libSBML C++ API  5.18.0
printNotes.cpp

Prints the notes strings for each element in a given model.

/**
* @file printNotes.cpp
* @brief Prints notes strings 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;
void printNotes(SBase *sb, const string& id = "")
{
if (!sb->isSetNotes()) return;
string pid = id;
if (pid == "" && sb->isSetId())
{
pid = sb->getId();
}
cout << "----- " << sb->getElementName() << " (" << pid
<< ") notes -----" << endl;
cout << sb->getNotesString() << endl;
cout << endl;
}
int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: printNotes 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();
cout << endl;
cout << "filename: " << filename << endl;
cout << endl;
if(errors > 0)
{
document->printErrors(cerr);
delete document;
return errors;
}
/* Model */
Model* m = document->getModel();
printNotes(m);
for(i=0; i < m->getNumReactions(); i++)
{
Reaction* re = m->getReaction(i);
printNotes(re);
/* SpeciesReference (Reacatant) */
for(j=0; j < re->getNumReactants(); j++)
{
if (rt->isSetNotes()) cout << " ";
printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
}
/* SpeciesReference (Product) */
for(j=0; j < re->getNumProducts(); j++)
{
if (rt->isSetNotes()) cout << " ";
printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
}
/* ModifierSpeciesReference (Modifier) */
for(j=0; j < re->getNumModifiers(); j++)
{
if (md->isSetNotes()) cout << " ";
printNotes(md, (md->isSetSpecies() ? md->getSpecies() : std::string("")) );
}
/* Kineticlaw */
if(re->isSetKineticLaw())
{
if (kl->isSetNotes()) cout << " ";
printNotes(kl);
/* Parameter */
for(j=0; j < kl->getNumParameters(); j++)
{
Parameter* pa = kl->getParameter(j);
if (pa->isSetNotes()) cout << " ";
printNotes(pa);
}
}
}
/* Species */
for(i=0; i < m->getNumSpecies(); i++)
{
Species* sp = m->getSpecies(i);
printNotes(sp);
}
/* Compartment */
for(i=0; i < m->getNumCompartments(); i++)
{
printNotes(sp);
}
/* FunctionDefinition */
for(i=0; i < m->getNumFunctionDefinitions(); i++)
{
printNotes(sp);
}
/* UnitDefinition */
for(i=0; i < m->getNumUnitDefinitions(); i++)
{
printNotes(sp);
}
/* Parameter */
for(i=0; i < m->getNumParameters(); i++)
{
Parameter* sp = m->getParameter(i);
printNotes(sp);
}
/* Rule */
for(i=0; i < m->getNumRules(); i++)
{
Rule* sp = m->getRule(i);
printNotes(sp);
}
/* InitialAssignment */
for(i=0; i < m->getNumInitialAssignments(); i++)
{
printNotes(sp);
}
/* Event */
for(i=0; i < m->getNumEvents(); i++)
{
Event* sp = m->getEvent(i);
printNotes(sp);
/* Trigger */
if(sp->isSetTrigger())
{
const Trigger* tg = sp->getTrigger();
if (tg->isSetNotes()) cout << " ";
printNotes(const_cast<Trigger*>(tg));
}
/* Delay */
if(sp->isSetDelay())
{
const Delay* dl = sp->getDelay();
if (dl->isSetNotes()) cout << " ";
printNotes(const_cast<Delay*>(dl));
}
/* EventAssignment */
for(j=0; j < sp->getNumEventAssignments(); j++)
{
if (ea->isSetNotes()) cout << " ";
printNotes(ea);
}
}
/* SpeciesType */
for(i=0; i < m->getNumSpeciesTypes(); i++)
{
printNotes(sp);
}
/* Constraint */
for(i=0; i < m->getNumConstraints(); i++)
{
printNotes(sp);
}
delete document;
return errors;
}