LCE_QuantiInit Class Reference

Set patch-specifiec initial genotypes values. More...

#include <LCEquanti.h>

Inheritance diagram for LCE_QuantiInit:

Collaboration diagram for LCE_QuantiInit:

Public Member Functions
	LCE_QuantiInit ()
virtual	~LCE_QuantiInit ()
virtual void	execute ()
void	init_trait_value (sex_t SEX, age_idx AGE, unsigned int size, unsigned int deme, double *values)
void	init_allele_freq (sex_t SEX, age_idx AGE, unsigned int size, unsigned int deme, double *values, double **all_val)
virtual LifeCycleEvent *	clone ()
virtual bool	setParameters ()
virtual void	loadFileServices (FileServices *loader)
virtual void	loadStatServices (StatServices *loader)
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)
virtual age_t	removeAgeClass ()
virtual age_t	addAgeClass ()
virtual age_t	requiredAgeClass ()
Public Member Functions inherited from LifeCycleEvent
	LifeCycleEvent (const char *name, const char *trait_link)
	Cstor. More...
virtual	~LifeCycleEvent ()
virtual void	init (Metapop *popPtr)
	Sets the pointer to the current Metapop and the trait link if applicable. More...
virtual bool	attach_trait (string trait)
virtual void	set_paramset (std::string name, bool required, SimComponent *owner)
virtual void	set_event_name (std::string &name)
	Set the name of the event (name of the ParamSet) and add the corresponding parameter to the set. More...
virtual void	set_event_name (const char *name)
virtual string &	get_event_name ()
	Accessor to the LCE's name. More...
virtual int	get_rank ()
	Accessor to the LCE rank in the life cycle. More...
virtual void	set_pop_ptr (Metapop *popPtr)
	Accessors for the population pointer. More...
virtual Metapop *	get_pop_ptr ()
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_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
TMatrix	_init_values
TMatrix	_init_freq
bool	_doByTraitValue
bool	_doByAlleleFreq
unsigned int	_nTraits
unsigned int	_nLoci
TProtoQuanti *	_QuantiProto

Additional Inherited Members
Protected Attributes inherited from LifeCycleEvent
std::string	_event_name
	The param name to be read in the init file. More...
Metapop *	_popPtr
	The ptr to the current Metapop. More...
std::string	_LCELinkedTraitType
	The name of the linked trait. More...
int	_LCELinkedTraitIndex
	The index in the individual's trait table of the linked trait. More...
Protected Attributes inherited from SimComponent
ParamSet *	_paramSet
	The parameters container. More...

Detailed Description

Set patch-specifiec initial genotypes values.

Constructor & Destructor Documentation

LCE_QuantiInit()

LCE_QuantiInit::LCE_QuantiInit

(

)

                                 : LifeCycleEvent("quanti_init","quant"), _doByTraitValue(0),
  _doByAlleleFreq(0), _nTraits(0), _nLoci(0), _QuantiProto(0)
 {
   add_parameter("quanti_init_trait_values",MAT,0,0,0,0);
   add_parameter("quanti_init_freq",MAT,0,0,0,0);
 }

References SimComponent::add_parameter(), and MAT.

Referenced by clone().

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~LCE_QuantiInit()

virtual LCE_QuantiInit::~LCE_QuantiInit ( )

inlinevirtual

{ }

Member Function Documentation

addAgeClass()

virtual age_t LCE_QuantiInit::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

clone()

virtual LifeCycleEvent * LCE_QuantiInit::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_QuantiInit();}

References LCE_QuantiInit().

execute()

void LCE_QuantiInit::execute ( )

virtual

Implements LifeCycleEvent.

{
  if(!(_popPtr->getCurrentGeneration() == 1)) return;
 
  unsigned int patchNbr = _popPtr->getPatchNbr();
  
  double *values = NULL; 
  
  if (_doByTraitValue) {
    
    values = new double[_nTraits];
    
    for (unsigned int i = 0; i < patchNbr ; i++) { 
      
      _init_values.getRowView(i, _nTraits, values);  
      
