END_TEST
START_TEST (test_ListOf_append)
{
Model_t *m = Model_create(2, 4);
Model_createCompartment(m);
ListOf_t *loc = Model_getListOfCompartments(m);
fail_unless(ListOf_size(loc) == 1);
SBase_t *c = (SBase_t*)Compartment_create(2, 4);
int i = ListOf_append(loc, c);
fail_unless(i == LIBSBML_OPERATION_SUCCESS);
fail_unless(ListOf_size(loc) == 2);
SBase_t *sp = (SBase_t*)Species_create(2, 4);
i = ListOf_append(loc, sp);
fail_unless(i == LIBSBML_INVALID_OBJECT);
fail_unless(ListOf_size(loc) == 2);
Model_free(m);
Species_free((Species_t*)sp);
}
END_TEST
START_TEST (test_SBMLDocument_setLevelAndVersion_Error)
{
SBMLDocument_t *d = SBMLDocument_create();
SBMLDocument_setLevelAndVersion(d, 2, 1);
Model_t *m1 = Model_create(2, 1);
/* add unitDefinition */
Unit_t * u = Unit_create(2, 1);
Unit_setKind(u, UnitKind_forName("mole"));
Unit_setOffset(u, 3.2);
UnitDefinition_t *ud =
UnitDefinition_create(2, 1);
UnitDefinition_setId(ud, "ud");
UnitDefinition_addUnit(ud, u);
Model_addUnitDefinition(m1, ud);
SBMLDocument_setModel(d, m1);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,2,2) == 0);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,2,3) == 0);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,1,2) == 0);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,1,1) == 0);
SBMLDocument_free(d);
Model_free(m1);
Unit_free(u);
UnitDefinition_free(ud);
}
END_TEST
START_TEST (test_L3_Model_free_NULL)
{
Model_free(NULL);
}
END_TEST
START_TEST (test_SBMLDocument_setModel)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t *m1 = Model_create(2, 4);
Model_t *m2 = Model_create(2, 4);
Model_t *mout;
fail_unless(SBMLDocument_getModel(d) == NULL);
fail_unless( SBMLDocument_isSetModel(d) == 0 );
int i = SBMLDocument_setModel(d, m1);
fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
mout = SBMLDocument_getModel(d);
fail_unless(mout != NULL);
fail_unless(mout != m1);
fail_unless( SBMLDocument_isSetModel(d) == 1 );
/* Reflexive case (pathological) */
i = SBMLDocument_setModel(d, SBMLDocument_getModel(d));
fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
mout = SBMLDocument_getModel(d);
fail_unless(mout != NULL);
fail_unless(mout != m1);
i = SBMLDocument_setModel(d, m2);
fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
mout = SBMLDocument_getModel(d);
fail_unless(mout != NULL);
fail_unless(mout != m2);
SBMLDocument_free(d);
Model_free(m1);
Model_free(m2);
}
END_TEST
START_TEST (test_L3_Model_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Model_t *m =
Model_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) m) == SBML_MODEL );
fail_unless( SBase_getMetaId ((SBase_t *) m) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) m) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) m) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) m) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) m) == 1 );
fail_unless( Model_getNamespaces (m) != NULL );
fail_unless( XMLNamespaces_getLength(Model_getNamespaces(m)) == 2 );
fail_unless( Model_getId (m) == NULL );
fail_unless( Model_getName (m) == NULL );
fail_unless( Model_getSubstanceUnits(m) == NULL );
fail_unless( Model_getTimeUnits(m) == NULL );
fail_unless( Model_getVolumeUnits(m) == NULL );
fail_unless( Model_getAreaUnits(m) == NULL );
fail_unless( Model_getLengthUnits(m) == NULL );
fail_unless( Model_getConversionFactor(m) == NULL );
fail_unless( !Model_isSetId (m) );
fail_unless( !Model_isSetName (m) );
fail_unless( !Model_isSetSubstanceUnits(m) );
fail_unless( !Model_isSetTimeUnits(m) );
fail_unless( !Model_isSetVolumeUnits(m) );
fail_unless( !Model_isSetAreaUnits(m) );
fail_unless( !Model_isSetLengthUnits(m) );
fail_unless( !Model_isSetConversionFactor(m) );
