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

Class Mitab25Writer

java.lang.Object

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

psidev.psi.mi.jami.tab.io.writer.extended.Mitab25Writer

All Implemented Interfaces:

InteractionWriter<Interaction>

Direct Known Subclasses:

Mitab26Writer

public class Mitab25Writer
extends AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

The simple MITAB 2.5 writer will write interactions using the JAMI interfaces. It will not check for MITAB extended objects (such as MitabAlias and DefaultMitabFeature). The default Complex expansion method is spoke expansion.

Since:

10/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
Mitab25Writer()	Constructor for Mitab25Writer.
Mitab25Writer(File file)	Constructor for Mitab25Writer.
Mitab25Writer(File file, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab25Writer(OutputStream output)	Constructor for Mitab25Writer.
Mitab25Writer(OutputStream output, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.
Mitab25Writer(Writer writer)	Constructor for Mitab25Writer.
Mitab25Writer(Writer writer, ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	Constructor for Mitab25Writer.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
MitabVersion	getVersion()	getVersion.
protected Writer	getWriter()	Getter for the field writer.
protected void	initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)	initialiseExpansionMethod.
protected void	initialiseFile(File file)	initialiseFile.
protected void	initialiseOutputStream(OutputStream output)	initialiseOutputStream.
protected void	initialiseSubWriters()	initialiseSubWriters.
protected void	initialiseWriter(Writer writer)	initialiseWriter.
void	reset()	reset.
protected void	setInteractionEvidenceWriter(Mitab25EvidenceWriter interactionEvidenceWriter)	Setter for the field interactionEvidenceWriter.
protected void	setModelledInteractionWriter(Mitab25ModelledWriter modelledInteractionWriter)	Setter for the field modelledInteractionWriter.
void	start()	start.
void	write(Interaction interaction)	write.

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

end, flush, getBinaryWriter, getExpansionMethod, hasStarted, initialiseContext, isWriteHeader, setBinaryWriter, setExpansionMethod, setStarted, setWriteHeader, write, write

Methods inherited from class java.lang.Object

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

Constructor Detail

Mitab25Writer

public Mitab25Writer()

Constructor for Mitab25Writer.

Mitab25Writer

public Mitab25Writer(File file)
              throws IOException

Constructor for Mitab25Writer.

Parameters:

file - a File object.

Throws:

IOException - if any.

Mitab25Writer

public Mitab25Writer(OutputStream output)

Constructor for Mitab25Writer.

Parameters:

output - a OutputStream object.

Mitab25Writer

public Mitab25Writer(Writer writer)

Constructor for Mitab25Writer.

Parameters:

writer - a Writer object.

Mitab25Writer

public Mitab25Writer(File file,
                     ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)
              throws IOException

Constructor for Mitab25Writer.

Parameters:

file - a File object.

expansionMethod - a ComplexExpansionMethod object.

Throws:

IOException - if any.

Mitab25Writer

public Mitab25Writer(OutputStream output,
                     ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)
              throws IOException

Constructor for Mitab25Writer.

Parameters:

output - a OutputStream object.

expansionMethod - a ComplexExpansionMethod object.

Throws:

IOException - if any.

Mitab25Writer

public Mitab25Writer(Writer writer,
                     ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)
              throws IOException

Constructor for Mitab25Writer.

Parameters:

writer - a Writer object.

expansionMethod - a ComplexExpansionMethod object.

Throws:

IOException - if any.

Method Detail

getVersion

public MitabVersion getVersion()

getVersion.

Specified by:

getVersion in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Returns:

a MitabVersion object.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<Interaction>

Overrides:

close in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<Interaction>

Overrides:

reset in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Throws:

MIIOException - if any.

initialiseExpansionMethod

protected void initialiseExpansionMethod(ComplexExpansionMethod<Interaction,BinaryInteraction> expansionMethod)

initialiseExpansionMethod.

Specified by:

initialiseExpansionMethod in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Parameters:

expansionMethod - a ComplexExpansionMethod object.

initialiseWriter

protected void initialiseWriter(Writer writer)

initialiseWriter.

Specified by:

initialiseWriter in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Parameters:

writer - a Writer object.

initialiseOutputStream

protected void initialiseOutputStream(OutputStream output)

initialiseOutputStream.

Specified by:

initialiseOutputStream in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Parameters:

output - a OutputStream object.

initialiseFile

protected void initialiseFile(File file)
                       throws IOException

initialiseFile.

Specified by:

initialiseFile in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Parameters:

file - a File object.

Throws:

IOException - if any.

start

public void start()
           throws MIIOException

start.

Specified by:

start in interface InteractionWriter<Interaction>

Overrides:

start in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Throws:

MIIOException - if any.

write

public void write(Interaction interaction)
           throws MIIOException

write.

Specified by:

write in interface InteractionWriter<Interaction>

Overrides:

write in class AbstractMitabWriter<Interaction,BinaryInteraction,Participant>

Parameters:

interaction - a T object.

Throws:

MIIOException - if any.

initialiseSubWriters

protected void initialiseSubWriters()

initialiseSubWriters.

setModelledInteractionWriter

protected void setModelledInteractionWriter(Mitab25ModelledWriter modelledInteractionWriter)

Setter for the field modelledInteractionWriter.

Parameters:

modelledInteractionWriter - a Mitab25ModelledWriter object.

setInteractionEvidenceWriter

protected void setInteractionEvidenceWriter(Mitab25EvidenceWriter interactionEvidenceWriter)

Setter for the field interactionEvidenceWriter.

Parameters:

interactionEvidenceWriter - a Mitab25EvidenceWriter object.

getWriter

protected Writer getWriter()

Getter for the field writer.

Returns:

a Writer object.