TTBDMI_SH Class Reference

StatHandler for the DBMI trait. More...

#include <ttbdmi.h>

Inheritance diagram for TTBDMI_SH:

Collaboration diagram for TTBDMI_SH:

Public Member Functions
	TTBDMI_SH (TProtoBDMI *TP)
virtual	~TTBDMI_SH ()
virtual bool	setStatRecorders (std::string &token)
void	addStats (age_t AGE)
void	setAdultStats ()
void	setOffsprgStats ()
void	setStats (age_idx agex, void(TTBDMI_SH::*cntFunc)(Patch *, sex_t, age_idx, double **, double **))
void	countAllele_haplo (Patch *patch, sex_t SEX, age_idx AGE, double **frqTab, double **icpTab)
void	countAllele_diplo (Patch *patch, sex_t SEX, age_idx AGE, double **frqTab, double **icpTab)
double	getFreq ()
double	getFreqIcmp ()
double	getPatchFreq (unsigned int i)
double	getPatchIcmp (unsigned int i)
Public Member Functions inherited from TraitStatHandler< TProtoBDMI, TTBDMI_SH >
	TraitStatHandler (TProtoBDMI *trait_proto)
virtual	~TraitStatHandler ()
Public Member Functions inherited from StatHandler< SH >
	StatHandler ()
virtual	~StatHandler ()
virtual void	clear ()
	Empties the _recorders list, they are destroyed in StatHandlerBase::reset(). More...
virtual StatRecorder< SH > *	add (std::string Title, std::string Name, age_t AGE, unsigned int ARG1, unsigned int ARG2, double(SH::*getStatNoArg)(void), double(SH::*getStatOneArg)(unsigned int), double(SH::*getStatTwoArg)(unsigned int, unsigned int), void(SH::*setStat)(void))
	Adds a StatRecorder to the list, it is also added to the StatHandlerBase::_stats list. More...
Public Member Functions inherited from StatHandlerBase
	StatHandlerBase ()
virtual	~StatHandlerBase ()
virtual void	reset ()
	Empties the _stats list and calls clear() (defined in the derived class). More...
Metapop *	get_pop_ptr ()
void	set_service (StatServices *srv)
StatServices *	get_service ()
unsigned int	getOccurrence ()
unsigned int	getNumOccurrences ()
unsigned int	getCurrentOccurrence ()
unsigned int	getNbRecorders ()
std::list< StatRecBase * > &	getStats ()
virtual void	add (StatRecBase *rec)
virtual void	init ()
virtual void	update ()
	This function is left empty as the StatServices calls StatRecorder::setVal directly. More...
Public Member Functions inherited from Handler
virtual void	init ()=0
	Inits state. More...
virtual void	update ()=0
	Updates the handler state. More...
virtual	~Handler ()

Private Attributes
double	_freq
double	_freqIcomp
double *	_patchFreq
double *	_patchIcmp

Additional Inherited Members
Protected Types inherited from StatHandler< SH >
typedef std::list< StatRecorder< SH > * >::iterator	REC_IT
Protected Attributes inherited from TraitStatHandler< TProtoBDMI, TTBDMI_SH >
TProtoBDMI *	_SHLinkedTrait
	Pointer to a TraitProtoype object. More...
int	_SHLinkedTraitIndex
	Index of the trait in the Individual::Traits table. More...
Protected Attributes inherited from StatHandler< SH >
std::list< StatRecorder< SH > * >	_recorders
	The list of stat recorders. More...
Protected Attributes inherited from StatHandlerBase
Metapop *	_pop
	Link to the current population, set through the link to the StatService. More...

Detailed Description

StatHandler for the DBMI trait.

Records the average allele frequencies at all loci, and the frequencies of incompatibilities (i.e. double heterozygotes).

Constructor & Destructor Documentation

TTBDMI_SH()

TTBDMI_SH::TTBDMI_SH ( TProtoBDMI *  TP )

inline

                            : TraitStatHandler< TProtoBDMI, TTBDMI_SH > (TP),
                               _patchFreq(0), _patchIcmp(0) {}

~TTBDMI_SH()

virtual TTBDMI_SH::~TTBDMI_SH ( )

inlinevirtual

{if(_patchFreq)delete[]_patchFreq;if(_patchIcmp)delete[]_patchIcmp;}

References _patchFreq, and _patchIcmp.

