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

Class AbstractMitab25BinaryWriter<T extends BinaryInteraction,P extends Participant>

java.lang.Object

psidev.psi.mi.jami.tab.io.writer.AbstractMitab25BinaryWriter<T,P>

All Implemented Interfaces:

InteractionWriter<T>

Direct Known Subclasses:

AbstractMitab26BinaryWriter, LightMitab25BinaryWriter, Mitab25BinaryEvidenceWriter, Mitab25BinaryEvidenceWriter, Mitab25BinaryWriter, Mitab25ModelledBinaryWriter, Mitab25ModelledBinaryWriter

public abstract class AbstractMitab25BinaryWriter<T extends BinaryInteraction,P extends Participant>
extends Object
implements InteractionWriter<T>

Abstract class for BinaryInteraction writer.

Since:

19/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractMitab25BinaryWriter()	Constructor for AbstractMitab25BinaryWriter.
AbstractMitab25BinaryWriter(File file)	Constructor for AbstractMitab25BinaryWriter.
AbstractMitab25BinaryWriter(OutputStream output)	Constructor for AbstractMitab25BinaryWriter.
AbstractMitab25BinaryWriter(Writer writer)	Constructor for AbstractMitab25BinaryWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	end()	end.
void	flush()	flush.
protected MitabColumnFeeder<T,P>	getColumnFeeder()	Getter for the field columnFeeder.
MitabVersion	getVersion()	Getter for the field version.
protected Writer	getWriter()	Getter for the field writer.
protected boolean	hasStarted()	hasStarted.
protected abstract void	initialiseColumnFeeder()	initialiseColumnFeeder.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
boolean	isWriteHeader()	isWriteHeader.
void	reset()	reset.
protected void	setColumnFeeder(MitabColumnFeeder<T,P> columnFeeder)	Setter for the field columnFeeder.
protected void	setStarted(boolean start)	setStarted.
protected void	setVersion(MitabVersion version)	Setter for the field version.
void	setWriteHeader(boolean writeHeader)	Setter for the field writeHeader.
void	start()	start.
void	write(Collection<? extends T> interactions)	Writes a collection of binary interactions.
void	write(Iterator<? extends T> interactions)	Writes Interaction objects using iterator
void	write(T interaction)	Writes a binary interaction.
protected void	writeBinary(T interaction, P a, P b)	Writes the binary interaction and its participants in MITAB 2.5
protected void	writeHeader()	Write the header

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractMitab25BinaryWriter

public AbstractMitab25BinaryWriter()

Constructor for AbstractMitab25BinaryWriter.

AbstractMitab25BinaryWriter

public AbstractMitab25BinaryWriter(File file)
                            throws IOException

Constructor for AbstractMitab25BinaryWriter.

Parameters:

file - a File object.

Throws:

IOException - if any.

AbstractMitab25BinaryWriter

public AbstractMitab25BinaryWriter(OutputStream output)

Constructor for AbstractMitab25BinaryWriter.

Parameters:

output - a OutputStream object.

AbstractMitab25BinaryWriter

public AbstractMitab25BinaryWriter(Writer writer)

Constructor for AbstractMitab25BinaryWriter.

Parameters:

writer - a Writer object.

Method Detail

getVersion

public MitabVersion getVersion()

Getter for the field version.

Returns:

a MitabVersion object.

isWriteHeader

public boolean isWriteHeader()

isWriteHeader.

Returns:

a boolean.

setWriteHeader

public void setWriteHeader(boolean writeHeader)

Setter for the field writeHeader.

Parameters:

writeHeader - a boolean.

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<T extends BinaryInteraction>

Parameters:

options - : the options given by the user

end

public void end()
         throws MIIOException

end.

Specified by:

end in interface InteractionWriter<T extends BinaryInteraction>

Throws:

MIIOException - if any.

start

public void start()
           throws MIIOException

start.

Specified by:

start in interface InteractionWriter<T extends BinaryInteraction>

Throws:

MIIOException - if any.

write

public void write(T 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<T extends BinaryInteraction>

Parameters:

interaction - a T object.

Throws:

MIIOException - if any.

write

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

Writes a collection of binary interactions. 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<T extends BinaryInteraction>

Parameters:

interactions - a Collection object.

Throws:

MIIOException - if any.

write

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

Writes Interaction objects using iterator

Specified by:

write in interface InteractionWriter<T extends BinaryInteraction>

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<T extends BinaryInteraction>

Throws:

MIIOException - if any.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<T extends BinaryInteraction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<T extends BinaryInteraction>

Throws:

MIIOException - if any.

getColumnFeeder

protected MitabColumnFeeder<T,P> getColumnFeeder()

Getter for the field columnFeeder.

Returns:

a MitabColumnFeeder object.

setColumnFeeder

protected void setColumnFeeder(MitabColumnFeeder<T,P> columnFeeder)

Setter for the field columnFeeder.

Parameters:

columnFeeder - a MitabColumnFeeder object.

initialiseColumnFeeder

protected abstract void initialiseColumnFeeder()

initialiseColumnFeeder.

writeBinary

protected void writeBinary(T interaction,
                           P a,
                           P b)
                    throws IOException

Writes the binary interaction and its participants in MITAB 2.5

Parameters:

interaction - a T object.

a - a P object.

b - a P object.

Throws:

IOException - if any.

getWriter

protected Writer getWriter()

Getter for the field writer.

Returns:

a Writer object.

writeHeader

protected void writeHeader()
                    throws IOException

Write the header

Throws:

IOException - if any.

setVersion

protected void setVersion(MitabVersion version)

Setter for the field version.

Parameters:

version - a MitabVersion object.

hasStarted

protected boolean hasStarted()

hasStarted.

Returns:

a boolean.

setStarted

protected void setStarted(boolean start)

setStarted.

Parameters:

start - a boolean.