void writeSpatialSBML() {
/*
// SBMLNamespaces of SBML Level 3 Version 1 with Spatial Version 1
SBMLNamespaces sbmlns(3,1,"spatial",1);
// SpatialPkgNamespaces spatialns(3,1,1);
// add Required Elements package namespace
sbmlns.addPkgNamespace("req", 1);
*/
// SBMLNamespaces of SBML Level 3 Version 1 with 'req' Version 1
// then add 'spatial' package namespace.
RequiredElementsPkgNamespaces sbmlns(3,1,1);
sbmlns.addPkgNamespace("spatial",1);
// create the L3V1 document with spatial package
SBMLDocument document(&sbmlns);
// set 'required' attribute on document for 'spatial' and 'req' packages to 'T'??
SBMLDocumentPlugin* dplugin;
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("spatial"));
dplugin->setRequired(true);
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("req"));
dplugin->setRequired(true);
// create the Model
Model *model = document.createModel();
model-> setId("trial_spatial");
model-> setName("trial_spatial");
// create the Compartments
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
// create the Species
Species* species1 = model->createSpecies();
species1->setId("ATPc");
species1->setCompartment("cytosol");
species1->setInitialConcentration(1.0);
species1->setHasOnlySubstanceUnits(false);
species1->setBoundaryCondition(false);
species1->setConstant(false);
// spatial package extension to species.
// required elements package extention to parameter
RequiredElementsSBasePlugin* reqplugin;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(species1->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
SpatialSpeciesRxnPlugin* srplugin;
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(species1->getPlugin("spatial"));
srplugin->setIsSpatial(true);
// add parameter for diff coeff of species1
Parameter* paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_dc");
paramSp->setValue(1.0);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
DiffusionCoefficient* diffCoeff = pplugin->getDiffusionCoefficient();
diffCoeff->setVariable(species1->getId());
diffCoeff->setCoordinateIndex(0);
// add parameter for adv coeff of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_ac");
paramSp->setValue(1.5);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
AdvectionCoefficient* advCoeff = pplugin->getAdvectionCoefficient();
advCoeff->setVariable(species1->getId());
advCoeff->setCoordinateIndex(0);
// add parameter for boundary condition of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_bc");
paramSp->setValue(2.0);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
BoundaryCondition* boundCon = pplugin->getBoundaryCondition();
boundCon->setVariable(species1->getId());
boundCon->setType("value");
boundCon->setCoordinateBoundary("Xmin");
Species* species2 = model->createSpecies();
species2->setId("ADPc");
species2->setCompartment("cytosol");
species2->setInitialConcentration(1);
species2->setHasOnlySubstanceUnits(false);
species2->setBoundaryCondition(false);
species2->setConstant(false);
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(species2->getPlugin("spatial"));
srplugin->setIsSpatial(true);
/* // create a parameter
Parameter* param = model->createParameter();
param->setId("k_1");
param->setValue(0.24);
param->setConstant(true);
// create an assignment rule
AssignmentRule* assignRule = model->createAssignmentRule();
assignRule->setVariable(species1->getId());
assignRule->setFormula("species2+k_1");
*/
/*
reqplugin = static_cast<RequiredElementsSBasePlugin*>(assignRule->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(false);
*/
Reaction* reaction = model->createReaction();
reaction->setId("rxn1");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("cytosol");
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(reaction->getPlugin("spatial"));
srplugin->setIsLocal(true);
//
// Get a SpatialModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
SpatialModelPlugin* mplugin;
mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
//
// Creates a geometry object via SpatialModelPlugin object.
//
Geometry* geometry = mplugin->getGeometry();
geometry->setCoordinateSystem("XYZ");
CoordinateComponent* coordX = geometry->createCoordinateComponent();
coordX->setSpatialId("coordComp1");
coordX->setComponentType("cartesian");
coordX->setSbmlUnit("umeter");
coordX->setIndex(1);
BoundaryMin* minX = coordX->createBoundaryMin();
minX->setSpatialId("Xmin");
minX->setValue(0.0);
BoundaryMax* maxX = coordX->createBoundaryMax();
maxX->setSpatialId("Xmax");
maxX->setValue(10.0);
Parameter* paramX = model->createParameter();
paramX->setId("x");
paramX->setValue(8.0);
// required elements package extention to parameter
// RequiredElementsSBasePlugin* reqplugin;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramX->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
// SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramX->getPlugin("spatial"));
SpatialSymbolReference* spSymRef = pplugin->getSpatialSymbolReference();
spSymRef->setSpatialId(coordX->getSpatialId());
spSymRef->setType(coordX->getElementName());
DomainType* domainType = geometry->createDomainType();
domainType->setSpatialId("dtype1");
domainType->setSpatialDimensions(3);
// Spatial package extension to compartment (mapping compartment with domainType)
// required elements package extention to compartment
reqplugin = static_cast<RequiredElementsSBasePlugin*>(compartment->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
SpatialCompartmentPlugin* cplugin;
cplugin = static_cast<SpatialCompartmentPlugin*>(compartment->getPlugin("spatial"));
CompartmentMapping* compMapping = cplugin->getCompartmentMapping();
compMapping->setSpatialId("compMap1");
compMapping->setCompartment(compartment->getId());
compMapping->setDomainType(domainType->getSpatialId());
compMapping->setUnitSize(1.0);
Domain* domain = geometry->createDomain();
domain->setSpatialId("domain1");
domain->setDomainType("dtype1");
domain->setImplicit(false);
domain->setShapeId("circle");
InteriorPoint* internalPt1 = domain->createInteriorPoint();
internalPt1->setCoord1(1.0);
domain = geometry->createDomain();
domain->setSpatialId("domain2");
domain->setDomainType("dtype1");
domain->setImplicit(false);
domain->setShapeId("square");
InteriorPoint* internalPt2 = domain->createInteriorPoint();
internalPt2->setCoord1(5.0);
AdjacentDomains* adjDomain = geometry->createAdjacentDomains();
adjDomain->setSpatialId("adjDomain1");
adjDomain->setDomain1("domain1");
adjDomain->setDomain2("domain2");
AnalyticGeometry* analyticGeom = geometry->createAnalyticGeometry();
analyticGeom->setSpatialId("analyticGeom1");
AnalyticVolume* analyticVol = analyticGeom->createAnalyticVolume();
analyticVol->setSpatialId("analyticVol1");
analyticVol->setDomainType(domainType->getSpatialId());
analyticVol->setFunctionType("squareFn");
analyticVol->setOrdinal(1);
const char* mathMLStr = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><apply xmlns=\"\"><plus /><apply><times /><ci>x</ci><ci>x</ci></apply><apply><minus /><cn>1.0</cn></apply></apply></math>";
