Exemplo n.º 1
0
END_TEST

START_TEST(test_parseModel_repressilator)
{
	doc = parseModel(EXAMPLES_FILENAME("repressilator.xml"), 0, 1);
	ck_assert(doc != NULL);
	model = SBMLDocument_getModel(doc);
	ck_assert(model != NULL);
	ck_assert(Model_getNumFunctionDefinitions(model) == 0);
	ck_assert(Model_getNumUnitDefinitions(model) == 0);
	ck_assert(Model_getNumCompartmentTypes(model) == 0);
	ck_assert(Model_getNumSpeciesTypes(model) == 0);
	ck_assert(Model_getNumCompartments(model) == 1);
	ck_assert(Model_getNumSpecies(model) == 6);
	ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
	ck_assert(Model_getNumParameters(model) == 3);
	ck_assert(Model_getNumInitialAssignments(model) == 0);
	ck_assert(Model_getNumRules(model) == 6);
	ck_assert(Model_getNumConstraints(model) == 0);
	ck_assert(Model_getNumReactions(model) == 0);
	ck_assert(Model_getNumEvents(model) == 0);
	CHECK_PARAMETER(model, 0, "alpha");
	CHECK_PARAMETER(model, 1, "beta");
	CHECK_PARAMETER(model, 2, "rho");
	CHECK_RULE(model, 0, "beta * (y1 - x1)");
	CHECK_RULE(model, 1, "beta * (y2 - x2)");
	CHECK_RULE(model, 2, "beta * (y3 - x3)");
	CHECK_RULE(model, 3, "alpha * x1 / (1 + x1 + rho * x3) - y1");
	CHECK_RULE(model, 4, "alpha * x2 / (1 + x2 + rho * x1) - y2");
	CHECK_RULE(model, 5, "alpha * x3 / (1 + x3 + rho * x2) - y3");
}
Exemplo n.º 2
0
END_TEST

START_TEST(test_parseModel_basic)
{
	doc = parseModel(EXAMPLES_FILENAME("basic.xml"), 0, 1);
	ck_assert(doc != NULL);
	model = SBMLDocument_getModel(doc);
	ck_assert(model != NULL);
	ck_assert(Model_getNumFunctionDefinitions(model) == 0);
	ck_assert(Model_getNumUnitDefinitions(model) == 0);
	ck_assert(Model_getNumCompartmentTypes(model) == 0);
	ck_assert(Model_getNumSpeciesTypes(model) == 0);
	ck_assert(Model_getNumCompartments(model) == 1);
	ck_assert(Model_getNumSpecies(model) == 2);
	ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
	ck_assert(Model_getNumParameters(model) == 1);
	ck_assert(Model_getNumInitialAssignments(model) == 0);
	ck_assert(Model_getNumRules(model) == 0);
	ck_assert(Model_getNumConstraints(model) == 0);
	ck_assert(Model_getNumReactions(model) == 2);
	ck_assert(Model_getNumEvents(model) == 0);
	CHECK_PARAMETER(model, 0, "k_1");
	CHECK_REACTION(model, 0, "R1", "k_1 * S1");
	CHECK_REACTION(model, 1, "R2", "k_2 * S2");
}
Exemplo n.º 3
0
int
main (int argc, char *argv[])
{
  const char *filename;

  SBMLDocument_t *d;
  Model_t        *m;

  unsigned int level, version;


  if (argc != 2)
  {
    printf("Usage: printSBML filename\n");
    return 2;
  }


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

  SBMLDocument_printErrors(d, stdout);

  m = SBMLDocument_getModel(d);

  level   = SBMLDocument_getLevel  (d);
  version = SBMLDocument_getVersion(d);

  printf("\n");
  printf("File: %s (Level %u, version %u)\n", filename, level, version);

  if (m == NULL)
  {
    printf("No model present.");
    return 1;
  }

  printf("         ");
  printf("  model id: %s\n",  Model_isSetId(m) ? Model_getId(m) : "(empty)");

  printf( "functionDefinitions: %d\n",  Model_getNumFunctionDefinitions(m) );
  printf( "    unitDefinitions: %d\n",  Model_getNumUnitDefinitions    (m) );
  printf( "   compartmentTypes: %d\n",  Model_getNumCompartmentTypes   (m) );
  printf( "        specieTypes: %d\n",  Model_getNumSpeciesTypes       (m) );
  printf( "       compartments: %d\n",  Model_getNumCompartments       (m) );
  printf( "            species: %d\n",  Model_getNumSpecies            (m) );
  printf( "         parameters: %d\n",  Model_getNumParameters         (m) );
  printf( " initialAssignments: %d\n",  Model_getNumInitialAssignments (m) );
  printf( "              rules: %d\n",  Model_getNumRules              (m) );
  printf( "        constraints: %d\n",  Model_getNumConstraints        (m) );
  printf( "          reactions: %d\n",  Model_getNumReactions          (m) );
  printf( "             events: %d\n",  Model_getNumEvents             (m) );
  printf( "\n" );

