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

Class MIJsonBinaryWriter

java.lang.Object

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

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

psidev.psi.mi.jami.json.binary.MIJsonBinaryWriter

All Implemented Interfaces:

InteractionWriter<BinaryInteraction>

public class MIJsonBinaryWriter
extends AbstractMIJsonBinaryWriter<BinaryInteraction>

JSON writer for mix of modelled and experimental interactions and

Since:

03/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MIJsonBinaryWriter()	Constructor for MIJsonBinaryWriter.
MIJsonBinaryWriter(File file, OntologyTermFetcher fetcher)	Constructor for MIJsonBinaryWriter.
MIJsonBinaryWriter(OutputStream output, OntologyTermFetcher fetcher)	Constructor for MIJsonBinaryWriter.
MIJsonBinaryWriter(Writer writer, OntologyTermFetcher fetcher)	Constructor for MIJsonBinaryWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	flush()	flush.
protected void	initExpansionMethodInteractionWriter(Integer expansionId)	initExpansionMethodInteractionWriter.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected void	initialiseInteractionWriter()	initialiseInteractionWriter.
protected void	initialiseSubWritersWith(Writer writer)	initialiseSubWritersWith.
void	reset()	reset.
void	write(BinaryInteraction interaction)	write.

Methods inherited from class psidev.psi.mi.jami.json.binary.AbstractMIJsonBinaryWriter

getExpansionId, setExpansionId, 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, writeEnd, writeStart

Methods inherited from class java.lang.Object

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

Constructor Detail

MIJsonBinaryWriter

public MIJsonBinaryWriter()

Constructor for MIJsonBinaryWriter.

MIJsonBinaryWriter

public MIJsonBinaryWriter(File file,
                          OntologyTermFetcher fetcher)
                   throws IOException

Constructor for MIJsonBinaryWriter.

Parameters:

file - a File object.

fetcher - a OntologyTermFetcher object.

Throws:

IOException - if any.

MIJsonBinaryWriter

public MIJsonBinaryWriter(OutputStream output,
                          OntologyTermFetcher fetcher)

Constructor for MIJsonBinaryWriter.

Parameters:

output - a OutputStream object.

fetcher - a OntologyTermFetcher object.

MIJsonBinaryWriter

public MIJsonBinaryWriter(Writer writer,
                          OntologyTermFetcher fetcher)

Constructor for MIJsonBinaryWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

Method Detail

write

public void write(BinaryInteraction interaction)
           throws MIIOException

write.

Specified by:

write in interface InteractionWriter<BinaryInteraction>

Overrides:

write in class AbstractMIJsonWriter<BinaryInteraction>

Parameters:

interaction - a I object.

Throws:

MIIOException - if any.

initialiseSubWritersWith

protected void initialiseSubWritersWith(Writer writer)

initialiseSubWritersWith.

Parameters:

writer - a Writer object.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<BinaryInteraction>

Overrides:

close in class AbstractMIJsonBinaryWriter<BinaryInteraction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<BinaryInteraction>

Overrides:

reset in class AbstractMIJsonBinaryWriter<BinaryInteraction>

Throws:

MIIOException - if any.

initialiseInteractionWriter

protected void initialiseInteractionWriter()

initialiseInteractionWriter.

Specified by:

initialiseInteractionWriter in class AbstractMIJsonWriter<BinaryInteraction>

flush

public void flush()
           throws MIIOException

flush.

Specified by:

flush in interface InteractionWriter<BinaryInteraction>

Overrides:

flush in class AbstractMIJsonBinaryWriter<BinaryInteraction>

Throws:

MIIOException - if any.

initExpansionMethodInteractionWriter

protected void initExpansionMethodInteractionWriter(Integer expansionId)

initExpansionMethodInteractionWriter.

Specified by:

initExpansionMethodInteractionWriter in class AbstractMIJsonBinaryWriter<BinaryInteraction>

Parameters:

expansionId - a Integer object.

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<BinaryInteraction>

Overrides:

initialiseContext in class AbstractMIJsonBinaryWriter<BinaryInteraction>

Parameters:

options - : the options given by the user