Ejemplo n.º 1
0
END_TEST


START_TEST (test_SBMLConvert_convertToL3_parameter)
{
  SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
  Model_t        *m = SBMLDocument_createModel(d);

  const char   *sid = "C";
  Parameter_t  *p = Model_createParameter(m);
  Parameter_t *p1;

  Parameter_setId   ( p, sid );

  fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);

  p1 = Model_getParameter(m, 0);

  fail_unless(Parameter_hasRequiredAttributes(p1) == 1);

  SBMLDocument_free(d);
}
Ejemplo n.º 2
0
int
main (int argc, char* argv[])
{
  unsigned int i,j,errors;
  const char* filename   = argv[1];
  SBMLDocument_t* document;
  Model_t* m;

  if (argc != 3)
  {
    printf("\nUsage: unsetNotes <input-filename> <output-filename>\n");
    return 1;
  }

  filename = argv[1];  
  document = readSBML(filename);

  errors =  SBMLDocument_getNumErrors(document);

  if(errors > 0)
  {
    SBMLDocument_printErrors(document, stderr);
    SBMLDocument_free(document);
    return errors;
  }

  m = SBMLDocument_getModel( document );
  SBase_unsetNotes((SBase_t*)m);

  for(i=0; i < Model_getNumReactions(m); i++)
  {
    Reaction_t* re = Model_getReaction(m, i);
    SBase_unsetNotes((SBase_t*)re);

    for(j=0; j < Reaction_getNumReactants(re); j++)
    {
      SpeciesReference_t* rt = Reaction_getReactant(re,j);
      SBase_unsetNotes((SBase_t*)rt);
    }

    for(j=0; j < Reaction_getNumProducts(re); j++)
    {
      SpeciesReference_t* rt = Reaction_getProduct(re,j);
      SBase_unsetNotes((SBase_t*)rt);
    }

    for(j=0; j < Reaction_getNumModifiers(re); j++)
    {
      SpeciesReference_t* md = Reaction_getModifier(re,j);
      SBase_unsetNotes((SBase_t*)md);
    }

    if(Reaction_isSetKineticLaw(re))
    {
      KineticLaw_t* kl =  Reaction_getKineticLaw(re);
      SBase_unsetNotes((SBase_t*)kl);

      for(j=0; j < KineticLaw_getNumParameters(kl); j++)
      {
        Parameter_t* pa = KineticLaw_getParameter(kl, j);
        SBase_unsetNotes((SBase_t*)pa);
      }
    }

  }

  for(i=0; i < Model_getNumSpecies(m); i++)
  {
    Species_t* sp = Model_getSpecies(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumCompartments(m); i++)
  {
    Compartment_t* sp = Model_getCompartment(m,i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
  {
    FunctionDefinition_t* sp = Model_getFunctionDefinition(m,i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumUnitDefinitions(m); i++)
  {
    UnitDefinition_t* sp = Model_getUnitDefinition(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumParameters(m); i++)
  {
    Parameter_t* sp = Model_getParameter(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumRules(m); i++)
  {
    Rule_t* sp = Model_getRule(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumInitialAssignments(m); i++)
  {
    InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumEvents(m); i++)
  {
    Event_t* sp = Model_getEvent(m, i);
    SBase_unsetNotes((SBase_t*)sp);

    for(j=0; j < Event_getNumEventAssignments(sp); j++)
    {
      EventAssignment_t* ea = Event_getEventAssignment(sp, j);
      SBase_unsetNotes((SBase_t*)ea);
    }
  }

  for(i=0; i < Model_getNumSpeciesTypes(m); i++)
  {
    SpeciesType_t* sp = Model_getSpeciesType(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumConstraints(m); i++)
  {
    Constraint_t* sp = Model_getConstraint(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  writeSBML(document, argv[2]);

  SBMLDocument_free(document);
  return errors;
}
Ejemplo n.º 3
0
int
main (int argc, char* argv[])
{
  unsigned int i,j,errors;
  const char* filename;
  SBMLDocument_t* document;
  Model_t* m;

  if (argc != 2)
  {
    printf("\nUsage: printNotes filename\n\n");
    return 1;
  }

  filename  = argv[1];
  document  = readSBML(filename);

  errors = SBMLDocument_getNumErrors( document);

  printf("\n%s\n\n", filename);

  if(errors > 0)
  {
    SBMLDocument_printErrors(document, stderr);
    SBMLDocument_free(document);
    return errors;
  }


