJAXBInteractorType.

Parameters:

interactorType - a CvTerm object.

setJAXBOrganism

public void setJAXBOrganism(Organism organism)

setJAXBOrganism.

Parameters:

organism - a Organism object.

setSequence

public void setSequence(String value)

Sets the value of the sequence property.

Parameters:

value - allowed object is String

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.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper wrapper)

Gets the value of the attributeList property.

Parameters:

wrapper - a AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper object.

createDefaultInteractorType

protected abstract void createDefaultInteractorType()

createDefaultInteractorType.

getSequence

public String getSequence()

getSequence.

Returns:

a String object.

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class Object

Returns:

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

sourceLocation

public Locator sourceLocation()

Specified by:

sourceLocation in interface com.sun.xml.bind.Locatable

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

setSourceLocation

public void setSourceLocation(PsiXmlLocator sourceLocator)

setSourceLocation.

Parameters:

sourceLocator - a PsiXmlLocator object.

initialiseAnnotationWrapper

protected abstract void initialiseAnnotationWrapper()

initialiseAnnotationWrapper.

getNamesContainer

protected AbstractNamesContainer getNamesContainer()

Getter for the field namesContainer.

Returns:

a AbstractNamesContainer object.