Package psidev.psi.mi.jami.html

Class AbstractMIHtmlWriter<T extends Interaction,P extends Participant,F extends Feature>

java.lang.Object

psidev.psi.mi.jami.html.AbstractMIHtmlWriter<T,P,F>

All Implemented Interfaces:

InteractionWriter<T>

Direct Known Subclasses:

LightMIHtmlWriter, MIEvidenceHtmlWriter, MIHtmlWriter, MIModelledHtmlWriter

public abstract class AbstractMIHtmlWriter<T extends Interaction,P extends Participant,F extends Feature>
extends Object
implements InteractionWriter<T>

Abstract class for MI HTML writer

Since:

06/12/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractMIHtmlWriter(File file, AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.
AbstractMIHtmlWriter(OutputStream output, AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.
AbstractMIHtmlWriter(Writer writer, AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.
AbstractMIHtmlWriter(AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)	Constructor for AbstractMIHtmlWriter.

Method Summary

Modifier and Type	Method	Description
void	close()	close
void	end()	end
void	flush()	flush
protected Set<ModelledInteraction>	getComplexesToWrite()	Getter for the field complexesToWrite.
protected AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature>	getComplexWriter()	Getter for the field complexWriter.
protected Set<Object>	getProcessedObjects()	Getter for the field processedObjects.
protected Writer	getWriter()	Getter for the field writer.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
void	reset()	reset
void	setWriteHeader(boolean writeHeader)	Setter for the field writeHeader.
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
protected abstract void	writeConfidences(P participant)	writeConfidences
protected abstract void	writeConfidences(T interaction)	writeConfidences
protected abstract void	writeCooperativeEffects(T interaction)	writeCooperativeEffects
protected void	writeCvTerm(String label, CvTerm term)	writeCvTerm
protected abstract void	writeDetectionMethods(F feature)	writeDetectionMethods
protected void	writeEndDocument()	writeEndDocument
protected abstract void	writeExperiment(T interaction)	writeExperiment
protected abstract void	writeExperimentalPreparations(P participant)	writeExperimentalPreparations
protected abstract void	writeExperimentalRole(P participant)	writeExperimentalRole
protected abstract void	writeExpressedInOrganism(P participant)	writeExpressedInOrganism
protected void	writeFeature(F feature)	writeFeature
protected abstract void	writeGeneralProperties(T interaction)	writeGeneralProperties
protected void	writeHeader()	writeHeader
protected void	writeHtmlStyle()	writeHtmlStyle
protected void	writeInteractionAnchor(Interaction interaction)	writeInteractionAnchor
protected void	writeInteractionList()	writeInteractionList
protected void	writeInteractor(Interactor interactor)	writeInteractor
protected void	writeModelledInteraction(ModelledInteraction c)	writeModelledInteraction
protected void	writeOrganism(String label, Organism organism)	writeOrganism
protected abstract void	writeParameters(P participant)	writeParameters
protected abstract void	writeParameters(T interaction)	writeParameters
protected void	writeParticipant(P participant)	writeParticipant
protected abstract void	writeParticipantIdentificationMethods(P participant)	writeParticipantIdentificationMethods
protected void	writeProperty(String property, String value)	writeProperty
protected void	writePropertyWithQualifier(String property, String value, String qualifier)	writePropertyWithQualifier
protected void	writerEndBody()	writerEndBody
protected void	writerStartBody()	writerStartBody
protected void	writeStartDocument()	writeStartDocument
protected void	writeSubTitle(String subTitle)	writeSubTitle
protected void	writeTag(String property)	writeTag

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractMIHtmlWriter

public AbstractMIHtmlWriter(AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)

Constructor for AbstractMIHtmlWriter.

Parameters:

complexWriter - a AbstractMIHtmlWriter object.

AbstractMIHtmlWriter

public AbstractMIHtmlWriter(File file,
                            AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)
                     throws IOException

Constructor for AbstractMIHtmlWriter.

Parameters:

file - a File object.

complexWriter - a AbstractMIHtmlWriter object.

Throws:

IOException - if any.

AbstractMIHtmlWriter

public AbstractMIHtmlWriter(OutputStream output,
                            AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)

Constructor for AbstractMIHtmlWriter.

Parameters:

output - a OutputStream object.

complexWriter - a AbstractMIHtmlWriter object.

AbstractMIHtmlWriter

public AbstractMIHtmlWriter(Writer writer,
                            AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> complexWriter)

Constructor for AbstractMIHtmlWriter.

Parameters:

writer - a Writer object.

complexWriter - a AbstractMIHtmlWriter object.

Method Detail

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

start

public void start()
           throws MIIOException

start

Specified by:

start in interface InteractionWriter<T extends Interaction>

Throws:

MIIOException - if any.

end

public void end()
         throws MIIOException

end

Specified by:

end in interface InteractionWriter<T extends Interaction>

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<T extends Interaction>

Parameters:

options - : the options given by the user

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.

setWriteHeader

public void setWriteHeader(boolean writeHeader)

Setter for the field writeHeader.