  /* Model */

  m = SBMLDocument_getModel(document);
  printNotes((SBase_t*)m, Model_getId(m));

  for(i=0; i < Model_getNumReactions(m); i++)
  {
    Reaction_t* re = Model_getReaction( m, i);
    printNotes((SBase_t*)re, Reaction_getId(re));

    /* SpeciesReference (Reactant) */

    for(j=0; j < Reaction_getNumReactants( re); j++)
    {
      SpeciesReference_t* rt =  Reaction_getReactant(re, j);
      if (SBase_isSetNotes((SBase_t*) rt)) printf("   ");
      printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
    }

    /* SpeciesReference (Product) */

    for(j=0; j < Reaction_getNumProducts( re ); j++)
    {
      SpeciesReference_t* rt = Reaction_getProduct( re, j);
      if (SBase_isSetNotes((SBase_t*) rt)) printf("   ");
      printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
    }

    /* ModifierSpeciesReference (Modifiers) */

    for(j=0; j < Reaction_getNumModifiers( re ); j++)
    {
      SpeciesReference_t* md = Reaction_getModifier(re, j);
      if (SBase_isSetNotes((SBase_t*) md)) printf("   ");
      printNotes((SBase_t*)md, SpeciesReference_getSpecies( md ) );
    }

    /* KineticLaw */

    if(Reaction_isSetKineticLaw( re ))
    {
      KineticLaw_t* kl = Reaction_getKineticLaw( re );
      if (SBase_isSetNotes((SBase_t*) kl)) printf("   ");
      printNotes((SBase_t*)kl, "");

      /* Parameter */

      for(j=0; j < KineticLaw_getNumParameters( kl ); j++)
      {
        Parameter_t* pa = KineticLaw_getParameter( kl, j);
        if (SBase_isSetNotes((SBase_t*) pa)) printf("   ");
        printNotes((SBase_t*)pa, Parameter_getId(pa));
      }
    }

  }

  /* Species */

  for(i=0; i < Model_getNumSpecies(m); i++)
  {
    Species_t* sp = Model_getSpecies(m, i);
    printNotes((SBase_t*)sp, Species_getId(sp));
  }

  /* Compartments */

  for(i=0; i < Model_getNumCompartments( m ); i++)
  {
    Compartment_t* sp = Model_getCompartment(m, i);
    printNotes((SBase_t*)sp, Compartment_getId(sp));
  }

  /* FunctionDefinition */

  for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
  {
    FunctionDefinition_t* sp = Model_getFunctionDefinition(m, i);
    printNotes((SBase_t*)sp, FunctionDefinition_getId(sp));
  }

  /* UnitDefinition */

  for(i=0; i < Model_getNumUnitDefinitions(m); i++)
  {
    UnitDefinition_t* sp = Model_getUnitDefinition( m, i);
    printNotes((SBase_t*)sp, UnitDefinition_getId(sp));
  }

  /* Parameter */

  for(i=0; i < Model_getNumParameters( m ); i++)
  {
    Parameter_t* sp = Model_getParameter( m, i);
    printNotes((SBase_t*)sp, Parameter_getId(sp));
  }

  /* Rule */

  for(i=0; i < Model_getNumReactions( m ); i++)
  {
    Rule_t* sp = Model_getRule(m, i);
    printNotes((SBase_t*)sp, "");
  }

  /* InitialAssignment */

  for(i=0; i < Model_getNumInitialAssignments(m); i++)
  {
    InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
    printNotes((SBase_t*)sp, "");
  }

  /* Event */

  for(i=0; i < Model_getNumEvents(m); i++)
  {
    Event_t* sp = Model_getEvent(m, i);
    printNotes((SBase_t*)sp, Event_getId(sp));

    /* Trigger */

    if(Event_isSetTrigger( sp ))
    {
      Trigger_t* tg = Event_getTrigger(sp);
      if (SBase_isSetNotes( (SBase_t*) tg)) printf( "   " );
      printNotes((SBase_t*)tg, "");
    }

    /* Delay */

    if(Event_isSetDelay(sp))
    {
      Delay_t* dl = Event_getDelay(sp);
      if (SBase_isSetNotes( (SBase_t*) dl)) printf( "   " );
      printNotes((SBase_t*) dl, "");
    }

