Nemo  2.3.46
ttdeletmutations_bitstring.h
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1 
29 #ifndef TTDELETMUTATIONS_BITSTR_H
30 #define TTDELETMUTATIONS_BITSTR_H
31 
32 #include "ttrait.h"
33 #include "types.h"
34 #include "stathandler.h"
35 #include "filehandler.h"
36 #include "datatable.h"
37 #include "metapop.h"
38 #include "bitstring.h"
39 #include "Uniform.h"
40 
41 class TTDeletMutBitstrSH;
42 class TTDeletMutBitstrFH;
44 
45 
48 private:
49 
51 
54  unsigned int _nb_locus;
55  unsigned int _fitness_model;
57  double _init_freq;
58  double _mut_rate;
60  double _strength;
61  double _dominance;
67  //globs:
68  static float** _effects;
69 
70  //counters:
71  unsigned int _nb_mutations;
72  unsigned int _nb_hmz_mutations;
73  unsigned int _nb_htz_mutations;
74 
75  bitstring* sequence[2];
76  bitstring *_htz, *_hmz;
77  double _phenotype;
78 
80 
81  void set_nb_mutations ( );
82  void set_nb_htz_mutations ( );
83  void set_nb_hmz_mutations ( );
84 
85 
86 public:
87 
88  //'tors:
90  : _myProto(0), _nb_locus(0), _fitness_model(0), _fitness_scaling_factor(1), _init_freq(0),
91  _mut_rate(0), _genomic_mut_rate(0), _strength(0), _dominance(0), _continuous_effects(0),
92  _viability_func_ptr(0), _inherit_func_ptr(0),_mutation_func_ptr(0), _nb_mutations(0),
93  _nb_hmz_mutations(0),_nb_htz_mutations(0), _htz(0), _hmz(0), _phenotype(0), _type(DELE)
94  {sequence[0] = sequence[1] = NULL;}
95 
97  : _myProto(T._myProto), _nb_locus(T._nb_locus), _fitness_model(T._fitness_model),
98  _fitness_scaling_factor(T._fitness_scaling_factor),
99  _init_freq(T._init_freq), _mut_rate(T._mut_rate), _genomic_mut_rate(T._genomic_mut_rate),
100  _strength(T._strength), _dominance(T._dominance), _continuous_effects(T._continuous_effects),
102  _mutation_func_ptr(T._mutation_func_ptr), _nb_mutations(0), _nb_hmz_mutations(0),
103  _nb_htz_mutations(0), _htz(0), _hmz(0), _phenotype(0), _type(DELE)
104  {sequence[0] = sequence[1] = NULL;}
105 
107 
108 
111  unsigned int get_nb_mutations ( ) {return _nb_mutations;}
112  unsigned int get_nb_mut_atLocus (unsigned int loc) {return (*sequence[0])[loc] + (*sequence[1])[loc];}
113  unsigned int get_nb_htz_mutations ( ) {return _nb_htz_mutations;}
114  unsigned int get_nb_hmz_mutations ( ) {return _nb_hmz_mutations;}
115  bool get_hmz_atLocus (unsigned int loc) {return (*sequence[0])[loc] & (*sequence[1])[loc];}
116  bool get_htz_atLocus (unsigned int loc) {return (*sequence[0])[loc] ^ (*sequence[1])[loc];}
117  float** get_effects ( ) const {return _effects;}
121  void set_proto (TProtoDeletMutations_bitstring* proto) {_myProto = proto;}
122  void set_nb_locus (int val) {_nb_locus = val;}
123  void set_mut_rate (double val, int nloc) {_mut_rate = val; _genomic_mut_rate = 2*nloc*_mut_rate;}
124  void set_strength (double val) {_strength = val;}
125  void set_dominance (double val) {_dominance = val;}
126  void set_viability_func_ptr (unsigned int f_model, bool is_cont);
127  void set_inherit_func_ptr (void(TProtoDeletMutations_bitstring::* theFunc)(sex_t, bitstring*, bitstring**))
128  {_inherit_func_ptr = theFunc;}
129  void set_mutation_func_ptr (unsigned int m_model);
130  void set_fitness_scaling_factor (double val) {_fitness_scaling_factor = val;}
131  void set_init_freq (double val) {_init_freq = val;}
132  void set_fitness_model (int val) {_fitness_model = val;}
133  void set_continuous_effects (bool val) {_continuous_effects = val;}
135 
136  double viability_multi ( );
137  double viability_epist ( );
138  double viability_multi_continuous ( );
139  double viability_epist_continuous ( );