  SBMLDocument_free(d);
  return 0;
}
Exemplo n.º 4
0
END_TEST

START_TEST(test_parseModel_huang96)
{
	doc = parseModel(EXAMPLES_FILENAME("huang96.xml"), 0, 1);
	ck_assert(doc != NULL);
	model = SBMLDocument_getModel(doc);
	ck_assert(model != NULL);
	ck_assert(Model_getNumFunctionDefinitions(model) == 0);
	ck_assert(Model_getNumUnitDefinitions(model) == 0);
	ck_assert(Model_getNumCompartmentTypes(model) == 0);
	ck_assert(Model_getNumSpeciesTypes(model) == 0);
	ck_assert(Model_getNumCompartments(model) == 1);
	ck_assert(Model_getNumSpecies(model) == 22);
	ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
	ck_assert(Model_getNumParameters(model) == 0);
	ck_assert(Model_getNumInitialAssignments(model) == 0);
	ck_assert(Model_getNumRules(model) == 0);
	ck_assert(Model_getNumConstraints(model) == 0);
	ck_assert(Model_getNumReactions(model) == 20);
	ck_assert(Model_getNumEvents(model) == 0);
	CHECK_REACTION(model, 0, "r1a", "a1 * E1 * KKK - d1 * E1_KKK");
	CHECK_REACTION(model, 1, "r1b", "k2 * E1_KKK");
	CHECK_REACTION(model, 2, "r2a", "a2 * E2 * P_KKK - d2 * E2_P_KKK");
	CHECK_REACTION(model, 3, "r2b", "k2 * E2_P_KKK");
	CHECK_REACTION(model, 4, "r3a", "a3 * KK * P_KKK - d3 * P_KKK_KK");
	CHECK_REACTION(model, 5, "r3b", "k3 * P_KKK_KK");
	CHECK_REACTION(model, 6, "r4a", "a4 * P_KK * KKPase - d4 * KKPase_P_KK");
	CHECK_REACTION(model, 7, "r4b", "k4 * KKPase_P_KK");
	CHECK_REACTION(model, 8, "r5a", "a5 * P_KK * P_KKK - d5 * P_KKK_P_KK");
	CHECK_REACTION(model, 9, "r5b", "k5 * P_KKK_P_KK");
	CHECK_REACTION(model, 10, "r6a", "a6 * PP_KK * KKPase - d6 * KKPase_PP_KK");
	CHECK_REACTION(model, 11, "r6b", "k6 * KKPase_PP_KK");
	CHECK_REACTION(model, 12, "r7a", "a7 * K * PP_KK - d7 * PP_KK_K");
	CHECK_REACTION(model, 13, "r7b", "k7 * PP_KK_K");
	CHECK_REACTION(model, 14, "r8a", "a8 * P_K * KPase - d8 * KPase_P_K");
	CHECK_REACTION(model, 15, "r8b", "k8 * KPase_P_K");
	CHECK_REACTION(model, 16, "r9a", "a9 * P_K * PP_KK - d9 * PP_KK_P_K");
	CHECK_REACTION(model, 17, "r9b", "k9 * PP_KK_P_K");
	CHECK_REACTION(model, 18, "r10a", "a10 * PP_K * KPase - d10 * KPase_PP_K");
	CHECK_REACTION(model, 19, "r10b", "k10 * KPase_PP_K");
	/* TODO */
}
Exemplo n.º 5
0
END_TEST

START_TEST(test_parseModel_events_1_event_1_assignment_l2)
{
	doc = parseModel(EXAMPLES_FILENAME("events-1-event-1-assignment-l2.xml"), 0, 1);
	ck_assert(doc != NULL);
	model = SBMLDocument_getModel(doc);
	ck_assert(model != NULL);
	ck_assert(Model_getNumFunctionDefinitions(model) == 0);
	ck_assert(Model_getNumUnitDefinitions(model) == 0);
	ck_assert(Model_getNumCompartmentTypes(model) == 0);
	ck_assert(Model_getNumSpeciesTypes(model) == 0);
	ck_assert(Model_getNumCompartments(model) == 1);
	ck_assert(Model_getNumSpecies(model) == 2);
	ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
	ck_assert(Model_getNumParameters(model) == 0);
	ck_assert(Model_getNumInitialAssignments(model) == 0);
	ck_assert(Model_getNumRules(model) == 0);
	ck_assert(Model_getNumConstraints(model) == 0);
	ck_assert(Model_getNumReactions(model) == 1);
	ck_assert(Model_getNumEvents(model) == 1);
	CHECK_REACTION(model, 0, "R", "S1");
	/* TODO */
}