libSBML C++ API  5.18.0
printUnits.cpp

A command-line program that prints information about the units of measurement used in a given SBML file.

/**
* @file printUnits.cpp
* @brief Prints some unit information about the model
* @author Sarah Keating
* @author Michael Hucka
*
* <!--------------------------------------------------------------------------
* This sample program is distributed under a different license than the rest
* of libSBML. This program uses the open-source MIT license, as follows:
*
* Copyright (c) 2013-2018 by the California Institute of Technology
* (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
* and the University of Heidelberg (Germany), with support from the National
* Institutes of Health (USA) under grant R01GM070923. All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the "Software"),
* to deal in the Software without restriction, including without limitation
* the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
* THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS IN THE SOFTWARE.
*
* Neither the name of the California Institute of Technology (Caltech), nor
* of the European Bioinformatics Institute (EMBL-EBI), nor of the University
* of Heidelberg, nor the names of any contributors, may be used to endorse
* or promote products derived from this software without specific prior
* written permission.
* ------------------------------------------------------------------------ -->
*/
#include <iostream>
#include <sbml/SBMLTypes.h>
#include <sbml/units/UnitFormulaFormatter.h>
#include <sbml/units/FormulaUnitsData.h>
using namespace std;
int
main (int argc, char *argv[])
{
if (argc != 2)
{
cout << endl << "Usage: printUnits filename" << endl << endl;
return 1;
}
const char* filename = argv[1];
SBMLDocument* document = readSBML(filename);
if (document->getNumErrors() > 0)
{
cerr << "Encountered the following SBML errors:" << endl;
document->printErrors(cerr);
return 1;
}
Model* model = document->getModel();
if (model == 0)
{
cout << "No model present." << endl;
return 1;
}
unsigned int i,j;
for (i = 0; i < model->getNumSpecies(); i++)
{
Species* s = model->getSpecies(i);
cout << "Species " << i << ": "
}
for (i = 0; i < model->getNumCompartments(); i++)
{
Compartment *c = model->getCompartment(i);
cout << "Compartment " << i << ": "
<< endl;
}
for (i = 0; i < model->getNumParameters(); i++)
{
Parameter *p = model->getParameter(i);
cout << "Parameter " << i << ": "
<< endl;
}
for (i = 0; i < model->getNumInitialAssignments(); i++)
{
cout << "InitialAssignment " << i << ": "
cout << " undeclared units: ";
cout << (ia->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
for (i = 0; i < model->getNumEvents(); i++)
{
Event *e = model->getEvent(i);
cout << "Event " << i << ": " << endl;
if (e->isSetDelay())
{
cout << "Delay: "
cout << " undeclared units: ";
cout << (e->getDelay()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
for (j = 0; j < e->getNumEventAssignments(); j++)
{
cout << "EventAssignment " << j << ": "
cout << " undeclared units: ";
cout << (ea->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
}
for (i = 0; i < model->getNumReactions(); i++)
{
Reaction *r = model->getReaction(i);
cout << "Reaction " << i << ": " << endl;
if (r->isSetKineticLaw())
{
cout << "Kinetic Law: "
cout << " undeclared units: ";
cout << (r->getKineticLaw()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
for (j = 0; j < r->getNumReactants(); j++)
{
{
cout << "Reactant stoichiometryMath" << j << ": "
cout << " undeclared units: ";
cout << (sr->getStoichiometryMath()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
{
cout << "Product stoichiometryMath" << j << ": "
cout << " undeclared units: ";
cout << (sr->getStoichiometryMath()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
}
}
for (i = 0; i < model->getNumRules(); i++)
{
Rule *r = model->getRule(i);
cout << "Rule " << i << ": "
cout << " undeclared units: ";
cout << (r->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
delete document;
return 0;
}