140  void mutate_redraw ( );
141  void mutate_noredraw ( );
142 
143  void set_sequence (bitstring** seq);
144  //glob setters:
145  static void set_effects (float** fx);
146  static void set_recomb_template (unsigned int size);
147 
150  virtual void init ( );
151  virtual void init_sequence ( );
152  virtual void reset ( );
153  virtual void* set_trait (void* value) {return NULL;}
154  virtual void** get_sequence ( ) const {return (void**)&sequence[0];}
155  virtual double get_allele_value (int loc, int all);
156  /*Be aware that the set_allele_value here changes the mutation effect for all individuals in the pop!!*/
157  virtual void set_allele_value (unsigned int locus, unsigned int allele, double value);
158  virtual void set_sequence (void** seq) {}
159  virtual trait_t get_type ( ) const {return _type;}
160  virtual void inherit (TTrait* mother, TTrait* father);
161  virtual void mutate ( ) {(this->*_mutation_func_ptr)();}
162  virtual void set_value ( );
163  virtual void* getValue ( ) const {return (void*)&_phenotype;}
164  virtual void show_up ( );
166  virtual TTDeletMutations_bitstring& operator=(const TTrait& T);
167  virtual bool operator==(const TTrait& T);
168  virtual bool operator!=(const TTrait& T);
169 
170  //implements StorableComponent:
171  virtual void store_data (BinaryStorageBuffer* saver); // {saver->store(sequence[0], _nb_locus); saver->store(sequence[1], _nb_locus);}
172  virtual bool retrieve_data (BinaryStorageBuffer* reader); // {reader->read(sequence[0], _nb_locus); reader->read(sequence[1], _nb_locus);return true;}
174 };
175 
176 // ------------------------------------------------------------------------------
177 
178 // TProtoDeletMutations
179 
180 // ------------------------------------------------------------------------------
183 public:
187 
188  int get_nb_locus ( ) {return _nb_locus;}
189  double get_mut_rate ( ) {return _mut_rate;}
190  double get_strength ( ) {return _strength;}
191  double get_dominance ( ) {return _dominance;}
194 
195  void set_effects ( );
196  double set_effects_exp ( ) {return RAND::Exponential(_strength);}
199  float* get_s_continous ( ) {return _effects[1];}
200  float* get_hs_continous ( ) {return _effects[0];}
201 
202  void inherit_low (sex_t SEX, bitstring* seq, bitstring** parent);
203  void inherit_free (sex_t SEX, bitstring* seq, bitstring** parent);
204 
205  bool setSelectionParameters ();
206 
207  //implements TraitPrototype
208  virtual void init (){setParameters();};
209 
210  virtual void reset (){TTProtoWithMap::reset();}
211 
212  virtual TTDeletMutations_bitstring* hatch ();
213 
215 
216  virtual trait_t get_type () const {return DELE;}
217  //implements StorageComponent
218  virtual void store_data (BinaryStorageBuffer* saver);
219 
220  virtual bool retrieve_data (BinaryStorageBuffer* reader);
221  //implements SimComponent
222  virtual bool setParameters ( );
223 
224  virtual void loadFileServices ( FileServices* loader );
225 
226  virtual void loadStatServices ( StatServices* loader );
227 
228 private:
229 
230  unsigned int _nb_locus;
231  unsigned int _fitness_model;
232  unsigned int _mutation_model;
235  double _init_freq;
236  double _mut_rate;
237  double _strength;
238  double _dominance;
239  double _dist_p1; //parameter 1 of random effects distribution (mu or shape)
240  double _dist_p2; //parameter 2 of random effects distribution (sigma or scale)
244  void (TProtoDeletMutations_bitstring::* _inherit_func_ptr) (sex_t, bitstring*, bitstring**);
245 
249  float** _effects;
250 };
251 
253 class TTDeletMutBitstrSH : public TraitStatHandler<TProtoDeletMutations_bitstring, TTDeletMutBitstrSH> {
