| _all_chooser | TProtoQuanti | private |
| _allele_model | TProtoQuanti | protected |
| _allele_value | TProtoQuanti | private |
| _chrsmLength | TTProtoWithMap | protected |
| _diallele_datatype | TProtoQuanti | protected |
| _doInitMutation | TProtoQuanti | private |
| _dominance_effects | TProtoQuanti | private |
| _dominance_model | TProtoQuanti | private |
| _effects_bivar | TProtoQuanti | private |
| _effects_multivar | TProtoQuanti | private |
| _epistasis | TProtoQuanti | private |
| _epistatic_coefs_indices | TProtoQuanti | private |
| _epistatic_coefs_matrix | TProtoQuanti | private |
| _eval | TProtoQuanti | private |
| _eVariance | TProtoQuanti | private |
| _evect | TProtoQuanti | private |
| _freqExtractor | TProtoQuanti | private |
| _genomic_mutation_rate | TProtoQuanti | protected |
| _getGenotypeWithDominance | TProtoQuanti | private |
| _getMutationValues | TProtoQuanti | private |
| _getMutationValuesVarPleio | 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 |
| _init_variance | TProtoQuanti | private |
| _isRegistered | TTProtoWithMap | private |
| _lociMapPositions | TTProtoWithMap | protected |
| _locus_table | TProtoQuanti | private |
| _locusByteSize | TProtoQuanti | private |
| _map | TTProtoWithMap | static |
| _mapIndex | TTProtoWithMap | protected |
| _mapResolution | TTProtoWithMap | protected |
| _mutation_correlation | TProtoQuanti | private |
| _mutation_func_ptr | TProtoQuanti | private |
| _mutation_rate | TProtoQuanti | protected |
| _mutation_sigma | TProtoQuanti | private |
| _mutationEffectIsFixedDiAllele | TProtoQuanti | private |
| _mutationVarianceIsLocusSpecific | TProtoQuanti | private |
| _num_epi_coefs | TProtoQuanti | private |
| _num_locus | TProtoQuanti | protected |
| _num_traits | TProtoQuanti | protected |
| _numChromosome | TTProtoWithMap | protected |
| _numLoci | TTProtoWithMap | protected |
| _numLociPerChrmsm | TTProtoWithMap | protected |
| _ohtaStats | TProtoQuanti | private |
| _paramPrefix | TTProtoWithMap | private |
| _paramSet | SimComponent | protected |
| _phenotypes | TProtoQuanti | private |
| _pleio_matx | TProtoQuanti | private |
| _pleio_type | TProtoQuanti | protected |
| _reader | TProtoQuanti | private |
| _recombRate | TTProtoWithMap | protected |
| _recombRatePerChrmsm | TTProtoWithMap | protected |
| _seq_length | TProtoQuanti | protected |
| _sequence_diallele_values | TProtoQuanti | private |
| _set_genotype_func_ptr | TProtoQuanti | private |
| _set_trait_value_func_ptr | TProtoQuanti | private |
| _sizeofLocusType | TProtoQuanti | private |
| _stats | TProtoQuanti | private |
| _totRecombEventsMean | TTProtoWithMap | protected |
| _trait_locus_table | TProtoQuanti | private |
| _trait_table | TProtoQuanti | private |
| _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 | |
| allocate_gsl_mutation_matrix_space(unsigned int num_locus) | TProtoQuanti | |
| areGeneticMapParamSet(string prefix) | TTProtoWithMap | |
| clone() | TProtoQuanti | inlinevirtual |
| deallocate_gsl_mutation_matrix_space() | TProtoQuanti | |
| do_epistasis() | TProtoQuanti | inline |
| get_allele_model() | TProtoQuanti | inline |
| get_allele_position(const unsigned int locus, const unsigned int trait) | TProtoQuanti | |
| get_allele_value(const TTQuanti *ind, const unsigned int allele, const unsigned int locus, const unsigned int trait) | TProtoQuanti | |
| get_diallele_value(unsigned int locus, unsigned int allele) | TProtoQuanti | inline |
