| _chrsmLength | TTProtoWithMap | protected |
| _diploGenotTableCoding3x3 | TProtoBDMI | privatestatic |
| _diploGenotTableCoding4x4 | TProtoBDMI | privatestatic |
| _gamete_recomb_func_ptr | TProtoBDMI | private |
| _genomic_mut_rate | TProtoBDMI | private |
| _genoTable | TProtoBDMI | private |
| _index | TraitPrototype | protected |
| _inherit_func_ptr | TProtoBDMI | private |
| _init_freq | TProtoBDMI | private |
| _isHaploid | TProtoBDMI | private |
| _isInitSet | TProtoBDMI | private |
| _isRegistered | TTProtoWithMap | private |
| _lociMapPositions | TTProtoWithMap | protected |
| _map | TTProtoWithMap | static |
| _mapIndex | TTProtoWithMap | protected |
| _mapResolution | TTProtoWithMap | protected |
| _mut_rate | TProtoBDMI | private |
| _mutation_func_ptr | TProtoBDMI | private |
| _npair | TProtoBDMI | private |
| _num_locus | TProtoBDMI | private |
| _numChromosome | TTProtoWithMap | protected |
| _numLoci | TTProtoWithMap | protected |
| _numLociPerChrmsm | TTProtoWithMap | protected |
| _paramPrefix | TTProtoWithMap | private |
| _paramSet | SimComponent | protected |
| _recomb_rate | TProtoBDMI | private |
| _recombRate | TTProtoWithMap | protected |
| _recombRatePerChrmsm | TTProtoWithMap | protected |
| _stater | TProtoBDMI | private |
| _totRecombEventsMean | TTProtoWithMap | protected |
| _type | TProtoBDMI | private |
| _viability_func_ptr | TProtoBDMI | private |
| _writer | TProtoBDMI | private |
| add_parameter(Param *param) | SimComponent | inlinevirtual |
| add_parameter(std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd) | SimComponent | inlinevirtual |
| add_parameter(std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater) | SimComponent | inlinevirtual |
| addGeneticMapParameters(string prefix) | TTProtoWithMap | |
| areGeneticMapParamSet(string prefix) | TTProtoWithMap | |
| clone() | TProtoBDMI | inlinevirtual |
| gamete_recombination(sex_t SEX, bitstring &seq, const bitstring *parent) | TProtoBDMI | inline |
| get_index() | TraitPrototype | inlinevirtual |
| get_init_freq(unsigned int i) | TProtoBDMI | inline |
| get_mut_rate() | TProtoBDMI | inline |
| get_name() | SimComponent | inlinevirtual |
| get_num_locus() | TProtoBDMI | inline |
| get_parameter(std::string name) | SimComponent | inlinevirtual |
| get_parameter_value(std::string name) | SimComponent | inlinevirtual |
| get_paramset() | SimComponent | inlinevirtual |
| get_type() const | TProtoBDMI | inlinevirtual |
| getGenoFitnessDiplo(unsigned int row, unsigned int posA, unsigned int posB) | TProtoBDMI | inline |
| getGenoFitnessDiplo(unsigned int row, unsigned int pos) | TProtoBDMI | inline |
| getGenoFitnessHaplo(unsigned int row, unsigned int pos) | TProtoBDMI | inline |
| getMapIndex() | TTProtoWithMap | inline |
| has_parameter(std::string name) | SimComponent | inlinevirtual |
| hatch() | TProtoBDMI | virtual |
| inherit_free(sex_t SEX, bitstring &seq, const bitstring *parent) | TProtoBDMI | inline |
| inherit_low(sex_t SEX, bitstring &seq, const bitstring *parent) | TProtoBDMI | inline |
| init() | TProtoBDMI | inlinevirtual |
| isHaploid() | TProtoBDMI | inline |
| isInitSet() | TProtoBDMI | inline |
| isRecombinationFree(string prefix) | TTProtoWithMap | |
| loadFileServices(FileServices *loader) | TProtoBDMI | virtual |
| loadStatServices(StatServices *loader) | TProtoBDMI | virtual |
| loadUpdaters(UpdaterServices *loader) | SimComponent | inlinevirtual |
| recombine(unsigned long indID) | TTProtoWithMap | static |
| recordRandomMap() | TTProtoWithMap | |
| registerGeneticMap() | TTProtoWithMap | |
| reset() | TTProtoWithMap | virtual |
| reset_recombination_pointers() | TTProtoWithMap | |
| resetParameterFromSource(std::string param, SimComponent *cmpt) | TProtoBDMI | inlinevirtual |
| retrieve_data(BinaryStorageBuffer *reader) | TProtoBDMI | virtual |
| set_index(int idx) | TraitPrototype | inlinevirtual |
| set_init_freq(double *val, unsigned int size) | TProtoBDMI | |
| set_paramset(ParamSet *paramset) | SimComponent | inlinevirtual |
| set_paramset(std::string name, bool required, SimComponent *owner) | SimComponent | inlinevirtual |
| set_paramsetFromCopy(const ParamSet &PSet) | SimComponent | inlinevirtual |
| setGeneticMapParameters(string prefix) | TTProtoWithMap | |
| setGenoFitnessValue(unsigned int row, unsigned int geno, double value) | TProtoBDMI | inline |
| setMapIndex(unsigned int idx) | TTProtoWithMap | inline |
| setNumLociPerChromosome(string param_name) | TTProtoWithMap | |
| setParameters() | TProtoBDMI | virtual |
| setRecombinationMapFixed() | TTProtoWithMap | |
| setRecombinationMapNonRandom(vector< vector< double > > *lociPositions) | TTProtoWithMap | |
| setRecombinationMapRandom() | TTProtoWithMap | |
| showGenoTable(unsigned int nrows) | TProtoBDMI | |
| SimComponent() | SimComponent | inline |
| store_data(BinaryStorageBuffer *saver) | TProtoBDMI | inlinevirtual |
| TProtoBDMI() | TProtoBDMI | |
| TProtoBDMI(const TProtoBDMI &TP) | TProtoBDMI | |
| TT_BDMI class | TProtoBDMI | friend |
| TTProtoWithMap() | TTProtoWithMap | inline |
| TTProtoWithMap(const TTProtoWithMap &TP) | TTProtoWithMap | |
| unregisterFromGeneticMap() | TTProtoWithMap | |
| ~SimComponent() | SimComponent | inlinevirtual |
| ~StorableComponent() | StorableComponent | inlinevirtual |
| ~TProtoBDMI() | TProtoBDMI | virtual |
| ~TTProtoWithMap() | TTProtoWithMap | virtual |