254 
256  //props and viability:
258  //0: outbred from migrants, 1: outbred from residants
259  //2: inbred from half-sibs, 3: inbred from full-sibs
260  //4: selfed offsprg
261 
264  //table to store the deleterious mutations freq per locus:
266 
268 
269 public:
270 
273  { _isContinuousEffect = TP->get_iscontinuous(); }
274 
275  virtual ~TTDeletMutBitstrSH () {if(_deletFreqTable != 0) delete [] _deletFreqTable;}
276 
277  virtual bool setStatRecorders (std::string& token);
278 
279  void setStatsForDeletMutations (age_t AGE);
280  void setViabStats (age_t AGE);
281  void setDeletStats (age_t AGE);
282  void setLethalEquivalents (age_t AGE);
283  void setFst (age_t AGE);
286  void setViability (age_idx agex);
289  void setMeanViability (age_idx agex);
290 
291 
292  double getMeanFecWithPatchMate(bool HOME);
293  double getBtheta () {return fecWithHomePatchMate;}
294  double getBalpha () {return fecWithOtherPatchMate;}
295  double getHeterosis ();
296  double getLoad ();
297  double getPatchLoad (unsigned int i);
298  double getDeletAllFreq () {return _freq;}
299  double getDeletAllHmz () {return _Hmz;}
300  double getDeletAllHtz () {return _Ho;}
301  double getFixedDeletLoci () {return _fixloc;}
303  double getSegregatingDeletLoci () {return _segrloc;}
306  double getHs () {return _Hs;}
307  double getHt () {return _Ht;}
308  double getFst () {return _Fst;}
309  double getLethalEquivalents () {return _letheq;}
312 
313  double getViability (unsigned int v) {return _viability[v];}
314  double getMeanViability () {return _meanViab;}
315  double getMeanViability (unsigned int a) {setMeanViability(static_cast<age_idx> (a)); return _meanViab;}
316 
317  double getSibProportions (unsigned int i) {return _SibProps[i];}
318 
319 };
320 
321 
324 class TTDeletMutBitstrFH : public TraitFileHandler<TProtoDeletMutations_bitstring> {
325 
326 public:
327 
330 
331  virtual ~TTDeletMutBitstrFH ( ) { }
332 
333  virtual void FHwrite ();
334  virtual void FHread (string& filename);
335 };
336 
337 
338 #endif //TTDELETMUTATIONS_BITSTR_H
void setLethalEquivalents(age_t AGE)
Definition: stats_delet_bitstring.cc:343
unsigned int get_nb_hmz_mutations()
Definition: ttdeletmutations_bitstring.h:114
double viability_multi_continuous()
Definition: ttdeletmutations_bitstring.cc:735
float * get_s_continous()
Definition: ttdeletmutations_bitstring.h:199
Template class for the trait's FileHandler.
Definition: filehandler.h:217
double fecWithOtherPatchMate
Definition: ttdeletmutations_bitstring.h:255
virtual trait_t get_type() const
Definition: ttdeletmutations_bitstring.h:159
int get_dominance_model()
Definition: ttdeletmutations_bitstring.h:192
bool _continuous_effects
Definition: ttdeletmutations_bitstring.h:241
virtual ~TTDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.h:106
TTDeletMutBitstrFH(TProtoDeletMutations_bitstring *TP)
Definition: ttdeletmutations_bitstring.h:328
float * get_hs_continous()
Definition: ttdeletmutations_bitstring.h:200
virtual void reset()
Definition: ttdeletmutations_bitstring.cc:534
The Service class used to manage the StatHandler objects.
Definition: statservices.h:50
void(TProtoDeletMutations_bitstring::* _inherit_func_ptr)(sex_t, bitstring *, bitstring **)
Definition: ttdeletmutations_bitstring.h:64
virtual void store_data(BinaryStorageBuffer *saver)
Definition: ttdeletmutations_bitstring.cc:760
double _fixLocPerPatch
Definition: ttdeletmutations_bitstring.h:262
#define ADULTS
Adults age class flag (breeders).
Definition: types.h:54
std::string trait_t
Trait types.
