libSBML C++ API  5.18.0
getAllElementsWithNotes.cpp

Demonstrates how to use the element filter class to search the model for elements with specific attributes .

/**
* @file getAllElementsWithNotes.cpp
* @brief Utility program, demontrating how to use the element filter
* class to search the model for elements with specific attributes
* @author Frank T. Bergmann
*
* <!--------------------------------------------------------------------------
* 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
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*/
#include <iostream>
#include <sstream>
#include <vector>
#include <string>
#include <sbml/SBMLTypes.h>
#include "util.h"
using namespace std;
/**
* This class implements an element filter, that can be used to find elements
* with notes
*/
class NotesFilter : public ElementFilter
{
public:
NotesFilter() : ElementFilter()
{
}
/**
* The function performing the filtering, here we just check
* that we have a valid element, and that it has notes.
*/
virtual bool filter(const SBase* element)
{
// return in case we don't have a valid element
if (element == NULL || !element->isSetNotes())
return false;
// otherwise we have notes set and want to keep the element
if (element->isSetId())
cout << " found : "
<< element->getId() << endl;
else
cout << " found : "
<< "element without id" << endl;
return true;
}
};
int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: getAllElementsWithNotes filename" << endl << endl;
return 1;
}
const char* filename = argv[1];
SBMLDocument* document;
SBMLReader reader;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
start = getCurrentMillis();
document = reader.readSBML(filename);
stop = getCurrentMillis();
unsigned int errors = document->getNumErrors(LIBSBML_SEV_ERROR);
cout << endl;
cout << " filename: " << filename << endl;
cout << " read time (ms): " << stop - start << endl;
if (errors > 0)
{
cout << " error(s): " << errors << endl;
document->printErrors(cerr);
delete document;
return errors;
}
start = stop;
// create the filter we want to use
NotesFilter filter;
// get a list of all elements with notes
cout << " searching ......:" << endl;
List* allElements = document->getAllElements(&filter);
stop = getCurrentMillis();
cout << " search time (ms): " << stop - start << endl;
cout << " elements with notes: " << allElements->getSize() << endl;
delete document;
return errors;
}