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_nb_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	inherit (sex_t SEX, bitstring *seq, bitstring **parent)
Implementations
virtual void	init ()
virtual TTrait *	hatch ()
virtual TraitPrototype *	clone ()
virtual trait_t	get_type () const
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
virtual bool	setParameters ()
virtual void	loadFileServices (FileServices *loader)
virtual void	loadStatServices (StatServices *loader)
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)
Public Member Functions inherited from TTProtoWithMap
	TTProtoWithMap ()
	TTProtoWithMap (const TTProtoWithMap &TP)
virtual	~TTProtoWithMap ()
void	setMapIndex (unsigned int idx)
unsigned int	getMapIndex ()
bool	setGeneticMapParameters (string prefix)
void	addGeneticMapParameters (string prefix)
bool	setRecombinationMapRandom ()
bool	setRecombinationMapNonRandom (vector< vector< double > > *lociPositions)
bool	setRecombinationMapFixed ()
bool	setNumLociPerChromosome (string param_name)
void	reset_recombination_pointers ()
void	registerGeneticMap ()
void	unregisterFromGeneticMap ()
bool	areGeneticMapParamSet (string prefix)
bool	isRecombinationFree (string prefix)
void	recordRandomMap ()
virtual void	reset ()
Public Member Functions inherited from TraitPrototype
virtual void	reset ()=0
	Called at the end of a simulation to reset the Traits' prototypes (e.g. More...
virtual TTrait *	hatch ()=0
	Creates the trait of which it is the prototype, called by IndFactory::makePrototype(). More...
virtual TraitPrototype *	clone ()=0
	Returns a copy of itself. More...
virtual trait_t	get_type () const =0
	Type accessor. More...
virtual void	set_index (int idx)
	Sets the traits index. More...
virtual int	get_index ()
	Index getter. More...
Public Member Functions inherited from StorableComponent
virtual void	store_data (BinaryStorageBuffer *saver)=0
	Interface to store the component data (e.g. gene values) into a binary buffer. More...
virtual bool	retrieve_data (BinaryStorageBuffer *reader)=0
	Interface to retrieve the same data from the binary buffer. More...
virtual	~StorableComponent ()
Public Member Functions inherited from SimComponent
	SimComponent ()
virtual	~SimComponent ()
virtual void	loadUpdaters (UpdaterServices *loader)
	Loads the parameters and component updater onto the updater manager. More...
virtual void	set_paramset (ParamSet *paramset)
	Sets the ParamSet member. More...
virtual void	set_paramset (std::string name, bool required, SimComponent *owner)
	Sets a new ParamSet and name it. More...
virtual void	set_paramsetFromCopy (const ParamSet &PSet)
	Reset the set of parameters from a another set. More...
virtual ParamSet *	get_paramset ()
	ParamSet accessor. More...
virtual void	add_parameter (Param *param)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater)
	Interface to add a parameter and its updater to the set. More...
virtual Param *	get_parameter (std::string name)
	Param getter. More...
virtual double	get_parameter_value (std::string name)
	Param value getter. More...
virtual string	get_name ()
	Returnd the name of the ParamSet, i.e. More...
virtual bool	has_parameter (std::string name)
	Param getter. More...

Private Attributes
trait_t	_type
bool	_isHaploid
unsigned int	_nb_locus
double	_mut_rate
double	_genomic_mut_rate
double	_recomb_rate
double *	_init_freq
bool	_isInitSet
void(TT_BDMI::*	_inherit_func_ptr )(TTrait *, TTrait *)
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	_diploGenotTableCoding [3][3] = {{0,1,2},{3,4,5},{6,7,8}}

Additional Inherited Members
Static Public Member Functions inherited from TTProtoWithMap
static void	recombine (unsigned long indID)
Static Public Attributes inherited from TTProtoWithMap
static GeneticMap	_map
Protected Attributes inherited from TTProtoWithMap
unsigned int	_mapIndex
double	_totRecombEventsMean
double	_recombRate
double	_mapResolution
unsigned int	_numChromosome
unsigned int	_numLoci
double *	_recombRatePerChrmsm
unsigned int *	_numLociPerChrmsm
unsigned int *	_chrsmLength
unsigned int *	_lociMapPositions
Protected Attributes inherited from TraitPrototype
int	_index
	The trait index in the Individual traits table. More...
Protected Attributes inherited from SimComponent
ParamSet *	_paramSet
	The parameters container. More...

Constructor & Destructor Documentation

TProtoBDMI() [1/2]

TProtoBDMI::TProtoBDMI

(

)

                       : 
_type("dmi"), _isHaploid(1), _nb_locus(0), _mut_rate(0), _recomb_rate(0), _init_freq(0),
_isInitSet(0), _inherit_func_ptr(0), _mutation_func_ptr(0), _viability_func_ptr(0),
_genoTable(0), _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), _nb_locus(TP._nb_locus), _mut_rate(TP._mut_rate),
_recomb_rate(TP._recomb_rate), _init_freq(0), _isInitSet(0), _inherit_func_ptr(TP._inherit_func_ptr),
_mutation_func_ptr(TP._mutation_func_ptr), _viability_func_ptr(TP._viability_func_ptr),
_genoTable(0), _writer(0), _stater(0)
{
  _paramSet = new ParamSet( *TP._paramSet );
  
  if(TP._genoTable) 
    _genoTable = new TMatrix( *TP._genoTable );
  else 
    _genoTable = NULL;
 
}

References _genoTable, and SimComponent::_paramSet.

