29#ifndef TTDELETMUTATIONS_BITSTR_H
30#define TTDELETMUTATIONS_BITSTR_H
139 virtual void init ( );
141 virtual void reset ( );
146 virtual void set_allele_value (
unsigned int locus,
unsigned int allele,
double value);
353 virtual void FHread (
string& filename);
A class to store any kind of data in a char buffer before unloading it in a binary data file.
Definition: binarystoragebuffer.h:44
A class to manage the files associated with each components of the simulation.
Definition: fileservices.h:52
static double Exponential(double mu)
Definition: Uniform.h:448
static double LogNormal(double zeta, double sigma)
Definition: Uniform.h:358
static double Gamma(double a, double b)
Definition: Uniform.h:386
Interface to all basic components of a simulation (traits, life cycle events, pop,...
Definition: simcomponent.h:45
The Service class used to manage the StatHandler objects.
Definition: statservices.h:50
Prototype class of the bitstring-deleterious mutations trait class.
Definition: ttdeletmutations_bitstring.h:171
double get_mut_rate()
Definition: ttdeletmutations_bitstring.h:180
virtual TTDeletMutations_bitstring * hatch()
Definition: ttdeletmutations_bitstring.cc:384
virtual void reset()
Definition: ttdeletmutations_bitstring.h:221
TTDeletMutBitstrFH * _writer
Definition: ttdeletmutations_bitstring.h:266
void reset_effect_table()
Definition: ttdeletmutations_bitstring.cc:293
virtual bool resetParameterFromSource(std::string param, SimComponent *cmpt)
Definition: ttdeletmutations_bitstring.cc:512
virtual TProtoDeletMutations_bitstring * clone()
Definition: ttdeletmutations_bitstring.h:225
unsigned int _mutation_model
Definition: ttdeletmutations_bitstring.h:250
double _strength
Definition: ttdeletmutations_bitstring.h:256
unsigned int _nb_locus
Definition: ttdeletmutations_bitstring.h:248
~TProtoDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.cc:103
double get_dominance()
Definition: ttdeletmutations_bitstring.h:183
float ** _effects
Definition: ttdeletmutations_bitstring.h:268
float * get_hs_continous()
Definition: ttdeletmutations_bitstring.h:189
void inherit_low(sex_t SEX, bitstring *seq, bitstring **parent)
Definition: ttdeletmutations_bitstring.cc:410
double(TProtoDeletMutations_bitstring::* _set_effects_func)(void)
Definition: ttdeletmutations_bitstring.h:262
virtual trait_t get_type() const
Definition: ttdeletmutations_bitstring.h:227
int get_nb_locus()
Definition: ttdeletmutations_bitstring.h:179
double get_init_freq()
Definition: ttdeletmutations_bitstring.h:186
float get_effect(unsigned int at, unsigned int loc)
Definition: ttdeletmutations_bitstring.h:191
bool setSelectionParameters()
Definition: ttdeletmutations_bitstring.cc:173
virtual void init()
Definition: ttdeletmutations_bitstring.h:219
virtual void loadFileServices(FileServices *loader)
Definition: ttdeletmutations_bitstring.cc:342
virtual bool retrieve_data(BinaryStorageBuffer *reader)
Definition: ttdeletmutations_bitstring.cc:482
virtual void store_data(BinaryStorageBuffer *saver)
Definition: ttdeletmutations_bitstring.cc:468
double set_effects_lognorm()
Definition: ttdeletmutations_bitstring.h:200
virtual bool setParameters()
Definition: ttdeletmutations_bitstring.cc:119
double _fitness_scaling_factor
Definition: ttdeletmutations_bitstring.h:252
double get_fitness_scaling_factor()
Definition: ttdeletmutations_bitstring.h:187
void write_effects_to_parameter()
Definition: ttdeletmutations_bitstring.cc:309
double get_backmutation_rate()
Definition: ttdeletmutations_bitstring.h:181
int get_dominance_model()
Definition: ttdeletmutations_bitstring.h:184
double set_effects_gamma()
Definition: ttdeletmutations_bitstring.h:199
void set_effects()
Definition: ttdeletmutations_bitstring.cc:266
virtual void loadStatServices(StatServices *loader)
Definition: ttdeletmutations_bitstring.cc:331
double set_effects_exp()
Definition: ttdeletmutations_bitstring.h:198
void(TProtoDeletMutations_bitstring::* _inherit_func_ptr)(sex_t, bitstring *, bitstring **)
Definition: ttdeletmutations_bitstring.h:263
void set_effect(unsigned int at, unsigned int loc, float val)
