Package psidev.psi.mi.jami.tab.io.writer

Class Mitab25BinaryWriter

java.lang.Object

psidev.psi.mi.jami.tab.io.writer.AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

psidev.psi.mi.jami.tab.io.writer.Mitab25BinaryWriter

All Implemented Interfaces:

InteractionWriter<BinaryInteraction>

Direct Known Subclasses:

Mitab25BinaryWriter

public class Mitab25BinaryWriter
extends AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

The basic Mitab 2.5 writer for BinaryInteraction

Since:

19/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
Mitab25BinaryWriter()	Constructor for Mitab25BinaryWriter.
Mitab25BinaryWriter(File file)	Constructor for Mitab25BinaryWriter.
Mitab25BinaryWriter(OutputStream output)	Constructor for Mitab25BinaryWriter.
Mitab25BinaryWriter(Writer writer)	Constructor for Mitab25BinaryWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
protected void	initialiseColumnFeeder()	initialiseColumnFeeder.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected void	initialiseSubWritersWith(Writer writer)	initialiseSubWritersWith.
void	reset()	reset.
protected void	setBinaryEvidenceWriter(AbstractMitab25BinaryWriter<BinaryInteractionEvidence,ParticipantEvidence> binaryEvidenceWriter)	Setter for the field binaryEvidenceWriter.
protected void	setModelledBinaryWriter(AbstractMitab25BinaryWriter<ModelledBinaryInteraction,ModelledParticipant> modelledBinaryWriter)	Setter for the field modelledBinaryWriter.
void	setWriteHeader(boolean writeHeader)	Setter for the field writeHeader.
void	start()	start.
void	write(BinaryInteraction interaction)	Writes a binary interaction.

Methods inherited from class psidev.psi.mi.jami.tab.io.writer.AbstractMitab25BinaryWriter

end, flush, getColumnFeeder, getVersion, getWriter, hasStarted, isWriteHeader, setColumnFeeder, setStarted, setVersion, write, write, writeBinary, writeHeader

Methods inherited from class java.lang.Object

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

Constructor Detail

Mitab25BinaryWriter

public Mitab25BinaryWriter()

Constructor for Mitab25BinaryWriter.

Mitab25BinaryWriter

public Mitab25BinaryWriter(File file)
                    throws IOException

Constructor for Mitab25BinaryWriter.

Parameters:

file - a File object.

Throws:

IOException - if any.

Mitab25BinaryWriter

public Mitab25BinaryWriter(OutputStream output)

Constructor for Mitab25BinaryWriter.

Parameters:

output - a OutputStream object.

Mitab25BinaryWriter

public Mitab25BinaryWriter(Writer writer)

Constructor for Mitab25BinaryWriter.

Parameters:

writer - a Writer 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<BinaryInteraction>

Overrides:

initialiseContext in class AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

Parameters:

options - : the options given by the user

start

public void start()
           throws MIIOException

start.

Specified by:

start in interface InteractionWriter<BinaryInteraction>

Overrides:

start in class AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

Throws:

MIIOException - if any.

write

public void write(BinaryInteraction interaction)
           throws MIIOException

Writes a binary interaction. Does not write any extended properties from participants, interaction and features This method will write empty columns for interaction detection method, publication author and identifier, source and confidences. It will also ignore experimental roles, host organism, interaction parameters and participant identification methods

Specified by:

write in interface InteractionWriter<BinaryInteraction>

Overrides:

write in class AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

Parameters:

interaction - a T object.

Throws:

MIIOException - if any.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<BinaryInteraction>

Overrides:

close in class AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<BinaryInteraction>

Overrides:

reset in class AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

Throws:

MIIOException - if any.

initialiseSubWritersWith

protected void initialiseSubWritersWith(Writer writer)

initialiseSubWritersWith.

Parameters:

writer - a Writer object.

initialiseColumnFeeder

protected void initialiseColumnFeeder()

initialiseColumnFeeder.

Specified by:

initialiseColumnFeeder in class AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

setWriteHeader

public void setWriteHeader(boolean writeHeader)

Setter for the field writeHeader.

Overrides:

setWriteHeader in class AbstractMitab25BinaryWriter<BinaryInteraction,Participant>

Parameters:

writeHeader - a boolean.

setModelledBinaryWriter

protected void setModelledBinaryWriter(AbstractMitab25BinaryWriter<ModelledBinaryInteraction,ModelledParticipant> modelledBinaryWriter)

Setter for the field modelledBinaryWriter.

Parameters:

modelledBinaryWriter - a AbstractMitab25BinaryWriter object.

setBinaryEvidenceWriter

protected void setBinaryEvidenceWriter(AbstractMitab25BinaryWriter<BinaryInteractionEvidence,ParticipantEvidence> binaryEvidenceWriter)

Setter for the field binaryEvidenceWriter.

Parameters:

binaryEvidenceWriter - a AbstractMitab25BinaryWriter object.