ASTNode* mathNode = readMathMLFromString(mathMLStr);
analyticVol->setMath(mathNode);
SampledFieldGeometry* sfg = geometry->createSampledFieldGeometry();
sfg->setSpatialId("sampledFieldGeom1");
SampledField* sampledField = sfg->createSampledField();
sampledField->setSpatialId("sampledField1");
sampledField->setNumSamples1(4);
sampledField->setNumSamples2(4);
sampledField->setNumSamples3(2);
sampledField->setDataType("double");
sampledField->setInterpolationType("linear");
sampledField->setEncoding("encoding1");
//int samples[5] = {1, 2, 3, 4, 5};
int samples[32] = {
// z=0
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0,
// z=1
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0
};
ImageData* id = sampledField->createImageData();
id->setDataType("compressed");
id->setSamples(samples, 32);
SampledVolume* sampledVol = sfg->createSampledVolume();
sampledVol->setSpatialId("sv_1");
sampledVol->setDomainType(domainType->getSpatialId());
sampledVol->setSampledValue(128.0);
sampledVol->setMinValue(0.0);
sampledVol->setMaxValue(255.0);
ParametricGeometry* pg = geometry->createParametricGeometry();
pg->setSpatialId("parametricGeom1");
ParametricObject* paramObj = pg->createParametricObject();
paramObj->setSpatialId("po_1");
paramObj->setDomain(domain->getSpatialId());
paramObj->setPolygonType("hexagon");
int ptIndices[5] = {1, 2, 3, 4, 5};
PolygonObject* po = paramObj->createPolygonObject();
po->setPointIndices(ptIndices, 5);
SpatialPoint* spPt = pg->createSpatialPoint();
spPt->setSpatialId("sp_1");
spPt->setDomain(domain->getSpatialId());
spPt->setCoord1(1);
spPt->setCoord2(2);
spPt->setCoord3(3);
CSGeometry* csg = geometry->createCSGeometry();
csg->setSpatialId("csGeom1");
CSGObject* csgObj = csg->createCSGObject();
csgObj->setSpatialId("csg_csgo_1");
csgObj->setDomainType(domainType->getSpatialId());
csgObj->setOrdinal(1);
CSGScale* scale = csgObj->createCSGScale();
scale->setScaleX(2.0);
scale->setScaleY(3.0);
scale->setScaleZ(4.0);
CSGPrimitive* prim1 = scale->createCSGPrimitive();
prim1->setPrimitiveType("SOLID_SPHERE");
csgObj = csg->createCSGObject();
csgObj->setSpatialId("csg_csgo_2");
csgObj->setDomainType(domainType->getSpatialId());
CSGSetOperator* setUnion = csgObj->createCSGSetOperator();
setUnion->setOperationType("UNION");
/* CSGPrimitive* prim = setUnion->createCSGPrimitive();
prim->setPrimitiveType("SOLID_SPHERE");
CSGPrimitive* prim2 = setUnion->createCSGPrimitive();
prim2->setPrimitiveType("SOLID_CONE");
*/
CSGPrimitive* prim2 = new CSGPrimitive(3,1,1);
prim2->setSpatialId("cone0");
prim2->setPrimitiveType("SOLID_CONE");
CSGTranslation* translatedCone = new CSGTranslation(3,1,1);
translatedCone->setSpatialId("translation0");
translatedCone->setTranslateX(2.0);
translatedCone->setTranslateY(2.0);
translatedCone->setTranslateZ(2.0);
translatedCone->setChild(prim2);
int n = setUnion->addCSGNodeChild(translatedCone);
CSGPrimitive* prim3 = new CSGPrimitive(3,1,1);
prim3->setSpatialId("sphere0");
prim3->setPrimitiveType("SOLID_SPHERE");
n = setUnion->addCSGNodeChild(prim3);
writeSBML(&document, "spatial_example0.xml");
}
void readSpatialSBML() {
SBMLDocument *document2 = readSBML("spatial_example0.xml");
Model *model2 = document2->getModel();
Compartment *comp;
SpatialCompartmentPlugin* cplugin;
RequiredElementsSBasePlugin* reqplugin;
for (unsigned int i = 0; i < model2->getNumCompartments(); i++) {
comp = model2->getCompartment(i);
cout << "Compartment" << i << ": " << comp->getId() << endl;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(comp->getPlugin("req"));
if (!reqplugin->getMathOverridden().empty()) {
cout << "Comp" << i << " req mathOverridden: " << reqplugin->getMathOverridden() << endl;
}
cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
if (cplugin->getCompartmentMapping()->isSetSpatialId()) {
cout << "Comp" << i << " CMSpId: " << cplugin->getCompartmentMapping()->getSpatialId() << endl;
cout << "Comp" << i << " CM_Comp: " << cplugin->getCompartmentMapping()->getCompartment() << endl;
cout << "Comp" << i << " CM_DType: " << cplugin->getCompartmentMapping()->getDomainType() << endl;
cout << "Comp" << i << " CM_UnitSz: " << cplugin->getCompartmentMapping()->getUnitSize() << endl;
}
}
Species *sp;
SpatialSpeciesRxnPlugin* srplugin;
for (unsigned int i = 0; i < model2->getNumSpecies(); i++) {
sp = model2->getSpecies(i);
cout << "Species" << i << ": " << sp->getId() << endl;
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(sp->getPlugin("spatial"));
if (srplugin->getIsSpatial()) {
cout << "species" << i << " isSpatial: " << srplugin->getIsSpatial() << endl;
}
}
Parameter *param;
SpatialParameterPlugin* pplugin;
for (unsigned int i = 0; i < model2->getNumParameters(); i++) {
param = model2->getParameter(i);
cout << "Parameter" << i << ": " << param->getId() << endl;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(param->getPlugin("req"));
if (!reqplugin->getMathOverridden().empty()) {
cout << "Parameter" << i << " req mathOverridden: " << reqplugin->getMathOverridden() << endl;
}
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
if (pplugin->getSpatialSymbolReference()->isSetSpatialId()) {
cout << "Parameter" << i << " SpRefId: " << pplugin->getSpatialSymbolReference()->getSpatialId() << endl;
cout << "Parameter" << i << " SpRefType: " << pplugin->getSpatialSymbolReference()->getType() << endl;
}
if (pplugin->getDiffusionCoefficient()->isSetVariable()) {
cout << "Diff_" << i << " SpeciesVarId: " << pplugin->getDiffusionCoefficient()->getVariable() << endl;
cout << "Diff_" << i << " SpCoordIndex: " << pplugin->getDiffusionCoefficient()->getCoordinateIndex() << endl;
}
if (pplugin->getAdvectionCoefficient()->isSetVariable()) {
cout << "Adv_" << i << " SpeciesVarId: " << pplugin->getAdvectionCoefficient()->getVariable() << endl;
cout << "Adv_" << i << " SpCoordIndex: " << pplugin->getAdvectionCoefficient()->getCoordinateIndex() << endl;
}
if (pplugin->getBoundaryCondition()->isSetVariable()) {
cout << "BC_" << i << " SpeciesVarId: " << pplugin->getBoundaryCondition()->getVariable() << endl;
cout << "BC_" << i << " SpCoordBoundary: " << pplugin->getBoundaryCondition()->getCoordinateBoundary() << endl;
cout << "BC_" << i << " SpBoundaryType: " << pplugin->getBoundaryCondition()->getType() << endl;
}
}
Reaction *rxn;
for (unsigned int i = 0; i < model2->getNumReactions(); i++) {
rxn = model2->getReaction(i);
cout << "Reaction" << i << ": " << rxn->getId() << endl;
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(rxn->getPlugin("spatial"));
if (srplugin->getIsLocal()) {
cout << "rxn" << i << " isLocal: " << srplugin->getIsLocal() << endl;
}
}
Rule *rule;
for (unsigned int i = 0; i < model2->getNumRules(); i++) {
rule = model2->getRule(i);
cout << "Rule" << i << ": " << rule->getVariable() << endl;
}
//
// Get a SpatialModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be cast for the
// corresponding derived class.
