inc

Model

class Model

Public Functions

bool getIsValid() const

const QString &getErrorMessage() const

bool getHasUnsavedChanges() const

const QString &getCurrentFilename() const

void setName(const QString &name)

QString getName() const

ModelCompartments &getCompartments()

const ModelCompartments &getCompartments() const

ModelGeometry &getGeometry()

const ModelGeometry &getGeometry() const

ModelMembranes &getMembranes()

const ModelMembranes &getMembranes() const

ModelSpecies &getSpecies()

const ModelSpecies &getSpecies() const

ModelReactions &getReactions()

const ModelReactions &getReactions() const

ModelFunctions &getFunctions()

const ModelFunctions &getFunctions() const

ModelParameters &getParameters()

const ModelParameters &getParameters() const

ModelEvents &getEvents()

const ModelEvents &getEvents() const

ModelUnits &getUnits()

const ModelUnits &getUnits() const

ModelMath &getMath()

const ModelMath &getMath() const

simulate::SimulationData &getSimulationData()

const simulate::SimulationData &getSimulationData() const

SimulationSettings &getSimulationSettings()

const SimulationSettings &getSimulationSettings() const

MeshParameters &getMeshParameters()

const MeshParameters &getMeshParameters() const

simulate::OptimizeOptions &getOptimizeOptions()

const simulate::OptimizeOptions &getOptimizeOptions() const

const std::vector<QRgb> &getSampledFieldColours() const

explicit Model()

Model(Model&&) noexcept = default

Model &operator=(Model&&) noexcept = default

Model &operator=(const Model&) = delete

Model(const Model&) = delete

~Model()

void createSBMLFile(const std::string &name)

void importSBMLFile(const std::string &filename)

void importSBMLString(const std::string &xml, const std::string &filename = {})

void exportSBMLFile(const std::string &filename)

void importFile(const std::string &filename)

void exportSMEFile(const std::string &filename)

QString getXml()

void clear()

SpeciesGeometry getSpeciesGeometry(const QString &speciesID) const

std::string inlineExpr(const std::string &mathExpression) const

DisplayOptions getDisplayOptions() const

void setDisplayOptions(const DisplayOptions &displayOptions)

ModelCompartments

class ModelCompartments

Public Functions

ModelCompartments()

ModelCompartments(libsbml::Model *model, ModelMembranes *membranes, const ModelUnits *units, simulate::SimulationData *data)

void setGeometryPtr(ModelGeometry *geometry)

void setSpeciesPtr(ModelSpecies *species)

void setReactionsPtr(ModelReactions *reactions)

void setSimulationDataPtr(simulate::SimulationData *data)

const QStringList &getIds() const

const QStringList &getNames() const

const QVector<QRgb> &getColours() const

QString add(const QString &name)

bool remove(const QString &id)

QString getName(const QString &id) const

QString setName(const QString &id, const QString &name)

std::optional<std::vector<QPointF>> getInteriorPoints(const QString &id) const

void setInteriorPoints(const QString &id, const std::vector<QPointF> &points)

void setColour(const QString &id, QRgb colour)

QRgb getColour(const QString &id) const

QString getIdFromColour(QRgb colour) const

const std::vector<std::unique_ptr<geometry::Compartment>> &getCompartments() const

geometry::Compartment *getCompartment(const QString &id)

const geometry::Compartment *getCompartment(const QString &id) const

double getSize(const QString &id) const

const std::map<std::string, double, std::less<>> &getInitialCompartmentSizes() const

void clear()

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelEvents

class ModelEvents

Public Functions

ModelEvents()

explicit ModelEvents(libsbml::Model *model, ModelParameters *parameters = nullptr, ModelSpecies *species = nullptr)

const QStringList &getIds() const

const QStringList &getNames() const

QString setName(const QString &id, const QString &name)

QString getName(const QString &id) const

void setVariable(const QString &id, const QString &variable)

QString getVariable(const QString &id) const

void setTime(const QString &id, double time)

double getTime(const QString &id) const

void setExpression(const QString &id, const QString &expr)

QString getExpression(const QString &id) const

QString add(const QString &name, const QString &variable)

bool isParameter(const QString &id) const

double getValue(const QString &id) const

void remove(const QString &id)

void removeAnyUsingVariable(const QString &variable)

void applyEvent(const QString &id)

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelFunctions

class ModelFunctions

Public Functions

ModelFunctions()

explicit ModelFunctions(libsbml::Model *model)

const QStringList &getIds() const

const QStringList &getNames() const

QString setName(const QString &id, const QString &name)

QString getName(const QString &id) const

void setExpression(const QString &id, const QString &expression)

QString getExpression(const QString &id) const

QStringList getArguments(const QString &id) const

QString addArgument(const QString &functionId, const QString &argumentId)

void removeArgument(const QString &functionId, const QString &argumentId)

