Package psidev.psi.mi.jami.html

Class MIEvidenceHtmlWriter

java.lang.Object

psidev.psi.mi.jami.html.AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

psidev.psi.mi.jami.html.MIEvidenceHtmlWriter

All Implemented Interfaces:

InteractionWriter<InteractionEvidence>

public class MIEvidenceHtmlWriter
extends AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

HTML writer for PSI-MI interaction evidences. This writer is based on the JAMI interfaces

Since:

02/04/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	writeConfidences(InteractionEvidence interaction)	writeConfidences
protected void	writeConfidences(ParticipantEvidence participant)	writeConfidences
protected void	writeCooperativeEffects(InteractionEvidence interaction)	writeCooperativeEffects
protected void	writeDetectionMethods(FeatureEvidence feature)	writeDetectionMethods
protected void	writeExperiment(InteractionEvidence interaction)	writeExperiment
protected void	writeExperimentalPreparations(ParticipantEvidence participant)	writeExperimentalPreparations
protected void	writeExperimentalRole(ParticipantEvidence participant)	writeExperimentalRole
protected void	writeExpressedInOrganism(ParticipantEvidence participant)	writeExpressedInOrganism
protected void	writeGeneralProperties(InteractionEvidence interaction)	writeGeneralProperties
protected void	writeParameters(InteractionEvidence interaction)	writeParameters
protected void	writeParameters(ParticipantEvidence participant)	writeParameters
protected void	writeParticipantIdentificationMethods(ParticipantEvidence participant)	writeParticipantIdentificationMethods
protected void	writePublication(Publication publication)	writePublication

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

close, end, flush, getComplexesToWrite, getComplexWriter, getProcessedObjects, getWriter, initialiseContext, reset, setWriteHeader, start, write, write, write, 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

MIEvidenceHtmlWriter

public MIEvidenceHtmlWriter()

Constructor for MIEvidenceHtmlWriter.

MIEvidenceHtmlWriter

public MIEvidenceHtmlWriter(File file)
                     throws IOException

Constructor for MIEvidenceHtmlWriter.

Parameters:

file - a File object.

Throws:

IOException - if any.

MIEvidenceHtmlWriter

public MIEvidenceHtmlWriter(OutputStream output)

Constructor for MIEvidenceHtmlWriter.

Parameters:

output - a OutputStream object.

MIEvidenceHtmlWriter

public MIEvidenceHtmlWriter(Writer writer)

Constructor for MIEvidenceHtmlWriter.

Parameters:

writer - a Writer object.

Method Detail

writeCooperativeEffects

protected void writeCooperativeEffects(InteractionEvidence interaction)

writeCooperativeEffects

Specified by:

writeCooperativeEffects in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

interaction - a T object.

writeConfidences

protected void writeConfidences(InteractionEvidence interaction)
                         throws IOException

writeConfidences

Specified by:

writeConfidences in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeParameters

protected void writeParameters(InteractionEvidence interaction)
                        throws IOException

writeParameters

Specified by:

writeParameters in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeExperiment

protected void writeExperiment(InteractionEvidence interaction)
                        throws IOException

writeExperiment

Specified by:

writeExperiment in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

interaction - a InteractionEvidence object.

Throws:

IOException - if any.

writeConfidences

protected void writeConfidences(ParticipantEvidence participant)
                         throws IOException

writeConfidences

Specified by:

writeConfidences in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParameters

protected void writeParameters(ParticipantEvidence participant)
                        throws IOException

writeParameters

Specified by:

writeParameters in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExperimentalPreparations

protected void writeExperimentalPreparations(ParticipantEvidence participant)
                                      throws IOException

writeExperimentalPreparations

Specified by:

writeExperimentalPreparations in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExpressedInOrganism

protected void writeExpressedInOrganism(ParticipantEvidence participant)
                                 throws IOException

writeExpressedInOrganism

Specified by:

writeExpressedInOrganism in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeExperimentalRole

protected void writeExperimentalRole(ParticipantEvidence participant)
                              throws IOException

writeExperimentalRole

Specified by:

writeExperimentalRole in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeParticipantIdentificationMethods

protected void writeParticipantIdentificationMethods(ParticipantEvidence participant)
                                              throws IOException

writeParticipantIdentificationMethods

Specified by:

writeParticipantIdentificationMethods in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

participant - a P object.

Throws:

IOException - if any.

writeGeneralProperties

protected void writeGeneralProperties(InteractionEvidence interaction)
                               throws IOException

writeGeneralProperties

Specified by:

writeGeneralProperties in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

interaction - a T object.

Throws:

IOException - if any.

writeDetectionMethods

protected void writeDetectionMethods(FeatureEvidence feature)
                              throws IOException

writeDetectionMethods

Specified by:

writeDetectionMethods in class AbstractMIHtmlWriter<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

feature - a F object.

Throws:

IOException - if any.

writePublication

protected void writePublication(Publication publication)
                         throws IOException

writePublication

Parameters:

publication - a Publication object.

Throws:

IOException - if any.