//
SpatialModelPlugin* mplugin2;
mplugin2 = static_cast<SpatialModelPlugin*>(model2->getPlugin("spatial"));
cout << "URI: " << mplugin2->getURI() << endl;
cout << "prefix: " << mplugin2->getPrefix() << endl;
// get a Geometry object via SpatialModelPlugin object.
Geometry* geometry2 = mplugin2->getGeometry();
cout << "Geometry coordSystem: " << geometry2->getCoordinateSystem() << endl;
// get a CoordComponent object via the Geometry object.
CoordinateComponent* coordComp = geometry2->getCoordinateComponent(0);
std::cout << "CoordComponent spatialId: " << coordComp->getSpatialId() << std::endl;
std::cout << "CoordComponent compType: " << coordComp->getComponentType() << std::endl;
std::cout << "CoordComponent sbmlUnit: " << coordComp->getSbmlUnit() << std::endl;
std::cout << "CoordComponent index: " << coordComp->getIndex() << std::endl;
BoundaryMin* minX = coordComp->getBoundaryMin();
std::cout << "minX name: " << minX->getSpatialId() << std::endl;
std::cout << "minX value: " << minX->getValue() << std::endl;
BoundaryMax* maxX = coordComp->getBoundaryMax();
std::cout << "maxX name: " << maxX->getSpatialId() << std::endl;
std::cout << "maxX value: " << maxX->getValue() << std::endl;
// get a DomainType object via the Geometry object.
DomainType* domainType2 = geometry2->getDomainType(0);
std::cout << "DomainType spatialId: " << domainType2->getSpatialId() << std::endl;
std::cout << "DomainType spatialDim: " << domainType2->getSpatialDimensions() << std::endl;
// get a Domain object via the Geometry object.
Domain* domain = geometry2->getDomain(0);
std::cout << "Domain1 spatialId: " << domain->getSpatialId() << std::endl;
std::cout << "Domain1 implicit: " << domain->getImplicit() << std::endl;
std::cout << "Domain1 domainType: " << domain->getDomainType() << std::endl;
std::cout << "Domain1 Shape: " << domain->getShapeId() << std::endl;
// get an internal point via the domain object
InteriorPoint* internalPt = domain->getInteriorPoint(0);
std::cout << "InternalPt_1 coord1: " << internalPt->getCoord1() << std::endl;
// get a Domain object via the Geometry object.
domain = geometry2->getDomain(1);
std::cout << "Domain2 spatialId: " << domain->getSpatialId() << std::endl;
std::cout << "Domain2 implicit: " << domain->getImplicit() << std::endl;
std::cout << "Domain2 domainType: " << domain->getDomainType() << std::endl;
std::cout << "Domain2 Shape: " << domain->getShapeId() << std::endl;
// get an internal point via the domain object
internalPt = domain->getInteriorPoint(0);
std::cout << "InternalPt_2 coord1: " << internalPt->getCoord1() << std::endl;
// get an AdjacentDomains object via the Geometry object.
AdjacentDomains* adjDomain = geometry2->getAdjacentDomains(0);
std::cout << "AdjDomain spatialId: " << adjDomain->getSpatialId() << std::endl;
std::cout << "AdjDomain domain1: " << adjDomain->getDomain1() << std::endl;
std::cout << "AdjDomain domain2: " << adjDomain->getDomain2() << std::endl;
// get the different GeometryDefinition objects via the Geometry object.
GeometryDefinition* gd;
for (unsigned int i = 0; i < geometry2->getNumGeometryDefinitions(); i++) {
gd = geometry2->getGeometryDefinition(i);
if (gd->isAnalyticGeometry()) {
AnalyticGeometry* analyticalGeom = static_cast<AnalyticGeometry*>(gd);
std::cout << "AnalGeom spatialId: " << analyticalGeom->getSpatialId() << std::endl;
// analVol from analGeom.
AnalyticVolume* av = analyticalGeom->getAnalyticVolume(0);
std::cout << "AnalVol spatialId: " << av->getSpatialId() << std::endl;
std::cout << "AnalVol domainType: " << av->getDomainType() << std::endl;
std::cout << "AnalVol funcType: " << av->getFunctionType() << std::endl;
std::cout << "AnalVol ordinal: " << av->getOrdinal() << std::endl;
const ASTNode* mathNode = av->getMath();
char* mathStr = writeMathMLToString(mathNode);
std::cout << "AnalVol math: " << mathStr << std::endl;
}
if (gd->isSampledFieldGeometry()) {
SampledFieldGeometry* sfGeom = static_cast<SampledFieldGeometry*>(gd);
std::cout << "SampledFieldGeom spatialId: " << sfGeom->getSpatialId() << std::endl;
// sampledField from sfGeom
SampledField* sf = sfGeom->getSampledField();
std::cout << "SampledField spatialId: " << sf->getSpatialId() << std::endl;
std::cout << "SampledField dataType: " << sf->getDataType() << std::endl;
std::cout << "SampledField interpolation: " << sf->getInterpolationType() << std::endl;
std::cout << "SampledField encoding: " << sf->getEncoding() << std::endl;
std::cout << "SampledField numSamples1: " << sf->getNumSamples1() << std::endl;
std::cout << "SampledField numSamples2: " << sf->getNumSamples2() << std::endl;
std::cout << "SampledField numSamples3: " << sf->getNumSamples3() << std::endl;
const ImageData* id = sf->getImageData();
int* samples = new int[id->getSamplesLength()];
id->getSamples(samples);
std::cout << "ImageData samples[0]: " << samples[0] << std::endl;
std::cout << "ImageData samplesLen: " << id->getSamplesLength() << std::endl;
std::cout << "ImageData dataType: " << id->getDataType() << std::endl;
// sampledVolVol from sfGeom.
SampledVolume* sv = sfGeom->getSampledVolume(0);
std::cout << "SampledVol spatialId: " << sv->getSpatialId() << std::endl;
std::cout << "SampledVol domainType: " << sv->getDomainType() << std::endl;
std::cout << "SampledVol sampledVal: " << sv->getSampledValue() << std::endl;
std::cout << "SampledVol min: " << sv->getMinValue() << std::endl;
std::cout << "SampledVol max: " << sv->getMaxValue() << std::endl;
}
if (gd->isParametricGeometry()) {
ParametricGeometry* pGeom = static_cast<ParametricGeometry*>(gd);
std::cout << "ParametricGeometry spatialId: " << pGeom->getSpatialId() << std::endl;
// parametricObject from pGeom
ParametricObject* pObj = pGeom->getParametricObject(0);
std::cout << "ParametricObj spatialId: " << pObj->getSpatialId() << std::endl;
std::cout << "ParametricObj domain: " << pObj->getDomain() << std::endl;
std::cout << "ParametricObj polygonType: " << pObj->getPolygonType() << std::endl;
const PolygonObject* po = pObj->getPolygonObject();
int* ptInd = new int[po->getIndicesLength()];
po->getPointIndices(ptInd);
std::cout << "PolygonObj ptIndices[0]: " << ptInd[0] << std::endl;
std::cout << "PolygonObj indLen: " << po->getIndicesLength() << std::endl;
// SpatialPoint from pGeom.