      _QuantiProto->set_init_values(values, _nTraits); // the individuals use the proto to set the init values
 
      init_trait_value(FEM, OFFSx, _popPtr->size(FEM, OFFSPRG, i), i, values);
      init_trait_value(MAL, OFFSx, _popPtr->size(MAL, OFFSPRG, i), i, values);
      init_trait_value(FEM, ADLTx, _popPtr->size(FEM, ADULTS, i), i, values);
      init_trait_value(MAL, ADLTx, _popPtr->size(MAL, ADULTS, i), i, values);
    }
  }
  
  if (_doByAlleleFreq) {
    
    if(values) delete [] values;
    
    values = new double[_nLoci];
    
    double **allele_val = dynamic_cast<TProtoQuanti*> ( _popPtr->getTraitPrototype("quant") )->get_allele_values();
    
    for (unsigned int i = 0; i < patchNbr ; i++) { 
      
      _init_freq.getRowView(i, _nLoci, values);  
      
      init_allele_freq(FEM, OFFSx, _popPtr->size(FEM, OFFSPRG, i), i, values, allele_val);
      init_allele_freq(MAL, OFFSx, _popPtr->size(MAL, OFFSPRG, i), i, values, allele_val);
      init_allele_freq(FEM, ADLTx, _popPtr->size(FEM, ADULTS, i), i, values, allele_val);
      init_allele_freq(MAL, ADLTx, _popPtr->size(MAL, ADULTS, i), i, values, allele_val);
    }
  }
  
  if(values) delete [] values;
}

References _doByAlleleFreq, _doByTraitValue, _init_freq, _init_values, _nLoci, _nTraits, LifeCycleEvent::_popPtr, _QuantiProto, ADLTx, ADULTS, FEM, Metapop::getCurrentGeneration(), Metapop::getPatchNbr(), TMatrix::getRowView(), IndFactory::getTraitPrototype(), init_allele_freq(), init_trait_value(), MAL, OFFSPRG, OFFSx, TProtoQuanti::set_init_values(), and Metapop::size().

init_allele_freq()

void LCE_QuantiInit::init_allele_freq	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	size,
		unsigned int	deme,
		double *	values,
		double **	all_val
	)

{ 
  if(!size) return;
  
  Individual* ind;
  TTQuanti* trait;
  unsigned int num_A, num_a;
  unsigned int *ind_A = 0, *ind_a = 0;
  
  for(unsigned a = 0; a < 2; a++) {
    for(unsigned l = 0; l < _nLoci; l++) {
 
      num_A = (unsigned int)(size * values[l]);
      num_a = size - num_A;
      
      ind_A = new unsigned int [num_A];
      ind_a = new unsigned int [num_a];
      
      RAND::SampleSeqWithReciprocal(0, size, 1, num_A, (int*)ind_A, num_a, (int*)ind_a); //sample individuals within deme, without replacement
      
      for (unsigned int i = 0; i < num_A ; i++) {
        ind = _popPtr->get(SEX, age, ind_A[i], deme);
        trait = dynamic_cast<TTQuanti*> ( ind->getTrait(_LCELinkedTraitIndex) );
        trait->set_allele(l, a, all_val[l][0]);
      }
      for (unsigned int i = 0; i < num_a ; i++) {
        ind = _popPtr->get(SEX, age, ind_a[i], deme);
        trait = dynamic_cast<TTQuanti*> ( ind->getTrait(_LCELinkedTraitIndex) );
        trait->set_allele(l, a, all_val[l][1]);
      }
      
      delete [] ind_A;
      delete [] ind_a;
    }
  }
  
  for (unsigned int i = 0; i < size; ++i) {
    ind = _popPtr->get(SEX, age, i, deme);
    trait = dynamic_cast<TTQuanti*> ( ind->getTrait(_LCELinkedTraitIndex) );
    trait->set_value();
  }
  
}

References LifeCycleEvent::_LCELinkedTraitIndex, _nLoci, LifeCycleEvent::_popPtr, Metapop::get(), Individual::getTrait(), RAND::SampleSeqWithReciprocal(), TTQuanti::set_allele(), and TTQuanti::set_value().

Referenced by execute().

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init_trait_value()

void LCE_QuantiInit::init_trait_value	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	size,
		unsigned int	deme,
		double *	values
	)

{ 
  Individual* ind;
  TTQuanti* trait;
 
  for (unsigned int i = 0; i < size ; i++) {
    ind = _popPtr->get(SEX, age, i, deme);
    trait = dynamic_cast<TTQuanti*> ( ind->getTrait(_LCELinkedTraitIndex) );
//    trait->set_init_value(values);
    trait->init_sequence(); // this function reads the init values from the trait prototype
    trait->set_value();
  }
 
}

References LifeCycleEvent::_LCELinkedTraitIndex, LifeCycleEvent::_popPtr, Metapop::get(), Individual::getTrait(), TTQuanti::init_sequence(), and TTQuanti::set_value().

