printMath.cpp

Prints the rule, reaction, and event formulas in a given SBML document.

/**
 * @file    printMath.cpp
 * @brief   Prints Rule, Reaction, and Event formulas in a given SBML Document
 * @author  Ben Bornstein
 * @author  Sarah Keating
 *
 * <!--------------------------------------------------------------------------
 * 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>
 
 
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
 
void
printFunctionDefinition (unsigned int n, const FunctionDefinition* fd)
{
  const ASTNode* math;
  char* formula;
 
 
  if ( fd->isSetMath() )
  {
    cout << "FunctionDefinition " << n << ", " << fd->getId();
 
    math = fd->getMath();
 
    /* Print function arguments. */
    if (math->getNumChildren() > 1)
    {
      cout << "(" << ( math->getLeftChild() )->getName();
 
      for (n = 1; n < math->getNumChildren() - 1; ++n)
      {
        cout <<", " << ( math->getChild(n) )->getName();
      }
    }
 
    cout <<") := ";
 
    /* Print function body. */
    if (math->getNumChildren() == 0)
    {
      cout << "(no body defined)";
    }
    else
    {
      math    = math->getChild(math->getNumChildren() - 1);
      formula = SBML_formulaToString(math);
      cout << formula << endl;
      free(formula);
    }
  }
}
 
 
void
printRuleMath (unsigned int n, const Rule* r)
{
  char* formula;
 
 
  if ( r->isSetMath() )
  {
    formula = SBML_formulaToString( r->getMath() );
 
    if (r->getVariable().length() > 0)
    {
      cout << "Rule " << n << ", formula: "
       << r->getVariable() << " = " << formula << endl;
    }
    else
    {
      cout << "Rule " << n << ", formula: "
       << formula << " = 0" << endl;
    }
 
    free(formula);
  }
}
 
 
void
printReactionMath (unsigned int n, const Reaction* r)
{
  char* formula;
  const KineticLaw* kl;
 
 
  if (r->isSetKineticLaw())
  {
    kl = r->getKineticLaw();
 
    if ( kl->isSetMath() )
    {
      formula = SBML_formulaToString( kl->getMath() );
      cout << "Reaction " << n << ", formula: " << formula << endl;
      free(formula);
    }
  }
}
 
 
void
printEventAssignmentMath (unsigned int n, const EventAssignment* ea)
{
  std::string variable;
  char* formula;
 
 
  if ( ea->isSetMath() )
  {
    variable = ea->getVariable();
    formula  = SBML_formulaToString( ea->getMath() );
 
    cout <<"  EventAssignment " << n
         << ", trigger: " << variable << " = " << formula << endl;
 
    free(formula);
  }
}
 
 
void
printEventMath (unsigned int n, const Event* e)
{
  char* formula;
  unsigned int i;
 
 
  if ( e->isSetDelay() )
  {
    formula = SBML_formulaToString( e->getDelay()->getMath() );
    cout << "Event " << n << " delay: " << formula << endl;
    free(formula);
  }
 
  if ( e->isSetTrigger() )
  {
    formula = SBML_formulaToString( e->getTrigger()->getMath() );
    cout << "Event " << n << " trigger: " << formula << endl;
    free(formula);
  }
 
  for (i = 0; i < e->getNumEventAssignments(); ++i)
  {
    printEventAssignmentMath(i + 1, e->getEventAssignment(i));
  }
 
  cout << endl;
}
 
 
void
printMath (const Model* m)
{
  unsigned int  n;
 
 
  for (n = 0; n < m->getNumFunctionDefinitions(); ++n)
  {
    printFunctionDefinition(n + 1, m->getFunctionDefinition(n));
  }
 
  for (n = 0; n < m->getNumRules(); ++n)
  {
    printRuleMath(n + 1, m->getRule(n));
  }
 
  cout << endl;
 
  for (n = 0; n < m->getNumReactions(); ++n)
  {
    printReactionMath(n + 1, m->getReaction(n));
  }
 
  cout << endl;
 
  for (n = 0; n < m->getNumEvents(); ++n)
  {
    printEventMath(n + 1, m->getEvent(n));
  }
}
 
 
int
main (int argc, char* argv[])
{
  if (argc != 2)
  {
    cout << endl << "Usage: printMath filename" << endl << endl;
    return 1;
  }
 
  const char* filename   = argv[1];
  SBMLDocument* document = readSBML(filename);
 
  if (document->getNumErrors() > 0)
  {
    cerr << "Encountered the following SBML errors:" << endl;
    document->printErrors(cerr);
    return 1;
  }
 
  Model* model = document->getModel();
 
  if (model == 0)
  {
    cout << "No model present." << endl;
    return 1;
  }
 
  printMath(model);
  cout << endl;
 
  delete document;
  return 0;
}