TProtoBDMI Class Reference

#include <ttbdmi.h>

Inheritance diagram for TProtoBDMI:

Collaboration diagram for TProtoBDMI:

Public Member Functions
	TProtoBDMI ()
	TProtoBDMI (const TProtoBDMI &TP)
virtual	~TProtoBDMI ()
int	get_num_locus ()
double	get_mut_rate ()
bool	isHaploid ()
void	set_init_freq (double *val, unsigned int size)
double	get_init_freq (unsigned int i)
bool	isInitSet ()
double	getGenoFitnessHaplo (unsigned int row, unsigned int pos)
double	getGenoFitnessDiplo (unsigned int row, unsigned int posA, unsigned int posB)
double	getGenoFitnessDiplo (unsigned int row, unsigned int pos)
void	setGenoFitnessValue (unsigned int row, unsigned int geno, double value)
void	showGenoTable (unsigned int nrows)
void	gamete_recombination (sex_t SEX, bitstring &seq, const bitstring *parent)
void	inherit_free (sex_t SEX, bitstring &seq, const bitstring *parent)
void	inherit_low (sex_t SEX, bitstring &seq, const bitstring *parent)
TraitPrototype Implementation
virtual void	init ()
virtual TTrait *	hatch ()
virtual TraitPrototype *	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 void	reset ()
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
trait_t	_type
bool	_isHaploid
unsigned int	_num_locus
unsigned int	_npair
double	_mut_rate
double	_genomic_mut_rate
double	_recomb_rate
double *	_init_freq
bool	_isInitSet
void(TT_BDMI::*	_inherit_func_ptr )(const TTrait *, const TTrait *)
void(TProtoBDMI::*	_gamete_recomb_func_ptr )(sex_t SEX, bitstring &seq, const bitstring *parent)
void(TT_BDMI::*	_mutation_func_ptr )(void)
double(TT_BDMI::*	_viability_func_ptr )(void)
TMatrix	_genoTable
TTBDMI_SH *	_stater
TTBDMI_FH *	_writer

Static Private Attributes
static unsigned int	_diploGenotTableCoding3x3 [3][3] = {{0,1,2},{3,4,5},{6,7,8}}
static unsigned int	_diploGenotTableCoding4x4 [4][4] = {{0,1,2,3},{4,5,6,7},{8,9,10,11},{12,13,14,15}}

Friends
class	TT_BDMI

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...

Constructor & Destructor Documentation

TProtoBDMI() [1/2]

TProtoBDMI::TProtoBDMI

(

)

                       : 
_type("dmi"), _isHaploid(1), _num_locus(0), _npair(0), _mut_rate(0), _genomic_mut_rate(0), _recomb_rate(0),
_init_freq(0), _isInitSet(0), _inherit_func_ptr(0), _gamete_recomb_func_ptr(0), _mutation_func_ptr(0),
_viability_func_ptr(0), _genoTable(), _writer(0), _stater(0)
{
  set_paramset("dmi", false, this);
  
  add_parameter("dmi_loci",INT,true,false, 0, 0);
  add_parameter("dmi_is_haploid",BOOL,false,false, 0, 0);
  add_parameter("dmi_mutation_rate",DBL,true,true, 0, 1, 0);
  add_parameter("dmi_genot_table", MAT, true, 0, 0, 0);
 
  //genetic map parameters:
  TTProtoWithMap::addGeneticMapParameters("dmi");
  
  add_parameter("dmi_save_genotype", BOOL, false, false, 0, 0, 0);
  add_parameter("dmi_logtime", INT, false, false, 0, 0);
  add_parameter("dmi_output_dir", STR, 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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TProtoBDMI() [2/2]

TProtoBDMI::TProtoBDMI

(

const TProtoBDMI &

TP

)

                                           : 
_type("dmi"), _isHaploid(TP._isHaploid), _num_locus(TP._num_locus), _npair(TP._npair),
_mut_rate(TP._mut_rate), _genomic_mut_rate(TP._genomic_mut_rate), _recomb_rate(TP._recomb_rate),
_init_freq(0), _isInitSet(0), _inherit_func_ptr(TP._inherit_func_ptr),
_gamete_recomb_func_ptr(TP._gamete_recomb_func_ptr),
_mutation_func_ptr(TP._mutation_func_ptr), _viability_func_ptr(TP._viability_func_ptr),
_genoTable(TP._genoTable), _writer(0), _stater(0)
{
  _paramSet = new ParamSet( *TP._paramSet );
}

References SimComponent::_paramSet.

