/** * Returns the number of {@link Reaction}s of this {@link Model}. * * @return the number of {@link Reaction}s of this {@link Model}. * @libsbml.deprecated use {@link #getReactionCount()} */ public int getNumReactions() { return getReactionCount(); }
/** * Returns the number of {@link NamedSBaseWithDerivedUnit}s in the {@link Model}, so elements * that can have a name and a derived unit in SBML L3V1 or below. * * @return the number of {@link NamedSBaseWithDerivedUnit}s in the {@link Model}. */ public int getNamedSBaseWithDerivedUnitCount() { return getQuantityCount() + getFunctionDefinitionCount() + getReactionCount(); }
/** * Initializes the Converter */ private void init() { svariables = new ArrayList<SBase>(); reactants = new HashSet<String>(); for (int i = 0; i < model.getReactionCount(); i++) { if (model.getReaction(i).isSetListOfProducts()) { for (SpeciesReference sref : model.getReaction(i).getListOfProducts()) { reactants.add(sref.getSpecies()); } } if (model.getReaction(i).isSetListOfReactants()) { for (SpeciesReference sref : model.getReaction(i).getListOfReactants()) { reactants.add(sref.getSpecies()); } } } // Build the graph the matching and try to improve the matching buildGraph(); buildMatching(); augmentMatching(); }
UnitDefinition firstUD = null; if (m.getReactionCount() > 0) { for (Reaction r : m.getListOfReactions()) { if (r.isSetKineticLaw()) {
for (i = 0; i < model.getReactionCount(); i++) { Reaction r = model.getReaction(i);
for (int i = 0; i < model.getReactionCount(); i++) { Reaction reaction = model.getReaction(i); if (reaction.isSetCompartment()