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setNamesFromIds.cpp

Program that changes all objects' "name" attribute values to match their "id" attribute values.

/**
* @file setNamesFromIds.cpp
* @brief Utility program, renaming all Names to match their ids.
*
* @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) 2013-2014 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 <sstream>
#include <vector>
#include <string>
#include <sbml/SBMLTypes.h>
#include "util.h"
using namespace std;
/**
* The NameIdTransformer class transforms the name of a given SBase
* element by replacing it with its id.
*
* It won't do anything if the name is the same as the id, or if
* no id is set.
*/
class NameIdTransformer : public IdentifierTransformer
{
public:
NameIdTransformer()
: IdentifierTransformer()
{
}
/**
* The actual transform implementation
*/
int transform(SBase* element)
{
// return in case we don't have a valid element
if (element == NULL || element->getTypeCode() == SBML_LOCAL_PARAMETER)
// or if there is nothing to do
if (!element->isSetId() || element->getId() == element->getName())
// set it
element->setName(element->getId());
}
};
int
main (int argc, char* argv[])
{
if (argc != 3)
{
cout << endl << "Usage: setNamesFromIds filename output" << endl << endl;
return 1;
}
const char* filename = argv[1];
const char* output = argv[2];
SBMLDocument* document;
SBMLReader reader;
unsigned long long start, stop;
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;
// get a list of all elements, as we will need to know all identifiers
List* allElements = document->getAllElements();
// create the transformer
NameIdTransformer trans;
// rename the identifiers (using the elements we already gathered before)
document->getModel()->renameIDs(allElements, &trans);
stop = getCurrentMillis();
cout << " rename time (ms): " << stop - start << endl;
start = stop;
// write to file
writeSBMLToFile(document, output);
stop = getCurrentMillis();
cout << " write time (ms): " << stop - start << endl;
cout << endl;
delete document;
return errors;
}