private org.opencb.bionetdb.core.models.Complex createComplex(BioPAXElement bioPAXElement) { org.opencb.bionetdb.core.models.Complex complex = new org.opencb.bionetdb.core.models.Complex(); Complex complexBP = (Complex) bioPAXElement; // Common properties setPhysicalEntityCommonProperties(complexBP, complex); // Complex properties // Components Set<PhysicalEntity> components = complexBP.getComponent(); for (PhysicalEntity component : components) { complex.getComponents().add(component.getRDFId().split("#")[1]); } // Stoichiometry List<Map<String, Object>> stoichiometry = new ArrayList<>(); Set<Stoichiometry> stoichiometryItems = complexBP.getComponentStoichiometry(); for (Stoichiometry stoichiometryItem : stoichiometryItems) { Map<String, Object> stchmtr = new HashMap<>(); stchmtr.put("component", stoichiometryItem.getPhysicalEntity().toString().split("#")[1]); stchmtr.put("coefficient", stoichiometryItem.getStoichiometricCoefficient()); stoichiometry.add(stchmtr); } complex.setStoichiometry(stoichiometry); return complex; }
private Set<PhysicalEntity> getPEsRecursively(Set<PhysicalEntity> pes, Fetcher fetcher) { Model m = BioPAXLevel.L3.getDefaultFactory().createModel(); for(PhysicalEntity pe : pes) { if(pe instanceof Complex) fetcher.fetch(pe,m); else if(!m.containsID(pe.getRDFId())) m.add(pe); } return m.getObjects(PhysicalEntity.class); }
private org.opencb.bionetdb.core.models.Catalysis createCatalysis(BioPAXElement bioPAXElement) { org.opencb.bionetdb.core.models.Catalysis catalysis = new org.opencb.bionetdb.core.models.Catalysis(); Catalysis catalysisBP = (Catalysis) bioPAXElement; // Common Interaction properties setInteractionCommonProperties(catalysisBP, catalysis); // Catalysis properties // controllers Set<Controller> controllers = catalysisBP.getController(); for (Controller controller: controllers) { catalysis.getControllers().add(controller.getRDFId().split("#")[1]); } // controlled Set<Process> controlledProcesses = catalysisBP.getControlled(); for (Process controlledProcess: controlledProcesses) { catalysis.getControlledProcesses().add(controlledProcess.getRDFId().split("#")[1]); } // controlType catalysis.setControlType(catalysisBP.getControlType().toString()); // cofactor Set<PhysicalEntity> cofactors = catalysisBP.getCofactor(); for (PhysicalEntity cofactor: cofactors) { catalysis.getCofactors().add(cofactor.getRDFId().split("#")[1]); } return catalysis; }
} else log.debug("Non complex PE member for complex (" + member.getRDFId() + "->" + complex .getRDFId() + "). Skipping");
reaction.getProducts().add(product.getRDFId().split("#")[1]); Set<PhysicalEntity> lefts = conversionBP.getLeft(); for (PhysicalEntity left : lefts) { leftItems.add(left.getRDFId().split("#")[1]); Set<PhysicalEntity> rights = conversionBP.getRight(); for (PhysicalEntity right : rights) { rightItems.add(right.getRDFId().split("#")[1]);