~TProtoBDMI()

TProtoBDMI::~TProtoBDMI ( )

virtual

{
  if(_stater) delete _stater;
  if(_writer) delete _writer;
  if(_init_freq) delete [] _init_freq; 
}

References _init_freq, _stater, and _writer.

Member Function Documentation

clone()

virtual TraitPrototype* TProtoBDMI::clone ( )

inlinevirtual

Implements TraitPrototype.

{return new TProtoBDMI(*this);}

References TProtoBDMI().

gamete_recombination()

void TProtoBDMI::gamete_recombination ( sex_t  SEX, bitstring &  seq, const bitstring *  parent  )

inline

{
  (this->* _gamete_recomb_func_ptr)(SEX, seq, parent);
}

References _gamete_recomb_func_ptr.

Referenced by TT_BDMI::inherit_diplo(), and TT_BDMI::inherit_haplo().

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get_allele_number()

virtual int TProtoBDMI::get_allele_number ( )

inlinevirtual

Returns the number of allele per locus.

Implements TraitPrototype.

{return 2;}

get_init_freq()

double TProtoBDMI::get_init_freq ( unsigned int  i )

inline

{return _init_freq[i];}

References _init_freq.

Referenced by TT_BDMI::init_sequence().

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get_locus_number()

virtual int TProtoBDMI::get_locus_number ( )

inlinevirtual

Returns the number of locus.

Implements TraitPrototype.

{return _num_locus;}

References _num_locus.

get_mut_rate()

double TProtoBDMI::get_mut_rate ( )

inline

{return _mut_rate;}

References _mut_rate.

get_num_locus()

int TProtoBDMI::get_num_locus ( )

inline

{return _num_locus;}

References _num_locus.

Referenced by TTBDMI_SH::countAllele_diplo(), TTBDMI_SH::countAllele_haplo(), TTBDMI_FH::FHwrite(), LCE_Init_BDMI::setParameters(), TTBDMI_SH::setStats(), TTBDMI_FH::write_diplo(), and TTBDMI_FH::write_haplo().

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get_phenotype_dimension()

virtual int TProtoBDMI::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_type()

virtual trait_t TProtoBDMI::get_type ( ) const

inlinevirtual

Implements TraitPrototype.

{return _type;}

References _type.

Referenced by TT_BDMI::get_type(), and TT_BDMI::operator==().

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getGenoFitnessDiplo() [1/2]

double TProtoBDMI::getGenoFitnessDiplo ( unsigned int  row, unsigned int  pos  )

inline

  {
    assert(pos < 16);
    return _genoTable.get(row, pos);
  }

References _genoTable, and TMatrix::get().

getGenoFitnessDiplo() [2/2]

double TProtoBDMI::getGenoFitnessDiplo ( unsigned int  row, unsigned int  posA, unsigned int  posB  )

inline

  {
    return _genoTable.get(row, _diploGenotTableCoding4x4[posA][posB] );
  }

References _diploGenotTableCoding4x4, _genoTable, and TMatrix::get().

Referenced by TT_BDMI::get_allele_value(), and TT_BDMI::viability_diplo().

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getGenoFitnessHaplo()

double TProtoBDMI::getGenoFitnessHaplo ( unsigned int  row, unsigned int  pos  )

inline

                                                                                    {
    assert(pos < 4);
    return _genoTable.get(row, pos);
  }

References _genoTable, and TMatrix::get().

Referenced by TT_BDMI::get_allele_value(), and TT_BDMI::viability_haplo().