Member Function Documentation

addStats()

void TTBDMI_SH::addStats

(

age_t

AGE

)

{
  string prefix = (AGE == ADULTS ? "adlt." : "off.");
  ostringstream name;
  void (TTBDMI_SH::* setter) () = (AGE == ADULTS ?
                                            &TTBDMI_SH::setAdultStats :
                                            &TTBDMI_SH::setOffsprgStats);
  
  add("", prefix + "dmi.freq", AGE, 0, 0, &TTBDMI_SH::getFreq, 0, 0, setter);
  add("", prefix + "dmi.icmp", AGE, 0, 0, &TTBDMI_SH::getFreqIcmp, 0, 0, 0);
  for (unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
    name << prefix << "dmi.p" << i+1;
    add("", name.str(), AGE, i, 0, 0, &TTBDMI_SH::getPatchFreq, 0, 0);
    name.str(""); //reset the string
  }
  for (unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
    name << prefix << "icmp.p" << i+1;
    add("", name.str(), AGE, i, 0, 0, &TTBDMI_SH::getPatchIcmp, 0, 0);
    name.str("");
  }
  
}

References StatHandlerBase::_pop, StatHandler< SH >::add(), ADULTS, getFreq(), getFreqIcmp(), getPatchFreq(), getPatchIcmp(), Metapop::getPatchNbr(), setAdultStats(), and setOffsprgStats().

Referenced by setStatRecorders().

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countAllele_diplo()

void TTBDMI_SH::countAllele_diplo	(	Patch *	patch,
		sex_t	SEX,
		age_idx	AGE,
		double **	frqTab,
		double **	icpTab
	)

{
  TT_BDMI* trait;
  unsigned int l, a1, a2, num_pair = _SHLinkedTrait->get_nb_locus()/2;
  
  for(unsigned int j = 0; j < patch->size(SEX, AGE); ++j) {
    
    trait = dynamic_cast< TT_BDMI* > ( patch->get( SEX, AGE, j )->getTrait( _SHLinkedTraitIndex ) );
    
    l = 0;
    for(unsigned int k = 0; k < num_pair; ++k) {
      
      a1 = trait->get_num_mut_diplo(l);
      frqTab[patch->getID()][l++] += a1;
      
      a2 = trait->get_num_mut_diplo(l);
      frqTab[patch->getID()][l++] += a2;
      
      icpTab[patch->getID()][k] += ((a1 == 1) && (a2 == 1));
    }
  }
}

References TraitStatHandler< TProtoBDMI, TTBDMI_SH >::_SHLinkedTrait, TraitStatHandler< TProtoBDMI, TTBDMI_SH >::_SHLinkedTraitIndex, Patch::get(), TProtoBDMI::get_nb_locus(), TT_BDMI::get_num_mut_diplo(), Patch::getID(), Individual::getTrait(), and Patch::size().

Referenced by setAdultStats(), and setOffsprgStats().

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countAllele_haplo()

void TTBDMI_SH::countAllele_haplo	(	Patch *	patch,
		sex_t	SEX,
		age_idx	AGE,
		double **	frqTab,
		double **	icpTab
	)

{
  TT_BDMI* trait;
  unsigned int l, a1, a2, num_pair = _SHLinkedTrait->get_nb_locus()/2;
  
  for(unsigned int j = 0; j < patch->size(SEX, AGE); ++j) {
    
    trait = dynamic_cast< TT_BDMI* > ( patch->get( SEX, AGE, j )->getTrait( _SHLinkedTraitIndex ) );
    
    l = 0;
    for(unsigned int k = 0; k < num_pair; ++k) {
      
      a1 = trait->get_num_mut_haplo(l);
      frqTab[patch->getID()][l++] += a1;
      
      a2 = trait->get_num_mut_haplo(l);
      frqTab[patch->getID()][l++] += a2;
      
      icpTab[patch->getID()][k] += a1 ^ a2;
    }
  }
}

References TraitStatHandler< TProtoBDMI, TTBDMI_SH >::_SHLinkedTrait, TraitStatHandler< TProtoBDMI, TTBDMI_SH >::_SHLinkedTraitIndex, Patch::get(), TProtoBDMI::get_nb_locus(), TT_BDMI::get_num_mut_haplo(), Patch::getID(), Individual::getTrait(), and Patch::size().

Referenced by setAdultStats(), and setOffsprgStats().

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getFreq()

double TTBDMI_SH::getFreq ( )

inline

{return _freq;}

References _freq.

Referenced by addStats().

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getFreqIcmp()

double TTBDMI_SH::getFreqIcmp ( )

inline

{return _freqIcomp;}

References _freqIcomp.

Referenced by addStats().

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getPatchFreq()

double TTBDMI_SH::getPatchFreq ( unsigned int  i )

inline

{return _patchFreq[i];}

References _patchFreq.

Referenced by addStats().

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getPatchIcmp()

double TTBDMI_SH::getPatchIcmp ( unsigned int  i )

inline

{return _patchIcmp[i];}

References _patchIcmp.

Referenced by addStats().

