Package psidev.psi.mi.jami.json.binary

Class AbstractMIJsonBinaryWriter<I extends BinaryInteraction>

java.lang.Object

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

psidev.psi.mi.jami.json.binary.AbstractMIJsonBinaryWriter<I>

All Implemented Interfaces:

InteractionWriter<I>

Direct Known Subclasses:

LightMIJsonBinaryWriter, MIJsonBinaryEvidenceWriter, MIJsonBinaryWriter, MIJsonModelledBinaryWriter

public abstract class AbstractMIJsonBinaryWriter<I extends BinaryInteraction>
extends AbstractMIJsonWriter<I>

Abstract JSON writer for binary interactions (binary json format)

Since:

03/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	flush()	flush.
protected Integer	getExpansionId()	Getter for the field expansionId.
protected abstract void	initExpansionMethodInteractionWriter(Integer expansionId)	initExpansionMethodInteractionWriter.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
void	reset()	reset.
void	setExpansionId(Integer expansionId)	Setter for the field expansionId.
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, initialiseInteractionWriter, 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

AbstractMIJsonBinaryWriter

public AbstractMIJsonBinaryWriter()

Constructor for AbstractMIJsonBinaryWriter.

AbstractMIJsonBinaryWriter

public AbstractMIJsonBinaryWriter(File file,
                                  OntologyTermFetcher fetcher)
                           throws IOException

Constructor for AbstractMIJsonBinaryWriter.

Parameters:

file - a File object.

fetcher - a OntologyTermFetcher object.

Throws:

IOException - if any.

AbstractMIJsonBinaryWriter

public AbstractMIJsonBinaryWriter(OutputStream output,
                                  OntologyTermFetcher fetcher)

Constructor for AbstractMIJsonBinaryWriter.

Parameters:

output - a OutputStream object.

fetcher - a OntologyTermFetcher object.

AbstractMIJsonBinaryWriter

public AbstractMIJsonBinaryWriter(Writer writer,
                                  OntologyTermFetcher fetcher)

Constructor for AbstractMIJsonBinaryWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

AbstractMIJsonBinaryWriter

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

Constructor for AbstractMIJsonBinaryWriter.

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.

AbstractMIJsonBinaryWriter

protected AbstractMIJsonBinaryWriter(Map<String,String> processedInteractors,
                                     Map<Feature,Integer> processedFeatures,
                                     Map<Entity,Integer> processedParticipants,
                                     IncrementalIdGenerator idGenerator)

Constructor for AbstractMIJsonBinaryWriter.

Parameters:

processedInteractors - a Map object.

processedFeatures - a Map object.

processedParticipants - a Map object.

idGenerator - a IncrementalIdGenerator object.

Method Detail

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<I extends BinaryInteraction>

Overrides:

close in class AbstractMIJsonWriter<I extends BinaryInteraction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<I extends BinaryInteraction>

Overrides:

reset in class AbstractMIJsonWriter<I extends BinaryInteraction>

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<I extends BinaryInteraction>

Overrides:

initialiseContext in class AbstractMIJsonWriter<I extends BinaryInteraction>

Parameters:

options - : the options given by the user

flush

public void flush()
           throws MIIOException

flush.

Specified by:

flush in interface InteractionWriter<I extends BinaryInteraction>

Overrides:

flush in class AbstractMIJsonWriter<I extends BinaryInteraction>

Throws:

MIIOException - if any.

setExpansionId

public void setExpansionId(Integer expansionId)

Setter for the field expansionId.

Parameters:

expansionId - a Integer object.

initExpansionMethodInteractionWriter

protected abstract void initExpansionMethodInteractionWriter(Integer expansionId)

initExpansionMethodInteractionWriter.

Parameters:

expansionId - a Integer object.

getExpansionId

protected Integer getExpansionId()

Getter for the field expansionId.

Returns:

a Integer object.

writeComplex

protected void writeComplex(Complex complex)

writeComplex.

Specified by:

writeComplex in class AbstractMIJsonWriter<I extends BinaryInteraction>

Parameters:

complex - a Complex object.