Model_free(m);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_SBMLDocument_setModel3)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m1 = Model_create(2, 2);
int i = SBMLDocument_setModel(d, m1);
fail_unless ( i == LIBSBML_OPERATION_SUCCESS);
fail_unless (SBMLDocument_getModel(d) != 0);
SBMLDocument_free(d);
Model_free(m1);
}
END_TEST
START_TEST (test_SBMLDocument_setModel1)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m1 = Model_create(2, 1);
int i = SBMLDocument_setModel(d, m1);
fail_unless ( i == LIBSBML_VERSION_MISMATCH);
fail_unless (SBMLDocument_getModel(d) == 0);
SBMLDocument_free(d);
Model_free(m1);
}
END_TEST
START_TEST (test_SBMLDocument_setLevelAndVersion)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m1 = Model_create(2, 2);
SBMLDocument_setModel(d, m1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,3) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,1) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,2) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,1) == 0);
SBMLDocument_free(d);
Model_free(m1);
}
END_TEST
START_TEST (test_create_l1v1_units)
{
Model_t *m;
Compartment_t *c;
KineticLaw_t *kl;
Parameter_t *p;
Reaction_t *r;
Species_t *s;
SpeciesReference_t *sr;
Unit_t *u;
UnitDefinition_t *ud;
/**
* <sbml level="1" version="1">
*/
m = Model_create(2, 4);
/**
* <unitDefinition name="substance">
* <listOfUnits>
* <unit kind="mole" scale="-3"/>
* </listOfUnits>
* </unitDefinition>
*/
ud = Model_createUnitDefinition(m);
UnitDefinition_setName(ud, "substance");
u = Model_createUnit(m);
Unit_setKind(u,UNIT_KIND_MOLE);
Unit_setScale(u, -3);
/**
* <unitDefinition name="mls">
* <listOfUnits>
* <unit kind="mole" scale="-3"/>
* <unit kind="liter" exponent="-1"/>
* <unit kind="second" exponent="-1"/>
* </listOfUnits>
* </unitDefinition>
*/
ud = Model_createUnitDefinition(m);
UnitDefinition_setName(ud, "mls");
u = Model_createUnit(m);
Unit_setKind(u, UNIT_KIND_MOLE);
Unit_setScale(u, -3);
u = Model_createUnit(m);
Unit_setKind(u, UNIT_KIND_LITER);
Unit_setExponent(u, -1);
u = Model_createUnit(m);
Unit_setKind(u, UNIT_KIND_SECOND);
Unit_setExponent(u, -1);
/**
* <listOfCompartments>
* <compartment name="cell"/>
* </listOfCompartments>
*/
c = Model_createCompartment(m);
Compartment_setName(c, "cell");
/**
* <listOfSpecies>
* <specie name="x0" compartment="cell" initialAmount="1"/>
* <specie name="x1" compartment="cell" initialAmount="1"/>
* <specie name="s1" compartment="cell" initialAmount="1"/>
* <specie name="s2" compartment="cell" initialAmount="1"/>
* </listOfSpecies>
*/
s = Model_createSpecies(m);
Species_setName(s, "x0");
Species_setCompartment(s, "cell");
Species_setInitialAmount(s, 1);
s = Model_createSpecies(m);
Species_setName(s, "x1");
Species_setCompartment(s, "cell");
Species_setInitialAmount(s, 1);
s = Model_createSpecies(m);
Species_setName(s, "s1");
Species_setCompartment(s, "cell");
Species_setInitialAmount(s, 1);
s = Model_createSpecies(m);
Species_setName(s, "s2");
Species_setCompartment(s, "cell");
Species_setInitialAmount(s, 1);
/**
* <listOfParameters>
* <parameter name="vm" value="2" units="mls"/>
* <parameter name="km" value="2"/>
* </listOfParameters>
*/
p = Model_createParameter(m);
Parameter_setName (p, "vm");
Parameter_setUnits(p, "mls");
Parameter_setValue(p, 2);
p = Model_createParameter(m);
Parameter_setName (p, "km");
Parameter_setValue(p, 2);
/**
* <reaction name="v1">
* <listOfReactants>
* <specieReference specie="x0"/>
* </listOfReactants>
* <listOfProducts>
* <specieReference specie="s1"/>
* </listOfProducts>
* <kineticLaw formula="(vm * s1)/(km + s1)"/>
* </reaction>
*/
r = Model_createReaction(m);
Reaction_setName(r, "v1");
sr = Model_createReactant(m);
SpeciesReference_setSpecies(sr, "x0");