~TProtoBDMI()

TProtoBDMI::~TProtoBDMI ( )

virtual

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

References _genoTable, _init_freq, _stater, and _writer.

Member Function Documentation

clone()

virtual TraitPrototype * TProtoBDMI::clone ( )

inlinevirtual

Implements TraitPrototype.

{return new TProtoBDMI(*this);}

References TProtoBDMI().

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_mut_rate()

double TProtoBDMI::get_mut_rate ( )

inline

{return _mut_rate;}

References _mut_rate.

get_nb_locus()

int TProtoBDMI::get_nb_locus ( )

inline

{return _nb_locus;}

References _nb_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_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 < 9);
    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, _diploGenotTableCoding[posA][posB] );
  }

References _diploGenotTableCoding, _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_nb_locus(_nb_locus);
  chick->set_mut_rate(_mut_rate);
  chick->set_geno_rate(_genomic_mut_rate);
  chick->set_isHaploid(_isHaploid);
  chick->set_viability_func_ptr(_viability_func_ptr);
  chick->set_mutation_func_ptr(_mutation_func_ptr);
  chick->set_inherit_func_ptr(_inherit_func_ptr);
  chick->set_proto (this);
  return chick;
}

References _genomic_mut_rate, _inherit_func_ptr, _isHaploid, _mut_rate, _mutation_func_ptr, _nb_locus, _viability_func_ptr, TT_BDMI::set_geno_rate(), TT_BDMI::set_inherit_func_ptr(), TT_BDMI::set_isHaploid(), TT_BDMI::set_mut_rate(), TT_BDMI::set_mutation_func_ptr(), TT_BDMI::set_nb_locus(), TT_BDMI::set_proto(), and TT_BDMI::set_viability_func_ptr().

inherit()

void TProtoBDMI::inherit ( sex_t  SEX, bitstring *  seq, bitstring **  parent  )

inline

{
  
  register unsigned int nbRec, prevLoc = 0, chrm_bloc;
  register 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, TTProtoWithMap::_numChromosome, TTProtoWithMap::_numLociPerChrmsm, bitstring::copy(), GeneticMap::getFirstRecPosition(), and GeneticMap::getRecLoci().

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

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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->isMatrix()) {
      
      TMatrix temp;
      param->getMatrix(&temp);
      _writer->set_multi(true, true, 1, &temp, get_parameter("dmi_output_dir")->getArg());
      
    } 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("dmi_output_dir")->getArg(),this);
    }
    
    loader->attach(_writer);
    
  } else if(_writer != NULL) {
    delete _writer;
    _writer = NULL;
  }
}

References _writer, FileServices::attach(), SimComponent::get_parameter(), Param::getMatrix(), Param::getValue(), Param::isMatrix(), Param::isSet(), TraitFileHandler< TP >::set(), and FileHandler::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 != _nb_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", _nb_locus, dummy_int);
    _nb_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, _nb_locus, BinaryStorageBuffer::read(), and warning().

set_init_freq()

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

{
  assert(size == _nb_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 _nb_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.

{
  _nb_locus = (unsigned int)get_parameter_value("dmi_loci");
  _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 = _nb_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:
  if(_genoTable) delete _genoTable;
  
  _genoTable = new TMatrix ();
  
  get_parameter("dmi_genot_table")->getMatrix(_genoTable);
  
  //checks on size of genoTable
  if(_isHaploid && _genoTable->getNbCols() != 4)
    return error("The genotype fitness table for DMI loci must have 4 columns in the haploid case.");
  
  if(!_isHaploid && _genoTable->getNbCols() != 9)
    return error("The genotype fitness table for DMI loci must have 9 columns in the diploid case.");
  
  
  _isInitSet = 0;
  
#ifdef _DEBUG_
  message("::TProtoBDMI::\nFitness table:\n");
  showGenoTable(_nb_locus/2);
#endif
 
 return TTProtoWithMap::setGeneticMapParameters ("dmi");
}

References _genomic_mut_rate, _genoTable, _inherit_func_ptr, _isHaploid, _isInitSet, _mut_rate, _mutation_func_ptr, _nb_locus, _viability_func_ptr, error(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getMatrix(), TMatrix::getNbCols(), TT_BDMI::inherit_diplo(), TT_BDMI::inherit_haplo(), message(), TT_BDMI::mutate_diplo(), TT_BDMI::mutate_haplo(), 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 : 9);
 
  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(&_nb_locus, sizeof(int));
    saver->store(&_isHaploid, sizeof(bool));
  }

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

Member Data Documentation

_diploGenotTableCoding

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

staticprivate

Referenced by getGenoFitnessDiplo().

_genomic_mut_rate

double TProtoBDMI::_genomic_mut_rate

private

Referenced by hatch(), and setParameters().

_genoTable

TMatrix* TProtoBDMI::_genoTable

private

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

_inherit_func_ptr

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

private

Referenced by hatch(), 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 hatch(), isHaploid(), retrieve_data(), setParameters(), showGenoTable(), and 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(), hatch(), and setParameters().

_mutation_func_ptr

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

private

Referenced by hatch(), and setParameters().

_nb_locus

unsigned int TProtoBDMI::_nb_locus

private

Referenced by get_nb_locus(), hatch(), retrieve_data(), set_init_freq(), setParameters(), and store_data().

_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 hatch(), and setParameters().

_writer

TTBDMI_FH* TProtoBDMI::_writer

private

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

---

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

• ttbdmi.h
• ttbdmi.cc