Package psidev.psi.mi.jami.model.impl

Class DefaultPublication

java.lang.Object

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

All Implemented Interfaces:

Publication

Direct Known Subclasses:

ImexPublication, MitabPublication

public class DefaultPublication
extends Object
implements Publication

Default implementation for a Publication Notes: The equals and hashcode methods have NOT been overridden because the Publication object is a complex object. To compare Publication objects, you can use some comparators provided by default: - DefaultPublicationComparator - UnambiguousPublicationComparator - DefaultCuratedPublicationComparator - UnambiguousCuratedPublicationComparator - PublicationComparator - CuratedPublicationComparator

Since:

22/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

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.
protected void	clearPropertiesLinkedToIdentifiers()	clearPropertiesLinkedToIdentifiers
protected void	clearPropertiesLinkedToXrefs()	clearPropertiesLinkedToXrefs
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
List<String>	getAuthors()	Getter for the field authors.
CurationDepth	getCurationDepth()	Getter for the field curationDepth.
String	getDoi()	Getter for the field doi.
Collection<Experiment>	getExperiments()	Getter for the field experiments.
Collection<Xref>	getIdentifiers()	Getter for the field identifiers.
String	getImexId()	Getter for the field imexId.
String	getJournal()	Getter for the field journal.
Date	getPublicationDate()	Getter for the field publicationDate.
String	getPubmedId()	Getter for the field pubmedId.
Date	getReleasedDate()	Getter for the field releasedDate.
Source	getSource()	Getter for the field source.
String	getTitle()	Getter for the field title.
Collection<Xref>	getXrefs()	Getter for the field xrefs.
protected void	initialiseAnnotations()	initialiseAnnotations
protected void	initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	initialiseAuthors()	initialiseAuthors
protected void	initialiseAuthorsWith(List<String> authors)	initialiseAuthorsWith
protected void	initialiseExperiments()	initialiseExperiments
protected void	initialiseExperimentsWith(Collection<Experiment> experiments)	initialiseExperimentsWith
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	initialiseXrefs()	initialiseXrefs
protected void	initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	processAddedXrefEvent(Xref added)	processAddedXrefEvent
protected void	processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
protected void	processRemovedXrefEvent(Xref removed)	processRemovedXrefEvent
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	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	setTitle(String title)	Set the publication title
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultPublication

public DefaultPublication()

Constructor for DefaultPublication.

DefaultPublication

public DefaultPublication(Xref identifier)

Constructor for DefaultPublication.

Parameters:

identifier - a Xref object.

DefaultPublication

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

Constructor for DefaultPublication.

Parameters:

identifier - a Xref object.

curationDepth - a CurationDepth object.

source - a Source object.

DefaultPublication

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

Constructor for DefaultPublication.

Parameters:

identifier - a Xref object.

imexId - a String object.

source - a Source object.

DefaultPublication

public DefaultPublication(String pubmed)

Constructor for DefaultPublication.

Parameters:

pubmed - a String object.

DefaultPublication

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

Constructor for DefaultPublication.

Parameters:

pubmed - a String object.

curationDepth - a CurationDepth object.

source - a Source object.

DefaultPublication

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

Constructor for DefaultPublication.

Parameters:

pubmed - a String object.

imexId - a String object.

source - a Source object.

DefaultPublication

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

Constructor for DefaultPublication.

Parameters:

title - a String object.

journal - a String object.

publicationDate - a Date object.

DefaultPublication

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

Constructor for DefaultPublication.

Parameters:

title - a String object.

journal - a String object.

publicationDate - a Date object.

curationDepth - a CurationDepth object.

source - a Source object.

DefaultPublication

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

Constructor for DefaultPublication.

Parameters:

title - a String object.

journal - a String object.

publicationDate - a Date object.

imexId - a String object.

source - a Source object.

Method Detail

initialiseAuthors

protected void initialiseAuthors()

initialiseAuthors

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations

initialiseExperiments

protected void initialiseExperiments()

initialiseExperiments

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

initialiseAuthorsWith

protected void initialiseAuthorsWith(List<String> authors)

initialiseAuthorsWith

Parameters:

authors - a List object.

initialiseXrefsWith

protected void initialiseXrefsWith(Collection<Xref> xrefs)

initialiseXrefsWith

Parameters:

xrefs - a Collection object.

initialiseAnnotationsWith

protected void initialiseAnnotationsWith(Collection<Annotation> annotations)

initialiseAnnotationsWith

Parameters:

annotations - a Collection object.

initialiseExperimentsWith

protected void initialiseExperimentsWith(Collection<Experiment> experiments)

initialiseExperimentsWith

Parameters:

experiments - a Collection object.

initialiseIdentifiersWith

protected void initialiseIdentifiersWith(Collection<Xref> identifiers)

initialiseIdentifiersWith

Parameters:

identifiers - a Collection object.

getPubmedId

public String getPubmedId()

Getter for the field pubmedId.

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()

Getter for the field doi.

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()

Getter for the field identifiers.

Specified by:

getIdentifiers in interface Publication

Returns:

a Collection object.

getImexId

public String getImexId()

Getter for the field imexId.

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()

Getter for the field title.

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()

Getter for the field journal.

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()

Getter for the field publicationDate.

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()

Getter for the field authors.

Specified by:

getAuthors in interface Publication

Returns:

a List object.

getXrefs

public Collection<Xref> getXrefs()

Getter for the field xrefs.

Specified by:

getXrefs in interface Publication

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

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()

Getter for the field curationDepth.

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

processAddedIdentifierEvent

protected void processAddedIdentifierEvent(Xref added)

processAddedIdentifierEvent

Parameters:

added - a Xref object.

processRemovedIdentifierEvent

protected void processRemovedIdentifierEvent(Xref removed)

processRemovedIdentifierEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToIdentifiers

protected void clearPropertiesLinkedToIdentifiers()

clearPropertiesLinkedToIdentifiers

processAddedXrefEvent

protected void processAddedXrefEvent(Xref added)

processAddedXrefEvent

Parameters:

added - a Xref object.

processRemovedXrefEvent

protected void processRemovedXrefEvent(Xref removed)

processRemovedXrefEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToXrefs

protected void clearPropertiesLinkedToXrefs()

clearPropertiesLinkedToXrefs

toString

public String toString()

Overrides:

toString in class Object