Пример #1
0
END_TEST


START_TEST (test_Rule_setFormula)
{
    const char *formula = "k1*X0";


    Rule_setFormula(R, formula);

    fail_unless( !strcmp(Rule_getFormula(R), formula) );
    fail_unless( Rule_isSetFormula(R) == 1 );

    if (Rule_getFormula(R) == formula)
    {
        fail("Rule_setFormula(...) did not make a copy of string.");
    }

    /* Reflexive case (pathological) */
    Rule_setFormula(R, Rule_getFormula(R));
    fail_unless( !strcmp(Rule_getFormula(R), formula) );

    Rule_setFormula(R, "");
    fail_unless( Rule_isSetFormula(R) == 0 );

    if (Rule_getFormula(R) != NULL)
    {
        fail("Rule_setFormula(R, NULL) did not clear string.");
    }
}
Пример #2
0
END_TEST


START_TEST (test_Rule_setFormula2)
{
  int i = Rule_setFormula(R, NULL);

  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
  fail_unless( !Rule_isSetFormula(R)   );
}
Пример #3
0
END_TEST


START_TEST (test_Rule_setFormula3)
{
  const char *formula = "k1 X0";

  int i = Rule_setFormula(R, formula);

  fail_unless( i == LIBSBML_INVALID_OBJECT);
  fail_unless( !Rule_isSetFormula(R)   );
}
Пример #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");
  } 
  
}