LCE_Init_BDMI Class Reference

Allelic frequency initialiser for the DBMI trait. More...

#include <ttbdmi.h>

Inheritance diagram for LCE_Init_BDMI:

Collaboration diagram for LCE_Init_BDMI:

Public Member Functions
	LCE_Init_BDMI ()
virtual	~LCE_Init_BDMI ()
bool	setSpatialPattern (TMatrix &freq_mat, unsigned int patchNbr)
bool	setPatchFreq (TMatrix &freq_mat, TMatrix &pat_mat, unsigned int patchNbr)
void	init_value (sex_t SEX, age_idx age, unsigned int size, unsigned int deme)
virtual void	execute ()
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	_nLocus

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

Allelic frequency initialiser for the DBMI trait.

It executes at the first generation of each replicate only.

Constructor & Destructor Documentation

LCE_Init_BDMI()

LCE_Init_BDMI::LCE_Init_BDMI

(

)

                               : LifeCycleEvent("dmi_init","dmi")
{
  add_parameter("dmi_init_freq", MAT, true, false, 0, 0, 0);
  add_parameter("dmi_init_patch", MAT, false, false, 0, 0, 0);
//  add_parameter("dmi_inoculum_alleles", MAT, false, false, 0, 0, 0);
//  add_parameter("dmi_inoculum_size", INT, false, false, 0, 0, 0);
}

References SimComponent::add_parameter(), and MAT.

Referenced by clone().

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~LCE_Init_BDMI()

virtual LCE_Init_BDMI::~LCE_Init_BDMI ( )

inlinevirtual

{ }

Member Function Documentation

addAgeClass()

virtual age_t LCE_Init_BDMI::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

clone()

virtual LifeCycleEvent * LCE_Init_BDMI::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_Init_BDMI();}

References LCE_Init_BDMI().

execute()

void LCE_Init_BDMI::execute ( )

virtual

Implements LifeCycleEvent.

{
  
  if(!(_popPtr->getCurrentGeneration() == 1)) return;
  
  unsigned int patchNbr = _popPtr->getPatchNbr();
  double *values = new double[_nLocus];
  TProtoBDMI* proto = dynamic_cast<TProtoBDMI*> ( _popPtr->getTraitPrototype("dmi") );
 
  for (unsigned int i = 0; i < patchNbr ; i++) { 
 
    _init_freq.getRowView(i, _nLocus, values);
    
    proto->set_init_freq(values, _nLocus);
    
    init_value(FEM, OFFSx, _popPtr->size(FEM, OFFSPRG, i), i);
    init_value(MAL, OFFSx, _popPtr->size(MAL, OFFSPRG, i), i);
    init_value(FEM, ADLTx, _popPtr->size(FEM, ADULTS, i), i);
    init_value(MAL, ADLTx, _popPtr->size(MAL, ADULTS, i), i);
    
  }
  
  delete [] values;
}

References _init_freq, _nLocus, LifeCycleEvent::_popPtr, ADLTx, ADULTS, FEM, Metapop::getCurrentGeneration(), Metapop::getPatchNbr(), TMatrix::getRowView(), IndFactory::getTraitPrototype(), init_value(), MAL, OFFSPRG, OFFSx, TProtoBDMI::set_init_freq(), and Metapop::size().

init_value()

void LCE_Init_BDMI::init_value	(	sex_t	SEX,
		age_idx	age,
		unsigned int	size,
		unsigned int	deme
	)

{ 
  Individual* ind;
  TT_BDMI* trait;
  
  for (unsigned int i = 0; i < size ; i++) {
    ind = _popPtr->get(SEX, age, i, deme);
    trait = dynamic_cast<TT_BDMI*> ( ind->getTrait(_LCELinkedTraitIndex) );
    trait->init_sequence();
    trait->set_value();
  }
}

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

Referenced by execute().

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loadFileServices()

virtual void LCE_Init_BDMI::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{}

loadStatServices()

virtual void LCE_Init_BDMI::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_Init_BDMI::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_Init_BDMI::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

setParameters()

bool LCE_Init_BDMI::setParameters ( )

virtual

Implements SimComponent.

{
  TMatrix freq_mat, pat_mat;
  unsigned int patchNbr = _popPtr->getPatchNbr();
  TProtoBDMI* proto = dynamic_cast<TProtoBDMI*> ( _popPtr->getTraitPrototype("dmi") );
  bool isPatchSpecific = false;
  
  _nLocus = proto->get_nb_locus();
  
  _paramSet->getMatrix("dmi_init_freq", &freq_mat);
  
  if(get_parameter("dmi_init_patch")->isSet()) {
    _paramSet->getMatrix("dmi_init_patch", &pat_mat);
    isPatchSpecific = true;
  }
  
  unsigned int ncol = freq_mat.getNbCols(); //nbr of loci = nbr of col
  unsigned int npat = freq_mat.getNbRows(); //nbr of diff. value / locus, may be <= patchNbr
  