Definition: types.h:63
virtual void FHread(string &filename)
Definition: ttdeletmutations_bitstring.cc:1065
void set_nb_htz_mutations()
Definition: ttdeletmutations_bitstring.cc:701
virtual void show_up()
Definition: ttdeletmutations_bitstring.cc:790
virtual void store_data(BinaryStorageBuffer *saver)
Definition: ttdeletmutations_bitstring.cc:383
virtual TProtoDeletMutations_bitstring * clone()
Definition: ttdeletmutations_bitstring.h:214
virtual void loadStatServices(StatServices *loader)
Definition: ttdeletmutations_bitstring.cc:244
void setStatsForDeletMutations(age_t AGE)
Definition: ttdeletmutations_bitstring.cc:864
static double Exponential(double mu)
Definition: Uniform.h:424
virtual bool setParameters()
Definition: ttdeletmutations_bitstring.cc:115
age_idx
Array index of the age classes in the patch sizes and containers arrays.
Definition: types.h:41
unsigned int _nb_htz_mutations
Definition: ttdeletmutations_bitstring.h:73
double _deletHtzLoci
Definition: ttdeletmutations_bitstring.h:262
double _freq
Definition: ttdeletmutations_bitstring.h:263
virtual ~TTDeletMutBitstrFH()
Definition: ttdeletmutations_bitstring.h:331
virtual void FHwrite()
Definition: ttdeletmutations_bitstring.cc:959
void set_fitness_scaling_factor(double val)
Definition: ttdeletmutations_bitstring.h:130
double(TTDeletMutations_bitstring::* _viability_func_ptr)(void)
Definition: ttdeletmutations_bitstring.h:242
virtual void mutate()
Definition: ttdeletmutations_bitstring.h:161
virtual void inherit(TTrait *mother, TTrait *father)
Definition: ttdeletmutations_bitstring.cc:627
virtual void init()
Definition: ttdeletmutations_bitstring.h:208
double _genomic_mut_rate
Definition: ttdeletmutations_bitstring.h:59
void inherit_free(sex_t SEX, bitstring *seq, bitstring **parent)
Definition: ttdeletmutations_bitstring.cc:317
double(TProtoDeletMutations_bitstring::* _set_effects_func)(void)
Definition: ttdeletmutations_bitstring.h:243
unsigned int age_t
Age class flags.
Definition: types.h:46
double getAdultsLetheq()
Definition: ttdeletmutations_bitstring.h:310
static double LogNormal(double zeta, double sigma)
Definition: Uniform.h:334
TTProtoWithMap.
Definition: ttrait_with_map.h:165
void(TTDeletMutations_bitstring::* _mutation_func_ptr)(void)
Definition: ttdeletmutations_bitstring.h:65
double _strength
Definition: ttdeletmutations_bitstring.h:60
double getBtheta()
Definition: ttdeletmutations_bitstring.h:293
void set_proto(TProtoDeletMutations_bitstring *proto)
Definition: ttdeletmutations_bitstring.h:121
void(TProtoDeletMutations_bitstring::* _inherit_func_ptr)(sex_t, bitstring *, bitstring **)
Definition: ttdeletmutations_bitstring.h:244
Non-template and faster implementation of std::bitset.
Definition: bitstring.h:56
virtual void * set_trait(void *value)
Definition: ttdeletmutations_bitstring.h:153
bool get_hmz_atLocus(unsigned int loc)
Definition: ttdeletmutations_bitstring.h:115
void set_nb_mutations()
Definition: ttdeletmutations_bitstring.cc:694
double getHeterosis()
Definition: stats_delet_bitstring.cc:72
unsigned int _nb_locus
Definition: ttdeletmutations_bitstring.h:54
void setFst(age_t AGE)
Definition: stats_delet_bitstring.cc:361
double getFixedDeletLoci()
Definition: ttdeletmutations_bitstring.h:301
TTDeletMutBitstrFH * _reader
Definition: ttdeletmutations_bitstring.h:248
virtual void init_sequence()
Definition: ttdeletmutations_bitstring.cc:594
double getMeanViability(unsigned int a)
Definition: ttdeletmutations_bitstring.h:315
TTDeletMutations_bitstring(const TTDeletMutations_bitstring &T)
Definition: ttdeletmutations_bitstring.h:96
virtual void * getValue() const
Definition: ttdeletmutations_bitstring.h:163
bitstring * sequence[2]
Definition: ttdeletmutations_bitstring.h:75
double get_dominance()
Definition: ttdeletmutations_bitstring.h:191
Interface for all trait types, declares all basic trait operations.