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hatch()

TTrait * TProtoBDMI::hatch ( )

virtual

Implements TraitPrototype.

{
  TT_BDMI* chick = new TT_BDMI();
  
  chick->set_proto (this);
  return chick;
}

References TT_BDMI::set_proto(), and TT_BDMI.

inherit_free()

void TProtoBDMI::inherit_free ( sex_t  SEX, bitstring &  seq, const bitstring *  parent  )

inline

{
  for(unsigned int i = 0; i < _num_locus; ++i) {
   seq[i] = parent[RAND::RandBool()][i];
  }
}

References _num_locus, and RAND::RandBool().

Referenced by setParameters().

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inherit_low()

void TProtoBDMI::inherit_low ( sex_t  SEX, bitstring &  seq, const bitstring *  parent  )

inline

{
  
  unsigned int prevLoc = 0;
 
  
  //the table containing the loci at which x-overs happen; < position, side >
  vector< pair<unsigned int, unsigned int> > recTable = _map.reduceJunctions(SEX, _mapIndex);
 
 
#ifdef _REC_DEBUG_
  //number of x-overs
  unsigned int nbRec = recTable.size();
  cout << "TProtoBDMI::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++;
  }
  
  
//  bool flipper;
//
//  vector< unsigned int >& recTable = _map.getRecLoci(SEX, _mapIndex);
//  vector< bool > & firstRecPos = _map.getFirstRecPosition(SEX);
//
//  nbRec = recTable.size();
//
//  for(unsigned int c = 0, stride = 0, rec = 0; c < _numChromosome; ++c) {
//
//    flipper = firstRecPos[c];
//
//    chrm_bloc = stride + _numLociPerChrmsm[c]; //number of loci considered so far
//
//    prevLoc = stride; //stride is the first locus of a chromosome
//
//    //do recombination chromosome-wise
//    for(; recTable[rec] < chrm_bloc && rec < nbRec; rec++) {
//
//      seq->copy( *parent[flipper], prevLoc, recTable[rec]);
//
//      prevLoc = recTable[rec];
//
//      flipper = !flipper;
//    }
//
//    //copy what's left between the last x-over point and the end of the chrmsme
//    seq->copy( *parent[flipper], prevLoc, chrm_bloc);
//
//    stride += _numLociPerChrmsm[c];
//
//  }
 
}

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

Referenced by setParameters().

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init()

virtual void TProtoBDMI::init ( )

inlinevirtual

{setParameters();}

References setParameters().

isHaploid()

bool TProtoBDMI::isHaploid ( )

inline

{return _isHaploid;}

References _isHaploid.

Referenced by TTBDMI_FH::FHwrite(), TTBDMI_SH::setAdultStats(), TTBDMI_SH::setOffsprgStats(), and TTBDMI_SH::setStats().

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isInitSet()

bool TProtoBDMI::isInitSet ( )

inline

{return _isInitSet;}

References _isInitSet.

Referenced by TT_BDMI::init_sequence().

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loadFileServices()

void TProtoBDMI::loadFileServices ( FileServices *  loader )

virtual

Implements SimComponent.

{
  //writer
  if(get_parameter("dmi_save_genotype")->isSet()) {
    
    if(_writer == NULL) _writer = new TTBDMI_FH(this);
    
    Param* param = get_parameter("dmi_logtime");
    
    if(!param->isSet() )
      fatal("dmi trait::parameter \"dmi_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("dmi_output_dir")->getArg(), this);
      
    } else {      
      //           rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
      _writer->set(true, true, 1, (int)param->getValue(), 0, get_parameter("dmi_output_dir")->getArg(),this);
    }
    
    loader->attach(_writer);
    
  } else if(_writer != NULL) {
    delete _writer;
    _writer = NULL;
  }
}

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

loadStatServices()

void TProtoBDMI::loadStatServices ( StatServices *  loader )

virtual

Implements SimComponent.

{
  if(_stater != NULL) 
    delete _stater;
  
  _stater = new TTBDMI_SH(this);
  
  loader->attach(_stater);
}

References _stater, and StatServices::attach().

