TProtoDeletMutations_bitstring Class Reference

Prototype class of the bitstring-deleterious mutations trait class. More...

#include <ttdeletmutations_bitstring.h>

Inheritance diagram for TProtoDeletMutations_bitstring:

Collaboration diagram for TProtoDeletMutations_bitstring:

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
virtual int	get_phenotype_dimension ()
	Returns the dimension of the phenotype of the trait (size of the array accessed with TTrait::getValue() More...
virtual int	get_allele_number ()
	Returns the number of allele per locus. More...
virtual int	get_locus_number ()
	Returns the number of locus. More...
StorableComponent 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 ()
double	getRecombRate () const
bool	setGeneticMapParameters (string prefix, unsigned int numLoci=0)
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 bool	is_mappable ()
	Checks if the trait is mappable, i.e., if the loci can be placed on a genetic map. More...
virtual bool	is_mapped ()
	Checks if the trait's loci are placed on a genetic map. More...
virtual vector< unsigned int >	get_locus_map_positions ()
	Returns the map positions of the loci in vector. More...
Public Member Functions inherited from TraitPrototype
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	~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 GeneticMap &	getGeneticMapRef ()
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...

Detailed Description

Prototype class of the bitstring-deleterious mutations trait class.

Constructor & Destructor Documentation

TProtoDeletMutations_bitstring() [1/2]

TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring

(

)

: _nb_locus(0), _fitness_model(0), _mutation_model(0), _dominance_model(1), 
_fitness_scaling_factor(1), _init_freq(0),_mut_rate(0), _back_mutation_rate(0), _strength(0),
_dominance(0), _dist_p1(0), _dist_p2(0), _continuous_effects(0), _viability_func_ptr(0),
_set_effects_func(0), _inherit_func_ptr(0), _stats(0), _writer(0), _reader(0), _effects(0)
{
  set_paramset("delet", false, this);
  
  add_parameter("delet_loci",INT,true,false,0,0);
  
  add_parameter("delet_mutation_rate",DBL,true,true,0,1, 0);
  add_parameter("delet_backmutation_rate",DBL,false,true,0,1, 0);
  add_parameter("delet_mutation_model",INT,false,true,1,2, 0);
  add_parameter("delet_init_freq",DBL,false,true,0,1, 0);
  
  //genetic map parameters:
  TTProtoWithMap::addGeneticMapParameters("delet");
  
  //effects parameters
  add_parameter("delet_effects_mean",DBL,false,false,0,1, 0);
  add_parameter("delet_dominance_mean",DBL,false,true,0,1, 0);
  add_parameter("delet_fitness_model",INT,false,true,1,2, 0);
  add_parameter("delet_effects", MAT, false, false, 0, 0, 0);
  add_parameter("delet_effects_distribution",STR,false,false,0,0, 0);
  add_parameter("delet_effects_dist_param1",DBL,false,false,0,0, 0);
  add_parameter("delet_effects_dist_param2",DBL,false,false,0,0, 0);
  add_parameter("delet_fitness_scaling_factor",DBL,false,false,0,0, 0);
  add_parameter("delet_dominance_model", INT, false, true, 1, 2, 0);
  //for back compatibility:
//  add_parameter("delet_sel_coef",DBL,false,true,0,1, 0);
//  add_parameter("delet_dom_coef",DBL,false,true,0,1, 0);
  //output parameters:
  add_parameter("delet_save_genotype",BOOL,false,false,0,0);
  add_parameter("delet_genot_dir",STR,false,false,0,0);
  add_parameter("delet_genot_logtime",INT,false,false,0,0);
  
}

References SimComponent::add_parameter(), TTProtoWithMap::addGeneticMapParameters(), BOOL, DBL, INT, MAT, SimComponent::set_paramset(), and STR.

Referenced by clone().