Definition: ttrait.h:46
double _deletAllCount
Definition: ttdeletmutations_bitstring.h:263
double get_mut_rate()
Definition: ttdeletmutations_bitstring.h:189
virtual bool operator==(const TTrait &T)
Definition: ttdeletmutations_bitstring.cc:460
double getFixedDeletLociPerPatch()
Definition: ttdeletmutations_bitstring.h:302
virtual TTDeletMutations_bitstring & operator=(const TTrait &T)
Definition: ttdeletmutations_bitstring.cc:428
void setViability(age_idx agex)
Definition: stats_delet_bitstring.cc:86
virtual void init()
Definition: ttdeletmutations_bitstring.cc:520
double _init_freq
Definition: ttdeletmutations_bitstring.h:57
trait_t _type
Definition: ttdeletmutations_bitstring.h:79
bool _continuous_effects
Definition: ttdeletmutations_bitstring.h:62
bool get_htz_atLocus(unsigned int loc)
Definition: ttdeletmutations_bitstring.h:116
TTDeletMutBitstrFH * _writer
Definition: ttdeletmutations_bitstring.h:247
virtual TTDeletMutations_bitstring * clone()
Definition: ttdeletmutations_bitstring.h:165
double _dominance
Definition: ttdeletmutations_bitstring.h:238
void setAdultViab()
Definition: ttdeletmutations_bitstring.h:287
double viability_epist_continuous()
Definition: ttdeletmutations_bitstring.cc:749
unsigned int _fitness_model
Definition: ttdeletmutations_bitstring.h:55
static void set_recomb_template(unsigned int size)
TProtoDeletMutations_bitstring * _myProto
Definition: ttdeletmutations_bitstring.h:50
void set_nb_hmz_mutations()
Definition: ttdeletmutations_bitstring.cc:709
void setDeletStats(age_t AGE)
Definition: stats_delet_bitstring.cc:211
bitstring * _htz
Definition: ttdeletmutations_bitstring.h:76
virtual void reset()
Definition: ttrait_with_map.cc:505
virtual void set_allele_value(unsigned int locus, unsigned int allele, double value)
Definition: ttdeletmutations_bitstring.cc:574
virtual void reset()
Definition: ttdeletmutations_bitstring.h:210
void inherit_low(sex_t SEX, bitstring *seq, bitstring **parent)
Definition: ttdeletmutations_bitstring.cc:325
double _meanViab
Definition: ttdeletmutations_bitstring.h:257
double fecWithHomePatchMate
Definition: ttdeletmutations_bitstring.h:255
double set_effects_exp()
Definition: ttdeletmutations_bitstring.h:196
unsigned int _nb_mutations
Definition: ttdeletmutations_bitstring.h:71
unsigned int _fitness_model
Definition: ttdeletmutations_bitstring.h:231
virtual void set_sequence(void **seq)
Definition: ttdeletmutations_bitstring.h:158
double getMeanFecWithPatchMate(bool HOME)
Definition: stats_delet_bitstring.cc:41
void set_continuous_effects(bool val)
Definition: ttdeletmutations_bitstring.h:133
Template class for the trait's StatHandler.
Definition: stathandler.h:168
double set_effects_gamma()
Definition: ttdeletmutations_bitstring.h:197
void setOffsprgDeletStats()
Definition: ttdeletmutations_bitstring.h:285
double get_strength()
Definition: ttdeletmutations_bitstring.h:190
virtual bool setStatRecorders(std::string &token)
Definition: ttdeletmutations_bitstring.cc:820
double getBalpha()
Definition: ttdeletmutations_bitstring.h:294
void mutate_redraw()
Definition: ttdeletmutations_bitstring.cc:640
TProtoDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.cc:50
sex_t
Sex types, males are always 0 and females 1!!
Definition: types.h:36
Definition: types.h:42
double _Hs
Definition: ttdeletmutations_bitstring.h:263
bitstring * _hmz
Definition: ttdeletmutations_bitstring.h:76
virtual double get_allele_value(int loc, int all)
Definition: ttdeletmutations_bitstring.cc:560
double _deletHmzLoci
Definition: ttdeletmutations_bitstring.h:262
The FileHandler associated with the TTDeletMutations_bitstring trait.
