Nemo
2.3.56
Simulate forward-in-time genetic evolution in a spatially explicit, individual-based stochastic simulator
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Prototype class of the bitstring-deleterious mutations trait class. More...
#include <ttdeletmutations_bitstring.h>
Public Member Functions | |
TProtoDeletMutations_bitstring () | |
TProtoDeletMutations_bitstring (const TProtoDeletMutations_bitstring &T) | |
~TProtoDeletMutations_bitstring () | |
Getters | |
int | get_nb_locus () |
double | get_mut_rate () |
double | get_backmutation_rate () |
double | get_strength () |
double | get_dominance () |
int | get_dominance_model () |
bool | get_iscontinuous () |
double | get_init_freq () |
double | get_fitness_scaling_factor () |
float * | get_s_continous () |
float * | get_hs_continous () |
float ** | get_effects () const |
float | get_effect (unsigned int at, unsigned int loc) |
Setters | |
void | set_effects () |
void | set_effect (unsigned int at, unsigned int loc, float val) |
double | set_effects_exp () |
double | set_effects_gamma () |
double | set_effects_lognorm () |
void | reset_effect_table () |
void | write_effects_to_parameter () |
Parameter setters | |
bool | setSelectionParameters () |
bool | setEffectsFromInput () |
Inheritance functions | |
void | inherit_low (sex_t SEX, bitstring *seq, bitstring **parent) |
void | inherit_free (sex_t SEX, bitstring *seq, bitstring **parent) |
TraitPrototype implementations | |
virtual void | init () |
virtual void | reset () |
virtual TTDeletMutations_bitstring * | hatch () |
virtual TProtoDeletMutations_bitstring * | clone () |
virtual trait_t | get_type () const |
StorageComponent implementation | |
virtual void | store_data (BinaryStorageBuffer *saver) |
virtual bool | retrieve_data (BinaryStorageBuffer *reader) |
SimComponent implementation | |
virtual bool | setParameters () |
virtual void | loadFileServices (FileServices *loader) |
virtual void | loadStatServices (StatServices *loader) |
virtual bool | resetParameterFromSource (std::string param, SimComponent *cmpt) |
Public Member Functions inherited from TTProtoWithMap | |
TTProtoWithMap () | |
TTProtoWithMap (const TTProtoWithMap &TP) | |
virtual | ~TTProtoWithMap () |
void | setMapIndex (unsigned int idx) |
unsigned int | getMapIndex () |
bool | setGeneticMapParameters (string prefix) |
void | addGeneticMapParameters (string prefix) |
bool | setRecombinationMapRandom () |
bool | setRecombinationMapNonRandom (vector< vector< double > > *lociPositions) |
bool | setRecombinationMapFixed () |
bool | setNumLociPerChromosome (string param_name) |
void | reset_recombination_pointers () |
void | registerGeneticMap () |
void | unregisterFromGeneticMap () |
bool | areGeneticMapParamSet (string prefix) |
bool | isRecombinationFree (string prefix) |
void | recordRandomMap () |
virtual void | reset () |
Public Member Functions inherited from TraitPrototype | |
virtual void | reset ()=0 |
Called at the end of a simulation to reset the Traits' prototypes (e.g. More... | |
virtual TTrait * | hatch ()=0 |
Creates the trait of which it is the prototype, called by IndFactory::makePrototype() . More... | |
virtual TraitPrototype * | clone ()=0 |
Returns a copy of itself. More... | |
virtual trait_t | get_type () const =0 |
Type accessor. More... | |
virtual void | set_index (int idx) |
Sets the traits index. More... | |
virtual int | get_index () |
Index getter. More... | |
Public Member Functions inherited from StorableComponent | |
virtual void | store_data (BinaryStorageBuffer *saver)=0 |
Interface to store the component data (e.g. gene values) into a binary buffer. More... | |
virtual bool | retrieve_data (BinaryStorageBuffer *reader)=0 |
Interface to retrieve the same data from the binary buffer. More... | |
virtual | ~StorableComponent () |
Public Member Functions inherited from SimComponent | |
SimComponent () | |
virtual | ~SimComponent () |
virtual void | loadUpdaters (UpdaterServices *loader) |
Loads the parameters and component updater onto the updater manager. More... | |
virtual void | set_paramset (ParamSet *paramset) |
Sets the ParamSet member. More... | |
virtual void | set_paramset (std::string name, bool required, SimComponent *owner) |
Sets a new ParamSet and name it. More... | |
virtual void | set_paramsetFromCopy (const ParamSet &PSet) |
Reset the set of parameters from a another set. More... | |
virtual ParamSet * | get_paramset () |
ParamSet accessor. More... | |
virtual void | add_parameter (Param *param) |
Interface to add a parameter to the set. More... | |
virtual void | add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd) |
Interface to add a parameter to the set. More... | |
virtual void | add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater) |
Interface to add a parameter and its updater to the set. More... | |
virtual Param * | get_parameter (std::string name) |
Param getter. More... | |
virtual double | get_parameter_value (std::string name) |
Param value getter. More... | |
virtual string | get_name () |
Returnd the name of the ParamSet, i.e. More... | |
virtual bool | has_parameter (std::string name) |
Param getter. More... | |