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TProtoDeletMutations_bitstring() [2/2]

TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring

(

const TProtoDeletMutations_bitstring &

T

)

: _nb_locus(T._nb_locus), _fitness_model(T._fitness_model), _mutation_model(T._mutation_model),
_dominance_model(T._dominance_model),_fitness_scaling_factor(T._fitness_scaling_factor), 
_init_freq(T._init_freq), _mut_rate(T._mut_rate), _back_mutation_rate(T._back_mutation_rate),
_strength(T._strength), _dominance(T._dominance), _dist_p1(T._dist_p1), _dist_p2(T._dist_p2),
_continuous_effects(T._continuous_effects), _viability_func_ptr(T._viability_func_ptr),
_inherit_func_ptr(T._inherit_func_ptr), _set_effects_func(T._set_effects_func),
_stats(0), _writer(0), _reader(0), _effects(0)
{
  _paramSet = new ParamSet( *(T._paramSet) ) ;
}

References SimComponent::_paramSet.

~TProtoDeletMutations_bitstring()

TProtoDeletMutations_bitstring::~TProtoDeletMutations_bitstring

(

)

{
  if(_stats != NULL)      {delete _stats;     _stats = NULL;}
  if(_reader)             {delete _reader;    _reader= NULL;}
  if(_writer != NULL)     {delete _writer;   _writer = NULL;} 
  if(_effects != NULL)    {
    delete [] _effects[0];
    delete [] _effects[1];
    delete [] _effects;
    _effects = NULL;
  }
  
}

References _effects, _reader, _stats, and _writer.

Member Function Documentation

clone()

virtual TProtoDeletMutations_bitstring* TProtoDeletMutations_bitstring::clone ( )

inlinevirtual

Implements TraitPrototype.

{return new TProtoDeletMutations_bitstring((*this));}

References TProtoDeletMutations_bitstring().

get_allele_number()

virtual int TProtoDeletMutations_bitstring::get_allele_number ( )

inlinevirtual

Returns the number of allele per locus.

Implements TraitPrototype.

{return 2;}

get_backmutation_rate()

double TProtoDeletMutations_bitstring::get_backmutation_rate ( )

inline

{return _back_mutation_rate;}

References _back_mutation_rate.

Referenced by TTDeletMutations_bitstring::mutate_noredraw(), and TTDeletMutations_bitstring::set_mutation_func_ptr().

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get_dominance()

double TProtoDeletMutations_bitstring::get_dominance ( )

inline

{return _dominance;}

References _dominance.

Referenced by TTDeletMutations_bitstring::set_allele_value(), TTDeletMutations_bitstring::viability_epist(), and TTDeletMutations_bitstring::viability_multi().

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get_dominance_model()

int TProtoDeletMutations_bitstring::get_dominance_model ( )

inline

{return _dominance_model;}

References _dominance_model.

Referenced by TTDeletMutations_bitstring::set_allele_value().

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get_effect()

float TProtoDeletMutations_bitstring::get_effect ( unsigned int  at, unsigned int  loc  )

inline

{return _effects[at][loc];}

References _effects.

Referenced by TTDeletMutations_bitstring::get_allele_value(), and TTDeletMutations_bitstring::set_allele_value().

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get_effects()

float** TProtoDeletMutations_bitstring::get_effects ( ) const

inline

{return _effects;}

References _effects.

Referenced by resetParameterFromSource(), TTDeletMutations_bitstring::viability_epist_continuous(), and TTDeletMutations_bitstring::viability_multi_continuous().

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get_fitness_scaling_factor()

double TProtoDeletMutations_bitstring::get_fitness_scaling_factor ( )

inline

{return _fitness_scaling_factor;}

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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get_hs_continous()

float* TProtoDeletMutations_bitstring::get_hs_continous ( )

inline

{return _effects[0];}

References _effects.

Referenced by TTDeletMutBitstrFH::FHwrite().

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get_init_freq()

double TProtoDeletMutations_bitstring::get_init_freq ( )

inline

{return _init_freq; }

References _init_freq.

Referenced by TTDeletMutations_bitstring::init_sequence().

