Package psidev.psi.mi.jami.json.elements

Class SimpleJsonInteractionWriter<I extends Interaction>

java.lang.Object

psidev.psi.mi.jami.json.elements.SimpleJsonInteractionWriter<I>

All Implemented Interfaces:

JsonElementWriter<I>

Direct Known Subclasses:

SimpleJsonBinaryInteractionWriter, SimpleJsonInteractionEvidenceWriter, SimpleJsonModelledInteractionWriter

public class SimpleJsonInteractionWriter<I extends Interaction>
extends Object
implements JsonElementWriter<I>

Json writer for interactions

Since:

18/07/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
SimpleJsonInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants)	Constructor for SimpleJsonInteractionWriter.
SimpleJsonInteractionWriter(Writer writer, Map<Feature,Integer> processedFeatures, Map<String,String> processedInteractors, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for SimpleJsonInteractionWriter.

Method Summary

Modifier and Type	Method	Description
protected String[]	generateInteractionIdentifier(I object, Xref preferredIdentifier)	generateInteractionIdentifier.
JsonElementWriter<CvTerm>	getCvWriter()	Getter for the field cvWriter.
OntologyTermFetcher	getFetcher()	Getter for the field fetcher.
JsonElementWriter<Xref>	getIdentifierWriter()	Getter for the field identifierWriter.
IncrementalIdGenerator	getIdGenerator()	Getter for the field idGenerator.
JsonElementWriter	getParticipantWriter()	Getter for the field participantWriter.
protected Map<Feature,Integer>	getProcessedFeatures()	Getter for the field processedFeatures.
protected Map<String,String>	getProcessedInteractors()	Getter for the field processedInteractors.
protected Map<Entity,Integer>	getProcessedParticipants()	Getter for the field processedParticipants.
protected Writer	getWriter()	Getter for the field writer.
protected boolean	hasIdentifiers(I object)	hasIdentifiers.
protected void	initialiseDefaultParticipantWriter()	initialiseDefaultParticipantWriter.
void	setCvWriter(JsonElementWriter<CvTerm> cvWriter)	Setter for the field cvWriter.
void	setFetcher(OntologyTermFetcher fetcher)	Setter for the field fetcher.
void	setIdentifierWriter(JsonElementWriter<Xref> identifierWriter)	Setter for the field identifierWriter.
void	setIdGenerator(IncrementalIdGenerator idGenerator)	Setter for the field idGenerator.
void	setParticipantWriter(JsonElementWriter participantWriter)	Setter for the field participantWriter.
void	write(I object)	write.
protected void	writeAllIdentifiers(I object)	writeAllIdentifiers.
protected void	writeExpansionMethod(CvTerm expansion)	writeExpansionMethod.
protected void	writeOtherExpansionMethodProperties()	writeOtherExpansionMethodProperties.
protected void	writeOtherIdentifiers(I object)	writeOtherIdentifiers.
protected void	writeOtherProperties(I object)	writeOtherProperties.

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleJsonInteractionWriter

public SimpleJsonInteractionWriter(Writer writer,
                                   Map<Feature,Integer> processedFeatures,
                                   Map<String,String> processedInteractors,
                                   Map<Entity,Integer> processedParticipants)

Constructor for SimpleJsonInteractionWriter.

Parameters:

writer - a Writer object.

processedFeatures - a Map object.

processedInteractors - a Map object.

processedParticipants - a Map object.

SimpleJsonInteractionWriter

public SimpleJsonInteractionWriter(Writer writer,
                                   Map<Feature,Integer> processedFeatures,
                                   Map<String,String> processedInteractors,
                                   Map<Entity,Integer> processedParticipants,
                                   IncrementalIdGenerator idGenerator)

Constructor for SimpleJsonInteractionWriter.

Parameters:

writer - a Writer object.

processedFeatures - a Map object.

processedInteractors - a Map object.

processedParticipants - a Map object.

idGenerator - a IncrementalIdGenerator object.

