/** * Creates a new {@link Reaction} inside this {@link Model} and returns it. * * @param id * the id of the new element to create * @return the {@link Reaction} object created */ public Reaction createReaction(String id) { Reaction reaction = new Reaction(id, getLevel(), getVersion()); addReaction(reaction); return reaction; }
/** * Creates a new {@link IntraSpeciesReaction} inside this {@link MultiModelPlugin} and returns it. * * @param id * the id of the new element to create * @return the {@link IntraSpeciesReaction} object created */ public IntraSpeciesReaction createIntraSpeciesReaction(String id) { IntraSpeciesReaction reaction = new IntraSpeciesReaction(); reaction.setId(id); getModel().addReaction(reaction); return reaction; // TODO - put the IntraSpeciesReaction into a separate ListOf, either on the ModelPlugin or a new ListOf plugin ? }
private void addSBaseToModel(Model model, SBase sBase) { if (model != null && sBase != null) { sBase.removeFromParent(); if (sBase.getClass() == Reaction.class) { model.addReaction((Reaction) sBase); } else if (sBase.getClass() == Compartment.class) { model.addCompartment((Compartment) sBase); } else if (sBase.getClass() == Constraint.class) { model.addConstraint((Constraint) sBase); } else if (sBase.getClass() == Event.class) { model.addEvent((Event) sBase); } else if (sBase.getClass() == FunctionDefinition.class) { model.addFunctionDefinition((FunctionDefinition) sBase); } else if (sBase.getClass() == Parameter.class) { model.addParameter((Parameter) sBase); } else if (sBase.getClass() == Rule.class) { model.addRule((Rule) sBase); } else if (sBase.getClass() == Species.class) { model.addSpecies((Species) sBase); } else if (sBase.getClass() == UnitDefinition.class) { model.addUnitDefinition((UnitDefinition) sBase); } } }
ListOf.Type.listOfReactions)) { Reaction reaction = (Reaction) newContextObject; model.addReaction(reaction); reaction.initDefaults();
Reaction relatedReaction = model.getReaction(reactsIds[i]); subModel.addReaction(relatedReaction.clone());
targetModel.addReaction(reaction.clone());