Parameters:

writeHeader - a boolean.

writeCooperativeEffects

protected abstract void writeCooperativeEffects(T interaction)
                                         throws IOException

writeCooperativeEffects

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeConfidences

protected abstract void writeConfidences(T interaction)
                                  throws IOException

writeConfidences

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeParameters

protected abstract void writeParameters(T interaction)
                                 throws IOException

writeParameters

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeFeature

protected void writeFeature(F feature)
                     throws IOException

writeFeature

Parameters:

feature - a F object.

Throws:

IOException - if any.

writeDetectionMethods

protected abstract void writeDetectionMethods(F feature)
                                       throws IOException

writeDetectionMethods

Parameters:

feature - a F object.

Throws:

IOException - if any.

writeCvTerm

protected void writeCvTerm(String label,
                           CvTerm term)
                    throws IOException

writeCvTerm

Parameters:

label - a String object.

term - a CvTerm object.

Throws:

IOException - if any.

writeOrganism

protected void writeOrganism(String label,
                             Organism organism)
                      throws IOException

writeOrganism

Parameters:

label - a String object.

organism - a Organism object.

Throws:

IOException - if any.

writeInteractor

protected void writeInteractor(Interactor interactor)
                        throws IOException

writeInteractor

Parameters:

interactor - a Interactor object.

Throws:

IOException - if any.

writeGeneralProperties

protected abstract void writeGeneralProperties(T interaction)
                                        throws IOException

writeGeneralProperties

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeExperiment

protected abstract void writeExperiment(T interaction)
                                 throws IOException

writeExperiment

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeParticipant

protected void writeParticipant(P participant)
                         throws IOException

writeParticipant

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeConfidences

protected abstract void writeConfidences(P participant)
                                  throws IOException

writeConfidences

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParameters

protected abstract void writeParameters(P participant)
                                 throws IOException

writeParameters

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExperimentalPreparations

protected abstract void writeExperimentalPreparations(P participant)
                                               throws IOException

writeExperimentalPreparations

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExpressedInOrganism

protected abstract void writeExpressedInOrganism(P participant)
                                          throws IOException

writeExpressedInOrganism

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExperimentalRole

protected abstract void writeExperimentalRole(P participant)
                                       throws IOException

writeExperimentalRole

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParticipantIdentificationMethods

protected abstract void writeParticipantIdentificationMethods(P participant)
                                                       throws IOException

writeParticipantIdentificationMethods

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeSubTitle

protected void writeSubTitle(String subTitle)
                      throws IOException

writeSubTitle

Parameters:

subTitle - a String object.

Throws:

IOException - if any.

writeTag

protected void writeTag(String property)
                 throws IOException

writeTag

Parameters:

property - a String object.

Throws:

IOException - if any.

writeProperty

protected void writeProperty(String property,
                             String value)
                      throws IOException

writeProperty

Parameters:

property - a String object.

value - a String object.

Throws:

IOException - if any.

writePropertyWithQualifier

protected void writePropertyWithQualifier(String property,
                                          String value,
                                          String qualifier)
                                   throws IOException

writePropertyWithQualifier

Parameters:

property - a String object.

value - a String object.

qualifier - a String object.

Throws:

IOException - if any.

writeInteractionAnchor

protected void writeInteractionAnchor(Interaction interaction)
                               throws IOException

writeInteractionAnchor

Parameters:

interaction - a Interaction object.

Throws:

IOException - if any.

writeInteractionList

protected void writeInteractionList()
                             throws IOException

writeInteractionList

Throws:

IOException - if any.

writerStartBody

protected void writerStartBody()
                        throws IOException

writerStartBody

Throws:

IOException - if any.

writerEndBody

protected void writerEndBody()
                      throws IOException

writerEndBody

Throws:

IOException - if any.

writeStartDocument

protected void writeStartDocument()
                           throws IOException

writeStartDocument

Throws:

IOException - if any.

writeEndDocument

protected void writeEndDocument()
                         throws IOException

writeEndDocument

Throws:

IOException - if any.

writeHeader

protected void writeHeader()
                    throws IOException

writeHeader

Throws:

IOException - if any.

writeHtmlStyle

protected void writeHtmlStyle()
                       throws IOException

writeHtmlStyle

Throws:

IOException - if any.

getWriter

protected Writer getWriter()

Getter for the field writer.

Returns:

a Writer object.

getProcessedObjects

protected Set<Object> getProcessedObjects()

Getter for the field processedObjects.

Returns:

a Set object.

getComplexesToWrite

protected Set<ModelledInteraction> getComplexesToWrite()

Getter for the field complexesToWrite.

Returns:

a Set object.

getComplexWriter

protected AbstractMIHtmlWriter<ModelledInteraction,ModelledParticipant,ModelledFeature> getComplexWriter()

Getter for the field complexWriter.

Returns:

a AbstractMIHtmlWriter object.

writeModelledInteraction

protected void writeModelledInteraction(ModelledInteraction c)

writeModelledInteraction

Parameters:

c - a ModelledInteraction object.