| _2L | TProtoNeutralGenes | private |
| _allele_num | TProtoNeutralGenes | private |
| _chrsmLength | TTProtoWithMap | protected |
| _index | TraitPrototype | protected |
| _inherit_func_ptr | TProtoNeutralGenes | private |
| _init_model | TProtoNeutralGenes | private |
| _isRegistered | TTProtoWithMap | private |
| _lociMapPositions | TTProtoWithMap | protected |
| _locus_num | TProtoNeutralGenes | private |
| _map | TTProtoWithMap | static |
| _mapIndex | TTProtoWithMap | protected |
| _mapResolution | TTProtoWithMap | protected |
| _mut_model | TProtoNeutralGenes | private |
| _mut_rate | TProtoNeutralGenes | private |
| _mutate_func_ptr | TProtoNeutralGenes | private |
| _numChromosome | TTProtoWithMap | protected |
| _numLoci | TTProtoWithMap | protected |
| _numLociPerChrmsm | TTProtoWithMap | protected |
| _ohtaStats | TProtoNeutralGenes | private |
| _paramPrefix | TTProtoWithMap | private |
| _paramSet | SimComponent | protected |
| _ploidy | TProtoNeutralGenes | private |
| _recomb_rate | TProtoNeutralGenes | private |
| _recombRate | TTProtoWithMap | protected |
| _recombRatePerChrmsm | TTProtoWithMap | protected |
| _stats | TProtoNeutralGenes | private |
| _totRecombEventsMean | TTProtoWithMap | protected |
| _type | TProtoNeutralGenes | private |
| _writers | TProtoNeutralGenes | 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() | TProtoNeutralGenes | inlinevirtual |
| get_allele_num() | TProtoNeutralGenes | inline |
| get_genome_size() | TProtoNeutralGenes | inline |
| get_index() | TraitPrototype | inlinevirtual |
| get_init_model() | TProtoNeutralGenes | inline |
| get_locus_num() | TProtoNeutralGenes | inline |
| get_mut_rate() | TProtoNeutralGenes | inline |
| get_name() | SimComponent | inlinevirtual |
| get_num_mutations() | TProtoNeutralGenes | inline |
| get_parameter(std::string name) | SimComponent | inlinevirtual |
| get_parameter_value(std::string name) | SimComponent | inlinevirtual |
| get_paramset() | SimComponent | inlinevirtual |
| get_ploidy() | TProtoNeutralGenes | inline |
| get_stater() | TProtoNeutralGenes | inline |
| get_type() const | TProtoNeutralGenes | inlinevirtual |
| getMapIndex() | TTProtoWithMap | inline |
| has_parameter(std::string name) | SimComponent | inlinevirtual |
| hatch() | TProtoNeutralGenes | virtual |
| inherit_free(sex_t SEX, unsigned char *seq, const unsigned char **parent) | TProtoNeutralGenes | inline |
| inherit_low(sex_t SEX, unsigned char *seq, const unsigned char **parent) | TProtoNeutralGenes | inline |
| init() | TProtoNeutralGenes | inlinevirtual |
| isRecombinationFree(string prefix) | TTProtoWithMap | |
| loadFileServices(FileServices *loader) | TProtoNeutralGenes | virtual |
| loadStatServices(StatServices *loader) | TProtoNeutralGenes | virtual |
| loadUpdaters(UpdaterServices *loader) | SimComponent | inlinevirtual |
| recombine(unsigned long indID) | TTProtoWithMap | static |
| recordRandomMap() | TTProtoWithMap | |
| registerGeneticMap() | TTProtoWithMap | |
| reset() | TProtoNeutralGenes | inlinevirtual |
| reset_recombination_pointers() | TTProtoWithMap | |
| resetParameterFromSource(std::string param, SimComponent *cmpt) | TProtoNeutralGenes | virtual |
| retrieve_data(BinaryStorageBuffer *reader) | TProtoNeutralGenes | virtual |
| set_index(int idx) | TraitPrototype | inlinevirtual |
| 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 | |
| setMapIndex(unsigned int idx) | TTProtoWithMap | inline |
| setNumLociPerChromosome(string param_name) | TTProtoWithMap | |
| setParameters() | TProtoNeutralGenes | virtual |
| setRecombinationMapFixed() | TTProtoWithMap | |
| setRecombinationMapNonRandom(vector< vector< double > > *lociPositions) | TTProtoWithMap | |
| setRecombinationMapRandom() | TTProtoWithMap | |
| SimComponent() | SimComponent | inline |
| store_data(BinaryStorageBuffer *saver) | TProtoNeutralGenes | inlinevirtual |
| TProtoNeutralGenes() | TProtoNeutralGenes | |
| TProtoNeutralGenes(const TProtoNeutralGenes &T) | TProtoNeutralGenes | |
| TTProtoWithMap() | TTProtoWithMap | inline |
| TTProtoWithMap(const TTProtoWithMap &TP) | TTProtoWithMap | |
| unregisterFromGeneticMap() | TTProtoWithMap | |
| ~SimComponent() | SimComponent | inlinevirtual |
| ~StorableComponent() | StorableComponent | inlinevirtual |
| ~TProtoNeutralGenes() | TProtoNeutralGenes | virtual |
| ~TTProtoWithMap() | TTProtoWithMap | virtual |
