END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Amount)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Compartment_create(2, 4);
Species_t *s = Species_create(2, 4);
Compartment_setId ( c, sid );
Model_addCompartment( m, c );
Species_setCompartment ( s, sid );
Species_setInitialAmount( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL );
fail_unless( Species_getInitialAmount(s) == 2.34, NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_Species_setInitialAmount)
{
fail_unless( !Species_isSetInitialAmount (S) );
fail_unless( !Species_isSetInitialConcentration(S) );
Species_setInitialAmount(S, 1.2);
fail_unless( Species_isSetInitialAmount (S) );
fail_unless( !Species_isSetInitialConcentration(S) );
fail_unless( Species_getInitialAmount(S) == 1.2 );
}
END_TEST
START_TEST (test_Species_setInitialAmount1)
{
int i = Species_setInitialAmount(C, 2.0);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getInitialAmount(C) == 2.0 );
fail_unless( Species_isSetInitialAmount(C));
i = Species_unsetInitialAmount(C);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetInitialAmount(C));
}
END_TEST
START_TEST (test_L3_Species_initialAmount)
{
double initialAmount = 0.2;
fail_unless( !Species_isSetInitialAmount(S));
fail_unless( util_isNaN(Species_getInitialAmount(S)));
Species_setInitialAmount(S, initialAmount);
fail_unless( Species_getInitialAmount(S) == initialAmount );
fail_unless( Species_isSetInitialAmount(S) );
Species_unsetInitialAmount(S);
fail_unless( !Species_isSetInitialAmount(S) );
fail_unless( util_isNaN(Species_getInitialAmount(S)));
}
END_TEST
START_TEST (test_Species_setInitialAmount2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setInitialAmount(c, 4);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getInitialAmount(c) == 4.0 );
fail_unless( Species_isSetInitialAmount(c));
i = Species_unsetInitialAmount(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetInitialAmount(c));
Species_free(c);
}
/*
setValues: the user can enter a species name and
change its initial condition (amount or concentration)
*/
static void setValues(Model_t *m) {
char *species;
char *newIA;
char *newIC;
Species_t *s;
printf("Please enter the id of the species to change: ");
species = get_line(stdin);
species = util_trim(species);
if ( (s = Model_getSpeciesById(m,species) ) ) {
printf("\n");
printf("Id: %s\n", Species_getId(s));
if ( Species_isSetName(s) ) {
printf("Name: %s\n", Species_getName(s));
}
if ( Species_isSetInitialAmount(s) ) {
printf("Initial Amount: %g", Species_getInitialAmount(s));
}
else if (Species_isSetInitialConcentration(s) ) {
printf("Initial Concentration: %g", Species_getInitialConcentration(s));
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
} else {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
if ( Species_isSetSpatialSizeUnits(s) ) {
printf("%s%s", "/", Species_getSpatialSizeUnits(s));
}
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
printf(" (has only substance units)");
}
printf("\n");
if ( Species_isSetCharge(s) ) {
printf("Charge: %-10d", Species_getCharge(s));
}
printf("\n");
printf("%s ", Species_getBoundaryCondition(s) ?
"Species is a Boundary\n" : "\n");
printf("%s ", Species_getConstant(s) ?
"Species is set constant" : "\n");
printf("\n");
if ( Species_isSetInitialAmount(s) ) {
printf("Please enter new initial Amount: ");
newIA = get_line(stdin);
newIA = util_trim(newIA);
Species_setInitialAmount(s, (float) atof(newIA));
}
else if ( Species_isSetInitialConcentration(s) ) {
printf("Please enter new initial Concentration: ");
newIC = get_line(stdin);
newIC = util_trim(newIC);
Species_setInitialConcentration(s, (float) atof(newIC));
}
}
else {
printf("%s not found.\n", species);
}
}
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);
}
