@Override public boolean readAttribute(String attributeName, String prefix, String value) { boolean isAttributeRead = super.readAttribute(attributeName, prefix, value); if (!isAttributeRead) { isAttributeRead = true; if (attributeName.equals("stoichiometry")) { setStoichiometry(StringTools.parseSBMLDouble(value)); } else if (attributeName.equals("constant")) { setConstant(StringTools.parseSBMLBoolean(value)); } else if (attributeName.equals("denominator")) { setDenominator(StringTools.parseSBMLInt(value)); } else { isAttributeRead = false; } } return isAttributeRead; }
/** * Creates a SpeciesReference instance from a given SpeciesReference. * * @param speciesReference */ @SuppressWarnings("deprecation") public SpeciesReference(SpeciesReference speciesReference) { super(speciesReference); if (speciesReference.isSetStoichiometryMath()) { setStoichiometryMath(speciesReference.getStoichiometryMath() .clone()); } if (speciesReference.isSetStoichiometry()) { setStoichiometry(new Double(speciesReference.getStoichiometry())); } else { stoichiometry = speciesReference.stoichiometry == null ? null : new Double(speciesReference.stoichiometry); } if (speciesReference.isSetConstant()) { setConstant(new Boolean(speciesReference.isConstant())); } else { constant = speciesReference.constant == null ? null : new Boolean(speciesReference.constant); } if (speciesReference.isSetDenominator) { setDenominator(new Integer(speciesReference.getDenominator())); } else { denominator = speciesReference.denominator == null ? null : new Integer(speciesReference.denominator); } }
/** * This builds multiple reaction participants in one step and adds them to * the given list of {@link SpeciesReference}s. * * @param listOf * where to add new {@link SpeciesReference} * @param participants * the definition of stoichiometry and {@link Species} for which a * reaction participant is to be created. */ private static void buildParticipants(ListOf<SpeciesReference> listOf, Pair<Double, Species>... participants) { for (Pair<Double, Species> participant : participants) { SpeciesReference sr = new SpeciesReference(listOf.getLevel(), listOf.getVersion()); if (participant.isSetKey()) { sr.setStoichiometry(participant.getKey().doubleValue()); } if (participant.isSetValue()) { sr.setSpecies(participant.getValue()); } if (listOf.getLevel() > 2) { sr.setConstant(true); } listOf.add(sr); } }