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get_iscontinuous()

bool TProtoDeletMutations_bitstring::get_iscontinuous ( )

inline

{return _continuous_effects;}

References _continuous_effects.

Referenced by TTDeletMutBitstrFH::FHwrite(), and TTDeletMutBitstrSH::TTDeletMutBitstrSH().

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get_locus_number()

virtual int TProtoDeletMutations_bitstring::get_locus_number ( )

inlinevirtual

Returns the number of locus.

Implements TraitPrototype.

{return _nb_locus;}

References _nb_locus.

get_mut_rate()

double TProtoDeletMutations_bitstring::get_mut_rate ( )

inline

{return _mut_rate;}

References _mut_rate.

get_nb_locus()

int TProtoDeletMutations_bitstring::get_nb_locus ( )

inline

{return _nb_locus;}

References _nb_locus.

Referenced by TTDeletMutBitstrFH::FHread(), TTDeletMutBitstrFH::FHwrite(), TTDeletMutBitstrSH::setDeletStats(), and TTDeletMutBitstrSH::setLethalEquivalents().

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get_phenotype_dimension()

virtual int TProtoDeletMutations_bitstring::get_phenotype_dimension ( )

inlinevirtual

Returns the dimension of the phenotype of the trait (size of the array accessed with TTrait::getValue()

Implements TraitPrototype.

{return 1;}

get_s_continous()

float* TProtoDeletMutations_bitstring::get_s_continous ( )

inline

{return _effects[1];}

References _effects.

Referenced by TTDeletMutBitstrFH::FHwrite(), and TTDeletMutBitstrSH::setLethalEquivalents().

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get_strength()

double TProtoDeletMutations_bitstring::get_strength ( )

inline

{return _strength;}

References _strength.

Referenced by TTDeletMutations_bitstring::set_allele_value(), TTDeletMutBitstrSH::setLethalEquivalents(), TTDeletMutations_bitstring::viability_epist(), and TTDeletMutations_bitstring::viability_multi().

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get_type()

virtual trait_t TProtoDeletMutations_bitstring::get_type ( ) const

inlinevirtual

Implements TraitPrototype.

{return DELE;}

References DELE.

hatch()

TTDeletMutations_bitstring * TProtoDeletMutations_bitstring::hatch ( )

virtual

Implements TraitPrototype.

{
  TTDeletMutations_bitstring* new_trait = new TTDeletMutations_bitstring();
  
  new_trait->set_proto(this);
  
  new_trait->set_nb_locus(_nb_locus);
  new_trait->set_mut_rate(_mut_rate,_nb_locus);
  
  new_trait->set_is_continuous(_continuous_effects);
  new_trait->set_viability_func_ptr(_fitness_model, _continuous_effects);
  new_trait->set_inherit_func_ptr(_inherit_func_ptr);
  new_trait->set_mutation_func_ptr(_mutation_model);
  
  return new_trait;
}

References _continuous_effects, _fitness_model, _inherit_func_ptr, _mut_rate, _mutation_model, _nb_locus, TTDeletMutations_bitstring::set_inherit_func_ptr(), TTDeletMutations_bitstring::set_is_continuous(), 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().

inherit_free()

void TProtoDeletMutations_bitstring::inherit_free ( sex_t  SEX, bitstring *  seq, bitstring **  parent  )

inline

{ 
//  for(unsigned int i = 0; i < _nb_locus; )
//    seq[i] = (bool)(*parent[RAND::RandBool()])[i];
 
  // Word-level random recombination: for each 64-bit word, generate a random mask
  // offspring = (parent_chrom_a & mask) | (parent_chrom_b & ~mask)
  size_t nwords = parent[0]->nb_words();
 
  unsigned int first = RAND::RandBool();
  const bitstring& seq0 = *parent[first];
  const bitstring& seq1 = *parent[!first];
 
  for (size_t w = 0; w < nwords; w++) {
    bitstring::_ul mask = RAND::RandULong();
    bitstring::_ul result = (*seq0.getword_atIdx(w) & mask) |
        (*seq1.getword_atIdx(w) & ~mask);
    *(seq->getword_atIdx(w)) = result;
  }
}