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

retrieve_data()

bool TProtoBDMI::retrieve_data ( BinaryStorageBuffer *  reader )

virtual

Implements StorableComponent.

{
  int dummy_int;
  bool dummy_bool;
 
  reader->read(&dummy_int, sizeof(int));
 
  if(dummy_int != _num_locus) {
    warning("DMI 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", _num_locus, dummy_int);
    _num_locus = dummy_int;
  }
  reader->read(&_isHaploid, sizeof(bool));
 
  if(dummy_bool != _isHaploid){
    warning("DMI mutation trait::haploidy in binary source file differs from parameter value!\n\
 >>>> adjusting haploidy to match source population: %i set to %i\n", _isHaploid, dummy_bool);
    _isHaploid = dummy_bool;
  }
 
  return true;
}

References _isHaploid, _num_locus, BinaryStorageBuffer::read(), and warning().

set_init_freq()

void TProtoBDMI::set_init_freq	(	double *	val,
		unsigned int	size
	)

{
  assert(size == _num_locus);
  
  if(_init_freq) delete [] _init_freq;
  
  _init_freq = new double [size];
  
  memcpy(_init_freq, val, size*sizeof(double));
 
  _isInitSet = true;
}

References _init_freq, _isInitSet, and _num_locus.

Referenced by LCE_Init_BDMI::execute().

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setGenoFitnessValue()

void TProtoBDMI::setGenoFitnessValue ( unsigned int  row, unsigned int  geno, double  value  )

inline

  { _genoTable.set(row, geno, value); }

References _genoTable, and TMatrix::set().

Referenced by TT_BDMI::set_allele_value().

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setParameters()

bool TProtoBDMI::setParameters ( )

virtual

Implements SimComponent.

{
  _num_locus = (unsigned int)get_parameter_value("dmi_loci");
 
 if(_num_locus%2)
    return error("dmi trait: the number of loci must be an even number; incompatible loci go by pair!\n");
 
  _npair = _num_locus/2;
  _mut_rate = get_parameter_value("dmi_mutation_rate");
  
  if(get_parameter("dmi_is_haploid")->isSet())
    _isHaploid = (bool)get_parameter_value("dmi_is_haploid");
  else 
    _isHaploid = 0; //diploid by default
  
  _genomic_mut_rate = _num_locus * _mut_rate * (_isHaploid ? 1 : 2);
  
  if(_isHaploid){
    _inherit_func_ptr =   &TT_BDMI::inherit_haplo;
    _mutation_func_ptr =  &TT_BDMI::mutate_haplo;
    _viability_func_ptr = &TT_BDMI::viability_haplo;
  } else {
    _inherit_func_ptr =   &TT_BDMI::inherit_diplo;
    _mutation_func_ptr =  &TT_BDMI::mutate_diplo;
    _viability_func_ptr = &TT_BDMI::viability_diplo;
  }
  
  //setting the incompatibility table:
  get_parameter("dmi_genot_table")->getMatrix(&_genoTable);
  
  //checks on size of genoTable
  if(_isHaploid && _genoTable.ncols() != 4)
    return error("dmi trait: the genotype fitness table must have 4 elements per locus pair in the haploid case.");
  
  if(!_isHaploid) {
    if(_genoTable.ncols() != 9 && _genoTable.ncols() != 16)
      return error("dmi trait: the genotype fitness table must have 9 or 16 elements per locus pair in the diploid case.");
  }
  
  if(_genoTable.nrows() > _npair )
    return error("dmi trait: the number of rows of the genotype fitness table exceeds the number of locus pairs.\n");
  
  if(_genoTable.nrows() < _npair ) {
  // we need to expand the table, copying the existing rows to complete the table
    TMatrix cpymat(_genoTable);
 
    _genoTable.reset(_npair, cpymat.ncols());
 