sr = Model_createProduct(m);
SpeciesReference_setSpecies(sr, "s1");
kl = Model_createKineticLaw(m);
KineticLaw_setFormula(kl, "(vm * s1)/(km + s1)");
/**
* <reaction name="v2">
* <listOfReactants>
* <specieReference specie="s1"/>
* </listOfReactants>
* <listOfProducts>
* <specieReference specie="s2"/>
* </listOfProducts>
* <kineticLaw formula="(vm * s2)/(km + s2)"/>
* </reaction>
*/
r = Model_createReaction(m);
Reaction_setName(r, "v2");
sr = Model_createReactant(m);
SpeciesReference_setSpecies(sr, "s1");
sr = Model_createProduct(m);
SpeciesReference_setSpecies(sr, "s2");
kl = Model_createKineticLaw(m);
KineticLaw_setFormula(kl, "(vm * s2)/(km + s2)");
/**
* <reaction name="v3">
* <listOfReactants>
* <specieReference specie="s2"/>
* </listOfReactants>
* <listOfProducts>
* <specieReference specie="x1"/>
* </listOfProducts>
* <kineticLaw formula="(vm * s1)/(km + s1)"/>
* </reaction>
*/
r = Model_createReaction(m);
Reaction_setName(r, "v3");
sr = Model_createReactant(m);
SpeciesReference_setSpecies(sr, "s2");
sr = Model_createProduct(m);
SpeciesReference_setSpecies(sr, "x1");
kl = Model_createKineticLaw(m);
KineticLaw_setFormula(kl, "(vm * s1)/(km + s1)");
Model_free(m);
}
void
L3ModelTest_teardown (void)
{
Model_free(M);
}
int main(int argc, char **argv) {
double c = 1e-8;
/* number of kilobases separating the two sites */
double kb;
double u = 1e-6;
double relerr, relerr_tol = 0.004;
double odeAbsTol = 1e-7;
double odeRelTol = 1e-3;
int twoNsmp = 20;
int ok = 1;
int i, verbose = 0;
const char *statlbl;
size_t stateDim = Strobeck_stateDim();
double ystrobeck[stateDim], y_ode[stateDim], y_eq0[stateDim];
Model *model = Model_alloc("Strobeck", twoNsmp);
ODE *ode = ODE_new(model, odeAbsTol, odeRelTol);
assert(Model_stateDim(model) == stateDim);
switch (argc) {
case 1:
break;
case 2:
if(strncmp(argv[1], "-v", 2) != 0)
eprintf("usage: xstrobeck [-v]\n");
verbose = 1;
break;
default:
eprintf("usage: xhill [-v]\n");
}
/* Set up pophist */
EpochLink *linkedList = NULL;
linkedList = EpochLink_new(linkedList, 300.0, 1e5);
linkedList = EpochLink_new(linkedList, strtod("Inf", 0), 1e2);
PopHist *ph = PopHist_fromEpochLink(linkedList);
for(kb = 1.0; kb <= 300; kb += 5.0) {
double sep_bases = kb * 1000;
Strobeck_evolveDiscrete(ystrobeck, ph, c * sep_bases, u);
double sigdsq_hill = Strobeck_get_sigdsq(ystrobeck, twoNsmp);
double sigdsq_eq0 = ODE_ldEq(ode, c * sep_bases, u, ph, 0);
for(i = 0; i < Model_stateDim(model); ++i)
y_eq0[i] = ODE_stateVal(ode, i);
double sigdsq_ode = ODE_ld(ode, c * sep_bases, u, ph);
for(i = 0; i < Model_stateDim(model); ++i)
y_ode[i] = ODE_stateVal(ode, i);
if(verbose) {
printf("%8s %8s %8s %8s %8s %8s\n",
"param", "c", "hill", "ode", "relerr", "eqEpoch0");
}
for(i = 0; i < Model_stateDim(model); ++i) {
char buff[10];
snprintf(buff, sizeof(buff), "y[%d]", i);
relerr = fabs(y_ode[i] - ystrobeck[i]) / fabs(ystrobeck[i]);
if(verbose)
printf("%8s %8.6f %8.6f %8.6f %8.6f %8.6f\n",
buff, c * sep_bases, ystrobeck[i], y_ode[i], relerr,
y_eq0[i]);
}
relerr = fabs(sigdsq_hill - sigdsq_ode) / fabs(sigdsq_hill);
if(relerr > relerr_tol) {
ok = 0;
statlbl = "FAIL";
} else
statlbl = "OK";
if(verbose) {
printf("%8s %8.6f %8.6f %8.6f %8.6f %8.6f %6s\n",
"sigdsq", c * sep_bases, sigdsq_hill, sigdsq_ode, relerr,
sigdsq_eq0, statlbl);
}
}
if(verbose) {
printf("c=%lg u=%lg\n", c, u);
PopHist_print(ph, stdout);
}
if(verbose)
printf("State labels:");
for(i = 0; i < Model_stateDim(model); ++i) {
const char *lbl = Model_stateLbl(model, i);
if(verbose)
printf(" %s", lbl);
}
if(verbose)
putchar('\n');
Model_free(model);
ODE_free(ode);
EpochLink_free(linkedList);
PopHist_free(ph);
if(ok)
unitTstResult("Strobeck", "OK");
else
unitTstResult("Strobeck", "FAIL");
return 0;
}