References bitstring::getword_atIdx(), bitstring::nb_words(), RAND::RandBool(), and RAND::RandULong().

inherit_low()

void TProtoDeletMutations_bitstring::inherit_low ( sex_t  SEX, bitstring *  seq, bitstring **  parent  )

inline

{
  unsigned int prevLoc = 0, cEnd = 0;
 
  //the table containing the loci at which x-overs happen
  vector< pair<unsigned int, unsigned int> > recTable = _map.reduceJunctions(SEX, _mapIndex);
 
  //number of x-overs
  unsigned int nbRec = recTable.size();
 
#ifdef _REC_DEBUG_
  cout << "TProtoDeletMutations_bitstring::inherit_low; nb Rec = "<<nbRec - 1<<endl;
  cout << "   --sex = "<<SEX<<"\n";
#endif
 
  unsigned int num_copied = 0;
 
  vector< pair<unsigned int, unsigned int> >::const_iterator xover = recTable.begin();
 
  while(xover != recTable.end()) {
 
#ifdef _REC_DEBUG_
    cout<< "   copy seq from "<<prevLoc<<" to "<<xover->first
        <<" ("<<(xover->first - prevLoc)<<" loc) ("
        <<(xover->first - prevLoc)
        <<" bits) on side "<<xover->second<<std::endl;
#endif
 
    seq->copy( *parent[ xover->second ], prevLoc, xover->first);
 
    prevLoc = xover->first;
 
    xover++;
  }
 
}

References TTProtoWithMap::_map, TTProtoWithMap::_mapIndex, bitstring::copy(), and GeneticMap::reduceJunctions().

Referenced by setParameters().

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init()

virtual void TProtoDeletMutations_bitstring::init ( )

inlinevirtual

{setParameters();};

References setParameters().

loadFileServices()

void TProtoDeletMutations_bitstring::loadFileServices ( FileServices *  loader )

virtual

Implements SimComponent.

{ 
  // --- THE READER ---
  //always add the reader:
  if(_reader) delete _reader;
  _reader = new TTDeletMutBitstrFH(this);
  //set to read mode:
  _reader->set_isInputHandler(true);
  //attach to file manager:
  loader->attach_reader(_reader);
  
  //writer
  if(get_parameter("delet_save_genotype")->isSet()) {
    
    if(_writer)  delete _writer;
 
    _writer = new TTDeletMutBitstrFH(this);
    
    Param* param = get_parameter("delet_genot_logtime");
    
    if(!param->isSet() )
      fatal("delet trait::parameter \"delet_genot_logtime\" is required to set the periodicity of the output file\n");
 
    if(param->isMatrix()) {
      
      TMatrix temp;
      param->getMatrix(&temp);
      _writer->set_multi(true, true, 1, &temp, get_parameter("delet_genot_dir")->getArg(), this);
      
    } else {      
      //           rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
      _writer->set(true, true, 1, (param->isSet() ? (int)param->getValue() : 0),
                   0, get_parameter("delet_genot_dir")->getArg(),this);
    }
    
    loader->attach(_writer);
    
  } else if(_writer != NULL) {
    delete _writer;
    _writer = NULL;
  }
}

References _reader, _writer, FileServices::attach(), FileServices::attach_reader(), fatal(), SimComponent::get_parameter(), Param::getMatrix(), Param::getValue(), Param::isMatrix(), Param::isSet(), TraitFileHandler< TP >::set(), FileHandler::set_isInputHandler(), and TraitFileHandler< TP >::set_multi().

loadStatServices()

void TProtoDeletMutations_bitstring::loadStatServices ( StatServices *  loader )

virtual

Implements SimComponent.