SpatialPoint* sp = pGeom->getSpatialPoint(0);
std::cout << "SpatialPt spatialId: " << sp->getSpatialId() << std::endl;
std::cout << "SpatialPt domain: " << sp->getDomain() << std::endl;
std::cout << "SpatialPt coord1: " << sp->getCoord1() << std::endl;
std::cout << "SpatialPt coord2: " << sp->getCoord2() << std::endl;
std::cout << "SpatialPt coord3: " << sp->getCoord3() << std::endl;
}
if (gd->isCSGeometry()) {
CSGeometry* csGeom = static_cast<CSGeometry*>(gd);
std::cout << "CSGeometry spatialId: " << csGeom->getSpatialId() << std::endl;
// CSGObject-CSGOperator from csGeom
CSGObject* csgo;
for (unsigned int i = 0; i < csGeom->getNumCSGObjects(); i++) {
csgo = csGeom->getCSGObject(i);
std::cout << "CSGObject spatialId: " << csgo->getSpatialId() << std::endl;
std::cout << "CSGObject domainType: " << csgo->getDomainType() << std::endl;
const CSGNode* csgnode = csgo->getCSGNodeRoot();
if (csgnode->isCSGTransformation()) {
CSGTransformation* transf = (CSGTransformation*)csgnode;
if (transf->isCSGScale()) {
CSGScale* scale = static_cast<CSGScale*>(transf);
std::cout << "CSGScale scaleX: " << scale->getScaleX() << std::endl;
std::cout << "CSGScale scaleY: " << scale->getScaleY() << std::endl;
std::cout << "CSGScale scaleZ: " << scale->getScaleZ() << std::endl;
const CSGNode* scaleChild = scale->getChild();
if (scaleChild->isCSGPrimitive()) {
CSGPrimitive* prim = (CSGPrimitive*)scaleChild;
std::cout << "CSGPrimitive primitiveType: " << prim->getPrimitiveType() << std::endl;
}
}
}
if (csgnode->isCSGSetOperator()) {
CSGSetOperator* setop = (CSGSetOperator*)(csgnode);
std::cout << "CSGSetOperator opType: " << setop->getOperationType() << std::endl;
for (unsigned int k = 0; k < setop->getNumCSGNodeChildren(); k++) {
CSGNode* csgNode = setop->getCSGNodeChild(k);
std::cout << "CSGNode type: " << csgNode->getTypeCode() << std::endl;
}
}
}
}
}
delete document2;
}
END_TEST
START_TEST(test_FbcExtension_create_and_write_new_geneassociation
)
{
FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 2);
// create the document
SBMLDocument document(sbmlns);
document.setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE, false);
// create the Model
Model* model = document.createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("compartment");
compartment->setConstant(true);
compartment->setSize(1);
// create the Species
Species* species = model->createSpecies();
species->setId("Node1");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
// use fbc
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
FluxBound* bound = mplugin->createFluxBound();
bound->setId("bound1");
bound->setReaction("J0");
bound->setOperation("equal");
bound->setValue(10);
Objective* objective = mplugin->createObjective();
objective->setId("obj1");
objective->setType("maximize");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J0");
fluxObjective->setCoefficient(1);
FbcReactionPlugin* rplug = dynamic_cast<FbcReactionPlugin*>(reaction->getPlugin("fbc"));
fail_unless(rplug != NULL);
GeneProductAssociation * ga = rplug->createGeneProductAssociation();
ga->setId("ga1");
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
delete sbmlns;
}
void writeSpatialSBML()
{
// SBMLNamespaces of SBML Level 3 Version 1 with 'req' Version 1
// then add 'spatial' package namespace.
SpatialPkgNamespaces sbmlns(3,1,1);
// create the L3V1 document with spatial package
SBMLDocument document(&sbmlns);
// set 'required' attribute on document for 'spatial' and 'req' packages to 'T'??
SBMLDocumentPlugin* dplugin;
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("spatial"));
dplugin->setRequired(true);
// create the Model
Model *model = document.createModel();
model-> setId("trial_spatial");
model-> setName("trial_spatial");
// create the Compartments
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
// create the Species
Species* species1 = model->createSpecies();
species1->setId("ATPc");
species1->setCompartment("cytosol");
species1->setInitialConcentration(1.0);
species1->setHasOnlySubstanceUnits(false);
species1->setBoundaryCondition(false);
species1->setConstant(false);
// spatial package extension to species.
SpatialSpeciesPlugin* srplugin;
srplugin = static_cast<SpatialSpeciesPlugin*>(species1->getPlugin("spatial"));
srplugin->setIsSpatial(true);
// add parameter for diff coeff of species1
Parameter* paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_dc");
paramSp->setValue(1.0);
// spatial package extension to parameter.
SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
DiffusionCoefficient* diffCoeff = pplugin->createDiffusionCoefficient();
diffCoeff->setVariable(species1->getId());
diffCoeff->setType(SPATIAL_DIFFUSIONKIND_ANISOTROPIC);
CoordinateReference* coordRef = diffCoeff->createCoordinateReference();
coordRef->setCoordinate(SPATIAL_COORDINATEKIND_CARTESIAN_X);
// add parameter for adv coeff of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_ac");
paramSp->setValue(1.5);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
AdvectionCoefficient* advCoeff = pplugin->createAdvectionCoefficient();
advCoeff->setVariable(species1->getId());
advCoeff->setCoordinate(SPATIAL_COORDINATEKIND_CARTESIAN_X);
// add parameter for boundary condition of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_bc");
paramSp->setValue(2.0);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
BoundaryCondition* boundCon = pplugin->createBoundaryCondition();
boundCon->setVariable(species1->getId());
boundCon->setType(SPATIAL_BOUNDARYKIND_DIRICHLET);
boundCon->setCoordinateBoundary("Xmin");
Species* species2 = model->createSpecies();
species2->setId("ADPc");
species2->setCompartment("cytosol");
species2->setInitialConcentration(1);
species2->setHasOnlySubstanceUnits(false);
species2->setBoundaryCondition(false);
species2->setConstant(false);
srplugin = static_cast<SpatialSpeciesPlugin*>(species2->getPlugin("spatial"));
srplugin->setIsSpatial(true);
Reaction* reaction = model->createReaction();
reaction->setId("rxn1");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("cytosol");
SpatialReactionPlugin* rplugin = static_cast<SpatialReactionPlugin*>(reaction->getPlugin("spatial"));
rplugin->setIsLocal(true);
//
// Get a SpatialModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
SpatialModelPlugin* mplugin;
mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
//
// Creates a geometry object via SpatialModelPlugin object.