Method Detail

write

public void write(I object)
           throws IOException

write.

Specified by:

write in interface JsonElementWriter<I extends Interaction>

Parameters:

object - a I object.

Throws:

IOException - if any.

generateInteractionIdentifier

protected String[] generateInteractionIdentifier(I object,
                                                 Xref preferredIdentifier)

generateInteractionIdentifier.

Parameters:

object - a I object.

preferredIdentifier - a Xref object.

Returns:

an array of String objects.

writeExpansionMethod

protected void writeExpansionMethod(CvTerm expansion)
                             throws IOException

writeExpansionMethod.

Parameters:

expansion - a CvTerm object.

Throws:

IOException - if any.

writeOtherExpansionMethodProperties

protected void writeOtherExpansionMethodProperties()
                                            throws IOException

writeOtherExpansionMethodProperties.

Throws:

IOException - if any.

writeAllIdentifiers

protected void writeAllIdentifiers(I object)
                            throws IOException

writeAllIdentifiers.

Parameters:

object - a I object.

Throws:

IOException - if any.

writeOtherIdentifiers

protected void writeOtherIdentifiers(I object)
                              throws IOException

writeOtherIdentifiers.

Parameters:

object - a I object.

Throws:

IOException - if any.

hasIdentifiers

protected boolean hasIdentifiers(I object)

hasIdentifiers.

Parameters:

object - a I object.

Returns:

a boolean.

writeOtherProperties

protected void writeOtherProperties(I object)
                             throws IOException

writeOtherProperties.

Parameters:

object - a I object.

Throws:

IOException - if any.

getCvWriter

public JsonElementWriter<CvTerm> getCvWriter()

Getter for the field cvWriter.

Returns:

a JsonElementWriter object.

setCvWriter

public void setCvWriter(JsonElementWriter<CvTerm> cvWriter)

Setter for the field cvWriter.

Parameters:

cvWriter - a JsonElementWriter object.

getIdentifierWriter

public JsonElementWriter<Xref> getIdentifierWriter()

Getter for the field identifierWriter.

Returns:

a JsonElementWriter object.

setIdentifierWriter

public void setIdentifierWriter(JsonElementWriter<Xref> identifierWriter)

Setter for the field identifierWriter.

Parameters:

identifierWriter - a JsonElementWriter object.

getIdGenerator

public IncrementalIdGenerator getIdGenerator()

Getter for the field idGenerator.

Returns:

a IncrementalIdGenerator object.

setIdGenerator

public void setIdGenerator(IncrementalIdGenerator idGenerator)

Setter for the field idGenerator.

Parameters:

idGenerator - a IncrementalIdGenerator object.

getParticipantWriter

public JsonElementWriter getParticipantWriter()

Getter for the field participantWriter.

Returns:

a JsonElementWriter object.

initialiseDefaultParticipantWriter

protected void initialiseDefaultParticipantWriter()

initialiseDefaultParticipantWriter.

setParticipantWriter

public void setParticipantWriter(JsonElementWriter participantWriter)

Setter for the field participantWriter.

Parameters:

participantWriter - a JsonElementWriter object.

getFetcher

public OntologyTermFetcher getFetcher()

Getter for the field fetcher.

Returns:

a OntologyTermFetcher object.

setFetcher

public void setFetcher(OntologyTermFetcher fetcher)

Setter for the field fetcher.

Parameters:

fetcher - a OntologyTermFetcher object.

getWriter

protected Writer getWriter()

Getter for the field writer.

Returns:

a Writer object.

getProcessedInteractors

protected Map<String,String> getProcessedInteractors()

Getter for the field processedInteractors.

Returns:

a Map object.

getProcessedFeatures

protected Map<Feature,Integer> getProcessedFeatures()

Getter for the field processedFeatures.

Returns:

a Map object.

getProcessedParticipants

protected Map<Entity,Integer> getProcessedParticipants()

Getter for the field processedParticipants.

Returns:

a Map object.