/** * Returns the initialConcentration of this {@link Species}. * * @return the initialConcentration of this {@link Species} if it has been * set, o otherwise. */ public double getInitialConcentration() { if (isSetInitialConcentration()) { return getValue(); } return Double.NaN; }
@Override public boolean check(ValidationContext ctx, Species s) { Compartment c = s.getCompartmentInstance(); if (c != null && c.getSpatialDimensions() == 0 && s.isSetInitialConcentration()) { ValidationConstraint.logError(ctx, CORE_20604, s, s.getId(), s.getCompartment()); return false; } return true; } };
/** * Sets the initialAmount of this {@link Species}. * * @param initialAmount the initial amount */ public void setInitialAmount(double initialAmount) { // store initialConcentration in user define object to allow validation of incorrect SBML files if (isReadingInProgress() && isSetInitialConcentration()) { // TODO - replace by processInvalidAttribute and change the corresponding rule(s) AbstractReaderWriter.processUnknownAttribute("initialConcentration", "", getInitialConcentration() + "", "", this); } if (!amount) { amount = true; firePropertyChange(TreeNodeChangeEvent.initialAmount, Boolean.FALSE, Boolean.TRUE); } setValue(initialAmount); }
if (isSetInitialConcentration() && !isSetInitialAmount()) { attributes.put("initialConcentration", StringTools.toString(en, getInitialConcentration()));
} else if (species.isSetInitialConcentration()) { setInitialConcentration(new Double(species.getInitialConcentration()));
@Override public boolean check(ValidationContext ctx, Species s) { Model m = s.getModel(); if (m != null && !s.isSetInitialAmount() && !s.isSetInitialConcentration()) { boolean setByAssignment = false; if (s.isSetId()) { setByAssignment = m.getInitialAssignmentBySymbol(s.getId()) != null; if (!setByAssignment) { Rule r = m.getRuleByVariable(s.getId()); setByAssignment = r != null && r.isAssignment(); } } if (!setByAssignment) { // TODO - build a nice error message } return setByAssignment; } return true; } };
equals &= s.isSetInitialConcentration() == isSetInitialConcentration();
if (species.isSetInitialConcentration()) { speciesC.createAttribute(initialConcentration, species.getInitialConcentration(), false);
if (species.isSetInitialConcentration()) { speciesC.createAttribute(initialConcentration, species.getInitialConcentration(), false);