//
Geometry* geometry = mplugin->createGeometry();
geometry->setCoordinateSystem(SPATIAL_GEOMETRYKIND_CARTESIAN);
CoordinateComponent* coordX = geometry->createCoordinateComponent();
coordX->setId("coordComp1");
coordX->setType(SPATIAL_COORDINATEKIND_CARTESIAN_X);
coordX->setUnit("umeter");
Boundary* minX = coordX->createBoundaryMin();
minX->setId("Xmin");
minX->setValue(0.0);
Boundary* maxX = coordX->createBoundaryMax();
maxX->setId("Xmax");
maxX->setValue(10.0);
Parameter* paramX = model->createParameter();
paramX->setId("x");
paramX->setValue(8.0);
// spatial package extension to parameter.
// SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramX->getPlugin("spatial"));
SpatialSymbolReference* spSymRef = pplugin->createSpatialSymbolReference();
spSymRef->setSpatialRef(coordX->getId());
DomainType* domainType = geometry->createDomainType();
domainType->setId("dtype1");
domainType->setSpatialDimension(3);
// Spatial package extension to compartment (mapping compartment with domainType)
SpatialCompartmentPlugin* cplugin;
cplugin = static_cast<SpatialCompartmentPlugin*>(compartment->getPlugin("spatial"));
CompartmentMapping* compMapping = cplugin->createCompartmentMapping();
compMapping->setId("compMap1");
compMapping->setDomainType(domainType->getId());
compMapping->setUnitSize(1.0);
Domain* domain = geometry->createDomain();
domain->setId("domain1");
domain->setDomainType("dtype1");
InteriorPoint* internalPt1 = domain->createInteriorPoint();
internalPt1->setCoord1(1.0);
domain = geometry->createDomain();
domain->setId("domain2");
domain->setDomainType("dtype1");
InteriorPoint* internalPt2 = domain->createInteriorPoint();
internalPt2->setCoord1(5.0);
AdjacentDomains* adjDomain = geometry->createAdjacentDomains();
adjDomain->setId("adjDomain1");
adjDomain->setDomain1("domain1");
adjDomain->setDomain2("domain2");
AnalyticGeometry* analyticGeom = geometry->createAnalyticGeometry();
analyticGeom->setId("analyticGeom1");
AnalyticVolume* analyticVol = analyticGeom->createAnalyticVolume();
analyticVol->setId("analyticVol1");
analyticVol->setDomainType(domainType->getId());
analyticVol->setFunctionType(SPATIAL_FUNCTIONKIND_LAYERED);
analyticVol->setOrdinal(1);
const char* mathMLStr = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><apply xmlns=\"\"><plus /><apply><times /><ci>x</ci><ci>x</ci></apply><apply><minus /><cn>1.0</cn></apply></apply></math>";
ASTNode* mathNode = readMathMLFromString(mathMLStr);
analyticVol->setMath(mathNode);
SampledFieldGeometry* sfg = geometry->createSampledFieldGeometry();
sfg->setId("sampledFieldGeom1");
SampledField* sampledField = sfg->createSampledField();
sampledField->setId("sampledField1");
sampledField->setNumSamples1(4);
sampledField->setNumSamples2(4);
sampledField->setNumSamples3(2);
sampledField->setDataType("double");
sampledField->setInterpolationType("linear");
sampledField->setEncoding("encoding1");
//int samples[5] = {1, 2, 3, 4, 5};
int samples[32] = {
// z=0
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0,
// z=1
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0
};
ImageData* id = sampledField->createImageData();
id->setDataType("uint8");
id->setSamples(samples, 32);
SampledVolume* sampledVol = sfg->createSampledVolume();
sampledVol->setId("sv_1");
sampledVol->setDomainType(domainType->getId());
sampledVol->setSampledValue(128.0);
sampledVol->setMinValue(0.0);
sampledVol->setMaxValue(255.0);
writeSBML(&document, "spatial_example2.xml");
}
void readSpatialSBML() {
SBMLDocument *document2 = readSBML("spatial_example2.xml");
Model *model2 = document2->getModel();
Compartment *comp;
SpatialCompartmentPlugin* cplugin;
for (unsigned int i = 0; i < model2->getNumCompartments(); i++) {
comp = model2->getCompartment(i);
cout << "Compartment" << i << ": " << comp->getId() << endl;
cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
if (cplugin->getCompartmentMapping()->isSetId()) {
cout << "Comp" << i << " CMSpId: " << cplugin->getCompartmentMapping()->getId() << endl;
cout << "Comp" << i << " CM_DType: " << cplugin->getCompartmentMapping()->getDomainType() << endl;
cout << "Comp" << i << " CM_UnitSz: " << cplugin->getCompartmentMapping()->getUnitSize() << endl;
}
}
Species *sp;
SpatialSpeciesPlugin* srplugin;
for (unsigned int i = 0; i < model2->getNumSpecies(); i++) {
sp = model2->getSpecies(i);
cout << "Species" << i << ": " << sp->getId() << endl;
srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
if (srplugin->getIsSpatial()) {
cout << "species" << i << " isSpatial: " << srplugin->getIsSpatial() << endl;
}
}
Parameter *param;
SpatialParameterPlugin* pplugin;
for (unsigned int i = 0; i < model2->getNumParameters(); i++) {
param = model2->getParameter(i);
cout << "Parameter" << i << ": " << param->getId() << endl;
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
if (pplugin->isSetSpatialSymbolReference()) {
cout << "Parameter" << i << " SpRefId: " << pplugin->getSpatialSymbolReference()->getSpatialRef() << endl;
}
if (pplugin->isSetDiffusionCoefficient()) {
cout << "Diff_" << i << " SpeciesVarId: " << pplugin->getDiffusionCoefficient()->getVariable() << endl;
cout << "Diff_" << i << " Type: " << DiffusionKind_toString(pplugin->getDiffusionCoefficient()->getType()) << endl;
for (unsigned int j = 0; j < pplugin->getDiffusionCoefficient()->getNumCoordinateReferences(); ++j)
cout << "Diff_" << i << " SpCoordIndex " << j << " : " << CoordinateKind_toString(pplugin->getDiffusionCoefficient()->getCoordinateReference(j) ->getCoordinate()) << endl;
}
if (pplugin->isSetAdvectionCoefficient()) {
cout << "Adv_" << i << " SpeciesVarId: " << pplugin->getAdvectionCoefficient()->getVariable() << endl;
cout << "Adv_" << i << " SpCoordIndex: " << CoordinateKind_toString(pplugin->getAdvectionCoefficient()->getCoordinate()) << endl;
}
if (pplugin->isSetBoundaryCondition()) {
cout << "BC_" << i << " SpeciesVarId: " << pplugin->getBoundaryCondition()->getVariable() << endl;
cout << "BC_" << i << " SpCoordBoundary: " << pplugin->getBoundaryCondition()->getCoordinateBoundary() << endl;
cout << "BC_" << i << " SpBoundaryType: " << pplugin->getBoundaryCondition()->getType() << endl;
}
}
Reaction *rxn;
SpatialReactionPlugin* rplugin;
for (unsigned int i = 0; i < model2->getNumReactions(); i++) {
rxn = model2->getReaction(i);
cout << "Reaction" << i << ": " << rxn->getId() << endl;
rplugin = static_cast<SpatialReactionPlugin*>(rxn->getPlugin("spatial"));
if (rplugin->getIsLocal()) {
cout << "rxn" << i << " isLocal: " << rplugin->getIsLocal() << endl;
}
}
Rule *rule;
for (unsigned int i = 0; i < model2->getNumRules(); i++) {
rule = model2->getRule(i);
cout << "Rule" << i << ": " << rule->getVariable() << endl;
}
//
// Get a SpatialModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be cast for the
// corresponding derived class.
