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

Class AbstractMitabWriter<T extends Interaction,B extends BinaryInteraction,P extends Participant>

java.lang.Object

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

All Implemented Interfaces:

InteractionWriter<T>

Direct Known Subclasses:

LightMitab25Writer, Mitab25EvidenceWriter, Mitab25EvidenceWriter, Mitab25ModelledWriter, Mitab25ModelledWriter, Mitab25Writer, Mitab25Writer

public abstract class AbstractMitabWriter<T extends Interaction,B extends BinaryInteraction,P extends Participant>
extends Object
implements InteractionWriter<T>

Abstract writer for Mitab 2.5. The general options when calling method initialiseContext(java.util.Map<java.lang.String, java.lang.Object>) are : - output_file_key : File. Specifies the file where to write - output_stream_key : OutputStream. Specifies the stream where to write - output_writer_key : Writer. Specifies the writer. If these three options are given, output_file_key will take priority, then output_stream_key an finally output_writer_key. At leats one of these options should be provided when initialising the context of the writer - complex_expansion_key : ComplexExpansionMethod. Specifies the ComplexExpansion object to use. By default, it is SpokeExpansion if nothing is specified - mitab_header_key : Boolean. Specifies if the writer should write the MITAB header when starting to write or not

Since:

11/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractMitabWriter()	Constructor for AbstractMitabWriter.
AbstractMitabWriter(File file)	Constructor for AbstractMitabWriter.
AbstractMitabWriter(File file, ComplexExpansionMethod<T,B> expansionMethod)	Constructor for AbstractMitabWriter.
AbstractMitabWriter(OutputStream output)	Constructor for AbstractMitabWriter.
AbstractMitabWriter(OutputStream output, ComplexExpansionMethod<T,B> expansionMethod)	Constructor for AbstractMitabWriter.
AbstractMitabWriter(Writer writer)	Constructor for AbstractMitabWriter.
AbstractMitabWriter(Writer writer, ComplexExpansionMethod<T,B> expansionMethod)	Constructor for AbstractMitabWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
void	end()	end.
void	flush()	flush.
protected AbstractMitab25BinaryWriter<B,P>	getBinaryWriter()	Getter for the field binaryWriter.
protected ComplexExpansionMethod<T,B>	getExpansionMethod()	Getter for the field expansionMethod.
abstract MitabVersion	getVersion()	getVersion.
protected boolean	hasStarted()	hasStarted.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected abstract void	initialiseExpansionMethod(ComplexExpansionMethod<T,B> expansionMethod)	initialiseExpansionMethod.
protected abstract void	initialiseFile(File file)	initialiseFile.
protected abstract void	initialiseOutputStream(OutputStream output)	initialiseOutputStream.
protected abstract void	initialiseWriter(Writer writer)	initialiseWriter.
boolean	isWriteHeader()	isWriteHeader.
void	reset()	reset.
protected void	setBinaryWriter(AbstractMitab25BinaryWriter<B,P> binaryWriter)	Setter for the field binaryWriter.
protected void	setExpansionMethod(ComplexExpansionMethod<T,B> expansionMethod)	Setter for the field expansionMethod.
protected void	setStarted(boolean hasStarted)	setStarted.
void	setWriteHeader(boolean writeHeader)	setWriteHeader.
void	start()	start.
void	write(Collection<? extends T> interactions)	write.
void	write(Iterator<? extends T> interactions)	Writes Interaction objects using iterator
void	write(T interaction)	write.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractMitabWriter

public AbstractMitabWriter()

Constructor for AbstractMitabWriter.

AbstractMitabWriter

public AbstractMitabWriter(File file)
                    throws IOException

Constructor for AbstractMitabWriter.

Parameters:

file - a File object.

Throws:

IOException - if any.

AbstractMitabWriter

public AbstractMitabWriter(OutputStream output)

Constructor for AbstractMitabWriter.

Parameters:

output - a OutputStream object.

AbstractMitabWriter

public AbstractMitabWriter(Writer writer)

Constructor for AbstractMitabWriter.

Parameters:

writer - a Writer object.

AbstractMitabWriter

public AbstractMitabWriter(File file,
                           ComplexExpansionMethod<T,B> expansionMethod)
                    throws IOException

Constructor for AbstractMitabWriter.

Parameters:

file - a File object.

expansionMethod - a ComplexExpansionMethod object.

Throws:

IOException - if any.

AbstractMitabWriter

public AbstractMitabWriter(OutputStream output,
                           ComplexExpansionMethod<T,B> expansionMethod)

Constructor for AbstractMitabWriter.

Parameters:

output - a OutputStream object.

expansionMethod - a ComplexExpansionMethod object.

AbstractMitabWriter

public AbstractMitabWriter(Writer writer,
                           ComplexExpansionMethod<T,B> expansionMethod)

Constructor for AbstractMitabWriter.

Parameters:

writer - a Writer 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<T extends Interaction>

Parameters:

options - : the options given by the user

end

public void end()
         throws MIIOException

end.

Specified by:

end in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if any.

start

public void start()
           throws MIIOException

start.

Specified by:

start in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if any.

write

public void write(T interaction)
           throws MIIOException

write.

Specified by:

write in interface InteractionWriter<T extends Interaction>

Parameters:

interaction - a T object.

Throws:

MIIOException - if any.

write

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

write.

Specified by:

write in interface InteractionWriter<T extends Interaction>

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 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<T extends Interaction>

Throws:

MIIOException - if any.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if any.

getVersion

public abstract MitabVersion getVersion()

getVersion.

Returns:

a MitabVersion object.

isWriteHeader

public boolean isWriteHeader()

isWriteHeader.

Returns:

a boolean.

setWriteHeader

public void setWriteHeader(boolean writeHeader)

setWriteHeader.

Parameters:

writeHeader - a boolean.

initialiseExpansionMethod

protected abstract void initialiseExpansionMethod(ComplexExpansionMethod<T,B> expansionMethod)

initialiseExpansionMethod.

Parameters:

expansionMethod - a ComplexExpansionMethod object.

initialiseWriter

protected abstract void initialiseWriter(Writer writer)

initialiseWriter.

Parameters:

writer - a Writer object.

initialiseOutputStream

protected abstract void initialiseOutputStream(OutputStream output)

initialiseOutputStream.

Parameters:

output - a OutputStream object.

initialiseFile

protected abstract void initialiseFile(File file)
                                throws IOException

initialiseFile.

Parameters:

file - a File object.

Throws:

IOException - if any.

setExpansionMethod

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

Setter for the field expansionMethod.

Parameters:

expansionMethod - a ComplexExpansionMethod object.

setBinaryWriter

protected void setBinaryWriter(AbstractMitab25BinaryWriter<B,P> binaryWriter)

Setter for the field binaryWriter.

Parameters:

binaryWriter - a AbstractMitab25BinaryWriter object.

getBinaryWriter

protected AbstractMitab25BinaryWriter<B,P> getBinaryWriter()

Getter for the field binaryWriter.

Returns:

a AbstractMitab25BinaryWriter object.

getExpansionMethod

protected ComplexExpansionMethod<T,B> getExpansionMethod()

Getter for the field expansionMethod.

Returns:

a ComplexExpansionMethod object.

hasStarted

protected boolean hasStarted()

hasStarted.

Returns:

a boolean.

setStarted

protected void setStarted(boolean hasStarted)

setStarted.

Parameters:

hasStarted - a boolean.