| get_diallele_values() | TProtoQuanti | inline |
| get_doInitMutation() | TProtoQuanti | inline |
| get_dominance(unsigned int locus, unsigned int trait) | TProtoQuanti | inline |
| get_dominance_model() | TProtoQuanti | inline |
| get_env_var() | TProtoQuanti | inline |
| get_epi_coef_index() const | TProtoQuanti | inline |
| get_epi_coefs() const | TProtoQuanti | inline |
| 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_genotype_with_dominance(const double a1, const double a2, const unsigned int locus, const unsigned int trait) | TProtoQuanti | |
| get_genotypic_value(const TTQuanti *ind, const unsigned int trait) | 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_init_variance(unsigned int i) | TProtoQuanti | inline |
| get_locus_byte_size() | TProtoQuanti | inline |
| get_locus_ID(unsigned int locus, unsigned int trait) | TProtoQuanti | inline |
| get_locus_PD(unsigned int locus) | TProtoQuanti | inline |
| get_locus_seq_pos(unsigned int loc, unsigned int trait) | TProtoQuanti | inline |
| get_locus_start_pos(unsigned int locus) | TProtoQuanti | inline |
| get_name() | SimComponent | inlinevirtual |
| get_num_epi_coefs() | TProtoQuanti | inline |
| get_num_locus() | TProtoQuanti | inline |
| get_num_locus(unsigned int trait) | TProtoQuanti | inline |
| get_num_traits() | TProtoQuanti | inline |
| get_parameter(std::string name) | SimComponent | inlinevirtual |
| get_parameter_value(std::string name) | SimComponent | inlinevirtual |
| get_paramset() | SimComponent | inlinevirtual |
| get_phenotypic_value(const TTQuanti *ind, const unsigned int trait) | TProtoQuanti | inline |
| get_pleio_matrix() | TProtoQuanti | inline |
| get_pleiotropy_type() | TProtoQuanti | inline |
| get_seq_diallele_value(unsigned int position, unsigned int allele) | TProtoQuanti | inline |
| get_seq_length() | TProtoQuanti | inline |
| get_size_locus_type() | TProtoQuanti | inline |
| get_stater() | TProtoQuanti | inline |
| get_trait_mutation_variance(unsigned int trait) | TProtoQuanti | |
| get_type() const | TProtoQuanti | inlinevirtual |
| getMapIndex() | TTProtoWithMap | inline |
| getMutationEffectBivariateDiallelic(unsigned int loc) | TProtoQuanti | |
| getMutationEffectBivariateGaussian(unsigned int loc) | TProtoQuanti | |
| getMutationEffectBivariateGaussianLocSpec(unsigned int loc) | TProtoQuanti | |
| getMutationEffectMultivariateGaussian(unsigned int loc) | TProtoQuanti | |
| getMutationEffectMultivariateGaussianLocSpec(unsigned int loc) | TProtoQuanti | |
| getMutationEffects(unsigned int loc) | TProtoQuanti | inline |
| getMutationEffectsVarPleio(unsigned int loc) | TProtoQuanti | inline |
| getMutationEffectUnivariateDiallelic(unsigned int loc) | TProtoQuanti | |
| getMutationEffectUnivariateGaussian(unsigned int loc) | TProtoQuanti | |
| getMutationEffectUnivariateGaussianLocSpec(unsigned int loc) | TProtoQuanti | |
| has_parameter(std::string name) | SimComponent | inlinevirtual |
| hatch() | TProtoQuanti | virtual |
| inherit(sex_t SEX, TTQuanti *ind, const TTQuanti *parent) | TProtoQuanti | inline |
| inherit_free(sex_t SEX, TTQuanti *ind, const TTQuanti *parent) | TProtoQuanti | inline |