    /* EventAssignment */

    for(j=0; j < Event_getNumEventAssignments(sp); j++)
    {
      EventAssignment_t* ea = Event_getEventAssignment(sp, j);
      if (SBase_isSetNotes( (SBase_t*) ea)) printf( "   " );      
      printNotes((SBase_t*)ea, "");
    }
  }

  /* SpeciesType */

  for(i=0; i < Model_getNumSpeciesTypes(m); i++)
  {
    SpeciesType_t* sp = Model_getSpeciesType(m, i);
    printNotes((SBase_t*)sp, SpeciesType_getId(sp));
  }

  /* Constraints */

  for(i=0; i < Model_getNumConstraints(m); i++)
  {
    Constraint_t* sp = Model_getConstraint(m, i);
    printNotes((SBase_t*)sp, "");
  }

  SBMLDocument_free( document );
  return errors;
}
Ejemplo n.º 4
0
void printReactions(Model_t *m, FILE *f)
{
  
  int i,j,k;
  Reaction_t *r;
  SpeciesReference_t *sref;
  KineticLaw_t *kl;
  Rule_t *rl;
  AssignmentRule_t *asr;
  AlgebraicRule_t *alr;
  RateRule_t *rr;
  Event_t *e;
  EventAssignment_t *ea;
  Parameter_t *p;
  FunctionDefinition_t *fd;
  SBMLTypeCode_t type;
  const ASTNode_t *math;

  math = NULL;
  
  fprintf(f, "\n");
  for(i=0;i<Model_getNumParameters(m);i++){
    if(i==0)
      fprintf(f, "# Global parameters:\n");
    p = Model_getParameter(m,i);
    if(Parameter_isSetId(p))
      fprintf(f, "%s ",  Parameter_getId(p));
    if(Parameter_isSetName(p))
      fprintf(f, "(%s) ", Parameter_getName(p));
    if(Parameter_isSetValue(p))
      fprintf(f, "= %g; ", Parameter_getValue(p));
    if(Parameter_isSetUnits(p))
      fprintf(f, "[%s]; ", Parameter_getUnits(p));
    if(!Parameter_getConstant(p))
      fprintf(f, "(variable);");
    fprintf(f, "\n");
    
    if ( i==Model_getNumParameters(m)-1 )
      fprintf(f, "\n");
  }

  fprintf(f, "# Reactions:\n");
  for ( i=0; i<Model_getNumReactions(m); i++ ) {    
    r = Model_getReaction(m,i);
  
    fprintf(f, "%s: %s",
	   Reaction_isSetName(r) ? Reaction_getName(r) : Reaction_getId(r),
	   Reaction_getFast(r) ? "(fast)" : "");
    for ( k=0; k<Reaction_getNumReactants(r); k++ ) {
      sref = Reaction_getReactant(r,k);

      if ( SpeciesReference_isSetStoichiometryMath(sref) )	
	fprintf(f, "%s ",
		SBML_formulaToString(\
		SpeciesReference_getStoichiometryMath(sref)));
      else 
	if ( SpeciesReference_getStoichiometry(sref) != 1. )
	  fprintf(f, "%g ",  SpeciesReference_getStoichiometry(sref));
	
      fprintf(f, "%s", SpeciesReference_getSpecies(sref));
      if(k+1<Reaction_getNumReactants(r))
	fprintf(f, "%s", " + ");
    }
    
    fprintf(f, "%s", Reaction_getReversible(r) ? " <-> " : " -> ");
    for ( k=0; k<Reaction_getNumProducts(r); k++ ) {
      sref = Reaction_getProduct(r,k);
      if ( SpeciesReference_isSetStoichiometryMath(sref) )
	fprintf(f, "%s ",
	       SBML_formulaToString(\
		   SpeciesReference_getStoichiometryMath(sref)));
      else
	if ( SpeciesReference_getStoichiometry(sref) != 1. )
	  fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref));
      
      fprintf(f, "%s", SpeciesReference_getSpecies(sref));
      if(k+1<Reaction_getNumProducts(r))
	fprintf(f, "%s", " + ");
    }
    fprintf(f, ";  ");
    if(Reaction_isSetKineticLaw(r)){
      kl = Reaction_getKineticLaw(r);
      math = KineticLaw_getMath(kl);
      fprintf(f, "%s;", SBML_formulaToString(math));
      for(k=0;k<KineticLaw_getNumParameters(kl);k++){
	
