libSBML C++ API  libSBML 5.17.2 C++ API
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;
}
Reaction::getKineticLaw
const KineticLaw * getKineticLaw() const
Returns the KineticLaw object contained in this Reaction.
Definition: Reaction.cpp:391
SpeciesReference
A reference to an SBML species in a reaction.
Definition: SpeciesReference.h:271
Model::getNumInitialAssignments
unsigned int getNumInitialAssignments() const
Get the number of InitialAssignment objects in this Model.
Definition: Model.cpp:3266
Model::getNumParameters
unsigned int getNumParameters() const
Get the number of Parameter objects in this Model.
Definition: Model.cpp:3256
Parameter
An SBML parameter: a named symbol with a value.
Definition: Parameter.h:192
Event::getEventAssignment
const EventAssignment * getEventAssignment(unsigned int n) const
Return a specific EventAssignment object of this Event.
Definition: Event.cpp:1051
StoichiometryMath::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition object that expresses the units returned by the math expressi...
Definition: StoichiometryMath.cpp:476
Model::getParameter
const Parameter * getParameter(unsigned int n) const
Get the nth Parameter object in this Model.
Definition: Model.cpp:2710
Reaction
An SBML reaction between species in an SBML model.
Definition: Reaction.h:214
Model::getSpecies
const Species * getSpecies(unsigned int n) const
Get the nth Species object in this Model.
Definition: Model.cpp:2668
UnitDefinition::printUnits
static std::string printUnits(const UnitDefinition *ud, bool compact=false)
Expresses the given definition in a plain-text form.
Definition: UnitDefinition.cpp:1536
SBMLTypes.h
Include all SBML types in a single header file.
Rule::containsUndeclaredUnits
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this Rule contains parameters/numbers with undecla...
Event::getDelay
const Delay * getDelay() const
Get the assignment delay portion of this Event, if there is one.
Definition: Event.cpp:357
Model::getReaction
const Reaction * getReaction(unsigned int n) const
Get the nth Reaction object in this Model.
Definition: Model.cpp:3029
Reaction::getNumReactants
unsigned int getNumReactants() const
Returns the number of reactant species in this Reaction.
Definition: Reaction.cpp:1260
Reaction::isSetKineticLaw
bool isSetKineticLaw() const
Predicate returning true if this Reaction contains a kinetic law object.
Definition: Reaction.cpp:465
Model::getNumReactions
unsigned int getNumReactions() const
Get the number of Reaction objects in this Model.
Definition: Model.cpp:3296
Compartment::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment object's de...
Definition: Compartment.cpp:907
readSBML
SBMLDocument_t * readSBML(const char *filename)
Model::getInitialAssignment
const InitialAssignment * getInitialAssignment(unsigned int n) const
Get the nth InitialAssignment object in this Model.
Definition: Model.cpp:2752
Event
A discontinuous SBML event.
Definition: Event.h:345
Model::getCompartment
const Compartment * getCompartment(unsigned int n) const
Get the nth Compartment object in this Model.
Definition: Model.cpp:2626
InitialAssignment::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: InitialAssignment.cpp:268
Event::isSetDelay
bool isSetDelay() const
Predicate for testing whether the delay for this Event is set.
Definition: Event.cpp:456
Compartment
An SBML compartment, where species are located.
Definition: Compartment.h:480
Model::getNumEvents
unsigned int getNumEvents() const
Get the number of Event objects in this Model.
Definition: Model.cpp:3306
Delay::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: Delay.cpp:210
Parameter::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Parameter's value.
Definition: Parameter.cpp:531
SBMLDocument::getNumErrors
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1176
EventAssignment::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: EventAssignment.cpp:264
SBMLDocument::getModel
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition: SBMLDocument.cpp:353
InitialAssignment
An SBML initial assignment, evaluated once only.
Definition: InitialAssignment.h:279
EventAssignment
An assignment to a variable by an SBML event.
Definition: EventAssignment.h:286
InitialAssignment::containsUndeclaredUnits
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this InitialAssignment contains parameters/numbers...
Model
An SBML model.
Definition: Model.h:475
Model::getNumRules
unsigned int getNumRules() const
Get the number of Rule objects in this Model.
Definition: Model.cpp:3276
UnitDefinition.h
Definitions of UnitDefinition and ListOfUnitDefinitions.
Reaction::getNumProducts
unsigned int getNumProducts() const
Returns the number of product species in this Reaction.
Definition: Reaction.cpp:1270
SBMLDocument::printErrors
void printErrors(std::ostream &stream=std::cerr) const
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document...
Definition: SBMLDocument.cpp:1199
Rule::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: Rule.cpp:469
KineticLaw::containsUndeclaredUnits
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with u...
EventAssignment::containsUndeclaredUnits
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this EventAssignment contains literal numbers or p...
Reaction::getReactant
const SpeciesReference * getReactant(unsigned int n) const
Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reac...
Definition: Reaction.cpp:1126
Model::getNumSpecies
unsigned int getNumSpecies() const
Get the number of Species objects in this Model.
Definition: Model.cpp:3227
Delay::containsUndeclaredUnits
bool containsUndeclaredUnits()
Predicate returning true if the "math" expression in this Delay instance contains parameters with und...
Model::getEvent
const Event * getEvent(unsigned int n) const
Get the nth Event object in this Model.
Definition: Model.cpp:3135
Rule
Parent class for SBML rules in libSBML.
Definition: Rule.h:153
Event::getNumEventAssignments
unsigned int getNumEventAssignments() const
Returns the number of EventAssignment objects attached to this Event.
Definition: Event.cpp:1093
Model::getNumCompartments
unsigned int getNumCompartments() const
Get the number of Compartment objects in this Model.
Definition: Model.cpp:3217
KineticLaw::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the "math...
Definition: KineticLaw.cpp:847
SpeciesReference::getStoichiometryMath
const StoichiometryMath * getStoichiometryMath() const
Get the content of the "stoichiometryMath" subelement as an ASTNode tree.
Definition: SpeciesReference.cpp:230
SpeciesReference::isSetStoichiometryMath
bool isSetStoichiometryMath() const
Predicate returning true if this SpeciesReference's "stoichiometryMath" subelement is set.
Definition: SpeciesReference.cpp:271
Species
An SBML species – a pool of entities.
Definition: Species.h:419
Species::getDerivedUnitDefinition
UnitDefinition * getDerivedUnitDefinition()
Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or conc...
Definition: Species.cpp:1138
Model::getRule
const Rule * getRule(unsigned int n) const
Get the nth Rule object in this Model.
Definition: Model.cpp:2818
LIBSBML_CPP_NAMESPACE_USE
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:63
Reaction::getProduct
const SpeciesReference * getProduct(unsigned int n) const
Returns the nth product species (as a SpeciesReference object) in the list of products in this Reacti...
Definition: Reaction.cpp:1169
StoichiometryMath::containsUndeclaredUnits
bool containsUndeclaredUnits()
Predicate returning true if the math expression of this StoichiometryMath object contains literal num...
SBMLDocument
Overall SBML container object.
Definition: SBMLDocument.h:338