Definition: ttdeletmutations_bitstring.h:324
double _dist_p2
Definition: ttdeletmutations_bitstring.h:240
Bitstring implementation of TTDeletMutations with recombination.
Definition: ttdeletmutations_bitstring.h:47
TTDeletMutBitstrSH(TProtoDeletMutations_bitstring *TP)
Definition: ttdeletmutations_bitstring.h:271
virtual bool retrieve_data(BinaryStorageBuffer *reader)
Definition: ttdeletmutations_bitstring.cc:772
void set_nb_locus(int val)
Definition: ttdeletmutations_bitstring.h:122
double viability_multi()
Definition: ttdeletmutations_bitstring.cc:717
double _dominance
Definition: ttdeletmutations_bitstring.h:61
double _fitness_scaling_factor
Definition: ttdeletmutations_bitstring.h:234
void set_effects()
Definition: ttdeletmutations_bitstring.cc:211
double getOffsprgLetheq()
Definition: ttdeletmutations_bitstring.h:311
A class to store any kind of data in a char buffer before unloading it in a binary data file...
Definition: binarystoragebuffer.h:40
double getHt()
Definition: ttdeletmutations_bitstring.h:307
double set_effects_lognorm()
Definition: ttdeletmutations_bitstring.h:198
double getDeletAllHmz()
Definition: ttdeletmutations_bitstring.h:299
double _fitness_scaling_factor
Definition: ttdeletmutations_bitstring.h:56
float ** _effects
Definition: ttdeletmutations_bitstring.h:249
double _fixloc
Definition: ttdeletmutations_bitstring.h:263
unsigned int _mutation_model
Definition: ttdeletmutations_bitstring.h:232
bool setSelectionParameters()
Definition: ttdeletmutations_bitstring.cc:140
void set_viability_func_ptr(unsigned int f_model, bool is_cont)
Definition: ttdeletmutations_bitstring.cc:483
double viability_epist()
Definition: ttdeletmutations_bitstring.cc:727
double getDeletAllFreq()
Definition: ttdeletmutations_bitstring.h:298
#define DELE
Definition: types.h:66
double _Fst
Definition: ttdeletmutations_bitstring.h:263
double * _deletFreqTable
Definition: ttdeletmutations_bitstring.h:265
double getFst()
Definition: ttdeletmutations_bitstring.h:308
double getSegregatingDeletLociPerPatch()
Definition: ttdeletmutations_bitstring.h:304
double _segrloc
Definition: ttdeletmutations_bitstring.h:263
double _init_freq
Definition: ttdeletmutations_bitstring.h:235
double getLethalEquivalents()
Definition: ttdeletmutations_bitstring.h:309
~TProtoDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.cc:99
double getViability(unsigned int v)
Definition: ttdeletmutations_bitstring.h:313
virtual trait_t get_type() const
Definition: ttdeletmutations_bitstring.h:216
virtual void set_value()
Definition: ttdeletmutations_bitstring.cc:684
virtual ~TTDeletMutBitstrSH()
Definition: ttdeletmutations_bitstring.h:275
double getMeanViability()
Definition: ttdeletmutations_bitstring.h:314
void set_mutation_func_ptr(unsigned int m_model)
Definition: ttdeletmutations_bitstring.cc:506
virtual bool retrieve_data(BinaryStorageBuffer *reader)
Definition: ttdeletmutations_bitstring.cc:397
double _phenotype
Definition: ttdeletmutations_bitstring.h:77
TTDeletMutBitstrSH * _stats
Definition: ttdeletmutations_bitstring.h:246
double _letheq
Definition: ttdeletmutations_bitstring.h:263
Definition: types.h:42
double _dist_p1
Definition: ttdeletmutations_bitstring.h:239
void setViabStats(age_t AGE)
Definition: ttdeletmutations_bitstring.cc:912
double getDeletAllHtz()
Definition: ttdeletmutations_bitstring.h:300
unsigned int get_nb_mut_atLocus(unsigned int loc)
Definition: ttdeletmutations_bitstring.h:112
double(TTDeletMutations_bitstring::* _viability_func_ptr)(void)
Definition: ttdeletmutations_bitstring.h:63
#define OFFSPRG
Offspring age class flag.