Private Attributes | |
unsigned int | _nb_locus |
unsigned int | _fitness_model |
unsigned int | _mutation_model |
int | _dominance_model |
double | _fitness_scaling_factor |
double | _init_freq |
double | _mut_rate |
double | _back_mutation_rate |
double | _strength |
double | _dominance |
double | _dist_p1 |
double | _dist_p2 |
bool | _continuous_effects |
double(TTDeletMutations_bitstring::* | _viability_func_ptr )(void) |
double(TProtoDeletMutations_bitstring::* | _set_effects_func )(void) |
void(TProtoDeletMutations_bitstring::* | _inherit_func_ptr )(sex_t, bitstring *, bitstring **) |
TTDeletMutBitstrSH * | _stats |
TTDeletMutBitstrFH * | _writer |
TTDeletMutBitstrFH * | _reader |
float ** | _effects |
Additional Inherited Members | |
Static Public Member Functions inherited from TTProtoWithMap | |
static void | recombine (unsigned long indID) |
Static Public Attributes inherited from TTProtoWithMap | |
static GeneticMap | _map |
Protected Attributes inherited from TTProtoWithMap | |
unsigned int | _mapIndex |
double | _totRecombEventsMean |
double | _recombRate |
double | _mapResolution |
unsigned int | _numChromosome |
unsigned int | _numLoci |
double * | _recombRatePerChrmsm |
unsigned int * | _numLociPerChrmsm |
unsigned int * | _chrsmLength |
unsigned int * | _lociMapPositions |
Protected Attributes inherited from TraitPrototype | |
int | _index |
The trait index in the Individual traits table. More... | |
Protected Attributes inherited from SimComponent | |
ParamSet * | _paramSet |
The parameters container. More... | |
Prototype class of the bitstring-deleterious mutations trait class.
TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring | ( | ) |
References SimComponent::add_parameter(), TTProtoWithMap::addGeneticMapParameters(), BOOL, DBL, INT, MAT, SimComponent::set_paramset(), and STR.
Referenced by clone().
TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring | ( | const TProtoDeletMutations_bitstring & | T | ) |
References SimComponent::_paramSet.
TProtoDeletMutations_bitstring::~TProtoDeletMutations_bitstring | ( | ) |
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Implements TraitPrototype.
References TProtoDeletMutations_bitstring().
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References _back_mutation_rate.
Referenced by TTDeletMutations_bitstring::mutate_noredraw(), and TTDeletMutations_bitstring::set_mutation_func_ptr().
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References _dominance.
Referenced by TTDeletMutations_bitstring::set_allele_value(), TTDeletMutations_bitstring::viability_epist(), and TTDeletMutations_bitstring::viability_multi().
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References _dominance_model.
Referenced by TTDeletMutations_bitstring::set_allele_value().
References _effects.
Referenced by TTDeletMutations_bitstring::get_allele_value(), TTDeletMutations_bitstring::set_allele_value(), TTDeletMutations_bitstring::viability_epist_continuous(), and TTDeletMutations_bitstring::viability_multi_continuous().
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References _effects.
Referenced by resetParameterFromSource().
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References _fitness_scaling_factor.
Referenced by TTDeletMutations_bitstring::viability_epist(), TTDeletMutations_bitstring::viability_epist_continuous(), TTDeletMutations_bitstring::viability_multi(), and TTDeletMutations_bitstring::viability_multi_continuous().
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References _effects.
Referenced by TTDeletMutBitstrFH::FHwrite().
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References _init_freq.
Referenced by TTDeletMutations_bitstring::init_sequence().
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References _continuous_effects.
Referenced by TTDeletMutBitstrFH::FHwrite(), and TTDeletMutBitstrSH::TTDeletMutBitstrSH().
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References _nb_locus.
Referenced by TTDeletMutBitstrFH::FHread(), TTDeletMutBitstrFH::FHwrite(), TTDeletMutBitstrSH::setDeletStats(), and TTDeletMutBitstrSH::setLethalEquivalents().
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References _effects.
Referenced by TTDeletMutBitstrFH::FHwrite(), and TTDeletMutBitstrSH::setLethalEquivalents().
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References _strength.
Referenced by TTDeletMutations_bitstring::set_allele_value(), TTDeletMutBitstrSH::setLethalEquivalents(), TTDeletMutations_bitstring::viability_epist(), and TTDeletMutations_bitstring::viability_multi().
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Implements TraitPrototype.
References DELE.
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Implements TraitPrototype.
References _continuous_effects, _fitness_model, _inherit_func_ptr, _mut_rate, _mutation_model, _nb_locus, TTDeletMutations_bitstring::set_inherit_func_ptr(), TTDeletMutations_bitstring::set_mut_rate(), TTDeletMutations_bitstring::set_mutation_func_ptr(), TTDeletMutations_bitstring::set_nb_locus(), TTDeletMutations_bitstring::set_proto(), and TTDeletMutations_bitstring::set_viability_func_ptr().