| inherit_low(sex_t SEX, TTQuanti *ind, const TTQuanti *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_no_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_diallelic_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_diallelic_var_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_full_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_inplace_full_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_inplace_no_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_inplace_var_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_nill(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_no_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| mutate_var_pleio(TTQuanti *ind) | TProtoQuanti | inline |
| readMatrixFromQuantiMutationMatrix(vector< vector< double >> &varmat) | TProtoQuanti | |
| recombine(unsigned long indID) | TTProtoWithMap | static |
| recordRandomMap() | TTProtoWithMap | |
| registerGeneticMap() | TTProtoWithMap | |
| reset() | TProtoQuanti | inlinevirtual |
| 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 TTQuanti *ind, const unsigned int trait) | TProtoQuanti | |
| set_genotype_value_dominance(const TTQuanti *ind, const unsigned int trait) | TProtoQuanti | |
| set_gsl_mutation_matrix(unsigned int pleio_deg, const vector< double > &varcov) | TProtoQuanti | |
| set_gsl_mutation_matrix_from_sigma(unsigned int loc, unsigned int pleio_deg) | TProtoQuanti | |
| set_index(int idx) | TraitPrototype | inlinevirtual |
| set_init_values(const double *values, unsigned int nval) | TProtoQuanti | |
| set_mutation_matrix_decomposition(unsigned int loc, unsigned int pleio_deg) | 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 | inline |
| set_trait_value_VE(const TTQuanti *ind, const unsigned int trait) | TProtoQuanti | inline |
| setAlleleModel() | TProtoQuanti | |
| setContinuousMutationModel_full_pleio() | TProtoQuanti | |
| setContinuousMutationModel_no_pleio() | TProtoQuanti | |
| setContinuousMutationModel_var_pleio() | TProtoQuanti | |
| setDiallelicMutationModel() | TProtoQuanti | |
| setDominanceParameters() | TProtoQuanti | |
| setEpistasisParameters() | TProtoQuanti | |
| setGeneticMapParameters(string prefix) | TTProtoWithMap | |
| setGeneticMapParams() | TProtoQuanti | |
| setHeritabilityParams() | TProtoQuanti | |
| setInitialValuesParams() | TProtoQuanti | |
| setMapIndex(unsigned int idx) | TTProtoWithMap | inline |
| setMutationCorrelation() | TProtoQuanti | |
| setMutationModel_full_pleio() | TProtoQuanti | |
| setMutationModel_no_pleio() | TProtoQuanti | |
| setMutationModel_var_pleio() | TProtoQuanti | |
| setMutationSigmaFromQuantiMutationVariance() | TProtoQuanti | |
| setMutationSigmaFromQuantiMutationVariance_no_pleio() | TProtoQuanti | |
| setNumLociPerChromosome(string param_name) | TTProtoWithMap | |
| setParameters() | TProtoQuanti | virtual |
| setRecombinationMapFixed() | TTProtoWithMap | |
| setRecombinationMapNonRandom(vector< vector< double > > *lociPositions) | TTProtoWithMap | |
| setRecombinationMapRandom() | TTProtoWithMap | |
| setTraitAndLocusTables_full_pleio() | TProtoQuanti | |
| setTraitAndLocusTables_no_pleio(TMatrix &mat) | TProtoQuanti | |
| 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 class | TProtoQuanti | friend |
| TTQuanti_continuous class | TProtoQuanti | friend |
| TTQuanti_continuous_full_pleio class | TProtoQuanti | friend |
| TTQuanti_continuous_no_pleio class | TProtoQuanti | friend |
| TTQuanti_continuous_single class | TProtoQuanti | friend |
| TTQuanti_continuous_var_pleio class | TProtoQuanti | friend |
| unregisterFromGeneticMap() | TTProtoWithMap | |
| ~SimComponent() | SimComponent | inlinevirtual |
| ~StorableComponent() | StorableComponent | inlinevirtual |
| ~TProtoQuanti() | TProtoQuanti | virtual |
| ~TTProtoWithMap() | TTProtoWithMap | virtual |