//
SpatialModelPlugin* mplugin2;
mplugin2 = static_cast<SpatialModelPlugin*>(model2->getPlugin("spatial"));
cout << "URI: " << mplugin2->getURI() << endl;
cout << "prefix: " << mplugin2->getPrefix() << endl;
// get a Geometry object via SpatialModelPlugin object.
Geometry* geometry2 = mplugin2->getGeometry();
cout << "Geometry coordSystem: " << geometry2->getCoordinateSystem() << endl;
// get a CoordComponent object via the Geometry object.
CoordinateComponent* coordComp = geometry2->getCoordinateComponent(0);
std::cout << "CoordComponent Id: " << coordComp->getId() << std::endl;
std::cout << "CoordComponent type: " << CoordinateKind_toString( coordComp->getType()) << std::endl;
std::cout << "CoordComponent sbmlUnit: " << coordComp->getUnit() << std::endl;
if (coordComp->isSetBoundaryMin())
{
Boundary* minX = coordComp->getBoundaryMin();
std::cout << "minX name: " << minX->getId() << std::endl;
std::cout << "minX value: " << minX->getValue() << std::endl;
}
if (coordComp->isSetBoundaryMax())
{
Boundary* maxX = coordComp->getBoundaryMax();
std::cout << "maxX name: " << maxX->getId() << std::endl;
std::cout << "maxX value: " << maxX->getValue() << std::endl;
}
// get a DomainType object via the Geometry object.
DomainType* domainType2 = geometry2->getDomainType(0);
std::cout << "DomainType Id: " << domainType2->getId() << std::endl;
std::cout << "DomainType spatialDim: " << domainType2->getSpatialDimension() << std::endl;
// get a Domain object via the Geometry object.
Domain* domain = geometry2->getDomain(0);
std::cout << "Domain1 Id: " << domain->getId() << std::endl;
std::cout << "Domain1 domainType: " << domain->getDomainType() << std::endl;
// get an internal point via the domain object
InteriorPoint* internalPt = domain->getInteriorPoint(0);
std::cout << "InternalPt_1 coord1: " << internalPt->getCoord1() << std::endl;
// get a Domain object via the Geometry object.
domain = geometry2->getDomain(1);
std::cout << "Domain2 Id: " << domain->getId() << std::endl;
std::cout << "Domain2 domainType: " << domain->getDomainType() << std::endl;
// get an internal point via the domain object
internalPt = domain->getInteriorPoint(0);
std::cout << "InternalPt_2 coord1: " << internalPt->getCoord1() << std::endl;
// get an AdjacentDomains object via the Geometry object.
AdjacentDomains* adjDomain = geometry2->getAdjacentDomains(0);
std::cout << "AdjDomain Id: " << adjDomain->getId() << std::endl;
std::cout << "AdjDomain domain1: " << adjDomain->getDomain1() << std::endl;
std::cout << "AdjDomain domain2: " << adjDomain->getDomain2() << std::endl;
// get an AnalyticGeometry object via the Geometry object.
GeometryDefinition* gd;
for (unsigned int i = 0; i < geometry2->getNumGeometryDefinitions(); i++) {
gd = geometry2->getGeometryDefinition(i);
if (gd->isAnalyticGeometry()) {
AnalyticGeometry* analyticalGeom = static_cast<AnalyticGeometry*>(gd);
std::cout << "AnalGeom Id: " << analyticalGeom->getId() << std::endl;
// analVol from analGeom.
AnalyticVolume* av = analyticalGeom->getAnalyticVolume(0);
std::cout << "AnalVol Id: " << av->getId() << std::endl;
std::cout << "AnalVol domainType: " << av->getDomainType() << std::endl;
std::cout << "AnalVol funcType: " << av->getFunctionType() << std::endl;
std::cout << "AnalVol ordinal: " << av->getOrdinal() << std::endl;
const ASTNode* mathNode = av->getMath();
char* mathStr = writeMathMLToString(mathNode);
std::cout << "AnalVol math: " << mathStr << std::endl;
}
if (gd->isSampledFieldGeometry()) {
SampledFieldGeometry* sfGeom = static_cast<SampledFieldGeometry*>(gd);
std::cout << "SampledFieldGeom Id: " << sfGeom->getId() << std::endl;
// sampledField from sfGeom
SampledField* sf = sfGeom->getSampledField();
std::cout << "SampledField Id: " << sf->getId() << std::endl;
std::cout << "SampledField dataType: " << sf->getDataType() << std::endl;
std::cout << "SampledField interpolation: " << sf->getInterpolationType() << std::endl;
std::cout << "SampledField encoding: " << sf->getEncoding() << std::endl;
std::cout << "SampledField numSamples1: " << sf->getNumSamples1() << std::endl;
std::cout << "SampledField numSamples2: " << sf->getNumSamples2() << std::endl;
std::cout << "SampledField numSamples3: " << sf->getNumSamples3() << std::endl;
const ImageData* id = sf->getImageData();
int* samples = new int[id->getSamplesLength()];
id->getSamples(samples);
std::cout << "ImageData samples[0]: " << samples[0] << std::endl;
std::cout << "ImageData dtype: " << id->getDataType() << std::endl;
std::cout << "ImageData samplesLen: " << id->getSamplesLength() << std::endl;
// sampledVolVol from sfGeom.
