log.debug("interaction " + interaction.getId() + "/" + interaction.getImexId() + " was binary or intra molecular, no further processing involved."); interactions.add(interaction); log.debug("interaction " + interaction.getId() + "/" + interaction.getImexId() + " was inter molecular, reset stoichiometry of one of interactors"); interactions.add(interaction); } else {
log.debug("interaction " + interaction.getId() + "/" + interaction.getImexId() + " was binary or intra molecular, no further processing involved."); interactions.add(interaction); log.debug("interaction " + interaction.getId() + "/" + interaction.getImexId() + " was inter molecular, reset stoichiometry of one of interactors"); interactions.add(interaction); } else {
protected void psiStartConversion(Object psiObject) { String id = null; if (psiObject instanceof HasId) { id = String.valueOf(((HasId)psiObject).getId()); } if (psiObject instanceof Interaction) { final Interaction interaction = (Interaction) psiObject; if (interaction.getImexId() != null) { ConverterContext.getInstance().getLocation().newChild(new InteractionLocationItem(id, psiObject.getClass(), interaction.getImexId())); } else { ConverterContext.getInstance().getLocation().newChild(new LocationItem(id, psiObject.getClass())); } } else if (id != null) { ConverterContext.getInstance().getLocation().newChild(new LocationItem(id, psiObject.getClass())); } }
bpInteraction = createComplex(bpParticipants, interaction.getImexId(), interaction.getId()); } else if(isGeneticInteraction) { bpInteraction = createGeneticInteraction(bpParticipants, interactionVocabularies, interaction.getImexId(), interaction.getId() ); } else { bpInteraction = createMolecularInteraction(bpParticipants, interactionVocabularies, interaction.getImexId(), interaction.getId());
/** * 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; }
interaction.getImexId(), interaction.getId(), experimentDescription.getId());
jInteraction.setImexId( mInteraction.getImexId() );
jInteraction.setImexId( mInteraction.getImexId() );
String imexId = psiObject.getImexId(); if (imexId != null && !alreadyContainsImexXref(interaction)) { final InteractorXref imexXref = createImexXref(interaction, imexId);