Package psidev.psi.mi.jami.bridges.imex.extension

Class ImexPublication

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultPublication

psidev.psi.mi.jami.bridges.imex.extension.ImexPublication

All Implemented Interfaces:

Publication

public class ImexPublication
extends DefaultPublication

Extension of publication for imex central

Since:

29/10/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
ImexPublication(edu.ucla.mbi.imex.central.ws.v20.Publication delegate)	Constructor for ImexPublication.

Method Summary

Modifier and Type	Method	Description
void	assignImexId(String identifier)	Assign an IMEx id to a publication.
Date	getCreationDate()	Getter for the field creationDate.
CurationDepth	getCurationDepth()	Getter for the field curationDepth.
Collection<String>	getCurators()	Getter for the field curators.
String	getDoi()	Getter for the field doi.
Date	getExpectedPublicationDate()	Getter for the field expectedPublicationDate.
String	getImexId()	Getter for the field imexId.
String	getOwner()	getOwner.
String	getPaperAbstract()	getPaperAbstract.
String	getPubmedId()	Getter for the field pubmedId.
Source	getSource()	Getter for the field source.
List<Source>	getSources()	Getter for the field sources.
PublicationStatus	getStatus()	Getter for the field status.
protected void	initialiseAuthors()	initialiseAuthors
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	initialiseXrefs()	initialiseXrefs
void	setDoi(String doi)	Sets the doi.
void	setPubmedId(String pubmedId)	Sets the pubmed identifier.
void	setSource(Source source)	Sets the source who curated the publication.
void	setStatus(PublicationStatus status)	Setter for the field status.

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultPublication

addAllExperiments, addExperiment, clearPropertiesLinkedToIdentifiers, clearPropertiesLinkedToXrefs, getAnnotations, getAuthors, getExperiments, getIdentifiers, getJournal, getPublicationDate, getReleasedDate, getTitle, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseAuthorsWith, initialiseExperiments, initialiseExperimentsWith, initialiseIdentifiersWith, initialiseXrefsWith, processAddedIdentifierEvent, processAddedXrefEvent, processRemovedIdentifierEvent, processRemovedXrefEvent, removeAllExperiments, removeExperiment, setCurationDepth, setJournal, setPublicationDate, setReleasedDate, setTitle, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

ImexPublication

public ImexPublication(edu.ucla.mbi.imex.central.ws.v20.Publication delegate)

Constructor for ImexPublication.

Parameters:

delegate - a Publication object.

Method Detail

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

Overrides:

initialiseIdentifiers in class DefaultPublication

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

Overrides:

initialiseXrefs in class DefaultPublication

initialiseAuthors

protected void initialiseAuthors()

initialiseAuthors

Overrides:

initialiseAuthors in class DefaultPublication

getPubmedId

public String getPubmedId()

Getter for the field pubmedId.

Specified by:

getPubmedId in interface Publication

Overrides:

getPubmedId in class DefaultPublication

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

Overrides:

setPubmedId in class DefaultPublication

Parameters:

pubmedId - : pubmed identifier

getDoi

public String getDoi()

Getter for the field doi.

Specified by:

getDoi in interface Publication

Overrides:

getDoi in class DefaultPublication

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

Overrides:

setDoi in class DefaultPublication

Parameters:

doi - : DOI identifier

getImexId

public String getImexId()

Getter for the field imexId.

Specified by:

getImexId in interface Publication

Overrides:

getImexId in class DefaultPublication

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

Overrides:

assignImexId in class DefaultPublication

Parameters:

identifier - : the IMEx id from IMEx central

getCurationDepth

public CurationDepth getCurationDepth()

Getter for the field curationDepth.

Specified by:

getCurationDepth in interface Publication

Overrides:

getCurationDepth in class DefaultPublication

Returns:

a CurationDepth object.

getSource

public Source getSource()

Getter for the field source.

Specified by:

getSource in interface Publication

Overrides:

getSource in class DefaultPublication

Returns:

a Source object.

setSource

public void setSource(Source source)

Sets the source who curated the publication.

Specified by:

setSource in interface Publication

Overrides:

setSource in class DefaultPublication

Parameters:

source - : source for this publication

getPaperAbstract

public String getPaperAbstract()

getPaperAbstract.

Returns:

a String object.

getExpectedPublicationDate

public Date getExpectedPublicationDate()

Getter for the field expectedPublicationDate.

Returns:

a Date object.

getCreationDate

public Date getCreationDate()

Getter for the field creationDate.

Returns:

a Date object.

getStatus

public PublicationStatus getStatus()

Getter for the field status.

Returns:

a PublicationStatus object.

setStatus

public void setStatus(PublicationStatus status)

Setter for the field status.

Parameters:

status - a PublicationStatus object.

getOwner

public String getOwner()

getOwner.

Returns:

a String object.

getCurators

public Collection<String> getCurators()

Getter for the field curators.

Returns:

a Collection object.

getSources

public List<Source> getSources()

Getter for the field sources.

Returns:

a List object.