public GeneratedEntry addInteractionWithAc(String ac) { Interaction interaction = intactContext.getDataContext().getDaoFactory() .getInteractionDao().getByAc(ac); checkResult(interaction, ac, "interaction"); return addInteraction(interaction); }
public GeneratedEntry addInteractionWithAc(String ac) { Interaction interaction = intactContext.getDataContext().getDaoFactory() .getInteractionDao().getByAc(ac); checkResult(interaction, ac, "interaction"); return addInteraction(interaction); }
InteractionDao interactionDao = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao(); List<InteractionImpl> interactionsInIntact = interactionDao.getByAc(intactAcs); List<InteractionImpl> interactionsInIntactPassingExport = new ArrayList(interactionsInIntact);
/** * Filter the binary interactions of a given list of interactions and return a list composed with only binary interactions * @param interactionAcs : the list of interaction accessions * @param eligibleInteractions : the list of eligible interactions for uniprot export */ private void filterTrueBinaryInteractions(List<String> interactionAcs, List<String> eligibleInteractions) { // process each interaction of the list final int interactionCount = interactionAcs.size(); for (int i = 0; i < interactionCount; i++) { TransactionStatus status = IntactContext.getCurrentInstance().getDataContext().beginTransaction(); // get the IntAct interaction object String interactionAc = interactionAcs.get(i); Interaction interaction = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao().getByAc(interactionAc); // the interaction exists in IntAct if (interaction != null){ logger.info("\t\t Interaction: Shortlabel:" + interaction.getShortLabel() + " AC: " + interaction.getAc()); if (InteractionUtils.isBinaryInteraction(interaction)){ eligibleInteractions.add(interactionAc); } } IntactContext.getCurrentInstance().getDataContext().commitTransaction(status); } // i }
experiments = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao().getByAc(interaction.getAc()).getExperiments(); interaction.setExperiments(experiments); } else {
experiments = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao().getByAc(interaction.getAc()).getExperiments(); interaction.setExperiments(experiments); } else {
Interaction intactInteraction = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao().getByAc(interactionAc);
Interaction intactInteraction = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao().getByAc(interactionAc);
Interaction intactInteraction = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao().getByAc(interaction);