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

Class AbstractXmlCvTerm

java.lang.Object

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

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, CvTerm

Direct Known Subclasses:

AbstractXmlSource, XmlCvTerm, XmlOpenCvTerm

public abstract class AbstractXmlCvTerm
extends Object
implements CvTerm, FileSourceContext, com.sun.xml.bind.Locatable

Abstract cv term

Since:

19/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractXmlCvTerm.JAXBAttributeWrapper

Field Summary

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

PSI_MI, PSI_MI_MI, PSI_MOD, PSI_MOD_MI, PSI_PAR

Constructor Summary

Constructors

Constructor	Description
AbstractXmlCvTerm()	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName)	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName, String miIdentifier)	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName, String fullName, String miIdentifier)	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
Collection<Annotation>	getAnnotations()	getAnnotations.
protected AbstractXmlCvTerm.JAXBAttributeWrapper	getAttributeWrapper()	getAttributeWrapper.
String	getFullName()	getFullName.
Collection<Xref>	getIdentifiers()	getIdentifiers.
String	getMIIdentifier()	getMIIdentifier.
String	getMODIdentifier()	getMODIdentifier.
protected NamesContainer	getNamesContainer()	Getter for the field namesContainer.
String	getPARIdentifier()	getPARIdentifier.
String	getShortName()	getShortName.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
Collection<Alias>	getSynonyms()	getSynonyms.
protected CvTermXrefContainer	getXrefContainer()	Getter for the field xrefContainer.
Collection<Xref>	getXrefs()	getXrefs.
int	hashCode()
protected void	initialiseAnnotationWrapper()	initialiseAnnotationWrapper.
protected void	setAttributeWrapper(AbstractXmlCvTerm.JAXBAttributeWrapper jaxbAttributeWrapper)	setAttributeWrapper.
void	setFullName(String name)	Set the full name
void	setJAXBNames(NamesContainer value)	setJAXBNames.
void	setJAXBXref(CvTermXrefContainer value)	setJAXBXref.
void	setMIIdentifier(String mi)	Sets the PSI-MI identifier.
void	setMODIdentifier(String mod)	Sets the PSI-MOD identifier.
void	setPARIdentifier(String par)	Sets the PSI-PAR identifier.
void	setShortName(String name)	Set the short name
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
Locator	sourceLocation()
String	toString()	toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

AbstractXmlCvTerm

public AbstractXmlCvTerm()

Constructor for AbstractXmlCvTerm.

AbstractXmlCvTerm

public AbstractXmlCvTerm(String shortName)

Constructor for AbstractXmlCvTerm.

Parameters:

shortName - a String object.

AbstractXmlCvTerm

public AbstractXmlCvTerm(String shortName,
                         String miIdentifier)

Constructor for AbstractXmlCvTerm.

Parameters:

shortName - a String object.

miIdentifier - a String object.

AbstractXmlCvTerm

public AbstractXmlCvTerm(String shortName,
                         String fullName,
                         String miIdentifier)

Constructor for AbstractXmlCvTerm.

Parameters:

shortName - a String object.

fullName - a String object.

miIdentifier - a String object.

AbstractXmlCvTerm

public AbstractXmlCvTerm(String shortName,
                         Xref ontologyId)

Constructor for AbstractXmlCvTerm.

Parameters:

shortName - a String object.

ontologyId - a Xref object.

AbstractXmlCvTerm

public AbstractXmlCvTerm(String shortName,
                         String fullName,
                         Xref ontologyId)

Constructor for AbstractXmlCvTerm.

Parameters:

shortName - a String object.

fullName - a String object.

ontologyId - a Xref object.

Method Detail

getShortName

public String getShortName()

getShortName.

Specified by:

getShortName in interface CvTerm

Returns:

a String object.

setShortName

public void setShortName(String name)

Set the short name

Specified by:

setShortName in interface CvTerm

Parameters:

name - : short name

getFullName

public String getFullName()

getFullName.

Specified by:

getFullName in interface CvTerm

Returns:

a String object.

setFullName

public void setFullName(String name)

Set the full name

Specified by:

setFullName in interface CvTerm

Parameters:

name - : full name

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers.

Specified by:

getIdentifiers in interface CvTerm

Returns:

a Collection object.

getMIIdentifier

public String getMIIdentifier()

getMIIdentifier.

Specified by:

getMIIdentifier in interface CvTerm

Returns:

a String object.

getMODIdentifier

public String getMODIdentifier()

getMODIdentifier.

Specified by:

getMODIdentifier in interface CvTerm

Returns:

a String object.

getPARIdentifier

public String getPARIdentifier()

getPARIdentifier.

Specified by:

getPARIdentifier in interface CvTerm

Returns:

a String object.

setMIIdentifier

public void setMIIdentifier(String mi)

Sets the PSI-MI identifier. It will remove the previous PSI-MI identifier from the collection of identifiers, and add the new one in the collection of identifiers with qualifier identity. If mi is null, it will remove all the psi-mi identifiers from the collection of identifiers.

Specified by:

setMIIdentifier in interface CvTerm

Parameters:

mi - : mi identifier

setMODIdentifier

public void setMODIdentifier(String mod)

Sets the PSI-MOD identifier. It will remove the previous PSI-MOD identifier from the collection of xrefs, and add the new one in the collection of identifiers with qualifier identity. If mod is null, it will remove all the psi-mod identifiers from the collection of identifiers.

Specified by:

setMODIdentifier in interface CvTerm

Parameters:

mod - : mod identifier

setPARIdentifier

public void setPARIdentifier(String par)

Sets the PSI-PAR identifier. It will remove the previous PSI-PAR identifier from the collection of xrefs, and add the new one in the collection of identifiers with qualifier identity. If par is null, it will remove all the psi-par identifiers from the collection of identifiers.

Specified by:

setPARIdentifier in interface CvTerm

Parameters:

par - : par identifier

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface CvTerm

Returns:

a Collection object.

getSynonyms

public Collection<Alias> getSynonyms()

getSynonyms.

Specified by:

getSynonyms in interface CvTerm

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface CvTerm

Returns:

a Collection object.

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

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class 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

initialiseAnnotationWrapper

protected void initialiseAnnotationWrapper()

initialiseAnnotationWrapper.

getXrefContainer

protected CvTermXrefContainer getXrefContainer()

Getter for the field xrefContainer.

Returns:

a CvTermXrefContainer object.

setJAXBXref

public void setJAXBXref(CvTermXrefContainer value)

setJAXBXref.

Parameters:

value - a CvTermXrefContainer object.

getNamesContainer

protected NamesContainer getNamesContainer()

Getter for the field namesContainer.

Returns:

a NamesContainer object.

setJAXBNames

public void setJAXBNames(NamesContainer value)

setJAXBNames.

Parameters:

value - a NamesContainer object.

getAttributeWrapper

protected AbstractXmlCvTerm.JAXBAttributeWrapper getAttributeWrapper()

getAttributeWrapper.

Returns:

a AbstractXmlCvTerm.JAXBAttributeWrapper object.

setAttributeWrapper

protected void setAttributeWrapper(AbstractXmlCvTerm.JAXBAttributeWrapper jaxbAttributeWrapper)

setAttributeWrapper.

Parameters:

jaxbAttributeWrapper - a AbstractXmlCvTerm.JAXBAttributeWrapper object.