/** * Build a new Interaction with no participants but holding a copy of all other attributes of the given interaction. * <br/> WARNING: all attributes of the newly created interaction are the same as the source's (that is same object * instance). This is not an object clone. * * @param source the source interaction. * @return a target interaction which is a copy of the source interaction but the participants or * inferredInteractions. */ protected Interaction copyInteraction(Interaction source) { Interaction target = new Interaction(); // clone inner attributes target.setId(source.getId()); target.setImexId(source.getImexId()); // objects target.setNames(source.getNames()); target.setXref(source.getXref()); // collections target.getConfidences().addAll(source.getConfidences()); target.getExperiments().addAll(source.getExperiments()); target.getInteractionTypes().addAll(source.getInteractionTypes()); // added with mitab 27 target.setModelled(source.isModelled()); target.setIntraMolecular(source.isIntraMolecular()); target.setNegative(source.isNegative()); target.getParameters().addAll(source.getParameters()); target.getAttributes().addAll(source.getAttributes()); target.setAvailability(source.getAvailability()); return target; }
for (psidev.psi.mi.xml.model.Parameter parameter : interaction.getParameters()) { iParameters.add(new ParameterImpl(parameter.getTerm(), parameter.getFactor(),
interaction.getParameters().add(xmlParameter);
interaction.getParameters().add(parameter);
mInteraction.getParameters().add( parameterConverter.fromJaxb( jParameter ) );
mInteraction.getParameters().add( parameterConverter.fromJaxb( jParameter ) );
for ( Parameter pm : interaction.getParameters() ) { if ( pm.hasExperimentRef() ) { ExperimentRef eref = pm.getExperimentRef();
for ( Parameter mParameter : mInteraction.getParameters() ) { jInteraction.getParameterList().getParameters().add( parameterConverter.toJaxb( mParameter ) );
for ( Parameter mParameter : mInteraction.getParameters() ) { jInteraction.getParameterList().getParameters().add( parameterConverter.toJaxb( mParameter ) );
for (psidev.psi.mi.xml.model.Parameter psiParameter : psiObject.getParameters()){ InteractionParameter parameter = paramConverter.psiToIntact( psiParameter ); interaction.addParameter(parameter);