{
  if(_stats != NULL)
    delete _stats;
  
  _stats = new TTDeletMutBitstrSH(this);
  
  loader->attach(_stats);
}// ----------------------------------------------------------------------------------------

References _stats, and StatServices::attach().

reset()

virtual void TProtoDeletMutations_bitstring::reset ( )

inlinevirtual

Reimplemented from TTProtoWithMap.

{TTProtoWithMap::reset();}

References TTProtoWithMap::reset().

reset_effect_table()

void TProtoDeletMutations_bitstring::reset_effect_table

(

)

{
  if(_effects != NULL) {
    delete [] _effects[0];
    delete [] _effects[1];
    delete [] _effects;
  }
 
  _effects = new float* [2];
  _effects[0] = new float [_nb_locus];
  _effects[1] = new float [_nb_locus];
 
}

References _effects, and _nb_locus.

Referenced by resetParameterFromSource(), set_effects(), and setEffectsFromInput().

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resetParameterFromSource()

bool TProtoDeletMutations_bitstring::resetParameterFromSource ( std::string  param, SimComponent *  cmpt  )

virtual

Implements SimComponent.

{
  TProtoDeletMutations_bitstring *srceProto = dynamic_cast< TProtoDeletMutations_bitstring* >(cmpt);
 
  // this works only to reset the fitness effects
  if(param != "delet_effects") return false;
 
  float** efx = srceProto->get_effects();
 
  if(efx == NULL)
    return error("the binary source population did not properly set the fitness effects of\
 deleterious mutations, no effects received.\n");
 
  // the genetic architecture has already been checked in Metapop::loadPopFromBinarySource
  // we can skip the check of table size
 
  reset_effect_table(); // deallocate and re-allocate the _effects table
 
  //copy effects
  memcpy(_effects[0], efx[0], _nb_locus*sizeof(float));
  memcpy(_effects[1], efx[1], _nb_locus*sizeof(float));
 
  //record effects into the parameter
  write_effects_to_parameter();
 
  return true;
}

References _effects, _nb_locus, error(), get_effects(), reset_effect_table(), and write_effects_to_parameter().

retrieve_data()

bool TProtoDeletMutations_bitstring::retrieve_data ( BinaryStorageBuffer *  reader )

virtual

Implements StorableComponent.

{
  unsigned int dummy_int;
  reader->read(&dummy_int,sizeof(int));
 
  if(dummy_int != _nb_locus ){
      warning("Deleterious mutation trait::locus number in binary source file differs from parameter value!\n\
 >>>> adjusting locus number to match source population: %i set to %i\n", _nb_locus, dummy_int);
    _nb_locus = dummy_int;
  }
  
  char dummy_bool = 0;
  reader->read(&dummy_bool, 1);
 
  if(dummy_bool != _continuous_effects) {
    error("Deleterious mutation trait::mutation effects model in binary source file differ from parameter value!\n\
 >>>> adjusting model to match source population: continuous = %i to continuous = %i\n",
         _continuous_effects, (int)dummy_bool);
    _continuous_effects = dummy_bool;
  }
  
  if(_continuous_effects) {
    reader->read(_effects[0],_nb_locus * sizeof(float));
    reader->read(_effects[1],_nb_locus * sizeof(float));
  }
  return true;
}

References _continuous_effects, _effects, _nb_locus, error(), BinaryStorageBuffer::read(), and warning().

set_effect()

void TProtoDeletMutations_bitstring::set_effect ( unsigned int  at, unsigned int  loc, float  val  )

inline

{_effects[at][loc] = val;}

References _effects.

Referenced by TTDeletMutBitstrFH::FHread(), and TTDeletMutations_bitstring::set_allele_value().