    _genoTable.copy_recycle(cpymat);
  }
 
  if(_genoTable.ncols() == 9)
  {
    // expand to the 16 genotype values; we copy the heterozygotes values (aABB -> AaBB, etc)
    // the order is:
    // 9 elements: {0=AABB, 1=AABb/AAbB, 2=AAbb}, {3=AaBB/aABB, 4=AaBb/aABb/AabB/aAbB, 5=Aabb/aAbb}, {6=aaBB, 7=aaBb/aabB, 8=aabb}
    // 16 elements:{0=AABB, 1=AABb, 2=AAbB, 3=AAbb},{4=AaBB, 5=AaBb, 6=AabB, 7=Aabb},{8=aABB, 9=aABb, 10=aAbB, 11=aAbb},{12=aaBB, 13=aaBb, 14=aabB, 15=aabb}
 
    // indexes of elements in the 9-table to convert a 9-table into a 16-table:
    unsigned int index[16] = {0,1,1,2,3,4,4,5,3,4,4,5,6,7,7,8};
 
    //backup:
    TMatrix oldmat(_genoTable);
 
    //expand the genotable to hold 16 elements per row
    _genoTable.reset(oldmat.nrows(), 16);
 
    //copy values from the 9-table into the 16-table using the indexes of elements in the 9-table
    for(unsigned int i = 0; i < oldmat.nrows(); ++i)
      for(unsigned int j = 0; j < 16; ++j)
        _genoTable.set(i, j, oldmat.get(i, index[j]));
 
  }
  
  _isInitSet = 0;
  
#ifdef _DEBUG_
  message("::TProtoBDMI::\nFitness table:\n");
  showGenoTable(_npair);
#endif
 
  //  RECOMBINATION ------------------------------------------------------------------------------------
 
  //bypass the genetic map for free recombination to save significant time:
  //this is done whenever the recombination rate is set to 0.5
 
  if( TTProtoWithMap::isRecombinationFree("dmi")) { //test all possible options to set recomb rate = 0.5
 
    TTProtoWithMap::_recombRate = 0.5;
 
    _gamete_recomb_func_ptr = &TProtoBDMI::inherit_free;
 
  } else {
    // loci are not independent, ie recomb rate < 0.5
 
    // the loci positions will be registered in the genetic map
    if( !TTProtoWithMap::setGeneticMapParameters ("dmi") ) return false;
 
    _gamete_recomb_func_ptr = &TProtoBDMI::inherit_low;
 
  }
 
 return true;
}

References _gamete_recomb_func_ptr, _genomic_mut_rate, _genoTable, _inherit_func_ptr, _isHaploid, _isInitSet, _mut_rate, _mutation_func_ptr, _npair, _num_locus, TTProtoWithMap::_recombRate, _viability_func_ptr, TMatrix::copy_recycle(), error(), TMatrix::get(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getMatrix(), TT_BDMI::inherit_diplo(), inherit_free(), TT_BDMI::inherit_haplo(), inherit_low(), TTProtoWithMap::isRecombinationFree(), message(), TT_BDMI::mutate_diplo(), TT_BDMI::mutate_haplo(), TMatrix::ncols(), TMatrix::nrows(), TMatrix::reset(), TMatrix::set(), TTProtoWithMap::setGeneticMapParameters(), showGenoTable(), TT_BDMI::viability_diplo(), and TT_BDMI::viability_haplo().

Referenced by init().

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showGenoTable()

void TProtoBDMI::showGenoTable

(

unsigned int

nrows

)

{
  unsigned int len = (_isHaploid ? 4 : 16);
 
  if(_isHaploid)
    cout << "AB\taB\tAb\tab\n";
  else
    cout << "AABB\tAaBB\taaBB\t AABb\tAaBb\taaBb\t AAbb\tAabb\taabb\n";
  
  for (unsigned int i = 0; i < nrows; ++i) {
    cout << i+1 << ": ";
    for (unsigned int j = 0; j < len ; ++j) {
      cout << _genoTable.get(i, j) << "\t";
    }
  cout << endl;
  }
}

References _genoTable, _isHaploid, and TMatrix::get().

Referenced by setParameters(), and TT_BDMI::show_up().