SampledVolume* sv = sfGeom->getSampledVolume(0);
std::cout << "SampledVol Id: " << sv->getId() << std::endl;
std::cout << "SampledVol domainType: " << sv->getDomainType() << std::endl;
std::cout << "SampledVol sampledVal: " << sv->getSampledValue() << std::endl;
std::cout << "SampledVol min: " << sv->getMinValue() << std::endl;
std::cout << "SampledVol max: " << sv->getMaxValue() << std::endl;
}
}
delete document2;
}
END_TEST
START_TEST(test_FbcAssociation_parseFbcInfixAssociation_strange_labels)
{
const char* model1 =
"<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns:html='http://www.w3.org/1999/xhtml' xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version2' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless' fbc:strict='false'>"
" <listOfCompartments>"
" <compartment id=\"comp1\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>"
" </listOfCompartments>"
" <listOfSpecies>"
" <species id=\"S\" compartment=\"comp1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" fbc:charge=\"2\" fbc:chemicalFormula=\"S20\"/>"
" </listOfSpecies>"
" <listOfReactions>"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" fbc:lowerFluxBound=\"low\" fbc:upperFluxBound=\"up\">"
" <listOfReactants>"
" <speciesReference species=\"S1\" stoichiometry=\"1\" constant=\"true\"/>"
" </listOfReactants>"
" </reaction>"
" </listOfReactions>"
" </model>"
"</sbml>"
;
const char* expected =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns:html=\"http://www.w3.org/1999/xhtml\" xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" xmlns:fbc=\"http://www.sbml.org/sbml/level3/version1/fbc/version2\" level=\"3\" version=\"1\" fbc:required=\"false\">\n"
" <model id=\"M\" name=\"E\" timeUnits=\"dimensionless\" fbc:strict=\"false\">\n"
" <listOfCompartments>\n"
" <compartment id=\"comp1\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"S\" compartment=\"comp1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" fbc:charge=\"2\" fbc:chemicalFormula=\"S20\"/>\n"
" </listOfSpecies>\n"
" <listOfReactions>\n"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" fbc:lowerFluxBound=\"low\" fbc:upperFluxBound=\"up\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"S1\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <fbc:geneProductAssociation fbc:id=\"gg1\">\n"
" <fbc:and>\n"
" <fbc:geneProductRef fbc:geneProduct=\"gp_g__DOT__p\"/>\n"
" <fbc:geneProductRef fbc:geneProduct=\"gp___ONE__sd\"/>\n"
" </fbc:and>\n"
" </fbc:geneProductAssociation>\n"
" </reaction>\n"
" </listOfReactions>\n"
" <fbc:listOfGeneProducts>\n"
" <fbc:geneProduct fbc:id=\"gp_g__DOT__p\" fbc:label=\"g.p\"/>\n"
" <fbc:geneProduct fbc:id=\"gp___ONE__sd\" fbc:label=\"1sd\"/>\n"
" </fbc:listOfGeneProducts>\n"
" </model>\n"
"</sbml>\n"
;
std::string infix = "(g.p and 1sd)";
SBMLDocument* doc = readSBMLFromString(model1);
fail_unless(doc->getModel() != NULL);
FbcModelPlugin* fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneProducts() == 0);
Reaction * r = doc->getModel()->getReaction(0);
fail_unless(r != NULL);
FbcReactionPlugin * rplug = dynamic_cast<FbcReactionPlugin*>(r->getPlugin("fbc"));
fail_unless (rplug != NULL);
fail_unless(rplug->isSetGeneProductAssociation() == false);
GeneProductAssociation* gpa = rplug->createGeneProductAssociation();
gpa->setId("gg1");
FbcAssociation * fa = FbcAssociation::parseFbcInfixAssociation(infix, fbc);
fail_unless(fa->isFbcAnd() == true);
gpa->setAssociation(fa);
fail_unless(rplug->isSetGeneProductAssociation() == true);
fail_unless(fbc->getNumGeneProducts() == 2);
GeneProduct* gp = fbc->getGeneProduct(0);
fail_unless (gp->isSetId() == true);
fail_unless (gp->isSetLabel() == true);
FbcAssociation * fa_retrieved = gpa->getAssociation();
fail_unless(fa_retrieved->isFbcAnd() == true);
std::string out = fa_retrieved->toInfix();
// if it goes back to infix surely it should be the same infix that it started as
fail_unless(fa_retrieved->toInfix() == infix);
//GeneProductRef * gpref = dynamic_cast<GeneProductRef *>(gpa->getAssociation());
//fail_unless(gpref->isSetGeneProduct() == true);
//fail_unless(gpref->getGeneProduct() == gp->getId());
char * char_doc = writeSBMLToString(doc);
fail_unless(equals(expected, char_doc));
safe_free((void*)(char_doc));
delete fa;
delete doc;
}
END_TEST
START_TEST (test_SpatialExtension_read_L3V1V1_defaultNS)
{
string file = TestDataDirectory;
file += "/read_L3V1V1_defaultNS.xml";
SBMLDocument *document = readSBMLFromFile(file.c_str());
string sbmlDoc = writeSBMLToStdString(document);
Model *model = document->getModel();
//document->printErrors();
fail_unless(model != NULL);
//fail_unless(document->getNumErrors() == 0);
// model : compartment
fail_unless(model->getNumCompartments() == 1);
Compartment *comp = model->getCompartment(0);
// compartment : compartmentMapping
SpatialCompartmentPlugin* cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
fail_unless(cplugin != NULL);
CompartmentMapping *cMapping = cplugin->getCompartmentMapping();
if (cMapping->isSetId()) {
fail_unless(cMapping->getId() == "compMap1");
fail_unless(cMapping->getDomainType() == "dtype1");
fail_unless(cMapping->getUnitSize() == 1);
}
// model : species 1
fail_unless(model->getNumSpecies() == 2);
Species *sp = model->getSpecies(0);
SpatialSpeciesPlugin* srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
fail_unless(srplugin != NULL);
fail_unless(srplugin->getIsSpatial() == true);
// model : species 2
sp = model->getSpecies(1);
srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
fail_unless(srplugin != NULL);
fail_unless(srplugin->getIsSpatial() == true);
// model : parameters (species diffusion, advection coeffs, species boundary conditions, coordinate components from Geometry
fail_unless(model->getNumParameters() == 5);
// parameter 0 : diffusionCoefficient
Parameter *param = model->getParameter(0);
SpatialParameterPlugin* pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
fail_unless(pplugin->isSpatialParameter() == true);
fail_unless(pplugin->getType() == SBML_SPATIAL_DIFFUSIONCOEFFICIENT);
DiffusionCoefficient *diffCoeff = pplugin->getDiffusionCoefficient();
fail_unless(diffCoeff->getVariable() == "ATPc");
fail_unless(diffCoeff->isSetCoordinateReference1());
fail_unless(diffCoeff->getCoordinateReference1() == SPATIAL_COORDINATEKIND_CARTESIAN_X);
// parameter 1 : advectionCoefficient
param = model->getParameter(1);
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
fail_unless(pplugin->isSpatialParameter() == true);
fail_unless(pplugin->getType() == SBML_SPATIAL_ADVECTIONCOEFFICIENT);
AdvectionCoefficient *advCoeff = pplugin->getAdvectionCoefficient();
fail_unless(advCoeff->getVariable() == "ATPc");
fail_unless(advCoeff->getCoordinate() == SPATIAL_COORDINATEKIND_CARTESIAN_X);
// parameter 2 : boundaryCondition X
