libSBML C++ API  libSBML 5.18.0 C++ API
unsetNotes.cpp

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;
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++)
{
sp->unsetNotes();
}
for(i=0; i < m->getNumFunctionDefinitions(); i++)
{
sp->unsetNotes();
}
for(i=0; i < m->getNumUnitDefinitions(); 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++)
{
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++)
{
sp->unsetNotes();
}
for(i=0; i < m->getNumConstraints(); i++)
{
sp->unsetNotes();
}
writeSBML(document, argv[2]);
delete document;
return errors;
}
Reaction::getKineticLaw
const KineticLaw * getKineticLaw() const
Returns the KineticLaw object contained in this Reaction.
Definition: Reaction.cpp:395
SpeciesReference
@sbmlpackage{core}
Definition: SpeciesReference.h:276
Model::getNumInitialAssignments
unsigned int getNumInitialAssignments() const
Get the number of InitialAssignment objects in this Model.
Definition: Model.cpp:3274
Model::getNumParameters
unsigned int getNumParameters() const
Get the number of Parameter objects in this Model.
Definition: Model.cpp:3264
Model::getFunctionDefinition
const FunctionDefinition * getFunctionDefinition(unsigned int n) const
Get the nth FunctionDefinitions object in this Model.
Definition: Model.cpp:2466
Parameter
@sbmlpackage{core}
Definition: Parameter.h:197
Event::getEventAssignment
const EventAssignment * getEventAssignment(unsigned int n) const
Return a specific EventAssignment object of this Event.
Definition: Event.cpp:1055
Model::getParameter
const Parameter * getParameter(unsigned int n) const
Get the nth Parameter object in this Model.
Definition: Model.cpp:2718
Reaction
@sbmlpackage{core}
Definition: Reaction.h:219
SBase::unsetNotes
int unsetNotes()
Unsets the value of the "notes" subelement of this SBML object.
Definition: SBase.cpp:2612
Constraint
@sbmlpackage{core}
Definition: Constraint.h:153
Model::getSpecies
const Species * getSpecies(unsigned int n) const
Get the nth Species object in this Model.
Definition: Model.cpp:2676
KineticLaw
@sbmlpackage{core}
Definition: KineticLaw.h:198
SBMLTypes.h
Include all SBML types in a single header file.
UnitDefinition
@sbmlpackage{core}
Definition: UnitDefinition.h:277
Model::getNumConstraints
unsigned int getNumConstraints() const
Get the number of Constraint objects in this Model.
Definition: Model.cpp:3294
KineticLaw::getParameter
const Parameter * getParameter(unsigned int n) const
Returns the nth Parameter object in the list of parameters in this KineticLaw instance.
Definition: KineticLaw.cpp:732
Model::getNumSpeciesTypes
unsigned int getNumSpeciesTypes() const
Get the number of SpeciesType objects in this Model.
Definition: Model.cpp:3215
Model::getReaction
const Reaction * getReaction(unsigned int n) const
Get the nth Reaction object in this Model.
Definition: Model.cpp:3037
Reaction::getNumReactants
unsigned int getNumReactants() const
Returns the number of reactant species in this Reaction.
Definition: Reaction.cpp:1264
SBMLReader::readSBML
SBMLDocument * readSBML(const std::string &filename)
Reads an SBML document from the given file.
Definition: SBMLReader.cpp:107
Reaction::isSetKineticLaw
bool isSetKineticLaw() const
Predicate returning true if this Reaction contains a kinetic law object.
Definition: Reaction.cpp:469
Model::getNumReactions
unsigned int getNumReactions() const
Get the number of Reaction objects in this Model.
Definition: Model.cpp:3304
Model::getInitialAssignment
const InitialAssignment * getInitialAssignment(unsigned int n) const
Get the nth InitialAssignment object in this Model.
Definition: Model.cpp:2760
Event
@sbmlpackage{core}
Definition: Event.h:350
FunctionDefinition
@sbmlpackage{core}
Definition: FunctionDefinition.h:145
Reaction::getNumModifiers
unsigned int getNumModifiers() const
Returns the number of modifier species in this Reaction.
Definition: Reaction.cpp:1285
Model::getCompartment
const Compartment * getCompartment(unsigned int n) const
Get the nth Compartment object in this Model.
Definition: Model.cpp:2634
SBMLReader
@sbmlpackage{core}
Definition: SBMLReader.h:338
KineticLaw::getNumParameters
unsigned int getNumParameters() const
Returns the number of parameters in this KineticLaw instance.
Definition: KineticLaw.cpp:829
Compartment
@sbmlpackage{core}
Definition: Compartment.h:485
Model::getNumEvents
unsigned int getNumEvents() const
Get the number of Event objects in this Model.
Definition: Model.cpp:3314
Model::getNumUnitDefinitions
unsigned int getNumUnitDefinitions() const
Get the number of UnitDefinition objects in this Model.
Definition: Model.cpp:3195
SBMLDocument::getNumErrors
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1184
Model::getConstraint
const Constraint * getConstraint(unsigned int n) const
Get the nth Constraint object in this Model.
Definition: Model.cpp:3017
SBMLDocument::getModel
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition: SBMLDocument.cpp:361
InitialAssignment
@sbmlpackage{core}
Definition: InitialAssignment.h:284
EventAssignment
@sbmlpackage{core}
Definition: EventAssignment.h:291
Model
@sbmlpackage{core}
Definition: Model.h:480
SpeciesType
@sbmlpackage{core}
Definition: SpeciesType.h:104
Model::getNumRules
unsigned int getNumRules() const
Get the number of Rule objects in this Model.
Definition: Model.cpp:3284
Reaction::getNumProducts
unsigned int getNumProducts() const
Returns the number of product species in this Reaction.
Definition: Reaction.cpp:1274
Reaction::getModifier
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:1216
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:1207
Model::getSpeciesType
const SpeciesType * getSpeciesType(unsigned int n) const
Get the nth SpeciesType object in this Model.
Definition: Model.cpp:2592
Model::getNumFunctionDefinitions
unsigned int getNumFunctionDefinitions() const
Get the number of FunctionDefinition objects in this Model.
Definition: Model.cpp:3185
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:1130
Model::getNumSpecies
unsigned int getNumSpecies() const
Get the number of Species objects in this Model.
Definition: Model.cpp:3235
Model::getEvent
const Event * getEvent(unsigned int n) const
Get the nth Event object in this Model.
Definition: Model.cpp:3143
Rule
@sbmlpackage{core}
Definition: Rule.h:158
Model::getUnitDefinition
const UnitDefinition * getUnitDefinition(unsigned int n) const
Get the nth UnitDefinition object in this Model.
Definition: Model.cpp:2508
Event::getNumEventAssignments
unsigned int getNumEventAssignments() const
Returns the number of EventAssignment objects attached to this Event.
Definition: Event.cpp:1097
Model::getNumCompartments
unsigned int getNumCompartments() const
Get the number of Compartment objects in this Model.
Definition: Model.cpp:3225
Species
@sbmlpackage{core}
Definition: Species.h:424
util.h
Utility functions.
Model::getRule
const Rule * getRule(unsigned int n) const
Get the nth Rule object in this Model.
Definition: Model.cpp:2826
LIBSBML_CPP_NAMESPACE_USE
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:67
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:1173
SBMLDocument
@sbmlpackage{core}
Definition: SBMLDocument.h:343
writeSBML
int writeSBML(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file named by filename.
ModifierSpeciesReference
@sbmlpackage{core}
Definition: ModifierSpeciesReference.h:87