libSBML C++ API  5.18.0
renameSId.cpp

Program that renames a specific SId and updates all references to it in a given model.

/**
* @file renameSId.cpp
* @brief Utility program, renaming a specific SId
* while updating all references to it.
* @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
* written permission.
* ------------------------------------------------------------------------ -->
*/
#include <iostream>
#include <sbml/SBMLTypes.h>
#include "util.h"
using namespace std;
int
main (int argc, char* argv[])
{
if (argc != 5)
{
cout << endl << "Usage: renameSId filename oldSId newSId output" << endl << endl;
return 1;
}
const char* filename = argv[1];
const char* oldSId = argv[2];
const char* newSId = argv[3];
const char* output = argv[4];
if (strcmp(oldSId, newSId) == 0)
{
cout << "The Ids are identical, renaming stopped." << endl;
return 1;
}
if (!SyntaxChecker::isValidInternalSId(newSId))
{
cout << "The new SId '" << newSId
<< "' does not represent a valid SId."
<< endl;
return 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 << " file size: " << getFileSize(filename) << endl;
cout << " read time (ms): " << stop - start << endl;
cout << " error(s): " << errors << endl;
cout << endl;
if (errors > 0)
{
document->printErrors(cerr);
delete document;
return errors;
}
// find elements for old id
SBase* element = document->getElementBySId(oldSId);
if (element == NULL)
{
cout << "Found no element with SId '"
<< oldSId << "'." << endl;
return 1;
}
// found element --> renaming
element->setId(newSId);
// update all references to this element
List *allElements = document->getAllElements();
for (unsigned int i = 0; i < allElements->getSize(); ++i)
static_cast<SBase*>(allElements->get(i))->renameSIdRefs(oldSId, newSId);
// write to file
writeSBMLToFile(document, output);
delete document;
return errors;
}