Collection<ProteinImpl> proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByShortLabelLike("%afcs%");
public GeneratedEntry addInteractorWithUniprotId(String uniprotId) { List<ProteinImpl> interactors = intactContext.getDataContext().getDaoFactory() .getProteinDao().getByUniprotId(uniprotId); if (interactors.isEmpty()) { throw new IntactException("No interactors found with uniprot id: " + uniprotId); } for (Interactor interactor : interactors) { addInteractor(interactor); } return this; }
Protein result = getDaoFactory().getProteinDao().getByAc( ac ); if ( result == null ) {
Protein result = getDaoFactory().getProteinDao().getByAc( ac ); if ( result == null ) {
proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByAcLike(ac, false); } catch (IntactException e) { e.printStackTrace();
Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, identity, proteinId); Collection spliceVariants = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(protein.getAc()); Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, identity, id); proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, id);
Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, identity, proteinId); Collection spliceVariants = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(protein.getAc()); Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, identity, id); proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, id);
Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, identity, proteinId); Collection spliceVariants = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(protein.getAc()); Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, identity, id); proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(uniprot, id);
/** * Get a distinct set of Uniprot ID of the protein eligible to export in Swiss-Prot, * using a paginated query to avoid excessive memory usage. The pagination is done before * the selection of the distinct IDs, so the number of results obtained by this query * will be different than the number of maxResults if several rows for the same AC are * returned. * * @param firstResult First result of the page * @param maxResults Maximum number of results. * * @return a distinct set of Uniprot ID of the protein eligible to export in Swiss-Prot. */ public final Set<String> getEligibleProteins(int firstResult, int maxResults) throws SQLException, IntactException, DatabaseContentException { List<ProteinImpl> proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getProteinDao().getUniprotProteinsInvolvedInInteractions(firstResult, maxResults); return getEligibleProteins(proteins); }
getOut().println("ERROR: The splice variant having the AC(" + protein.getAc() + ") doesn't have it's master AC."); } else { master = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByAc(masterAc);
Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(proteinId); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().persist( (ProteinImpl)protein ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().update( (ProteinImpl)protein );
Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(proteinId); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().persist( (ProteinImpl)protein ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().update( (ProteinImpl)protein );
Collection proteins = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByXrefLike(proteinId); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().persist( (ProteinImpl)protein ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().update( (ProteinImpl)protein );