LLVMModelDataSymbols

class LLVMModelDataSymbols

stores the names of all the symbols in the sbml model and thier indexes in the ModelData arrays.

This class essentially maps symbol names into ModelData indexes.

The logic behind splitting up LLVMModelDataSymbols and LLVMModelSymbols is that LLVMModelSymbols contains all the ASTs from the model, and this contains only ModelData indices — once the all the model functions are generated, there is no need to keep AST information around, but we still need to know what symbol is at what index for the various Model accessor functions.

data storage: There can exist rules (assigment, rate, and eventually algebraic) rules that determine the value of a symbol.
All items for which a rate rule exists are stored in the modelData::rateRules array.
No space is allocated for items determined by rate rules.
All elements get an index value, even the dependent ones, this allows us uniquely identify them in the generated accessor functions.
Most of the indexes used in this class are indexes into ModelData arrays, therefore we use unsigned integers — these are less error prone and its easier to check if they are valid i.e. only check that they are less than the array size and we do not have to check that it is positive.
All symbols from the sbml are reordered such that the independent ones are first, followed by the dependent values.

Public Types

enum SpeciesReferenceType

Values:

enumerator Reactant

enumerator Product

enumerator Modifier

enumerator MultiReactantProduct

enum SymbolIndexType

The model frequently looks for indices to sbml symbols.

This is a list of the types of sbml symbols that this class keeps track of.

Values:

enumerator FLOATING_SPECIES

enumerator BOUNDARY_SPECIES

enumerator COMPARTMENT

enumerator GLOBAL_PARAMETER

enumerator REACTION

enumerator EVENT

enumerator STOICHIOMETRY

enumerator INVALID_SYMBOL

typedef std::map<std::string, uint> StringUIntMap

typedef std::map<std::string, std::vector<uint>> StringUIntVectorMap

typedef std::pair<std::string, uint> StringUIntPair

typedef std::unordered_map<uint, uint> UIntUIntMap

Public Functions

LLVMModelDataSymbols()

LLVMModelDataSymbols(libsbml::Model const *model, unsigned options)

LLVMModelDataSymbols(std::istream &in)

virtual ~LLVMModelDataSymbols()

const std::string &getModelName() const

int getCompartmentIndex(std::string const&) const

SymbolIndexType getSymbolIndex(const std::string &name, int &result) const

checks to see if we have the given symbol in the sbml.

Parameters:

name – the name of the sbml symbol to look up.
result – if successfull, this is set to the index

Returns:

the type of symbol, if no symbol is found, then INVALID_SYMBOL is returned.

int getFloatingSpeciesIndex(std::string const &id, bool requireIndependent = true) const

Get the index of a floating species.

Parameters:

id – the id of the species to retrieve.
requireIndependent – if true, the float species must be independent — not defined by a rule.

int getBoundarySpeciesIndex(std::string const &id) const

Get the index of a boundary species.

Parameters:: id – the id of the species to retrieve.

size_t getIndependentBoundarySpeciesSize() const: number of boundary species not defined by rules.

size_t getIndependentFloatingSpeciesSize() const

number of fully indenpendent species, these are species that have thier dynamics fully determined by the reaction rates / stoichiometric matrix — these DO NOT have any rules determining their dynamics.

This is size of the allocated array in the ModelData struct.

int getGlobalParameterIndex(std::string const&) const

index of a global param given its name.

