| _all_chooser | TProtoQuanti | private |
| _allele_model | TProtoQuanti | private |
| _allele_value | TProtoQuanti | private |
| _chrsmLength | TTProtoWithMap | protected |
| _doInitMutation | TProtoQuanti | private |
| _dominance_effects | TProtoQuanti | private |
| _dominance_is_constant | TProtoQuanti | private |
| _dominance_model | TProtoQuanti | private |
| _dominance_sd | TProtoQuanti | private |
| _effects_bivar | TProtoQuanti | private |
| _effects_multivar | TProtoQuanti | private |
| _eval | TProtoQuanti | private |
| _eVariance | TProtoQuanti | private |
| _evect | TProtoQuanti | private |
| _freqExtractor | TProtoQuanti | private |
| _genomic_mutation_rate | TProtoQuanti | private |
| _getGenotypeWithDominance | TProtoQuanti | private |
| _getMutationValues | TProtoQuanti | private |
| _gsl_mutation_matrix | TProtoQuanti | private |
| _h2 | TProtoQuanti | private |
| _h2_isBroad | TProtoQuanti | private |
| _h2_setTime | TProtoQuanti | private |
| _index | TraitPrototype | protected |
| _inherit_fun_ptr | TProtoQuanti | private |
| _init_value | TProtoQuanti | private |
| _isRegistered | TTProtoWithMap | private |
| _lociMapPositions | TTProtoWithMap | protected |
| _locusByteSize | TProtoQuanti | private |
| _map | TTProtoWithMap | static |
| _mapIndex | TTProtoWithMap | protected |
| _mapResolution | TTProtoWithMap | protected |
| _mutation_correlation | TProtoQuanti | private |
| _mutation_func_ptr | TProtoQuanti | private |
| _mutation_matrix | TProtoQuanti | private |
| _mutation_sigma | TProtoQuanti | private |
| _nb_locus | TProtoQuanti | private |
| _nb_traits | TProtoQuanti | private |
| _numChromosome | TTProtoWithMap | protected |
| _numLoci | TTProtoWithMap | protected |
| _numLociPerChrmsm | TTProtoWithMap | protected |
| _paramPrefix | TTProtoWithMap | private |
| _paramSet | SimComponent | protected |
| _phenotypes | TProtoQuanti | private |
| _reader | TProtoQuanti | private |
| _recombRate | TTProtoWithMap | protected |
| _recombRatePerChrmsm | TTProtoWithMap | protected |
| _seq_length | TProtoQuanti | private |
| _set_genotype_func_ptr | TProtoQuanti | private |
| _set_trait_value_func_ptr | TProtoQuanti | private |
| _sizeofLocusType | TProtoQuanti | private |
| _stats | TProtoQuanti | private |
| _totRecombEventsMean | TTProtoWithMap | protected |
| _writer | TProtoQuanti | private |
| _ws | TProtoQuanti | 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() | TProtoQuanti | inlinevirtual |
| get_allele_model() | TProtoQuanti | inline |
| get_allele_values() const | TProtoQuanti | inline |
| get_dominance(unsigned int locus, unsigned int trait) | TProtoQuanti | inline |
| get_dominance_effects() | TProtoQuanti | inline |
| get_dominance_model() | TProtoQuanti | inline |
| get_env_var() | TProtoQuanti | inline |
| get_genotype(const double a1, const double a2, const unsigned int locus, const unsigned int trait) | TProtoQuanti | |
| get_genotype_dominance_h(double a1, double a2, double h) | TProtoQuanti | inline |
| get_genotype_dominance_k(double a1, double a2, double k) | TProtoQuanti | inline |
| get_h2_isBroad() | TProtoQuanti | inline |
| get_h2_setTime() | TProtoQuanti | inline |
| get_heritability() | TProtoQuanti | inline |
| get_index() | TraitPrototype | inlinevirtual |
| get_init_value(unsigned int i) | TProtoQuanti | inline |
| get_mutation_correlation() | TProtoQuanti | inline |
| get_name() | SimComponent | inlinevirtual |
| get_nb_locus() | TProtoQuanti | inline |
| get_nb_traits() | TProtoQuanti | inline |
| get_parameter(std::string name) | SimComponent | inlinevirtual |
| get_parameter_value(std::string name) | SimComponent | inlinevirtual |
| get_paramset() | SimComponent | inlinevirtual |
| get_seq_length() | TProtoQuanti | inline |
| get_stater() | TProtoQuanti | inline |
| get_trait_var(unsigned int trait) | TProtoQuanti | inline |
| get_type() const | TProtoQuanti | inlinevirtual |
| getMapIndex() | TTProtoWithMap | inline |
