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

Class AbstractMIJsonWriter<I extends Interaction,B extends BinaryInteraction>

java.lang.Object

psidev.psi.mi.jami.json.binary.AbstractMIJsonWriter<I,B>

All Implemented Interfaces:

InteractionWriter<I>

Direct Known Subclasses:

LightMIJsonWriter, MIJsonEvidenceWriter, MIJsonModelledWriter, MIJsonWriter

public abstract class AbstractMIJsonWriter<I extends Interaction,B extends BinaryInteraction>
extends Object
implements InteractionWriter<I>

The jsonWriter which writes the interactions

Since:

05/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractMIJsonWriter()	Constructor for AbstractMIJsonWriter.
AbstractMIJsonWriter(File file, OntologyTermFetcher fetcher)	Constructor for AbstractMIJsonWriter.
AbstractMIJsonWriter(File file, OntologyTermFetcher fetcher, ComplexExpansionMethod<I,B> expansionMethod)	Constructor for AbstractMIJsonWriter.
AbstractMIJsonWriter(OutputStream output, OntologyTermFetcher fetcher)	Constructor for AbstractMIJsonWriter.
AbstractMIJsonWriter(OutputStream output, OntologyTermFetcher fetcher, ComplexExpansionMethod<I,B> expansionMethod)	Constructor for AbstractMIJsonWriter.
AbstractMIJsonWriter(Writer writer, OntologyTermFetcher fetcher)	Constructor for AbstractMIJsonWriter.
AbstractMIJsonWriter(Writer writer, OntologyTermFetcher fetcher, ComplexExpansionMethod<I,B> expansionMethod)	Constructor for AbstractMIJsonWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	end()	end.
void	flush()	flush.
protected AbstractMIJsonBinaryWriter<B>	getBinaryWriter()	Getter for the field binaryWriter.
protected abstract void	initialiseBinaryWriter(File file, OntologyTermFetcher fetcher)	initialiseBinaryWriter.
protected abstract void	initialiseBinaryWriter(OutputStream output, OntologyTermFetcher fetcher)	initialiseBinaryWriter.
protected abstract void	initialiseBinaryWriter(Writer writer, OntologyTermFetcher fetcher)	initialiseBinaryWriter.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected abstract void	initialiseDefaultBinaryWriter()	initialiseDefaultBinaryWriter.
protected abstract void	initialiseDefaultExpansionMethod()	initialiseDefaultExpansionMethod.
void	reset()	reset.
protected void	setBinaryWriter(AbstractMIJsonBinaryWriter<B> binaryWriter)	Setter for the field binaryWriter.
protected void	setExpansionMethod(ComplexExpansionMethod<I,B> expansionMethod)	Setter for the field expansionMethod.
void	start()	start.
void	write(I interaction)	write.
void	write(Collection<? extends I> interactions)	write.
void	write(Iterator<? extends I> interactions)	Writes Interaction objects using iterator

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractMIJsonWriter

public AbstractMIJsonWriter()

Constructor for AbstractMIJsonWriter.

AbstractMIJsonWriter

public AbstractMIJsonWriter(File file,
                            OntologyTermFetcher fetcher)
                     throws IOException

Constructor for AbstractMIJsonWriter.

Parameters:

file - a File object.

fetcher - a OntologyTermFetcher object.

Throws:

IOException - if any.

AbstractMIJsonWriter

public AbstractMIJsonWriter(OutputStream output,
                            OntologyTermFetcher fetcher)

Constructor for AbstractMIJsonWriter.

Parameters:

output - a OutputStream object.

fetcher - a OntologyTermFetcher object.

AbstractMIJsonWriter

public AbstractMIJsonWriter(Writer writer,
                            OntologyTermFetcher fetcher)

Constructor for AbstractMIJsonWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

AbstractMIJsonWriter

public AbstractMIJsonWriter(File file,
                            OntologyTermFetcher fetcher,
                            ComplexExpansionMethod<I,B> expansionMethod)
                     throws IOException

Constructor for AbstractMIJsonWriter.

Parameters:

file - a File object.

fetcher - a OntologyTermFetcher object.

expansionMethod - a ComplexExpansionMethod object.

Throws:

IOException - if any.

AbstractMIJsonWriter

public AbstractMIJsonWriter(OutputStream output,
                            OntologyTermFetcher fetcher,
                            ComplexExpansionMethod<I,B> expansionMethod)

Constructor for AbstractMIJsonWriter.

Parameters:

output - a OutputStream object.

fetcher - a OntologyTermFetcher object.

expansionMethod - a ComplexExpansionMethod object.

AbstractMIJsonWriter

public AbstractMIJsonWriter(Writer writer,
                            OntologyTermFetcher fetcher,
                            ComplexExpansionMethod<I,B> expansionMethod)

Constructor for AbstractMIJsonWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

expansionMethod - a ComplexExpansionMethod object.

Method Detail

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 Interaction>

Parameters:

options - : the options given by the user

start

public void start()
           throws MIIOException

start.

Specified by:

start in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

end

public void end()
         throws MIIOException

end.

Specified by:

end in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

write

public void write(I interaction)
           throws MIIOException

write.

Specified by:

write in interface InteractionWriter<I extends Interaction>

Parameters:

interaction - a I object.

Throws:

MIIOException - if any.

write

public void write(Collection<? extends I> interactions)
           throws MIIOException

write.

Specified by:

write in interface InteractionWriter<I extends Interaction>

Parameters:

interactions - a Collection object.

Throws:

MIIOException - if any.

write

public void write(Iterator<? extends I> interactions)
           throws MIIOException

Writes Interaction objects using iterator

Specified by:

write in interface InteractionWriter<I extends Interaction>

Parameters:

interactions - : the iterator of interactions to write

Throws:

MIIOException - : if cannot write

flush

public void flush()
           throws MIIOException

flush.

Specified by:

flush in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

getBinaryWriter

protected AbstractMIJsonBinaryWriter<B> getBinaryWriter()

Getter for the field binaryWriter.

Returns:

a AbstractMIJsonBinaryWriter object.

setBinaryWriter

protected void setBinaryWriter(AbstractMIJsonBinaryWriter<B> binaryWriter)

Setter for the field binaryWriter.

Parameters:

binaryWriter - a AbstractMIJsonBinaryWriter object.

setExpansionMethod

protected void setExpansionMethod(ComplexExpansionMethod<I,B> expansionMethod)

Setter for the field expansionMethod.

Parameters:

expansionMethod - a ComplexExpansionMethod object.

initialiseDefaultExpansionMethod

protected abstract void initialiseDefaultExpansionMethod()

initialiseDefaultExpansionMethod.

initialiseBinaryWriter

protected abstract void initialiseBinaryWriter(File file,
                                               OntologyTermFetcher fetcher)
                                        throws IOException

initialiseBinaryWriter.

Parameters:

file - a File object.

fetcher - a OntologyTermFetcher object.

Throws:

IOException - if any.

initialiseBinaryWriter

protected abstract void initialiseBinaryWriter(OutputStream output,
                                               OntologyTermFetcher fetcher)

initialiseBinaryWriter.

Parameters:

output - a OutputStream object.

fetcher - a OntologyTermFetcher object.

initialiseBinaryWriter

protected abstract void initialiseBinaryWriter(Writer writer,
                                               OntologyTermFetcher fetcher)

initialiseBinaryWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

initialiseDefaultBinaryWriter

protected abstract void initialiseDefaultBinaryWriter()

initialiseDefaultBinaryWriter.