Package psidev.psi.mi.jami.html

Class MIHtmlWriter

java.lang.Object

psidev.psi.mi.jami.html.AbstractMIHtmlWriter<Interaction,Participant,Feature>

psidev.psi.mi.jami.html.MIHtmlWriter

All Implemented Interfaces:

InteractionWriter<Interaction>

public class MIHtmlWriter
extends AbstractMIHtmlWriter<Interaction,Participant,Feature>

MI writer for a mix of interactions

Since:

09/12/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	close()	close
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
void	reset()	reset
void	write(Collection<? extends Interaction> interactions)	write
void	write(Iterator<? extends Interaction> interactions)	Writes Interaction objects using iterator
void	write(Interaction interaction)	write
protected void	writeConfidences(Interaction interaction)	writeConfidences
protected void	writeConfidences(Participant participant)	writeConfidences
protected void	writeCooperativeEffects(Interaction interaction)	writeCooperativeEffects
protected void	writeDetectionMethods(Feature feature)	writeDetectionMethods
protected void	writeExperiment(Interaction interaction)	writeExperiment
protected void	writeExperimentalPreparations(Participant participant)	writeExperimentalPreparations
protected void	writeExperimentalRole(Participant participant)	writeExperimentalRole
protected void	writeExpressedInOrganism(Participant participant)	writeExpressedInOrganism
protected void	writeGeneralProperties(Interaction interaction)	writeGeneralProperties
protected void	writeParameters(Interaction interaction)	writeParameters
protected void	writeParameters(Participant participant)	writeParameters
protected void	writeParticipantIdentificationMethods(Participant participant)	writeParticipantIdentificationMethods

Methods inherited from class psidev.psi.mi.jami.html.AbstractMIHtmlWriter

end, flush, getComplexesToWrite, getComplexWriter, getProcessedObjects, getWriter, setWriteHeader, start, writeCvTerm, writeEndDocument, writeFeature, writeHeader, writeHtmlStyle, writeInteractionAnchor, writeInteractionList, writeInteractor, writeModelledInteraction, writeOrganism, writeParticipant, writeProperty, writePropertyWithQualifier, writerEndBody, writerStartBody, writeStartDocument, writeSubTitle, writeTag

Methods inherited from class java.lang.Object

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

Constructor Detail

MIHtmlWriter

public MIHtmlWriter()

Constructor for MIHtmlWriter.

MIHtmlWriter

public MIHtmlWriter(File file)
             throws IOException

Constructor for MIHtmlWriter.

Parameters:

file - a File object.

Throws:

IOException - if any.

MIHtmlWriter

public MIHtmlWriter(OutputStream output)

Constructor for MIHtmlWriter.

Parameters:

output - a OutputStream object.

MIHtmlWriter

public MIHtmlWriter(Writer writer)

Constructor for MIHtmlWriter.

Parameters:

writer - a Writer object.

Method Detail

close

public void close()
           throws MIIOException

close

Specified by:

close in interface InteractionWriter<Interaction>

Overrides:

close in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Throws:

MIIOException - if any.

reset

public void reset()
           throws MIIOException

reset

Specified by:

reset in interface InteractionWriter<Interaction>

Overrides:

reset in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Throws:

MIIOException - if any.

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<Interaction>

Overrides:

initialiseContext in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

options - : the options given by the user

write

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

Writes Interaction objects using iterator

Specified by:

write in interface InteractionWriter<Interaction>

Overrides:

write in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interactions - : the iterator of interactions to write

Throws:

MIIOException - : if cannot write

write

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

write

Specified by:

write in interface InteractionWriter<Interaction>

Overrides:

write in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interactions - a Collection object.

Throws:

MIIOException - if any.

write

public void write(Interaction interaction)
           throws MIIOException

write

Specified by:

write in interface InteractionWriter<Interaction>

Overrides:

write in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interaction - a T object.

Throws:

MIIOException - if any.

writeCooperativeEffects

protected void writeCooperativeEffects(Interaction interaction)

writeCooperativeEffects

Specified by:

writeCooperativeEffects in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interaction - a T object.

writeConfidences

protected void writeConfidences(Interaction interaction)
                         throws IOException

writeConfidences

Specified by:

writeConfidences in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeParameters

protected void writeParameters(Interaction interaction)
                        throws IOException

writeParameters

Specified by:

writeParameters in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeDetectionMethods

protected void writeDetectionMethods(Feature feature)
                              throws IOException

writeDetectionMethods

Specified by:

writeDetectionMethods in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

feature - a F object.

Throws:

IOException - if any.

writeGeneralProperties

protected void writeGeneralProperties(Interaction interaction)
                               throws IOException

writeGeneralProperties

Specified by:

writeGeneralProperties in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeExperiment

protected void writeExperiment(Interaction interaction)
                        throws IOException

writeExperiment

Specified by:

writeExperiment in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeConfidences

protected void writeConfidences(Participant participant)
                         throws IOException

writeConfidences

Specified by:

writeConfidences in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParameters

protected void writeParameters(Participant participant)
                        throws IOException

writeParameters

Specified by:

writeParameters in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExperimentalPreparations

protected void writeExperimentalPreparations(Participant participant)
                                      throws IOException

writeExperimentalPreparations

Specified by:

writeExperimentalPreparations in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExpressedInOrganism

protected void writeExpressedInOrganism(Participant participant)
                                 throws IOException

writeExpressedInOrganism

Specified by:

writeExpressedInOrganism in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExperimentalRole

protected void writeExperimentalRole(Participant participant)
                              throws IOException

writeExperimentalRole

Specified by:

writeExperimentalRole in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParticipantIdentificationMethods

protected void writeParticipantIdentificationMethods(Participant participant)
                                              throws IOException

writeParticipantIdentificationMethods

Specified by:

writeParticipantIdentificationMethods in class AbstractMIHtmlWriter<Interaction,Participant,Feature>

Parameters:

participant - a P object.

Throws:

IOException - if any.