Definition: types.h:50
double getHs()
Definition: ttdeletmutations_bitstring.h:306
virtual TTDeletMutations_bitstring * hatch()
Definition: ttdeletmutations_bitstring.cc:295
unsigned int get_nb_htz_mutations()
Definition: ttdeletmutations_bitstring.h:113
void setOffsprgViab()
Definition: ttdeletmutations_bitstring.h:288
int _dominance_model
Definition: ttdeletmutations_bitstring.h:233
double _mut_rate
Definition: ttdeletmutations_bitstring.h:236
bool get_iscontinuous()
Definition: ttdeletmutations_bitstring.h:193
void set_fitness_model(int val)
Definition: ttdeletmutations_bitstring.h:132
double _Ho
Definition: ttdeletmutations_bitstring.h:263
double _SibProps[5]
Definition: ttdeletmutations_bitstring.h:257
Prototype class of the bitstring-deleterious mutations trait class.
Definition: ttdeletmutations_bitstring.h:182
int get_nb_locus()
Definition: ttdeletmutations_bitstring.h:188
void set_inherit_func_ptr(void(TProtoDeletMutations_bitstring::*theFunc)(sex_t, bitstring *, bitstring **))
Definition: ttdeletmutations_bitstring.h:127
The StatHandler for TTDeletMutations_bitstring.
Definition: ttdeletmutations_bitstring.h:253
void setMeanViability(age_idx agex)
Definition: stats_delet_bitstring.cc:139
double _segrLocPerPatch
Definition: ttdeletmutations_bitstring.h:262
void set_mut_rate(double val, int nloc)
Definition: ttdeletmutations_bitstring.h:123
float ** get_effects() const
Definition: ttdeletmutations_bitstring.h:117
static double Gamma(double a, double b)
Definition: Uniform.h:362
A class to manage the files associated with each components of the simulation.
Definition: fileservices.h:51
double _Hmz
Definition: ttdeletmutations_bitstring.h:263
static float ** _effects
Definition: ttdeletmutations_bitstring.h:68
void set_strength(double val)
Definition: ttdeletmutations_bitstring.h:124
double getSegregatingDeletLoci()
Definition: ttdeletmutations_bitstring.h:303
double getLoad()
Definition: stats_delet_bitstring.cc:165
virtual void loadFileServices(FileServices *loader)
Definition: ttdeletmutations_bitstring.cc:255
virtual void ** get_sequence() const
Definition: ttdeletmutations_bitstring.h:154
double _viability[5]
Definition: ttdeletmutations_bitstring.h:257
double getSibProportions(unsigned int i)
Definition: ttdeletmutations_bitstring.h:317
void set_dominance(double val)
Definition: ttdeletmutations_bitstring.h:125
bool _isContinuousEffect
Definition: ttdeletmutations_bitstring.h:267
unsigned int _nb_hmz_mutations
Definition: ttdeletmutations_bitstring.h:72
void setAdultDeletStats()
Definition: ttdeletmutations_bitstring.h:284
double getPatchLoad(unsigned int i)
Definition: stats_delet_bitstring.cc:185
double _mut_rate
Definition: ttdeletmutations_bitstring.h:58
double getDeletAllPerGenome()
Definition: ttdeletmutations_bitstring.h:305
void set_init_freq(double val)
Definition: ttdeletmutations_bitstring.h:131
TTDeletMutations_bitstring()
Definition: ttdeletmutations_bitstring.h:89
unsigned int _nb_locus
Definition: ttdeletmutations_bitstring.h:230
void mutate_noredraw()
Definition: ttdeletmutations_bitstring.cc:668
double _Ht
Definition: ttdeletmutations_bitstring.h:263
void set_sequence(bitstring **seq)
Definition: ttdeletmutations_bitstring.cc:551
double _strength
Definition: ttdeletmutations_bitstring.h:237
unsigned int get_nb_mutations()
Definition: ttdeletmutations_bitstring.h:111
virtual bool operator!=(const TTrait &T)
Definition: ttdeletmutations_bitstring.cc:473
static void set_effects(float **fx)
Definition: ttdeletmutations_bitstring.cc:41

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