Referenced by execute().

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loadFileServices()

virtual void LCE_QuantiInit::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{}

loadStatServices()

virtual void LCE_QuantiInit::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_QuantiInit::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_QuantiInit::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

setParameters()

bool LCE_QuantiInit::setParameters ( )

virtual

Implements SimComponent.

{
  TMatrix pat_mat;
 
  // setting default values
  unsigned int patchNbr = _popPtr->getPatchNbr();
  _QuantiProto = dynamic_cast<TProtoQuanti*> ( _popPtr->getTraitPrototype("quant") );
  _nTraits = _QuantiProto -> get_nb_traits();
  _nLoci   = _QuantiProto->get_nb_locus();
  _doByAlleleFreq = false;
  _doByTraitValue = false;
  
  // checking user's options
  if(_paramSet->isSet("quanti_init_trait_values")) {
  
    if(!get_parameter("quanti_init_trait_values")->isMatrix()) {
      fatal("\"quanti_init_trait_values\" accepts only a matrix as argument.\n");
      return false;
    }
    _paramSet->getMatrix("quanti_init_trait_values", &pat_mat);
  
    _doByTraitValue = setSpatialMatrix("quanti_init_trait_values", "num of quanti traits", &pat_mat, &_init_values, _nTraits, patchNbr);
  
  }
  
  if(_paramSet->isSet("quanti_init_freq")) {
    
    if (_QuantiProto->get_allele_model() > 2) {
      error("allelic model of quanti trait incompatible with initialization by allele frequency.\n");
      error("allelic model must be di-allelic instead of continuous.\n");
      return false;
    }
    _paramSet->getMatrix("quanti_init_freq", &pat_mat);
        
    _doByAlleleFreq = setSpatialMatrix("quanti_init_freq", "num of quanti trait loci", &pat_mat, &_init_freq, _nLoci, patchNbr);
    
  }
  
  if (_doByTraitValue && _doByAlleleFreq) {
    warning("LCE_QuantiInit:: trying to init quanti traits both by trait values and allele frequencies.");
    warning("LCE_QuantiInit:: forcing initialization by allele frequencies.\n");
    _doByTraitValue = false;
  }
  
  if (!_doByAlleleFreq && !_doByTraitValue) {
    error("either \"quanti_init_trait_values\" or \"quanti_init_freq\" are missing for LCE quanti_init\n");
  }
  
  return (_doByTraitValue || _doByAlleleFreq);
}

References _doByAlleleFreq, _doByTraitValue, _init_freq, _init_values, _nLoci, _nTraits, SimComponent::_paramSet, LifeCycleEvent::_popPtr, _QuantiProto, error(), fatal(), TProtoQuanti::get_allele_model(), TProtoQuanti::get_nb_locus(), SimComponent::get_parameter(), ParamSet::getMatrix(), Metapop::getPatchNbr(), IndFactory::getTraitPrototype(), ParamSet::isSet(), setSpatialMatrix(), and warning().

Member Data Documentation

_doByAlleleFreq

bool LCE_QuantiInit::_doByAlleleFreq

private

Referenced by execute(), and setParameters().

_doByTraitValue

bool LCE_QuantiInit::_doByTraitValue

private

Referenced by execute(), and setParameters().

_init_freq

TMatrix LCE_QuantiInit::_init_freq

private

Referenced by execute(), and setParameters().

_init_values

TMatrix LCE_QuantiInit::_init_values

private

Referenced by execute(), and setParameters().

_nLoci

unsigned int LCE_QuantiInit::_nLoci

private

Referenced by execute(), init_allele_freq(), and setParameters().

_nTraits

unsigned int LCE_QuantiInit::_nTraits

private

Referenced by execute(), and setParameters().

_QuantiProto

TProtoQuanti* LCE_QuantiInit::_QuantiProto

private

Referenced by execute(), and setParameters().

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

• LCEquanti.h
• LCEquanti.cc