Throws:: exception – if invalid name.

int getRateRuleIndex(std::string const&) const

size_t getRateRuleSize() const

std::string getRateRuleId(size_t indx) const: get the symbolic id of the i’th rate rule

size_t getIndependentGlobalParameterSize() const: number of global parameters which are not determined by rules.

int getReactionIndex(std::string const&) const

std::vector<std::string> getReactionIds() const

size_t getReactionSize() const

int getStoichiometryIndex(std::string const&) const

int getStoichiometryIndex(const std::string&, const std::string&) const

std::vector<std::string> getStoichiometryIds() const

size_t getStoichiometrySize() const

std::vector<std::string> getGlobalParameterIds() const

bool isRateRuleGlobalParameter(uint gid) const: is the global parameter index defined by a rate rule.

std::vector<std::string> getFloatingSpeciesIds() const: the list that is returned by ExecutableModel, so order must remain constant.

std::string getFloatingSpeciesId(size_t indx) const: get the symbolic id of the i’th floating species.

std::string getBoundarySpeciesId(size_t indx) const: get the symbolic id of the i’th boundary species.

std::string getCompartmentId(size_t indx) const: get the symbolic id of the i’th compartment.

std::string getGlobalParameterId(size_t indx) const: find the id of the given global parameter index.

size_t getFloatingSpeciesSize() const: total size of all floating species.

size_t getBoundarySpeciesSize() const

size_t getCompartmentsSize() const

size_t getGlobalParametersSize() const

std::vector<std::string> getCompartmentIds() const

size_t getIndependentCompartmentSize() const: number of compartments which are not determined by rules.

std::vector<std::string> getBoundarySpeciesIds() const

std::list<SpeciesReferenceInfo> getStoichiometryList() const

get a list of all the non-zero entries in the stoichiometry matrix.

in the list of pairs, first is the row (species) index, and second is the column (reaction) index.

void print() const: initialize and allocate the buffers (including the stoich matrix) for an existing ModelData struct.

bool isIndependentElement(const std::string &id) const

if there are no rules for an element, then they are considered independent.

These are only for elements, not init values, will return false for all init symbols.

Only valid after class has been constructed.

bool hasRateRule(const std::string &id) const

bool hasAssignmentRule(const std::string &id) const

bool hasInitialAssignmentRule(const std::string &id) const

bool isIndependentFloatingSpecies(const std::string &id) const

bool isIndependentBoundarySpecies(const std::string &id) const

bool isBoundarySpecies(const std::string &id) const

bool isIndependentGlobalParameter(const std::string &id) const

bool isIndependentCompartment(const std::string &id) const

bool isNamedSpeciesReference(const std::string &id) const

const SpeciesReferenceInfo &getNamedSpeciesReferenceInfo(const std::string &id)

bool isConservedMoietySpecies(const std::string &symbol) const

checks if the given symbol is a init value for a conserved species.

Global parameters or floating species can be conservied moieties,

a global parameter is a CM if it is defined by a inital assignment rules as a linear of one CM species and a set of indepdent floating species.

A floating species may be a CM if it is defined by a rule as a linear combination of independent species.

If a floating species is a CM, then it must by definition be a dependent floating species.

It can however have independent initial conditions defined either by intial values or initial assignment rules.

bool isConservedMoietySpecies(uint id, uint &result) const

checks if the given floating species id corresponds to to a conserved moiety species.

Parameters:

id – index of floating species
result – [out] the index of the conserved moiety if this is a conserved moiety species.

Returns:

true or false if this is a cm species or not.

bool isConservedMoietyParameter(uint id) const: check if the global parameter with the given id is a conserved moiety.

size_t getConservedMoietySize() const: get the number of conserved moieties.

int getDepSpeciesIndexForConservedMoietyId(std::string id) const: get the dependent species for a given conserved moiety id

const std::vector<uint> &getIndSpeciesIndexForConservedMoietyId(std::string id) const: get all the independent species for a given conserved moiety id

int getConservedMoietyGlobalParameterIndex(uint cmIndex) const: get the index of a global parameter given a conserved moiety index.

std::string getConservedMoietyId(size_t indx) const: find the id of the given conserved moiety index.

int getConservedMoietyIndex(const std::string &name) const: get the id of a conserved moiety given its name.

bool isConservedMoietyAnalysis() const: check if the conserved moiety is turned on for this model

const std::vector<unsigned char> &getEventAttributes() const

size_t getEventBufferSize(size_t eventId) const: get the size (in number of doubles) of the buffer that events need to save the event data to.

const std::vector<uint> &getStoichRowIndx() const: the row indices of non-zero stoichiometry values

const std::vector<uint> &getStoichColIndx() const: the column indices of non-zero stoichiometry values

bool isIndependentInitFloatingSpecies(const std::string &symbol) const

checks if the given symbol is an init value for an independent floating species.

