_chrsmLength | TTProtoWithMap | protected |
_diploGenotTableCoding | TProtoBDMI | privatestatic |
_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 |
_nb_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 |
get_index() | TraitPrototype | inlinevirtual |
get_init_freq(unsigned int i) | TProtoBDMI | inline |
get_mut_rate() | TProtoBDMI | inline |
get_name() | SimComponent | inlinevirtual |
get_nb_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(sex_t SEX, bitstring *seq, 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 | |
TTProtoWithMap() | TTProtoWithMap | inline |
TTProtoWithMap(const TTProtoWithMap &TP) | TTProtoWithMap | |
unregisterFromGeneticMap() | TTProtoWithMap | |
~SimComponent() | SimComponent | inlinevirtual |
~StorableComponent() | StorableComponent | inlinevirtual |
~TProtoBDMI() | TProtoBDMI | virtual |
~TTProtoWithMap() | TTProtoWithMap | virtual |