  //we have two possible configurations:
  // 1. ncol == 1; same value for all loci in a patch but varies among patches, with possible repetition of a pattern
  // 2. ncol == no loci && npat <= no patches; locus freq change in each patch following a pattern (same if npat == 1)
  if(npat > patchNbr) {
    error("The number of rows in \"dmi_init_freq\" is greater than the number of patches, must be at least equal to it.");
    return false;
  }  
  if(ncol > _nLocus) {
    error("The number of columns in \"dmi_init_freq\" is greater than number of loci, must be at least equal to it.\n");
    return false;
  }
  
  _init_freq.reset(patchNbr, _nLocus);
  
  bool status;
  if ( isPatchSpecific )
    status = setPatchFreq(freq_mat, pat_mat, patchNbr);
  else 
    status = setSpatialPattern(freq_mat, patchNbr);
  
  return status;
}

References _init_freq, _nLocus, SimComponent::_paramSet, LifeCycleEvent::_popPtr, error(), TProtoBDMI::get_nb_locus(), SimComponent::get_parameter(), ParamSet::getMatrix(), TMatrix::getNbCols(), TMatrix::getNbRows(), Metapop::getPatchNbr(), IndFactory::getTraitPrototype(), Param::isSet(), TMatrix::reset(), setPatchFreq(), and setSpatialPattern().

setPatchFreq()

bool LCE_Init_BDMI::setPatchFreq	(	TMatrix &	freq_mat,
		TMatrix &	pat_mat,
		unsigned int	patchNbr
	)

{
  unsigned int ncol = freq_mat.getNbCols();
  unsigned int nrow = freq_mat.getNbRows();
  unsigned int npatch = pat_mat.getNbCols();
  
  if(nrow != npatch && nrow != 1) {
    error("Row num. of \"dmi_init_freq\" is greater than column num. of \"dmi_init_patch\"\n\
          must match it or be 1.\n");
    return false;
  }
  
  for(unsigned int i = 0, pat, row; i < npatch; ++i) {
 
    pat = pat_mat.get(0, i) - 1; //patch index starts at 0!
    
    row = (nrow == 1 ? 0 : i);
    
    if(ncol == 1)
      for(unsigned int j = 0; j < _nLocus; j++) 
        _init_freq.set(pat, j, freq_mat.get(row, 0));
    else if (ncol < _nLocus)
      for(unsigned int j = 0; j < _nLocus; j++)
        _init_freq.set(pat, j, freq_mat.get(row, j % ncol));
    else
      for(unsigned int j = 0; j < _nLocus; j++)
        _init_freq.set(pat, j, freq_mat.get(row, j));
  }
  
  return true;
}

References _init_freq, _nLocus, error(), TMatrix::get(), TMatrix::getNbCols(), TMatrix::getNbRows(), and TMatrix::set().

Referenced by setParameters().

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setSpatialPattern()

bool LCE_Init_BDMI::setSpatialPattern	(	TMatrix &	freq_mat,
		unsigned int	patchNbr
	)

{  
  unsigned int ncol = freq_mat.getNbCols();
  unsigned int npat = freq_mat.getNbRows();
 
  for(unsigned int i = 0; i < patchNbr; ++i) {
    
    if(npat < patchNbr) {//repetition of a pattern
      
      if(ncol == 1)
        for(unsigned int j = 0; j < _nLocus; j++) 
          _init_freq.set(i, j, freq_mat.get(i % npat, 0));
      else if (ncol < _nLocus)
        for(unsigned int j = 0; j < _nLocus; j++)
          _init_freq.set(i, j, freq_mat.get(i % npat, j % ncol));
      else
       for(unsigned int j = 0; j < _nLocus; j++)
          _init_freq.set(i, j, freq_mat.get(i % npat, j));
      
    } else {//different values for each Patch
      
      if(ncol == 1)
        for(unsigned int j = 0; j < _nLocus; j++) 
          _init_freq.set(i, j, freq_mat.get(i, 0));
      else if (ncol < _nLocus)
        for(unsigned int j = 0; j < _nLocus; j++)
          _init_freq.set(i, j, freq_mat.get(i, j % ncol));
      else
        for(unsigned int j = 0; j < _nLocus; j++)
          _init_freq.set(i, j, freq_mat.get(i, j));
    }
  }
 
  return true;
}

References _init_freq, _nLocus, TMatrix::get(), TMatrix::getNbCols(), TMatrix::getNbRows(), and TMatrix::set().

Referenced by setParameters().

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Member Data Documentation

_init_freq

TMatrix LCE_Init_BDMI::_init_freq

private

Referenced by execute(), setParameters(), setPatchFreq(), and setSpatialPattern().

_nLocus

unsigned int LCE_Init_BDMI::_nLocus

private

Referenced by execute(), setParameters(), setPatchFreq(), and setSpatialPattern().

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

• ttbdmi.h
• ttbdmi.cc