QString add(const QString &name)

void remove(const QString &id)

std::vector<common::SymbolicFunction> getSymbolicFunctions() const

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelGeometry

class ModelGeometry

Public Functions

ModelGeometry()

explicit ModelGeometry(libsbml::Model *model, ModelCompartments *compartments, ModelMembranes *membranes, const ModelUnits *units, Settings *annotation)

void importSampledFieldGeometry(const libsbml::Model *model)

void importSampledFieldGeometry(const QString &filename)

void importGeometryFromImages(const common::ImageStack &imgs, bool keepColourAssignments)

void updateMesh()

void clear()

int getNumDimensions() const

const common::VolumeF &getVoxelSize() const

void setVoxelSize(const common::VolumeF &newVoxelSize, bool updateSBML = true)

const common::VoxelF &getPhysicalOrigin() const

const common::VolumeF &getPhysicalSize() const

common::VoxelF getPhysicalPoint(const common::Voxel &voxel) const

QString getPhysicalPointAsString(const common::Voxel &voxel) const

const common::ImageStack &getImages() const

mesh::Mesh2d *getMesh2d() const

mesh::Mesh3d *getMesh3d() const

bool getIsValid() const

bool getIsMeshValid() const

bool getHasImage() const

void writeGeometryToSBML() const

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelMath

class ModelMath

Public Functions

ModelMath()

explicit ModelMath(const libsbml::Model *model)

void parse(const std::string &expr)

double eval(const std::map<const std::string, std::pair<double, bool>> &vars = {}) const

bool isValid() const

const std::string &getErrorMessage() const

ModelMembranes

class ModelMembranes

Public Functions

const QStringList &getIds() const

const QStringList &getNames() const

QString setName(const QString &id, const QString &name)

QString getName(const QString &id) const

const std::vector<geometry::Membrane> &getMembranes() const

const geometry::Membrane *getMembrane(const QString &id) const

const std::vector<std::pair<std::string, std::pair<QRgb, QRgb>>> &getIdColourPairs() const

double getSize(const QString &id) const

void updateCompartmentNames(const QStringList &compartmentNames)

void updateCompartments(const std::vector<std::unique_ptr<geometry::Compartment>> &compartments)

void updateCompartmentImages(const common::ImageStack &imgs)

void importMembraneIdsAndNames()

void exportToSBML(const common::VolumeF &voxelSize)

explicit ModelMembranes(libsbml::Model *model = nullptr)

~ModelMembranes()

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelParameters

class ModelParameters

Public Functions

ModelParameters()

explicit ModelParameters(libsbml::Model *model)

void setEventsPtr(ModelEvents *events)

void setSpeciesPtr(ModelSpecies *species)

const QStringList &getIds() const

const QStringList &getNames() const

QString setName(const QString &id, const QString &name)

QString getName(const QString &id) const

void setExpression(const QString &id, const QString &expr)

QString getExpression(const QString &id) const

QString add(const QString &name)

void remove(const QString &id)

const SpatialCoordinates &getSpatialCoordinates() const

void setSpatialCoordinates(SpatialCoordinates coords)

std::vector<IdName> getSymbols(const QStringList &compartments = {}) const

std::vector<IdNameValue> getGlobalConstants() const

std::vector<IdNameExpr> getNonConstantParameters() const

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelReactions

class ModelReactions

Public Functions

ModelReactions()

explicit ModelReactions(libsbml::Model *model, const ModelCompartments *compartments, const ModelMembranes *membranes, bool isNonSpatialModel)

void makeReactionLocationsValid()

void applySpatialReactionRescalings(const std::vector<ReactionRescaling> &reactionRescalings)

std::vector<ReactionRescaling> getSpatialReactionRescalings() const

bool getIsIncompleteODEImport() const

QStringList getIds(const QString &locationId) const

QStringList getIds(const ReactionLocation &reactionLocation) const

std::vector<ReactionLocation> getReactionLocations() const

QString add(const QString &name, const QString &locationId, const QString &rateExpression = "1")

void remove(const QString &id)

void removeAllInvolvingSpecies(const QString &speciesId)

QString setName(const QString &id, const QString &name)

QString getName(const QString &id) const

QString getScheme(const QString &id) const

void setLocation(const QString &id, const QString &locationId)

QString getLocation(const QString &id) const

double getSpeciesStoichiometry(const QString &id, const QString &speciesId) const

void setSpeciesStoichiometry(const QString &id, const QString &speciesId, double stoichiometry)

QString getRateExpression(const QString &id) const

void setRateExpression(const QString &id, const QString &expression)

QStringList getParameterIds(const QString &id) const

QString setParameterName(const QString &reactionId, const QString &parameterId, const QString &name)