Conserved Moiety species are considered to have independent initial condtions as in this case, the assignment rule only applies at time t > 0.

bool isIndependentInitBoundarySpecies(const std::string &symbol) const

checks if the given symbol is an init value for an independent boundary species.

Conserved Moiety species are considered to have independent initial condtions as in this case, the assignment rule only applies at time t > 0.

bool isIndependentInitElement(const std::string &symbol) const

Is this sbml element an independent initial value.

True if this value does NOT have an assignment or initial assignment rule.

Independent initial values do not have assignment or initial assigment rules, but may have rate rules.

bool isIndependentInitCompartment(const std::string &symbol) const

bool isIndependentInitGlobalParameter(const std::string &symbol) const: has this std::string been found to be an independent init global param— is a global param and not having an assignment or init assignment rule.

bool isIndependentInitGlobalParameter(size_t id) const: is this global parameter id an independent init param — a global param without an init assignment rule.

int getFloatingSpeciesInitIndex(const std::string &symbol) const

get the index of a floating species initial value.

has the same index as the run time floating species.

int getBoundarySpeciesInitIndex(const std::string &symbol) const

get the index of a boundary species initial value.

has the same index as the run time boundary species.

int getCompartmentInitIndex(const std::string &symbol) const

get the index of a compartment initial value

has the same index as the run time compartment.

int getCompartmentIndexForFloatingSpecies(size_t floatIndex) const: get the index of a compartment for a float species.

int getCompartmentIndexForBoundarySpecies(size_t floatIndex) const: get the index of a compartment for a boundary species.

int getGlobalParameterInitIndex(const std::string &symbol) const

get the index of a global parameter initial value

has the same index as the run time global parameter.

size_t getInitCompartmentSize() const

size_t getInitFloatingSpeciesSize() const

size_t getInitBoundarySpeciesSize() const

size_t getInitGlobalParameterSize() const

std::vector<std::string> getEventIds() const

std::vector<std::string> getAssignmentRuleIds() const

std::vector<std::string> getRateRuleIds() const

std::vector<std::string> getInitialAssignmentIds() const

std::string getEventId(size_t indx) const

int getEventIndex(const std::string &id) const

void saveState(std::ostream&) const

void loadState(std::istream&)

Public Static Functions

static const char *getFieldName(ModelDataFields field): get the textual form of the field names.

Private Types

typedef std::map<std::string, SpeciesReferenceInfo> StringRefInfoMap: std::map of all identified species reference (species references with ids) to their indices in the stoichiometric matrix.

Private Functions

void initBoundarySpecies(const libsbml::Model*)

void initFloatingSpecies(const libsbml::Model *model, bool conservedMoieties)

init the floating species symbols.

Parameters:

model – the model to check.
conservedMoieties – are conserved moieties enabled?

void initCompartments(const libsbml::Model*)

void initGlobalParameters(const libsbml::Model *model, bool conservedMoieties)

get the global parameters, need to reorder them to set the independent ones first

Parameters:

model – the model to check.
conservedMoieties – are conserved moieties enabled?

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

void displayCompartmentInfo()

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

bool isValidFloatingSpeciesReference(const libsbml::SimpleSpeciesReference*, const std::string &reacOrProd)

determine is this species can be used as a species reference, in the sense that it will add a column to the stochiometry matrix.