param = model->getParameter(2);
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
fail_unless(pplugin->isSpatialParameter() == true);
fail_unless(pplugin->getType() == SBML_SPATIAL_BOUNDARYCONDITION);
BoundaryCondition *bc = pplugin->getBoundaryCondition();
fail_unless(bc->getVariable() == "ATPc");
fail_unless(bc->getCoordinateBoundary() == "Xmin");
fail_unless(bc->getType() == SPATIAL_BOUNDARYKIND_DIRICHLET);
// parameter 3 : SpatialSymbolReference (coordinateComponent from geometry)
param = model->getParameter(3);
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
SpatialSymbolReference *spSymRef = pplugin->getSpatialSymbolReference();
fail_unless(spSymRef->getSpatialRef() == "coordComp1");
// model : reaction
fail_unless(model->getNumReactions() == 1);
Reaction *rxn = model->getReaction(0);
SpatialReactionPlugin* rplugin = static_cast<SpatialReactionPlugin*>(rxn->getPlugin("spatial"));
fail_unless(rplugin != NULL);
fail_unless(rplugin->getIsLocal() == true);
// get the Geometry
SpatialModelPlugin* mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
fail_unless(mplugin != NULL);
Geometry *geometry = mplugin->getGeometry();
fail_unless(geometry != NULL);
fail_unless(geometry->getPackageName() == "spatial");
fail_unless(geometry->getCoordinateSystem() == SPATIAL_GEOMETRYKIND_CARTESIAN);
// geometry coordinateComponent
fail_unless(geometry->getNumCoordinateComponents() == 1);
fail_unless(geometry->getListOfCoordinateComponents()->getPackageName() == "spatial");
CoordinateComponent* coordComp = geometry->getCoordinateComponent(0);
fail_unless(coordComp->getId() == "coordComp1");
fail_unless(coordComp->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_X);
fail_unless(coordComp->getUnit() == "umeter");
fail_unless(coordComp->getPackageName() == "spatial");
// boundaryMin and boundayMax within coordinateComponent
Boundary *minX = coordComp->getBoundaryMin();
fail_unless(minX->getId() == "Xmin");
fail_unless(minX->getValue() == 0);
fail_unless(minX->getPackageName() == "spatial");
Boundary *maxX = coordComp->getBoundaryMax();
fail_unless(maxX->getId() == "Xmax");
fail_unless(maxX->getValue() == 10);
fail_unless(maxX->getPackageName() == "spatial");
// geometry domainType
fail_unless(geometry->getNumDomainTypes() == 1);
fail_unless(geometry->getListOfDomainTypes()->getPackageName() == "spatial");
DomainType *domainType = geometry->getDomainType(0);
fail_unless(domainType->getId() == "dtype1");
fail_unless(domainType->getSpatialDimensions() == 3);
fail_unless(domainType->getPackageName() == "spatial");
// geometry domains
fail_unless(geometry->getNumDomains() == 2);
fail_unless(geometry->getListOfDomains()->getPackageName() == "spatial");
Domain* domain = geometry->getDomain(0);
fail_unless(domain->getId() == "domain1");
fail_unless(domain->getDomainType() == "dtype1");
//fail_unless(domain->getImplicit() == false);
//fail_unless(domain->getShapeId() == "circle");
fail_unless(domain->getPackageName() == "spatial");
// interiorPoints in Domain
fail_unless(domain->getNumInteriorPoints() == 1);
fail_unless(domain->getListOfInteriorPoints()->getPackageName() == "spatial");
InteriorPoint* interiorPt = domain->getInteriorPoint(0);
fail_unless(interiorPt->getCoord1() == 1);
fail_unless(interiorPt->getPackageName() == "spatial");
// second domain in geometry
domain = geometry->getDomain(1);
fail_unless(domain->getId() == "domain2");
fail_unless(domain->getDomainType() == "dtype1");
//fail_unless(domain->getImplicit() == false);
//fail_unless(domain->getShapeId() == "square");
fail_unless(domain->getPackageName() == "spatial");
// Domain : interiorPoints
fail_unless(domain->getNumInteriorPoints() == 1);
fail_unless(domain->getListOfInteriorPoints()->getPackageName() == "spatial");
interiorPt = domain->getInteriorPoint(0);
fail_unless(interiorPt->getCoord1() == 5);
fail_unless(interiorPt->getPackageName() == "spatial");
// geometry adjacentDomains
fail_unless(geometry->getNumAdjacentDomains() == 1);
fail_unless(geometry->getListOfAdjacentDomains()->getPackageName() == "spatial");
AdjacentDomains* adjDomain = geometry->getAdjacentDomains(0);
fail_unless(adjDomain->getId() == "adjDomain1");
fail_unless(adjDomain->getDomain1() == "domain1");
fail_unless(adjDomain->getDomain2() == "domain2");
fail_unless(adjDomain->getPackageName() == "spatial");
// geometry : geometryDefinitions
fail_unless(geometry->getNumGeometryDefinitions() == 2);
fail_unless(geometry->getListOfGeometryDefinitions()->getPackageName() == "spatial");
GeometryDefinition *gd = geometry->getGeometryDefinition(0);
AnalyticGeometry *analyticGeom = static_cast<AnalyticGeometry*>(gd);
fail_unless(analyticGeom->getId() == "analyticGeom1");
fail_unless(analyticGeom->getPackageName() == "spatial");
// AnalyticGeometry : analyticVolumes
fail_unless(analyticGeom->getNumAnalyticVolumes() == 1);
fail_unless(analyticGeom->getListOfAnalyticVolumes()->getPackageName() == "spatial");
AnalyticVolume* av = analyticGeom->getAnalyticVolume(0);
fail_unless(av->getId() == "analyticVol1");
fail_unless(av->getDomainType() == "dtype1");
fail_unless(av->getFunctionType() == SPATIAL_FUNCTIONKIND_LAYERED);
fail_unless(av->getOrdinal() == 1);
fail_unless(av->getPackageName() == "spatial");
// ??????Math????
// geometry : sampledFieldGeometry
gd = geometry->getGeometryDefinition(1);
SampledFieldGeometry* sfGeom = static_cast<SampledFieldGeometry*>(gd);
fail_unless(sfGeom->getId() == "sampledFieldGeom1");
fail_unless(sfGeom->getPackageName() == "spatial");
// sampledFieldGeometry : SampledVolumes
fail_unless(sfGeom->getNumSampledVolumes() == 1);
fail_unless(sfGeom->getListOfSampledVolumes()->getPackageName() == "spatial");
SampledVolume* sv = sfGeom->getSampledVolume(0);
fail_unless(sv->getId() == "sv_1");
fail_unless(sv->getDomainType() == "dtype1");
fail_unless(sv->getSampledValue() == 128);
fail_unless(sv->getMinValue() == 0);
fail_unless(sv->getMaxValue() == 255);
fail_unless(sv->getPackageName() == "spatial");
// sampledFieldGeometry : SampledField
SampledField* sf = geometry->getSampledField( sfGeom->getSampledField() );
fail_unless(sf->getId() == "sampledField1");
fail_unless(sf->getDataType() == SPATIAL_DATAKIND_UINT8);
fail_unless(sf->getInterpolationType() == SPATIAL_INTERPOLATIONKIND_LINEAR);
fail_unless(sf->getCompression() == SPATIAL_COMPRESSIONKIND_UNCOMPRESSED);
fail_unless(sf->getNumSamples1() == 4);
fail_unless(sf->getNumSamples2() == 4);
fail_unless(sf->getNumSamples3() == 2);
fail_unless(sf->getPackageName() == "spatial");
// sampledField : ImageData
fail_unless(sf->getSamplesLength() == 32);
int* samples = new int[sf->getSamplesLength()];
sf->getSamples(samples);
fail_unless(samples[0] == 0);
string s2 = writeSBMLToStdString(document);
fail_unless(sbmlDoc==s2);
delete document;
delete[] samples;
}