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References _nb_locus, and RAND::RandBool().
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References TTProtoWithMap::_map, TTProtoWithMap::_mapIndex, TTProtoWithMap::_numChromosome, TTProtoWithMap::_numLociPerChrmsm, bitstring::copy(), GeneticMap::getFirstRecPosition(), and GeneticMap::getRecLoci().
Referenced by setParameters().
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References setParameters().
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Implements SimComponent.
References _reader, _writer, FileServices::attach(), FileServices::attach_reader(), SimComponent::get_parameter(), Param::getMatrix(), Param::getValue(), Param::isMatrix(), Param::isSet(), TraitFileHandler< TP >::set(), FileHandler::set_isInputHandler(), and FileHandler::set_multi().
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Implements SimComponent.
References _stats, and StatServices::attach().
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Reimplemented from TTProtoWithMap.
References TTProtoWithMap::reset().
void TProtoDeletMutations_bitstring::reset_effect_table | ( | ) |
References _effects, and _nb_locus.
Referenced by resetParameterFromSource(), set_effects(), and setEffectsFromInput().
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Implements SimComponent.
References _effects, _nb_locus, error(), get_effects(), reset_effect_table(), and write_effects_to_parameter().
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Implements StorableComponent.
References _continuous_effects, _effects, _nb_locus, error(), BinaryStorageBuffer::read(), and warning().
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References _effects.
Referenced by TTDeletMutBitstrFH::FHread(), and TTDeletMutations_bitstring::set_allele_value().
void TProtoDeletMutations_bitstring::set_effects | ( | ) |
References _dominance, _dominance_model, _effects, _nb_locus, _set_effects_func, _strength, reset_effect_table(), and write_effects_to_parameter().
Referenced by setSelectionParameters().
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References _strength, and RAND::Exponential().
Referenced by setSelectionParameters().
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References _dist_p1, _dist_p2, and RAND::Gamma().
Referenced by setSelectionParameters().
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References _dist_p1, _dist_p2, and RAND::LogNormal().
Referenced by setSelectionParameters().
bool TProtoDeletMutations_bitstring::setEffectsFromInput | ( | ) |
References _continuous_effects, _effects, _nb_locus, error(), TMatrix::get(), SimComponent::get_parameter(), Param::getMatrix(), TMatrix::getNbCols(), TMatrix::getNbRows(), and reset_effect_table().
Referenced by setSelectionParameters().
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Implements SimComponent.
References _back_mutation_rate, _fitness_model, _fitness_scaling_factor, _inherit_func_ptr, _init_freq, _mut_rate, _mutation_model, _nb_locus, error(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), inherit_low(), Param::isSet(), TTProtoWithMap::setGeneticMapParameters(), and setSelectionParameters().
Referenced by init().
bool TProtoDeletMutations_bitstring::setSelectionParameters | ( | ) |
References _continuous_effects, _dist_p1, _dist_p2, _dominance, _dominance_model, SimComponent::_paramSet, _set_effects_func, _strength, error(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), ParamSet::getArg(), set_effects(), set_effects_exp(), set_effects_gamma(), set_effects_lognorm(), and setEffectsFromInput().
Referenced by setParameters().
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Implements StorableComponent.
References _continuous_effects, _effects, _nb_locus, and BinaryStorageBuffer::store().
void TProtoDeletMutations_bitstring::write_effects_to_parameter | ( | ) |
References _effects, _nb_locus, SimComponent::get_parameter(), Param::setArg(), and Param::setIsSet().
Referenced by resetParameterFromSource(), and set_effects().
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Referenced by get_backmutation_rate(), and setParameters().
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Referenced by get_iscontinuous(), hatch(), retrieve_data(), setEffectsFromInput(), setSelectionParameters(), and store_data().
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Referenced by set_effects_gamma(), set_effects_lognorm(), and setSelectionParameters().
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Referenced by set_effects_gamma(), set_effects_lognorm(), and setSelectionParameters().
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Referenced by get_dominance(), set_effects(), and setSelectionParameters().
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Referenced by get_dominance_model(), set_effects(), and setSelectionParameters().
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Referenced by hatch(), and setParameters().
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Referenced by get_fitness_scaling_factor(), and setParameters().
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Referenced by hatch(), and setParameters().
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Referenced by get_init_freq(), and setParameters().
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Referenced by get_mut_rate(), hatch(), and setParameters().
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Referenced by hatch(), and setParameters().
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Referenced by loadFileServices(), and ~TProtoDeletMutations_bitstring().
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Referenced by set_effects(), and setSelectionParameters().
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Referenced by loadStatServices(), and ~TProtoDeletMutations_bitstring().
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Referenced by get_strength(), set_effects(), set_effects_exp(), and setSelectionParameters().
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Referenced by loadFileServices(), and ~TProtoDeletMutations_bitstring().