/** * Returns the id of a PluginSpeciesReference object's belonging species as * an object of type StringBuffer. * * @param ref * @return */ protected static final StringBuffer getSpecies(SpeciesReference ref) { return new StringBuffer(ref.getSpecies()); }
/** * Returns the id of a PluginSpeciesReference object's belonging species as * an object of type StringBuffer. * * @param ref * @return */ protected static final StringBuffer getSpecies(SpeciesReference ref) { return new StringBuffer(ref.getSpecies()); }
private void addCompounds(Reaction r, SpeciesReference sp, ONDEXConcept reaction, RelationType rt) { // process all lists of reactants and products String id = sp.getSpecies(); // this is compound which is consumed or produced by reaction ONDEXConcept fromConcept = concepts.get(id); if (fromConcept == null) { fireEventOccurred(new InconsistencyEvent( "fromConcept is empty for " + id, "[Parser - addSubstrates]")); return; } // create relation and add kinetics ONDEXRelation relation = graph.getFactory().createRelation(fromConcept, reaction, rt, evidence); addKinetics(r, relation, id); }
/** * 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(); }
.append(StringTools.encodeForHTML(reactant.getSpecies())); count++; reactionEqn.append(StringTools.encodeForHTML(product.getSpecies())); count++;
.append(StringTools.encodeForHTML(reactant.getSpecies())); count++; reactionEqn.append(StringTools.encodeForHTML(product.getSpecies())); count++;
for (SpeciesReference sr: r.getListOfProducts()) if (sr.getSpecies().equals(s.getId())) for (SpeciesReference sr: r.getListOfReactants()) if (sr.getSpecies().equals(s.getId()))
logger.warn(MessageFormat.format( bundle.getString("SBMLCoreParser.unknownReferenceError1"), "Species", "speciesID", speciesReference.getSpecies(), speciesReference.getElementName(), SBMLtools.getIdOrName(speciesReference))); bundle.getString("SBMLCoreParser.unknownReferenceError1"), "Species", "speciesID", speciesReference.getSpecies(), speciesReference.getElementName(), SBMLtools.getIdOrName(speciesReference)));