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set_effects()

void TProtoDeletMutations_bitstring::set_effects

(

)

{ 
  reset_effect_table (); //de-allocate, re-allocate memory
  
  double dom;
  double k = -1.0*log(2*_dominance) / _strength;
  
  for(unsigned int i = 0; i < _nb_locus; ++i){
    
    do{
      _effects[1][i] = (float)(this->*_set_effects_func)(); //homozygote effect: s
    }while(_effects[1][i] > 1); //truncate distribution
    
    if(_dominance_model == 1)
      dom = exp(-1.0*_effects[1][i]*k)/2.0; //scaling of h on s
    else dom = _dominance;
    
    _effects[0][i] = (float)(dom * _effects[1][i]); //heterozygote effect: hs
    
  }
 
  // save the effects to the parameter "delet_effects" will be written to the .log file
  write_effects_to_parameter();
}

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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set_effects_exp()

double TProtoDeletMutations_bitstring::set_effects_exp ( )

inline

{return RAND::Exponential(_strength);}

References _strength, and RAND::Exponential().

Referenced by setSelectionParameters().

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set_effects_gamma()

double TProtoDeletMutations_bitstring::set_effects_gamma ( )

inline

{return RAND::Gamma(_dist_p1, _dist_p2);}

References _dist_p1, _dist_p2, and RAND::Gamma().

Referenced by setSelectionParameters().

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set_effects_lognorm()

double TProtoDeletMutations_bitstring::set_effects_lognorm ( )

inline

{return RAND::LogNormal(_dist_p1, _dist_p2);}

References _dist_p1, _dist_p2, and RAND::LogNormal().

Referenced by setSelectionParameters().

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setEffectsFromInput()

bool TProtoDeletMutations_bitstring::setEffectsFromInput

(

)

{
  TMatrix tmp;
  
  get_parameter("delet_effects")->getMatrix(&tmp);
  
  if(tmp.getNbCols() != _nb_locus)
    return error("the number of mutational effects of the deleterious trait is not equal to its number of loci, please adjust.\n");
  
  if(tmp.getNbRows() != 2 )
    return error("the parameter \"delet_effects\" must have two rows, the first for\
 the mutational effect in heterozygotes, the second for the effects in homozygotes.\n");
  
  _continuous_effects = true;
  
  reset_effect_table ();
 
  for(unsigned int i = 0; i < _nb_locus; ++i){
    
    _effects[0][i] = (float)tmp.get(0, i); //heterozygote effect: hs
    _effects[1][i] = (float)tmp.get(1, i); //homozygote effect: s
  }
  
  return true;
}

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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setParameters()

bool TProtoDeletMutations_bitstring::setParameters ( )

virtual

Implements SimComponent.

{  
  _nb_locus = (int)get_parameter_value("delet_loci");
  _mut_rate = get_parameter_value("delet_mutation_rate");
  
  
  //we set the fitness model to 1 (multiplicative by default))
  if(get_parameter("delet_fitness_model")->isSet())
    _fitness_model = (int)get_parameter_value("delet_fitness_model");
  else
    _fitness_model = 1;
 
  //reverse mutation rate; we only store the ratio of back/forward mutation rate
  if( get_parameter("delet_backmutation_rate")->isSet() ) {
 
    _back_mutation_rate = get_parameter_value("delet_backmutation_rate");
 
    if(_back_mutation_rate > _mut_rate)
 
      return error("Deleterious mutations: The backward (reverse) mutation rate is larger than\
the forward mutation rate!\n");
 
    else
 
      _back_mutation_rate /= _mut_rate;
 
 
  } else
    _back_mutation_rate = 0; //by default we don't process backward mutations
 
  //mutation model
  if( get_parameter("delet_mutation_model")->isSet() )
    _mutation_model = (unsigned int)get_parameter_value("delet_mutation_model");
  else
    _mutation_model = 1;
  
  //initial allele frequency, applies to all loci equally
  if( (_init_freq = get_parameter_value("delet_init_freq")) == -1.0)
    _init_freq = 0;
  
  //selection parameters:
  if(!setSelectionParameters()) return false;
  
  
  if( (_fitness_scaling_factor = get_parameter_value("delet_fitness_scaling_factor")) == -1.0)
    _fitness_scaling_factor = 1.0;
 
  // we do not bypass the recombination map for rec rate = 0.5, it's too slow with bitstrings
  _inherit_func_ptr = &TProtoDeletMutations_bitstring::inherit_low;
 
  return TTProtoWithMap::setGeneticMapParameters ("delet");
}

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().

