Package psidev.psi.mi.jami.xml.model.extension.xml254

Class BibRef

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml254.BibRef

All Implemented Interfaces:

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

public class BibRef
extends Object
implements Publication, FileSourceContext, com.sun.xml.bind.Locatable

Xml implementation of a Publication

Since:

22/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BibRef.JAXBAttributeWrapper

Constructor Summary

Constructors

Constructor	Description
BibRef()	Constructor for BibRef.
BibRef(String pubmed)	Constructor for BibRef.
BibRef(String title, String journal, Date publicationDate)	Constructor for BibRef.
BibRef(String title, String journal, Date publicationDate, String imexId, Source source)	Constructor for BibRef.
BibRef(String title, String journal, Date publicationDate, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(String pubmed, String imexId, Source source)	Constructor for BibRef.
BibRef(String pubmed, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(Xref identifier)	Constructor for BibRef.
BibRef(Xref identifier, String imexId, Source source)	Constructor for BibRef.
BibRef(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for BibRef.

Method Summary

Modifier and Type	Method	Description
boolean	addAllExperiments(Collection<? extends Experiment> exps)	This method will add all the experiments and set the publication of the new experiments to this current publication
boolean	addExperiment(Experiment exp)	This method will add the experiment and set the publication of the new experiment to this current publication
void	assignImexId(String identifier)	Assign an IMEx id to a publication.
Collection<Annotation>	getAnnotations()	getAnnotations.
List<String>	getAuthors()	getAuthors.
CurationDepth	getCurationDepth()	getCurationDepth.
String	getDoi()	getDoi.
Collection<Experiment>	getExperiments()	Getter for the field experiments.
Collection<Xref>	getIdentifiers()	getIdentifiers.
String	getImexId()	getImexId.
String	getJournal()	getJournal.
Date	getPublicationDate()	getPublicationDate.
String	getPubmedId()	getPubmedId.
Date	getReleasedDate()	Getter for the field releasedDate.
Source	getSource()	Getter for the field source.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
String	getTitle()	getTitle.
Collection<Xref>	getXrefs()	getXrefs.
protected void	initialiseAnnotationWrapper()	initialiseAnnotationWrapper.
protected void	initialiseExperiments()	initialiseExperiments.
boolean	removeAllExperiments(Collection<? extends Experiment> exps)	This method will remove the experiments and set the publication of the removed experiments to null.
boolean	removeExperiment(Experiment exp)	This method will remove the experiment and set the publication of the removed experiment to null.
void	setCurationDepth(CurationDepth curationDepth)	Set the curation depth of the publication.
void	setDoi(String doi)	Sets the doi.
void	setJAXBAttributeWrapper(BibRef.JAXBAttributeWrapper wrapper)	setJAXBAttributeWrapper.
void	setJAXBXref(PublicationXrefContainer xrefContainer)	setJAXBXref.
void	setJournal(String journal)	Set the journal where the publication has been published
void	setPublicationDate(Date date)	Set the date of publication.
void	setPubmedId(String pubmedId)	Sets the pubmed identifier.
void	setReleasedDate(Date released)	Set the released date of the curated publication
void	setSource(Source source)	Sets the source who curated the publication.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
void	setTitle(String title)	Set the publication title
Locator	sourceLocation()
String	toString()	toString

Methods inherited from class java.lang.Object

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

Constructor Detail

BibRef

public BibRef()

Constructor for BibRef.

BibRef

public BibRef(Xref identifier)

Constructor for BibRef.

Parameters:

identifier - a Xref object.

BibRef

public BibRef(Xref identifier,
              CurationDepth curationDepth,
              Source source)

Constructor for BibRef.

Parameters:

identifier - a Xref object.

curationDepth - a CurationDepth object.

source - a Source object.

BibRef

public BibRef(Xref identifier,
              String imexId,
              Source source)

Constructor for BibRef.

Parameters:

identifier - a Xref object.

imexId - a String object.

source - a Source object.

BibRef

public BibRef(String pubmed)

Constructor for BibRef.

Parameters:

pubmed - a String object.

BibRef

public BibRef(String pubmed,
              CurationDepth curationDepth,
              Source source)

Constructor for BibRef.

Parameters:

pubmed - a String object.

curationDepth - a CurationDepth object.

source - a Source object.

BibRef

public BibRef(String pubmed,
              String imexId,
              Source source)

Constructor for BibRef.

Parameters:

pubmed - a String object.

imexId - a String object.

source - a Source object.

BibRef

public BibRef(String title,
              String journal,
              Date publicationDate)

Constructor for BibRef.

Parameters:

title - a String object.

journal - a String object.

publicationDate - a Date object.

BibRef

public BibRef(String title,
              String journal,
              Date publicationDate,
              CurationDepth curationDepth,
              Source source)

Constructor for BibRef.

Parameters:

title - a String object.

journal - a String object.

publicationDate - a Date object.

curationDepth - a CurationDepth object.

source - a Source object.

BibRef

public BibRef(String title,
              String journal,
              Date publicationDate,
              String imexId,
              Source source)

Constructor for BibRef.

Parameters:

title - a String object.

journal - a String object.

publicationDate - a Date object.

imexId - a String object.

source - a Source object.

Method Detail

getPubmedId

public String getPubmedId()

getPubmedId.