QString getParameterName(const QString &reactionId, const QString &parameterId) const

void setParameterValue(const QString &reactionId, const QString &parameterId, double value)

double getParameterValue(const QString &reactionId, const QString &parameterId) const

QString addParameter(const QString &reactionId, const QString &name, double value)

void removeParameter(const QString &reactionId, const QString &id)

bool dependOnVariable(const QString &variableId) const

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelSpecies

class ModelSpecies

Public Functions

ModelSpecies()

ModelSpecies(libsbml::Model *model, const ModelCompartments *compartments, const ModelGeometry *geometry, const ModelParameters *parameters, const ModelFunctions *functions, simulate::SimulationData *data, Settings *annotation)

void setReactionsPtr(ModelReactions *reactions)

void setSimulationDataPtr(simulate::SimulationData *data)

bool containsNonSpatialReactiveSpecies() const

QString add(const QString &name, const QString &compartmentId)

void remove(const QString &id)

QString setName(const QString &id, const QString &name)

QString getName(const QString &id) const

void updateCompartmentGeometry(const QString &compartmentId)

void setCompartment(const QString &id, const QString &compartmentId)

QString getCompartment(const QString &id) const

QStringList getIds(const QString &compartmentId) const

QStringList getNames(const QString &compartmentId) const

void setIsSpatial(const QString &id, bool isSpatial)

bool getIsSpatial(const QString &id) const

void setDiffusionConstant(const QString &id, double diffusionConstant)

double getDiffusionConstant(const QString &id) const

ConcentrationType getInitialConcentrationType(const QString &id) const

void setInitialConcentration(const QString &id, double concentration)

double getInitialConcentration(const QString &id) const

void setAnalyticConcentration(const QString &id, const QString &analyticExpression)

void setFieldConcAnalytic(geometry::Field &field, const std::string &expr, const std::map<std::string, double, std::less<>> &substitutions = {})

QString getAnalyticConcentration(const QString &id) const

void updateAllAnalyticConcentrations()

void setSampledFieldConcentration(const QString &id, const std::vector<double> &concentrationArray)

std::vector<double> getSampledFieldConcentration(const QString &id, bool maskAndInvertY = false) const

common::ImageStack getConcentrationImages(const QString &id) const

void setColour(const QString &id, QRgb colour)

QRgb getColour(const QString &id) const

void setIsConstant(const QString &id, bool constant)

bool getIsConstant(const QString &id) const

bool isReactive(const QString &id) const

void removeInitialAssignments()

QString getSampledFieldInitialAssignment(const QString &id) const

geometry::Field *getField(const QString &id)

const geometry::Field *getField(const QString &id) const

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

ModelUnits

class ModelUnits

Public Functions

explicit ModelUnits(libsbml::Model *model = nullptr)

const Unit &getTime() const

int getTimeIndex() const

const QVector<Unit> &getTimeUnits() const

QVector<Unit> &getTimeUnits()

void setTimeIndex(int index)

const Unit &getLength() const

int getLengthIndex() const

const QVector<Unit> &getLengthUnits() const

QVector<Unit> &getLengthUnits()

void setLengthIndex(int index)

const Unit &getVolume() const

int getVolumeIndex() const

const QVector<Unit> &getVolumeUnits() const

QVector<Unit> &getVolumeUnits()

void setVolumeIndex(int index)

const Unit &getAmount() const

int getAmountIndex() const

const QVector<Unit> &getAmountUnits() const

QVector<Unit> &getAmountUnits()

void setAmountIndex(int index)

const QString &getConcentration() const

const QString &getDiffusion() const

const QString &getCompartmentReaction() const

const QString &getMembraneReaction() const

bool getHasUnsavedChanges() const

void setHasUnsavedChanges(bool unsavedChanges)

Settings

struct Settings

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

SimulationSettings simulationSettings = {}

DisplayOptions displayOptions = {}

MeshParameters meshParameters = {}

std::map<std::string, QRgb> speciesColours = {}

sme::simulate::OptimizeOptions optimizeOptions = {}

std::vector<QRgb> sampledFieldColours = {}

struct SimulationSettings

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

std::vector<std::pair<std::size_t, double>> times = {}

simulate::Options options = {}

sme::simulate::SimulatorType simulatorType = {}

struct DisplayOptions

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

std::vector<bool> showSpecies = {}

bool showMinMax = {true}

bool normaliseOverAllTimepoints = {true}

bool normaliseOverAllSpecies = {true}

bool showGeometryGrid = {false}

bool showGeometryScale = {false}

bool invertYAxis = {false}

struct MeshParameters

Public Functions

template<class Archive> inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

std::vector<std::size_t> maxPoints = {}

std::vector<std::size_t> maxAreas = {}

std::size_t boundarySimplifierType = {0}