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setSelectionParameters()

bool TProtoDeletMutations_bitstring::setSelectionParameters

(

)

{
  
  if(get_parameter("delet_effects")->isSet())
    return setEffectsFromInput();
  
  //effects and dominance parameters:
  _strength = get_parameter_value("delet_effects_mean");
  _dominance = get_parameter_value("delet_dominance_mean");
  _dist_p1 = get_parameter_value("delet_effects_dist_param1");
  _dist_p2 = get_parameter_value("delet_effects_dist_param2");
  
  //for backward compatibility only, param removed
  _dominance_model = (int)get_parameter_value("delet_dominance_model");
 
  if(_dominance_model == -1) _dominance_model = 1; //1 means continuous; 2 means constant
  
  string distro = _paramSet->getArg("delet_effects_distribution");
  
  _continuous_effects = true;
  
  if(distro.empty() || distro == "constant") {
    
    _continuous_effects = false;
    
    _set_effects_func = 0;
    
  } else if(distro == "exponential") {
    
    _set_effects_func = &TProtoDeletMutations_bitstring::set_effects_exp;
    
  } else if(distro == "gamma") {
    
    _set_effects_func = &TProtoDeletMutations_bitstring::set_effects_gamma;
    //check params:
    if(_dist_p1 == -1) {
      return error("missing parameter 1 (shape) of the gamma distribution for the deleterious mutation effects.");
    }
    
    if(_dist_p2 == -1)
      _dist_p2 = _strength / _dist_p1; //mean of gamma == _strength = a*b with a == shape == _dist_p1
    
  } else if(distro == "lognormal") {
    
    _set_effects_func = &TProtoDeletMutations_bitstring::set_effects_lognorm;
    //check params:
    if(_dist_p1 == -1) {
      return error("missing parameter 1 (mu) of the log-normal distribution for the deleterious mutation effects.");
    }
    if(_dist_p2 == -1) {
      return error("missing parameter 2 (sigma) of the log-normal distribution for the deleterious mutation effects.");
    }
    
  } else {
    return error("Deleterious effects distribution \"%s\" not implemented.",distro.c_str());
  }
  
  
  if(_continuous_effects) set_effects();
  
  return true;
}

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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store_data()

void TProtoDeletMutations_bitstring::store_data ( BinaryStorageBuffer *  saver )

virtual

Implements StorableComponent.

{
  saver->store(&_nb_locus,sizeof(int));
  //store all bool on 1 byte
  char dummy = _continuous_effects;
  saver->store(&dummy, 1);
  if(_continuous_effects) {
    saver->store(_effects[0],_nb_locus * sizeof(float));
    saver->store(_effects[1],_nb_locus * sizeof(float));
  }
}

References _continuous_effects, _effects, _nb_locus, and BinaryStorageBuffer::store().

write_effects_to_parameter()

void TProtoDeletMutations_bitstring::write_effects_to_parameter

(

)

{
  ostringstream r0, r1;
 
  for(unsigned int i = 0; i < _nb_locus -1; ++i){
    // record the effects
    r0<<_effects[0][i]<<",";
    r1<<_effects[1][i]<<",";
  }
 
  r0<<_effects[0][_nb_locus -1];
  r1<<_effects[1][_nb_locus -1];
 
  // save the effects in a parameter; will be added to the .log simulation file
  string arg = "{{" + r0.str() + "} {" + r1.str() + "}}";
  get_parameter("delet_effects")->setArg(arg);
  get_parameter("delet_effects")->setIsSet(true);
 
}

References _effects, _nb_locus, SimComponent::get_parameter(), Param::setArg(), and Param::setIsSet().

Referenced by resetParameterFromSource(), and set_effects().

