LCE_NtrlInit Class Reference

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

#include <ttneutralgenes.h>

Inheritance diagram for LCE_NtrlInit:

Collaboration diagram for LCE_NtrlInit:

Public Member Functions
	LCE_NtrlInit ()
virtual	~LCE_NtrlInit ()
virtual void	execute ()
void	init_allele_freq (sex_t SEX, age_idx AGE, unsigned int size, unsigned int deme, double *values)
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_freq
unsigned int	_nLoci

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_NtrlInit()

LCE_NtrlInit::LCE_NtrlInit

(

)

                             : LifeCycleEvent("ntrl_init","ntrl"), _nLoci(0)
{
  add_parameter("ntrl_init_patch_freq",MAT,1,0,0,0);
}

References SimComponent::add_parameter(), and MAT.

Referenced by clone().

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~LCE_NtrlInit()

virtual LCE_NtrlInit::~LCE_NtrlInit ( )

inlinevirtual

{ }

Member Function Documentation

addAgeClass()

virtual age_t LCE_NtrlInit::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

clone()

virtual LifeCycleEvent * LCE_NtrlInit::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_NtrlInit();}

References LCE_NtrlInit().

execute()

void LCE_NtrlInit::execute ( )

virtual

Implements LifeCycleEvent.

{
  if(!(_popPtr->getCurrentGeneration() == 1)) return;
 
  unsigned int patchNbr = _popPtr->getPatchNbr();
 
  double *values = new double[_nLoci];
 
  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);
    init_allele_freq(MAL, OFFSx, _popPtr->size(MAL, OFFSPRG, i), i, values);
    init_allele_freq(FEM, ADLTx, _popPtr->size(FEM, ADULTS, i), i, values);
    init_allele_freq(MAL, ADLTx, _popPtr->size(MAL, ADULTS, i), i, values);
  }
 
  if(values) delete [] values;
}

References _init_freq, _nLoci, LifeCycleEvent::_popPtr, ADLTx, ADULTS, FEM, Metapop::getCurrentGeneration(), Metapop::getPatchNbr(), TMatrix::getRowView(), init_allele_freq(), MAL, OFFSPRG, OFFSx, and Metapop::size().

init_allele_freq()

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

{
  if(!size) return;
 
  Individual* ind;
  TTNeutralGenes* 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]);  //number of '0' allele
      num_a = size - num_A;                      //number of '1' allele
 
      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<TTNeutralGenes*> ( ind->getTrait(_LCELinkedTraitIndex) );
        trait->set_allele(l, a, 0);
      }
 
      for (unsigned int i = 0; i < num_a ; i++) {
        ind = _popPtr->get(SEX, age, ind_a[i], deme);
        trait = dynamic_cast<TTNeutralGenes*> ( ind->getTrait(_LCELinkedTraitIndex) );
        trait->set_allele(l, a, 1);
      }
 
      delete [] ind_A;
      delete [] ind_a;
    }
  }
}

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

Referenced by execute().

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loadFileServices()

virtual void LCE_NtrlInit::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{}

loadStatServices()

virtual void LCE_NtrlInit::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_NtrlInit::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_NtrlInit::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

setParameters()

bool LCE_NtrlInit::setParameters ( )

virtual

Implements SimComponent.

{
  TMatrix pat_mat;
  unsigned int patchNbr = _popPtr->getPatchNbr();
  TProtoNeutralGenes* proto = dynamic_cast<TProtoNeutralGenes*> ( _popPtr->getTraitPrototype("ntrl") );
 
  if(proto->get_allele_num() > 2) {
    error("LCE ntrl_init only works for di-allelic neutral loci, sorry.\n\
            Please consider using an FSTAT input file for more complex cases.\n");
    return false;
  }
 
  _nLoci   = proto->get_locus_num();
 
  _paramSet->getMatrix("ntrl_init_patch_freq", &pat_mat);
 
  if( !setSpatialMatrix("ntrl_init_patch_freq", "num of neutral loci", &pat_mat, &_init_freq, _nLoci, patchNbr) )
    return false;
 
  return true;
}

References _init_freq, _nLoci, SimComponent::_paramSet, LifeCycleEvent::_popPtr, error(), TProtoNeutralGenes::get_allele_num(), TProtoNeutralGenes::get_locus_num(), ParamSet::getMatrix(), Metapop::getPatchNbr(), IndFactory::getTraitPrototype(), and setSpatialMatrix().

Member Data Documentation

_init_freq

TMatrix LCE_NtrlInit::_init_freq

private

Referenced by execute(), and setParameters().

_nLoci

unsigned int LCE_NtrlInit::_nLoci

private

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

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

• ttneutralgenes.h
• ttneutralgenes.cc