libSBML C++ API  5.20.2
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unsetNotes.cpp

Unsets the notes for each element in the given SBML file.

Unsets the notes for each element in the given SBML file.

/**
* @file unsetNotes.cpp
* @brief unset notes for each element
* @author Akiya Jouraku
*
* <!--------------------------------------------------------------------------
* 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 "util.h"
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
int
main (int argc, char* argv[])
{
if (argc != 3)
{
cout << endl << "Usage: unsetNotes <input-filename> <output-filename>" << endl << endl;
return 1;
}
unsigned int i,j;
const char* filename = argv[1];
SBMLDocument* document;
SBMLReader reader;
document = reader.readSBML(filename);
unsigned int errors = document->getNumErrors();
if(errors > 0)
{
document->printErrors(cerr);
delete document;
return errors;
}
Model* m = document->getModel();
m->unsetNotes();
for(i=0; i < m->getNumReactions(); i++)
{
Reaction* re = m->getReaction(i);
re->unsetNotes();
for(j=0; j < re->getNumReactants(); j++)
{
rt->unsetNotes();
}
for(j=0; j < re->getNumProducts(); j++)
{
rt->unsetNotes();
}
for(j=0; j < re->getNumModifiers(); j++)
{
md->unsetNotes();
}
if(re->isSetKineticLaw())
{
kl->unsetNotes();
for(j=0; j < kl->getNumParameters(); j++)
{
Parameter* pa = kl->getParameter(j);
pa->unsetNotes();
}
}
}
for(i=0; i < m->getNumSpecies(); i++)
{
Species* sp = m->getSpecies(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumCompartments(); i++)
{
Compartment* sp = m->getCompartment(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumFunctionDefinitions(); i++)
{
FunctionDefinition* sp = m->getFunctionDefinition(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumUnitDefinitions(); i++)
{
UnitDefinition* sp = m->getUnitDefinition(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumParameters(); i++)
{
Parameter* sp = m->getParameter(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumRules(); i++)
{
Rule* sp = m->getRule(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumInitialAssignments(); i++)
{
InitialAssignment* sp = m->getInitialAssignment(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumEvents(); i++)
{
Event* sp = m->getEvent(i);
sp->unsetNotes();
for(j=0; j < sp->getNumEventAssignments(); j++)
{
ea->unsetNotes();
}
}
for(i=0; i < m->getNumSpeciesTypes(); i++)
{
SpeciesType* sp = m->getSpeciesType(i);
sp->unsetNotes();
}
for(i=0; i < m->getNumConstraints(); i++)
{
Constraint* sp = m->getConstraint(i);
sp->unsetNotes();
}
writeSBML(document, argv[2]);
delete document;
return errors;
}
Include all SBML types in a single header file.
int writeSBML(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file named by filename.
Definition Compartment.h:490
Definition Constraint.h:158
Definition EventAssignment.h:296
Definition Event.h:355
const EventAssignment * getEventAssignment(unsigned int n) const
Return a specific EventAssignment object of this Event.
Definition Event.cpp:1055
unsigned int getNumEventAssignments() const
Returns the number of EventAssignment objects attached to this Event.
Definition Event.cpp:1097
Definition FunctionDefinition.h:150
Definition InitialAssignment.h:289
Definition KineticLaw.h:203
unsigned int getNumParameters() const
Returns the number of parameters in this KineticLaw instance.
Definition KineticLaw.cpp:837
const Parameter * getParameter(unsigned int n) const
Returns the nth Parameter object in the list of parameters in this KineticLaw instance.
Definition KineticLaw.cpp:740
Definition ModifierSpeciesReference.h:92
Definition Parameter.h:202
Definition Reaction.h:224
unsigned int getNumReactants() const
Returns the number of reactant species in this Reaction.
Definition Reaction.cpp:1267
const KineticLaw * getKineticLaw() const
Returns the KineticLaw object contained in this Reaction.
Definition Reaction.cpp:396
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:1176
bool isSetKineticLaw() const
Predicate returning true if this Reaction contains a kinetic law object.
Definition Reaction.cpp:470
unsigned int getNumModifiers() const
Returns the number of modifier species in this Reaction.
Definition Reaction.cpp:1288
unsigned int getNumProducts() const
Returns the number of product species in this Reaction.
Definition Reaction.cpp:1277
const ModifierSpeciesReference * getModifier(unsigned int n) const
Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of t...
Definition Reaction.cpp:1219
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:1133
Definition Rule.h:163
Definition SBMLDocument.h:349
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition SBMLDocument.cpp:1163
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:1186
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition SBMLDocument.cpp:350
Definition SBMLReader.h:343
SBMLDocument * readSBML(const std::string &filename)
Reads an SBML document from the given file.
Definition SBMLReader.cpp:112
int unsetNotes()
Unsets the value of the "notes" subelement of this SBML object.
Definition SBase.cpp:2672
Definition Species.h:429
Definition SpeciesReference.h:281
Definition SpeciesType.h:109
Definition UnitDefinition.h:282
Utility functions.