Definition: ttdeletmutations_bitstring.h:197
double _init_freq
Definition: ttdeletmutations_bitstring.h:253
double _mut_rate
Definition: ttdeletmutations_bitstring.h:254
double _dominance
Definition: ttdeletmutations_bitstring.h:257
double get_strength()
Definition: ttdeletmutations_bitstring.h:182
bool setEffectsFromInput()
Definition: ttdeletmutations_bitstring.cc:238
void inherit_free(sex_t SEX, bitstring *seq, bitstring **parent)
Definition: ttdeletmutations_bitstring.cc:402
float ** get_effects() const
Definition: ttdeletmutations_bitstring.h:190
int _dominance_model
Definition: ttdeletmutations_bitstring.h:251
double _back_mutation_rate
Definition: ttdeletmutations_bitstring.h:255
double _dist_p2
Definition: ttdeletmutations_bitstring.h:259
unsigned int _fitness_model
Definition: ttdeletmutations_bitstring.h:249
TProtoDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.cc:50
double _dist_p1
Definition: ttdeletmutations_bitstring.h:258
TTDeletMutBitstrFH * _reader
Definition: ttdeletmutations_bitstring.h:267
double(TTDeletMutations_bitstring::* _viability_func_ptr)(void)
Definition: ttdeletmutations_bitstring.h:261
bool _continuous_effects
Definition: ttdeletmutations_bitstring.h:260
bool get_iscontinuous()
Definition: ttdeletmutations_bitstring.h:185
TTDeletMutBitstrSH * _stats
Definition: ttdeletmutations_bitstring.h:265
float * get_s_continous()
Definition: ttdeletmutations_bitstring.h:188
The FileHandler associated with the TTDeletMutations_bitstring trait.
Definition: ttdeletmutations_bitstring.h:343
TTDeletMutBitstrFH(TProtoDeletMutations_bitstring *TP)
Definition: ttdeletmutations_bitstring.h:347
virtual void FHread(string &filename)
Definition: ttdeletmutations_bitstring.cc:1227
virtual void FHwrite()
Definition: ttdeletmutations_bitstring.cc:1120
virtual ~TTDeletMutBitstrFH()
Definition: ttdeletmutations_bitstring.h:350
The StatHandler for TTDeletMutations_bitstring.
Definition: ttdeletmutations_bitstring.h:272
double _deletHmzLoci
Definition: ttdeletmutations_bitstring.h:281
virtual ~TTDeletMutBitstrSH()
Definition: ttdeletmutations_bitstring.h:294
void setStatsForDeletMutations(age_t AGE)
Definition: ttdeletmutations_bitstring.cc:1025
double getMeanViability()
Definition: ttdeletmutations_bitstring.h:333
bool _isContinuousEffect
Definition: ttdeletmutations_bitstring.h:286
double _deletHtzLoci
Definition: ttdeletmutations_bitstring.h:281
double getDeletAllFreq()
Definition: ttdeletmutations_bitstring.h:317
double _Hmz
Definition: ttdeletmutations_bitstring.h:282
void setFst(age_t AGE)
Definition: stats_delet_bitstring.cc:361
double _Fst
Definition: ttdeletmutations_bitstring.h:282
TTDeletMutBitstrSH(TProtoDeletMutations_bitstring *TP)
Definition: ttdeletmutations_bitstring.h:290
double getHs()
Definition: ttdeletmutations_bitstring.h:325
double _viability[5]
Definition: ttdeletmutations_bitstring.h:276
double getHt()
Definition: ttdeletmutations_bitstring.h:326
double getDeletAllHmz()
Definition: ttdeletmutations_bitstring.h:318
double getDeletAllHtz()
Definition: ttdeletmutations_bitstring.h:319
double getFst()
Definition: ttdeletmutations_bitstring.h:327
double _Ht
Definition: ttdeletmutations_bitstring.h:282
double getPatchLoad(unsigned int i)
Definition: stats_delet_bitstring.cc:185
double _fixLocPerPatch
Definition: ttdeletmutations_bitstring.h:281
double getMeanFecWithPatchMate(bool HOME)
Definition: stats_delet_bitstring.cc:41
double getLoad()
Definition: stats_delet_bitstring.cc:165
double _Ho
Definition: ttdeletmutations_bitstring.h:282
double getLethalEquivalents()
Definition: ttdeletmutations_bitstring.h:328
double getOffsprgLetheq()
Definition: ttdeletmutations_bitstring.h:330
double getFixedDeletLociPerPatch()
Definition: ttdeletmutations_bitstring.h:321
double getBtheta()
Definition: ttdeletmutations_bitstring.h:312
double getBalpha()
Definition: ttdeletmutations_bitstring.h:313
double getFixedDeletLoci()
Definition: ttdeletmutations_bitstring.h:320
double getSegregatingDeletLociPerPatch()
Definition: ttdeletmutations_bitstring.h:323
void setOffsprgDeletStats()
