Package psidev.psi.mi.jami.json.nary

Class MIJsonEvidenceWriter

java.lang.Object

psidev.psi.mi.jami.json.nary.AbstractMIJsonWriter<InteractionEvidence>

psidev.psi.mi.jami.json.nary.MIJsonEvidenceWriter

All Implemented Interfaces:

InteractionWriter<InteractionEvidence>

public class MIJsonEvidenceWriter
extends AbstractMIJsonWriter<InteractionEvidence>

Abstract JSON writer for interactions (n-ary json format)

Since:

03/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MIJsonEvidenceWriter()	Constructor for MIJsonEvidenceWriter.
MIJsonEvidenceWriter(File file, OntologyTermFetcher fetcher)	Constructor for MIJsonEvidenceWriter.
MIJsonEvidenceWriter(OutputStream output, OntologyTermFetcher fetcher)	Constructor for MIJsonEvidenceWriter.
MIJsonEvidenceWriter(Writer writer, OntologyTermFetcher fetcher)	Constructor for MIJsonEvidenceWriter.
MIJsonEvidenceWriter(Writer writer, OntologyTermFetcher fetcher, Map<String,String> processedInteractors, Map<Feature,Integer> processedFeatures, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for MIJsonEvidenceWriter.
MIJsonEvidenceWriter(Map<String,String> processedInteractors, Map<Feature,Integer> processedFeatures, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for MIJsonEvidenceWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	flush()	flush.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected void	initialiseInteractionWriter()	initialiseInteractionWriter.
void	reset()	reset.
protected void	writeComplex(Complex complex)	writeComplex.

Methods inherited from class psidev.psi.mi.jami.json.nary.AbstractMIJsonWriter

clear, end, getFetcher, getIdGenerator, getInteractionWriter, getInteractorWriter, getProcessedFeatures, getProcessedInteractors, getProcessedParticipants, getWriter, registerAndWriteInteractor, setFetcher, setInteractionWriter, start, write, write, write, writeEnd, writeStart

Methods inherited from class java.lang.Object

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

Constructor Detail

MIJsonEvidenceWriter

public MIJsonEvidenceWriter()

Constructor for MIJsonEvidenceWriter.

MIJsonEvidenceWriter

public MIJsonEvidenceWriter(File file,
                            OntologyTermFetcher fetcher)
                     throws IOException

Constructor for MIJsonEvidenceWriter.

Parameters:

file - a File object.

fetcher - a OntologyTermFetcher object.

Throws:

IOException - if any.

MIJsonEvidenceWriter

public MIJsonEvidenceWriter(OutputStream output,
                            OntologyTermFetcher fetcher)

Constructor for MIJsonEvidenceWriter.

Parameters:

output - a OutputStream object.

fetcher - a OntologyTermFetcher object.

MIJsonEvidenceWriter

public MIJsonEvidenceWriter(Writer writer,
                            OntologyTermFetcher fetcher)

Constructor for MIJsonEvidenceWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

MIJsonEvidenceWriter

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

Constructor for MIJsonEvidenceWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

processedInteractors - a Map object.

processedFeatures - a Map object.

processedParticipants - a Map object.

idGenerator - a IncrementalIdGenerator object.

MIJsonEvidenceWriter

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

Constructor for MIJsonEvidenceWriter.

Parameters:

processedInteractors - a Map object.

processedFeatures - a Map object.

processedParticipants - a Map object.

idGenerator - a IncrementalIdGenerator object.

Method Detail

flush

public void flush()
           throws MIIOException

flush.

Specified by:

flush in interface InteractionWriter<InteractionEvidence>

Overrides:

flush in class AbstractMIJsonWriter<InteractionEvidence>

Throws:

MIIOException - if any.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<InteractionEvidence>

Overrides:

close in class AbstractMIJsonWriter<InteractionEvidence>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<InteractionEvidence>

Overrides:

reset in class AbstractMIJsonWriter<InteractionEvidence>

Throws:

MIIOException - if any.

initialiseContext

public void initialiseContext(Map<String,Object> options)

Initialise the context of the InteractionWriter given a map of options

Specified by:

initialiseContext in interface InteractionWriter<InteractionEvidence>

Overrides:

initialiseContext in class AbstractMIJsonWriter<InteractionEvidence>

Parameters:

options - : the options given by the user

writeComplex

protected void writeComplex(Complex complex)

writeComplex.

Specified by:

writeComplex in class AbstractMIJsonWriter<InteractionEvidence>

Parameters:

complex - a Complex object.

initialiseInteractionWriter

protected void initialiseInteractionWriter()

initialiseInteractionWriter.

Specified by:

initialiseInteractionWriter in class AbstractMIJsonWriter<InteractionEvidence>