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Member Data Documentation

_back_mutation_rate

double TProtoDeletMutations_bitstring::_back_mutation_rate

private

Referenced by get_backmutation_rate(), and setParameters().

_continuous_effects

bool TProtoDeletMutations_bitstring::_continuous_effects

private

Referenced by get_iscontinuous(), hatch(), retrieve_data(), setEffectsFromInput(), setSelectionParameters(), and store_data().

_dist_p1

double TProtoDeletMutations_bitstring::_dist_p1

private

Referenced by set_effects_gamma(), set_effects_lognorm(), and setSelectionParameters().

_dist_p2

double TProtoDeletMutations_bitstring::_dist_p2

private

Referenced by set_effects_gamma(), set_effects_lognorm(), and setSelectionParameters().

_dominance

double TProtoDeletMutations_bitstring::_dominance

private

Referenced by get_dominance(), set_effects(), and setSelectionParameters().

_dominance_model

int TProtoDeletMutations_bitstring::_dominance_model

private

Referenced by get_dominance_model(), set_effects(), and setSelectionParameters().

_effects

float** TProtoDeletMutations_bitstring::_effects

private

Referenced by get_effect(), get_effects(), get_hs_continous(), get_s_continous(), reset_effect_table(), resetParameterFromSource(), retrieve_data(), set_effect(), set_effects(), setEffectsFromInput(), store_data(), write_effects_to_parameter(), and ~TProtoDeletMutations_bitstring().

_fitness_model

unsigned int TProtoDeletMutations_bitstring::_fitness_model

private

Referenced by hatch(), and setParameters().

_fitness_scaling_factor

double TProtoDeletMutations_bitstring::_fitness_scaling_factor

private

Referenced by get_fitness_scaling_factor(), and setParameters().

_inherit_func_ptr

void(TProtoDeletMutations_bitstring::* TProtoDeletMutations_bitstring::_inherit_func_ptr) (sex_t, bitstring *, bitstring **)

private

Referenced by hatch(), and setParameters().

_init_freq

double TProtoDeletMutations_bitstring::_init_freq

private

Referenced by get_init_freq(), and setParameters().

_mut_rate

double TProtoDeletMutations_bitstring::_mut_rate

private

Referenced by get_mut_rate(), hatch(), and setParameters().

_mutation_model

unsigned int TProtoDeletMutations_bitstring::_mutation_model

private

Referenced by hatch(), and setParameters().

_nb_locus

unsigned int TProtoDeletMutations_bitstring::_nb_locus

private

Referenced by get_locus_number(), get_nb_locus(), hatch(), reset_effect_table(), resetParameterFromSource(), retrieve_data(), set_effects(), setEffectsFromInput(), setParameters(), store_data(), and write_effects_to_parameter().

_reader

TTDeletMutBitstrFH* TProtoDeletMutations_bitstring::_reader

private

Referenced by loadFileServices(), and ~TProtoDeletMutations_bitstring().

_set_effects_func

double(TProtoDeletMutations_bitstring::* TProtoDeletMutations_bitstring::_set_effects_func) (void)

private

Referenced by set_effects(), and setSelectionParameters().

_stats

TTDeletMutBitstrSH* TProtoDeletMutations_bitstring::_stats

private

Referenced by loadStatServices(), and ~TProtoDeletMutations_bitstring().

_strength

double TProtoDeletMutations_bitstring::_strength

private

Referenced by get_strength(), set_effects(), set_effects_exp(), and setSelectionParameters().

_viability_func_ptr

double(TTDeletMutations_bitstring::* TProtoDeletMutations_bitstring::_viability_func_ptr) (void)

private

_writer

TTDeletMutBitstrFH* TProtoDeletMutations_bitstring::_writer

private

Referenced by loadFileServices(), and ~TProtoDeletMutations_bitstring().

---

The documentation for this class was generated from the following files:

• ttdeletmutations_bitstring.h
• ttdeletmutations_bitstring.cc