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store_data()

virtual void TProtoBDMI::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

  {
    saver->store(&_num_locus, sizeof(int));
    saver->store(&_isHaploid, sizeof(bool));
  }

References _isHaploid, _num_locus, and BinaryStorageBuffer::store().

Friends And Related Function Documentation

TT_BDMI

friend class TT_BDMI

friend

Referenced by hatch().

Member Data Documentation

_diploGenotTableCoding3x3

unsigned int TProtoBDMI::_diploGenotTableCoding3x3 = {{0,1,2},{3,4,5},{6,7,8}}

staticprivate

_diploGenotTableCoding4x4

unsigned int TProtoBDMI::_diploGenotTableCoding4x4 = {{0,1,2,3},{4,5,6,7},{8,9,10,11},{12,13,14,15}}

staticprivate

Referenced by getGenoFitnessDiplo().

_gamete_recomb_func_ptr

void(TProtoBDMI::* TProtoBDMI::_gamete_recomb_func_ptr) (sex_t SEX, bitstring &seq, const bitstring *parent)

private

Referenced by gamete_recombination(), and setParameters().

_genomic_mut_rate

double TProtoBDMI::_genomic_mut_rate

private

Referenced by TT_BDMI::mutate_diplo(), TT_BDMI::mutate_haplo(), and setParameters().

_genoTable

TMatrix TProtoBDMI::_genoTable

private

Referenced by getGenoFitnessDiplo(), getGenoFitnessHaplo(), setGenoFitnessValue(), setParameters(), and showGenoTable().

_inherit_func_ptr

void(TT_BDMI::* TProtoBDMI::_inherit_func_ptr) (const TTrait *, const TTrait *)

private

Referenced by TT_BDMI::inherit(), and setParameters().

_init_freq

double* TProtoBDMI::_init_freq

private

Referenced by get_init_freq(), set_init_freq(), and ~TProtoBDMI().

_isHaploid

bool TProtoBDMI::_isHaploid

private

Referenced by TT_BDMI::get_allele_value(), TT_BDMI::init(), TT_BDMI::init_sequence(), isHaploid(), TT_BDMI::operator=(), TT_BDMI::operator==(), retrieve_data(), TT_BDMI::retrieve_data(), TT_BDMI::set_sequence(), setParameters(), TT_BDMI::show_up(), showGenoTable(), store_data(), and TT_BDMI::store_data().

_isInitSet

bool TProtoBDMI::_isInitSet

private

Referenced by isInitSet(), set_init_freq(), and setParameters().

_mut_rate

double TProtoBDMI::_mut_rate

private

Referenced by get_mut_rate(), and setParameters().

_mutation_func_ptr

void(TT_BDMI::* TProtoBDMI::_mutation_func_ptr) (void)

private

Referenced by TT_BDMI::mutate(), and setParameters().

_npair

unsigned int TProtoBDMI::_npair

private

Referenced by setParameters(), TT_BDMI::show_up(), TT_BDMI::viability_diplo(), and TT_BDMI::viability_haplo().

_num_locus

unsigned int TProtoBDMI::_num_locus

private

Referenced by get_locus_number(), get_num_locus(), inherit_free(), TT_BDMI::init(), TT_BDMI::init_sequence(), TT_BDMI::mutate_diplo(), TT_BDMI::mutate_haplo(), TT_BDMI::operator=(), TT_BDMI::operator==(), retrieve_data(), set_init_freq(), setParameters(), TT_BDMI::show_up(), store_data(), TT_BDMI::viability_diplo(), and TT_BDMI::viability_haplo().

_recomb_rate

double TProtoBDMI::_recomb_rate

private

_stater

TTBDMI_SH* TProtoBDMI::_stater

private

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

_type

trait_t TProtoBDMI::_type

private

Referenced by get_type().

_viability_func_ptr

double(TT_BDMI::* TProtoBDMI::_viability_func_ptr) (void)

private

Referenced by TT_BDMI::set_value(), and setParameters().

_writer

TTBDMI_FH* TProtoBDMI::_writer

private

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

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

• ttbdmi.h
• ttbdmi.cc