Definition: ttdeletmutations_bitstring.h:304
double fecWithHomePatchMate
Definition: ttdeletmutations_bitstring.h:274
double * _deletFreqTable
Definition: ttdeletmutations_bitstring.h:284
void setAdultViab()
Definition: ttdeletmutations_bitstring.h:306
double _segrLocPerPatch
Definition: ttdeletmutations_bitstring.h:281
void setViability(age_idx agex)
Definition: stats_delet_bitstring.cc:86
double getHeterosis()
Definition: stats_delet_bitstring.cc:72
double getSegregatingDeletLoci()
Definition: ttdeletmutations_bitstring.h:322
void setOffsprgViab()
Definition: ttdeletmutations_bitstring.h:307
double getAdultsLetheq()
Definition: ttdeletmutations_bitstring.h:329
double _segrloc
Definition: ttdeletmutations_bitstring.h:282
double _meanViab
Definition: ttdeletmutations_bitstring.h:276
double getDeletAllPerGenome()
Definition: ttdeletmutations_bitstring.h:324
void setViabStats(age_t AGE)
Definition: ttdeletmutations_bitstring.cc:1073
void setMeanViability(age_idx agex)
Definition: stats_delet_bitstring.cc:139
double getViability(unsigned int v)
Definition: ttdeletmutations_bitstring.h:332
virtual bool setStatRecorders(std::string &token)
Definition: ttdeletmutations_bitstring.cc:981
double _letheq
Definition: ttdeletmutations_bitstring.h:282
double getMeanViability(unsigned int a)
Definition: ttdeletmutations_bitstring.h:334
double getSibProportions(unsigned int i)
Definition: ttdeletmutations_bitstring.h:336
void setDeletStats(age_t AGE)
Definition: stats_delet_bitstring.cc:211
double fecWithOtherPatchMate
Definition: ttdeletmutations_bitstring.h:274
double _freq
Definition: ttdeletmutations_bitstring.h:282
double _SibProps[5]
Definition: ttdeletmutations_bitstring.h:276
double _fixloc
Definition: ttdeletmutations_bitstring.h:282
double _Hs
Definition: ttdeletmutations_bitstring.h:282
void setLethalEquivalents(age_t AGE)
Definition: stats_delet_bitstring.cc:343
double _deletAllCount
Definition: ttdeletmutations_bitstring.h:282
void setAdultDeletStats()
Definition: ttdeletmutations_bitstring.h:303
Bitstring implementation of TTDeletMutations with recombination.
Definition: ttdeletmutations_bitstring.h:47
virtual bool operator!=(const TTrait &T)
Definition: ttdeletmutations_bitstring.cc:584
static void set_effects(float **fx)
bool get_hmz_atLocus(unsigned int loc)
Definition: ttdeletmutations_bitstring.h:108
unsigned int get_nb_htz_mutations()
Definition: ttdeletmutations_bitstring.h:106
TProtoDeletMutations_bitstring * _myProto
Definition: ttdeletmutations_bitstring.h:51
double viability_multi()
Definition: ttdeletmutations_bitstring.cc:875
unsigned int get_nb_mutations()
Definition: ttdeletmutations_bitstring.h:104
virtual void init_sequence()
Definition: ttdeletmutations_bitstring.cc:716
virtual void reset()
Definition: ttdeletmutations_bitstring.cc:653
virtual bool retrieve_data(BinaryStorageBuffer *reader)
Definition: ttdeletmutations_bitstring.cc:931
virtual ~TTDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.h:99
double viability_epist_continuous()
Definition: ttdeletmutations_bitstring.cc:908
static void set_recomb_template(unsigned int size)
unsigned int _nb_htz_mutations
Definition: ttdeletmutations_bitstring.h:69
TTDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.h:85
void set_nb_htz_mutations()
Definition: ttdeletmutations_bitstring.cc:859
virtual void set_value()
Definition: ttdeletmutations_bitstring.cc:842
double _phenotype
Definition: ttdeletmutations_bitstring.h:73
void set_inherit_func_ptr(void(TProtoDeletMutations_bitstring::*theFunc)(sex_t, bitstring *, bitstring **))
Definition: ttdeletmutations_bitstring.h:119
void set_mutation_func_ptr(unsigned int m_model)
Definition: ttdeletmutations_bitstring.cc:617
bitstring * _htz
Definition: ttdeletmutations_bitstring.h:72
virtual trait_t get_type() const
Definition: ttdeletmutations_bitstring.h:148
virtual void set_sequence(void **seq)
Definition: ttdeletmutations_bitstring.h:147
virtual void show_up()
Definition: ttdeletmutations_bitstring.cc:951
void mutate_noredraw_noBackMutation()
Definition: ttdeletmutations_bitstring.cc:827