| getMutationEffectBivariateDiallelic(unsigned int loc) | TProtoQuanti | |
| getMutationEffectBivariateGaussian(unsigned int loc) | TProtoQuanti | |
| getMutationEffectMultivariateGaussian(unsigned int loc) | TProtoQuanti | |
| getMutationEffectUnivariateDiallelic(unsigned int loc) | TProtoQuanti | |
| getMutationEffectUnivariateGaussian(unsigned int loc) | TProtoQuanti | |
| has_parameter(std::string name) | SimComponent | inlinevirtual |
| hatch() | TProtoQuanti | virtual |
| inherit(sex_t SEX, double *seq, const double **parent) | TProtoQuanti | inline |
| inherit_free(sex_t SEX, double *seq, const double **parent) | TProtoQuanti | inline |
| inherit_low(sex_t SEX, double *seq, const double **parent) | TProtoQuanti | inline |
| isRecombinationFree(string prefix) | TTProtoWithMap | |
| loadFileServices(FileServices *loader) | TProtoQuanti | virtual |
| loadStatServices(StatServices *loader) | TProtoQuanti | virtual |
| loadUpdaters(UpdaterServices *loader) | SimComponent | inlinevirtual |
| mutate(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_diallelic_HC(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_HC(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_nill(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_noHC(TTQuanti *ind) | TProtoQuanti | inline |
| recombine(unsigned long indID) | TTProtoWithMap | static |
| recordRandomMap() | TTProtoWithMap | |
| registerGeneticMap() | TTProtoWithMap | |
| reset() | TProtoQuanti | inlinevirtual |
| reset_mutation_pointers() | TProtoQuanti | |
| reset_recombination_pointers() | TTProtoWithMap | |
| resetParameterFromSource(std::string param, SimComponent *cmpt) | TProtoQuanti | inlinevirtual |
| retrieve_data(BinaryStorageBuffer *reader) | TProtoQuanti | inlinevirtual |
| set_eVarianceSD(unsigned int trait, double SD) | TProtoQuanti | |
| set_genotype_value_additive(const double **sequ, const unsigned int trait) | TProtoQuanti | |
| set_genotype_value_dominance(const double **sequ, const unsigned int trait) | TProtoQuanti | |
| set_index(int idx) | TraitPrototype | inlinevirtual |
| set_init_values(const double *values, unsigned int nval) | TProtoQuanti | |
| set_mutation_matrix_decomposition() | TProtoQuanti | |
| set_paramset(ParamSet *paramset) | SimComponent | inlinevirtual |
| set_paramset(std::string name, bool required, SimComponent *owner) | SimComponent | inlinevirtual |
| set_paramsetFromCopy(const ParamSet &PSet) | SimComponent | inlinevirtual |
| set_trait_value_func_ptr(bool withVe) | TProtoQuanti | |
| set_trait_value_noVE(const TTQuanti *ind, const unsigned int trait) | TProtoQuanti | |
| set_trait_value_VE(const TTQuanti *ind, const unsigned int trait) | TProtoQuanti | |
| setContinuousMutationModel() | TProtoQuanti | |
| setDiallelicMutationModel() | TProtoQuanti | |
| setDominanceParameters() | TProtoQuanti | |
| setGeneticMapParameters(string prefix) | TTProtoWithMap | |
| setMapIndex(unsigned int idx) | TTProtoWithMap | inline |
| setMutationParameters() | TProtoQuanti | |
| setNumLociPerChromosome(string param_name) | TTProtoWithMap | |
| setParameters() | TProtoQuanti | virtual |
| setRecombinationMapFixed() | TTProtoWithMap | |
| setRecombinationMapNonRandom(vector< vector< double > > *lociPositions) | TTProtoWithMap | |
| setRecombinationMapRandom() | TTProtoWithMap | |
| SimComponent() | SimComponent | inline |
| store_data(BinaryStorageBuffer *saver) | TProtoQuanti | inlinevirtual |
| TProtoQuanti() | TProtoQuanti | |
| TProtoQuanti(const TProtoQuanti &T) | TProtoQuanti | |
| TTProtoWithMap() | TTProtoWithMap | inline |
| TTProtoWithMap(const TTProtoWithMap &TP) | TTProtoWithMap | |
| TTQuanti | TProtoQuanti | friend |
| unregisterFromGeneticMap() | TTProtoWithMap | |
| ~SimComponent() | SimComponent | inlinevirtual |
| ~StorableComponent() | StorableComponent | inlinevirtual |
| ~TProtoQuanti() | TProtoQuanti | virtual |
| ~TTProtoWithMap() | TTProtoWithMap | virtual |