Specified by:

getPubmedId in interface Publication

Returns:

a String object.

setPubmedId

public void setPubmedId(String pubmedId)

Sets the pubmed identifier. It will remove the previous pubmed identifier from the collection of identifiers, and add the new one in the collection of identifiers with qualifier identity. If pubmedId is null, it will remove all the pubmed identifiers from the collection of identifiers.

Specified by:

setPubmedId in interface Publication

Parameters:

pubmedId - : pubmed identifier

getDoi

public String getDoi()

getDoi.

Specified by:

getDoi in interface Publication

Returns:

a String object.

setDoi

public void setDoi(String doi)

Sets the doi. It will remove the previous doi from the collection of identifiers, and add the new one in the collection of identifiers with qualifier identity. If doi is null, it will remove all the doi from the collection of identifiers.

Specified by:

setDoi in interface Publication

Parameters:

doi - : DOI identifier

getIdentifiers

public Collection<Xref> getIdentifiers()

getIdentifiers.

Specified by:

getIdentifiers in interface Publication

Returns:

a Collection object.

getImexId

public String getImexId()

getImexId.

Specified by:

getImexId in interface Publication

Returns:

a String object.

assignImexId

public void assignImexId(String identifier)

Assign an IMEx id to a publication. It will add a Xref imex with qualifier imex-primary to the list of xrefs.

Specified by:

assignImexId in interface Publication

Parameters:

identifier - : the IMEx id from IMEx central

getTitle

public String getTitle()

getTitle.

Specified by:

getTitle in interface Publication

Returns:

a String object.

setTitle

public void setTitle(String title)

Set the publication title

Specified by:

setTitle in interface Publication

Parameters:

title - : publication title

getJournal

public String getJournal()

getJournal.

Specified by:

getJournal in interface Publication

Returns:

a String object.

setJournal

public void setJournal(String journal)

Set the journal where the publication has been published

Specified by:

setJournal in interface Publication

Parameters:

journal - : the journal

getPublicationDate

public Date getPublicationDate()

getPublicationDate.

Specified by:

getPublicationDate in interface Publication

Returns:

a Date object.

setPublicationDate

public void setPublicationDate(Date date)

Set the date of publication.

Specified by:

setPublicationDate in interface Publication

Parameters:

date - : publication date

getAuthors

public List<String> getAuthors()

getAuthors.

Specified by:

getAuthors in interface Publication

Returns:

a List object.

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface Publication

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Publication

Returns:

a Collection object.

getExperiments

public Collection<Experiment> getExperiments()

Getter for the field experiments.

Specified by:

getExperiments in interface Publication

Returns:

a Collection object.

getCurationDepth

public CurationDepth getCurationDepth()

getCurationDepth.

Specified by:

getCurationDepth in interface Publication

Returns:

a CurationDepth object.

setCurationDepth

public void setCurationDepth(CurationDepth curationDepth)

Set the curation depth of the publication. If the curation depth is null, it should set the cuuration depth to CurationDepth.undefined

Specified by:

setCurationDepth in interface Publication

Parameters:

curationDepth - : the curation depth

getReleasedDate

public Date getReleasedDate()

Getter for the field releasedDate.

Specified by:

getReleasedDate in interface Publication

Returns:

a Date object.

setReleasedDate

public void setReleasedDate(Date released)

Set the released date of the curated publication

Specified by:

setReleasedDate in interface Publication

Parameters:

released - : the released date

getSource

public Source getSource()

Getter for the field source.

Specified by:

getSource in interface Publication

Returns:

a Source object.

setSource

public void setSource(Source source)

Sets the source who curated the publication.

Specified by:

setSource in interface Publication

Parameters:

source - : source for this publication

addExperiment

public boolean addExperiment(Experiment exp)

This method will add the experiment and set the publication of the new experiment to this current publication

Specified by:

addExperiment in interface Publication

Parameters:

exp - : experiment to add

Returns:

true if experiment is added to the list of experiments

removeExperiment

public boolean removeExperiment(Experiment exp)

This method will remove the experiment and set the publication of the removed experiment to null.

Specified by:

removeExperiment in interface Publication

Parameters:

exp - : experiment to remove

Returns:

true if experiment is removed from the list of experiments

addAllExperiments

public boolean addAllExperiments(Collection<? extends Experiment> exps)

This method will add all the experiments and set the publication of the new experiments to this current publication

Specified by:

addAllExperiments in interface Publication

Parameters:

exps - : experiments to add

Returns:

true if experiments are added to the list of experiments

removeAllExperiments

public boolean removeAllExperiments(Collection<? extends Experiment> exps)

This method will remove the experiments and set the publication of the removed experiments to null.

Specified by:

removeAllExperiments in interface Publication

Parameters:

exps - : experiments to remove

Returns:

true if experiments are removed from the list of experiments

setJAXBXref

public void setJAXBXref(PublicationXrefContainer xrefContainer)

setJAXBXref.

Parameters:

xrefContainer - a PublicationXrefContainer object.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(BibRef.JAXBAttributeWrapper wrapper)

setJAXBAttributeWrapper.

Parameters:

wrapper - a BibRef.JAXBAttributeWrapper 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

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.

initialiseExperiments

protected void initialiseExperiments()

initialiseExperiments.