virtual void set_allele_value(unsigned int locus, unsigned int allele, double value)
Definition: ttdeletmutations_bitstring.cc:694
unsigned int _nb_hmz_mutations
Definition: ttdeletmutations_bitstring.h:68
void set_mut_rate(double val, int nloc)
Definition: ttdeletmutations_bitstring.h:117
double _genomic_mut_rate
Definition: ttdeletmutations_bitstring.h:56
virtual double get_allele_value(int loc, int all)
Definition: ttdeletmutations_bitstring.cc:680
virtual void * set_trait(void *value)
Definition: ttdeletmutations_bitstring.h:142
virtual TTDeletMutations_bitstring * clone()
Definition: ttdeletmutations_bitstring.h:154
virtual void init()
Definition: ttdeletmutations_bitstring.cc:636
double viability_multi_continuous()
Definition: ttdeletmutations_bitstring.cc:893
bool get_htz_atLocus(unsigned int loc)
Definition: ttdeletmutations_bitstring.h:109
TTDeletMutations_bitstring(const TTDeletMutations_bitstring &T)
Definition: ttdeletmutations_bitstring.h:91
void set_sequence(bitstring **seq)
Definition: ttdeletmutations_bitstring.cc:670
void set_viability_func_ptr(unsigned int f_model, bool is_cont)
Definition: ttdeletmutations_bitstring.cc:594
unsigned int _nb_mutations
Definition: ttdeletmutations_bitstring.h:67
void set_proto(TProtoDeletMutations_bitstring *proto)
Definition: ttdeletmutations_bitstring.h:115
unsigned int _nb_locus
Definition: ttdeletmutations_bitstring.h:55
void set_nb_mutations()
Definition: ttdeletmutations_bitstring.cc:852
double(TTDeletMutations_bitstring::* _viability_func_ptr)(void)
Definition: ttdeletmutations_bitstring.h:58
void mutate_redraw()
Definition: ttdeletmutations_bitstring.cc:762
double viability_epist()
Definition: ttdeletmutations_bitstring.cc:885
virtual void mutate()
Definition: ttdeletmutations_bitstring.h:150
trait_t _type
Definition: ttdeletmutations_bitstring.h:75
void(TTDeletMutations_bitstring::* _mutation_func_ptr)(void)
Definition: ttdeletmutations_bitstring.h:60
virtual void ** get_sequence() const
Definition: ttdeletmutations_bitstring.h:143
void set_nb_hmz_mutations()
Definition: ttdeletmutations_bitstring.cc:867
bitstring * _hmz
Definition: ttdeletmutations_bitstring.h:72
virtual void inherit(TTrait *mother, TTrait *father)
Definition: ttdeletmutations_bitstring.cc:749
void(TProtoDeletMutations_bitstring::* _inherit_func_ptr)(sex_t, bitstring *, bitstring **)
Definition: ttdeletmutations_bitstring.h:59
virtual TTDeletMutations_bitstring & operator=(const TTrait &T)
Definition: ttdeletmutations_bitstring.cc:546
unsigned int get_nb_mut_atLocus(unsigned int loc)
Definition: ttdeletmutations_bitstring.h:105
bitstring * sequence[2]
Definition: ttdeletmutations_bitstring.h:71
void set_nb_locus(int val)
Definition: ttdeletmutations_bitstring.h:116
virtual void * getValue() const
Definition: ttdeletmutations_bitstring.h:152
virtual void store_data(BinaryStorageBuffer *saver)
Definition: ttdeletmutations_bitstring.cc:919
unsigned int get_nb_hmz_mutations()
Definition: ttdeletmutations_bitstring.h:107
virtual bool operator==(const TTrait &T)
Definition: ttdeletmutations_bitstring.cc:571
void mutate_noredraw()
Definition: ttdeletmutations_bitstring.cc:790
TTProtoWithMap.
Definition: ttrait_with_map.h:176
virtual void reset()
Definition: ttrait_with_map.cc:611
Interface for all trait types, declares all basic trait operations.
Definition: ttrait.h:46
Template class for the trait's FileHandler.
Definition: filehandler.h:217
Template class for the trait's StatHandler.
Definition: stathandler.h:168
Non-template and faster implementation of std::bitset.
Definition: bitstring.h:56
std::string trait_t
Trait types.
Definition: types.h:63
#define DELE
Definition: types.h:66
sex_t
Sex types, males are always 0 and females 1!!
Definition: types.h:36
unsigned int age_t
Age class flags.
Definition: types.h:46
#define ADULTS
Adults age class flag (breeders).
Definition: types.h:54
#define OFFSPRG
Offspring age class flag.
Definition: types.h:50
age_idx
Array index of the age classes in the patch sizes and containers arrays.
Definition: types.h:41
@ OFFSx
Definition: types.h:42
@ ADLTx
Definition: types.h:42