	p = KineticLaw_getParameter(kl,k);
	fprintf(f, " %s",  Parameter_getId(p));
	if(Parameter_isSetName(p))
	  fprintf(f, " (%s)", Parameter_getName(p));
	if(Parameter_isSetValue(p))
	  fprintf(f, " = %g", Parameter_getValue(p));
	if(Parameter_isSetUnits(p))
	  fprintf(f, " [%s]", Parameter_getUnits(p));
	if ( !Parameter_getConstant(p) )
	  fprintf(f, " (variable)");
	fprintf(f, ";");
      }
     /*  fprintf(f, "\n"); */
    }else
      fprintf(f, "#   no rate law is set for this reaction.");
    fprintf(f, "\n");
  }
    
  for(i=0;i<Model_getNumRules(m);i++){
    rl = Model_getRule(m,i);
    if ( i == 0 ) {
      fprintf(f, "# Rules:\n");
    }
    type = SBase_getTypeCode((SBase_t *)rl);
     
     
    if ( type == SBML_RATE_RULE ) {
      rr =  (RateRule_t *) rl;
      fprintf(f, " rateRule:       d%s/dt = ", RateRule_getVariable(rr));
    }
    if ( type == SBML_ALGEBRAIC_RULE ) {
      alr = (AlgebraicRule_t *) rl;
      fprintf(f, " algebraicRule:       0 = ");
    }
    if ( type == SBML_ASSIGNMENT_RULE ) {
      asr = (AssignmentRule_t *) rl;
      fprintf(f, " assignmentRule (%s): %s = ",
	     RuleType_toString(AssignmentRule_getType(asr)),
	     AssignmentRule_getVariable(asr));
    }
    if(!Rule_isSetMath(rl)){
      if(Rule_isSetFormula(rl)){
	Rule_setMathFromFormula(rl);
	
      }
    }
    if(Rule_isSetMath(rl))
      fprintf(f, "%s\n", SBML_formulaToString(Rule_getMath(rl)));
	     
  }
  fprintf(f, "\n");

  for(i=0;i<Model_getNumEvents(m);i++){
    if(i==0)
      fprintf(f, "# Events:\n");
    e = Model_getEvent(m,i);
    if(Event_isSetId(e))
      fprintf(f, "%s: ", Event_getId(e));
    if(Event_isSetName(e))
      fprintf(f, "(%s) ", Event_getName(e));   
    if(Event_isSetTrigger(e)) {
      math = Event_getTrigger(e);
      fprintf(f, "trigger: %s\n", SBML_formulaToString(math));
    }
    if(Event_isSetDelay(e))
      fprintf(f, "delay: %s;\n", SBML_formulaToString(Event_getDelay(e)));
    if(Event_isSetTimeUnits(e))
      fprintf(f, "time Units: %s;\n", Event_getTimeUnits(e));
    for(k=0;k<Event_getNumEventAssignments(e);k++){      
      ea = Event_getEventAssignment(e,k);
      if(EventAssignment_isSetVariable(ea))
	fprintf(f, "  event:  %s = %s;\n",
	       EventAssignment_getVariable(ea),
	       EventAssignment_isSetMath(ea) ?
	       SBML_formulaToString(EventAssignment_getMath(ea)) :
	       "# no math set;\n");
    }

    if(i==Model_getNumEvents(m)-1)
       fprintf(f, "\n"); 
  }  


  for ( i=0; i<Model_getNumFunctionDefinitions(m); i++ ) {

    if ( i==0 ) fprintf(f, "# Functions:\n");

    fd = Model_getFunctionDefinition(m,i);
    if ( FunctionDefinition_isSetName(fd) )
      fprintf(f, "%s: ", FunctionDefinition_getName(fd));
    if(FunctionDefinition_isSetId(fd) && FunctionDefinition_isSetMath(fd)){
      fprintf(f, "%s( ", FunctionDefinition_getId(fd));
      math = FunctionDefinition_getMath(fd);
	for(j=0;j<ASTNode_getNumChildren(math)-1;j++){
	  fprintf(f, "%s", SBML_formulaToString(ASTNode_getChild(math, j)));
	  if(j<ASTNode_getNumChildren(math)-2)
	    fprintf(f, ", ");
	  if(j==ASTNode_getNumChildren(math)-2)
	    fprintf(f, ") = ");
	}
      fprintf(f, "%s;", SBML_formulaToString(ASTNode_getRightChild(math)));
    }
    fprintf(f, "\n");
  } 
  
}