Boundary species are not consumed or produced in reactions. If this is invalid float species, such as its defined by a rule this will log the reason.

void setNamedSpeciesReferenceInfo(uint row, uint column, SpeciesReferenceType type)

set the type of all species references.

row is species, column is reaction

void saveStringRefInfoMap(std::ostream&, const StringRefInfoMap&) const

void loadStringRefInfoMap(std::istream&, StringRefInfoMap&)

void saveBinarySpeciesReferenceInfo(std::ostream&, SpeciesReferenceInfo &sri) const

void loadBinarySpeciesReferenceInfo(std::istream&, SpeciesReferenceInfo&)

Private Members

std::set<std::string> conservedMoietySpeciesSet: initialized in initFloatingSpecies.

std::vector<bool> conservedMoietyGlobalParameter: global parameter id conserved moiety status.

std::vector<uint> conservedMoietyGlobalParameterIndex

the index of a global parameter from a conserved moeity index.

This array will be the size of the number of CM, each value of this array will be a global parameter index.

UIntUIntMap floatingSpeciesToConservedMoietyIdMap

std::map of floating species ids to conserved moiety ids.

assume conserved moeity speces are stored in the sbml in the same order as the conserved moieties.

StringUIntMap conservedMoietyDepSpecies

StringUIntVectorMap conservedMoietyIndSpecies

std::set<std::string> initAssignmentRules

StringUIntMap initFloatingSpeciesMap

std::map of floating species init value symbols to thier index in the array.

All floating species are stored in this std::map, however they are reordered and only the ones with index < independentInitFloatingSpeciesSize are allocated storage.

StringUIntMap initBoundarySpeciesMap

StringUIntMap initCompartmentsMap

StringUIntMap initGlobalParametersMap

uint independentInitFloatingSpeciesSize

Elements that do NOT have assignment rules are considered independent initial conditions.

Ind init conditions CAN however defined by rules.

ind init conditions are all elements that do not have assignment or initial assignment rules. float species init array has floating species NOT defined by init assignment rules, assignment rules, but rate rules are OK. This does not contain the init values for conserved species.

uint independentInitBoundarySpeciesSize: boundary species not defined by any rule including init assignment rules.

uint independentInitGlobalParameterSize: global params not defined by any rule

uint independentInitCompartmentSize: compartments not defined by any rules.

std::vector<uint> floatingSpeciesCompartmentIndices: index of compartments for each float species.

std::vector<uint> boundarySpeciesCompartmentIndices: index of compartments for each boundary species.

std::string modelName

StringUIntMap floatingSpeciesMap

StringUIntMap boundarySpeciesMap

StringUIntMap compartmentsMap

StringUIntMap globalParametersMap

StringRefInfoMap namedSpeciesReferenceInfo

StringUIntMap reactionsMap: all reactions are named.

std::vector<uint> stoichColIndx

the stochiometry matrix is # reactions rows by # species columns.

the species indices go here.

std::vector<uint> stoichRowIndx: and the reaction indices go here.

std::vector<std::string> stoichIds: most species references are un-named, this is used so that if named ones have a rate rule, we can set the proper initial conditions.

std::vector<SpeciesReferenceType> stoichTypes

std::set<std::string> assignmentRules: the set of rule, these contain the variable name of the rule so that we can quickly see if a symbol has an associated rule.

StringUIntMap rateRules: rate rules, index by variable name.

std::vector<bool> globalParameterRateRules: are global params defined by rate rules, set in initGlobalParam

size_t independentFloatingSpeciesSize

size_t independentBoundarySpeciesSize

size_t independentGlobalParameterSize

size_t independentCompartmentSize

std::vector<size_t> eventAssignmentsSize: the number of assignments each event has

std::vector<unsigned char> eventAttributes

StringUIntMap eventIds: std::map of event ids

struct SpeciesReferenceInfo

info about an entry in the stoich matrix.

there is exactly one of these for each entry.

Public Members

uint row

uint column

SpeciesReferenceType type

std::string id