Loading [MathJax]/extensions/tex2jax.js
libSBML C++ API  5.20.2
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Modules Pages
setIdFromNames.cpp

Program that renames all SIds that also have names specified. The new identifiers will be derived from the name, with all invalid characters removed.

/**
* @file setIdFromNames.cpp
* @brief Utility program, renaming all SIds that also have
* names specified. The new id will be derived from
* the name, with all invalid characters removed.
* @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 <sstream>
#include <vector>
#include <string>
#include <sbml/SBMLTypes.h>
#include "util.h"
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
/**
* The NameIdTransformer class transforms the id of a given SBase
* element by replacing it with a string derived from the name.
*
* It won't do anything if the name is the same as the id, or if
* no name is set.
*/
class NameIdTransformer : public IdentifierTransformer
{
public:
NameIdTransformer(const vector<string> &ids)
: IdentifierTransformer()
, existingIds(ids)
{
}
/**
* 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->isSetName() || element->getId() == element->getName())
// find the new id
string newId = getValidIdForName(element->getName());
// set it
element->setId(newId);
// remember it
existingIds.push_back(newId);
}
private:
/**
* Cleans the name, so it represents a valid SId
*
* Taken from COPASI (released under the artistic license)
* https://github.com/copasi/COPASI/blob/master/copasi/utilities/utility.cpp
*/
std::string nameToSbmlId(const std::string & name)
{
// We convert all non allowed characters to '_'
// letter ::= 'a'..'z','A'..'Z'
// digit ::= '0'..'9'
// idChar ::= letter | digit | '_'
// SId ::= (letter | '_' ) idChar*
std::ostringstream IdStream;
std::string::const_iterator it = name.begin();
std::string::const_iterator end = name.end();
if ('0' <= *it && *it <= '9')
{
IdStream << '_';
}
for (; it != end; ++it)
{
// second, third or forth character of a multi-byte encoding
if (0x80 == (*it & 0xc0))
{
continue;
}
if (('0' <= *it && *it <= '9') ||
('a' <= *it && *it <= 'z') ||
('A' <= *it && *it <= 'Z'))
{
IdStream << *it;
}
else
{
IdStream << '_';
}
}
std::string Id = IdStream.str();
if (Id[Id.length() - 1] != '_')
{
return Id;
}
return Id.substr(0, Id.length() - 1);
}
/**
* Generates the id out of the name, and ensures it is unique.
* It does so by appending numbers to the original name.
*/
string getValidIdForName(const string& name)
{
string base = nameToSbmlId(name);
string id(base);
int count = 1;
while (containsId(id))
{
std::ostringstream idStream;
idStream << base << "_" << count;
id = idStream.str();
++count;
}
return id;
}
/**
* Checks whether the given id is already in the vector.
*/
bool containsId(string &id)
{
vector<string>::const_iterator it = existingIds.begin();
while(it != existingIds.end())
{
if ((*it) == id) return true;
++it;
}
return false;
}
vector<string> existingIds;
};
/**
* Returns a list of all ids from the given list of elements
*/
vector<string> getAllIds(List* allElements)
{
vector<string> result;
if (allElements == NULL || allElements->getSize() == 0)
return result;
for (unsigned long int i = 0; i < allElements->getSize(); ++i)
{
const SBase* current = static_cast<const SBase*>(allElements->get(i));
if (current->isSetId() && current->getTypeCode() != SBML_LOCAL_PARAMETER)
{
result.push_back(current->getId());
}
}
return result;
}
int
main (int argc, char* argv[])
{
if (argc != 3)
{
cout << endl << "Usage: setIdFromNames filename output" << endl << endl;
return 1;
}
const char* filename = argv[1];
const char* output = argv[2];
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;
// get a list of all elements, as we will need to know all identifiers
// so that we don't create duplicates.
List* allElements = document->getAllElements();
// get a list of all ids
const vector<string>& allIds = getAllIds(allElements);
// create the transformer with the ids
NameIdTransformer trans(allIds);
// 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 allElements;
delete document;
return errors;
}
@ SBML_LOCAL_PARAMETER
Definition: SBMLTypeCodes.h:94
Include all SBML types in a single header file.
int writeSBMLToFile(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file filename.
@ LIBSBML_SEV_ERROR
Definition: XMLError.h:534
Definition: List.h:174
void * get(unsigned int n) const
Get the nth item in this List.
Definition: List.cpp:219
unsigned int getSize() const
Get the number of items in this List.
Definition: List.cpp:347
Definition: SBMLDocument.h:349
unsigned int getNumErrors() const
Returns the number of errors or warnings encountered during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1163
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:1186
const Model * getModel() const
Returns the Model object stored in this SBMLDocument.
Definition: SBMLDocument.cpp:350
virtual List * getAllElements(ElementFilter *filter=NULL)
Returns a List of all child SBase objects, including those nested to an arbitrary depth.
Definition: SBMLDocument.cpp:432
Definition: SBMLReader.h:343
SBMLDocument * readSBML(const std::string &filename)
Reads an SBML document from the given file.
Definition: SBMLReader.cpp:112
Definition: SBase.h:191
virtual const std::string & getId() const
Returns the value of the "id" attribute of this SBML object, if it has one, or the "variable" attribu...
Definition: SBase.cpp:713
virtual int getTypeCode() const
Returns the libSBML type code for this object.
Definition: SBase.cpp:3500
virtual bool isSetName() const
Predicate returning true if this object's "name" attribute is set.
Definition: SBase.cpp:1125
virtual bool isSetId() const
Predicate returning true if a call to getId() returns a non-empty string.
Definition: SBase.cpp:1112
virtual const std::string & getName() const
Returns the value of the "name" attribute of this SBML object.
Definition: SBase.cpp:731
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this SBML object.
Definition: SBase.cpp:1233
Definitions of LIBSBML_EXTERN and related things.
#define BEGIN_C_DECLS
Definition: extern.h:110
#define END_C_DECLS
Definition: extern.h:111
Enumeration of values returned by operations within libSBML.
@ LIBSBML_OPERATION_SUCCESS
Definition: operationReturnValues.h:61
Utility functions.