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setAdultStats()

void TTBDMI_SH::setAdultStats

(

)

{
  if( _SHLinkedTrait->isHaploid()) setStats(ADLTx, &TTBDMI_SH::countAllele_haplo);
  else setStats(ADLTx, &TTBDMI_SH::countAllele_diplo);
}

References TraitStatHandler< TProtoBDMI, TTBDMI_SH >::_SHLinkedTrait, ADLTx, countAllele_diplo(), countAllele_haplo(), TProtoBDMI::isHaploid(), and setStats().

Referenced by addStats().

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setOffsprgStats()

void TTBDMI_SH::setOffsprgStats

(

)

{
  if( _SHLinkedTrait->isHaploid()) setStats(OFFSx, &TTBDMI_SH::countAllele_haplo);
  else setStats(OFFSx, &TTBDMI_SH::countAllele_diplo);
}

References TraitStatHandler< TProtoBDMI, TTBDMI_SH >::_SHLinkedTrait, countAllele_diplo(), countAllele_haplo(), TProtoBDMI::isHaploid(), OFFSx, and setStats().

Referenced by addStats().

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setStatRecorders()

bool TTBDMI_SH::setStatRecorders ( std::string &  token )

virtual

Implements StatHandlerBase.

{
#ifdef _DEBUG_
  message("-TTBDMI_SH::setStatRecorders ");
#endif
  if(token == "dmi") {
    
      addStats(OFFSPRG);
      addStats(ADULTS);
    
  } else if(token == "off.dmi") {
    
      addStats(OFFSPRG);
    
  } else if(token == "adlt.dmi") {
    
      addStats(ADULTS);
    
  } else
    return false;
  
  return true;
}

References addStats(), ADULTS, message(), and OFFSPRG.

setStats()

void TTBDMI_SH::setStats	(	age_idx	agex,
		void(TTBDMI_SH::*)(Patch *, sex_t, age_idx, double **, double **)	cntFunc
	)

{
  unsigned int i, nb_ind = 0, nb_patch = 0;
  unsigned int nb_locus = _SHLinkedTrait->get_nb_locus();
  unsigned int num_pair;
  unsigned int psize=0;
  unsigned int npatch=_pop->getPatchNbr();
 
  Patch* current_patch;
      
  num_pair = nb_locus/2;
 
  double* freqTable = new double [nb_locus];
  double* icmpTable = new double [num_pair];
  double** patchFreqTable = new double* [npatch];
  double** patchIcmpTable = new double* [npatch];
 
  for(i = 0; i < nb_locus; ++i)
    freqTable[i] = 0;
  
  for(i = 0; i < num_pair; ++i)
    icmpTable[i] = 0;
 
  //init patch tables:
  if(_patchFreq) delete [] _patchFreq;
  _patchFreq = new double [npatch];
  
  if(_patchIcmp) delete [] _patchIcmp;
  _patchIcmp = new double [npatch];
 
  //patch loop:
  for(i = 0; i < npatch; ++i) {
    
    current_patch = _pop->getPatch(i);
 
    patchFreqTable[i] = new double [nb_locus];
    for(unsigned int j = 0; j < nb_locus; ++j) patchFreqTable[i][j] = 0;
    
    patchIcmpTable[i] = new double [num_pair];
    for(unsigned int j = 0; j < num_pair; ++j) patchIcmpTable[i][j] = 0;
    
    _patchFreq[i] = 0;
    _patchIcmp[i] = 0;
 
    if( (psize = current_patch->size(agex)) == 0) continue;
    
    nb_patch++;
    
    nb_ind += psize;
 
    (this->* cntFunc) (current_patch, FEM, agex, patchFreqTable, patchIcmpTable);
    (this->* cntFunc) (current_patch, MAL, agex, patchFreqTable, patchIcmpTable);
    
    //mut frequ.
    for(unsigned int k = 0; k < nb_locus; ++k)
      _patchFreq[i] += patchFreqTable[i][k]/psize;
    
    if(_SHLinkedTrait->isHaploid()) _patchFreq[i] /= nb_locus;
    else _patchFreq[i] /= 2*nb_locus;
 
    //incompatibilities:
    for(unsigned int k = 0; k < num_pair; ++k)
      _patchIcmp[i] += patchIcmpTable[i][k]/psize;
    
    _patchIcmp[i] /= num_pair;
 
    
  }//end for Patch
  
  //set pop means
  //mut frequ:
  _freq = 0;
  
  for(i = 0; i < npatch; ++i)  _freq += _patchFreq[i];
  
  _freq /= npatch;
  
  //Incompatibilities:
  _freqIcomp = 0;
  
  for(i = 0; i < npatch; ++i)  _freqIcomp += _patchIcmp[i];
  
  _freqIcomp /= npatch;
  
  
  delete [] freqTable;
  delete [] icmpTable;
  for(i = 0; i < npatch; ++i) {
    delete [] patchFreqTable[i];
    delete [] patchIcmpTable[i];
  }
  delete [] patchFreqTable;
  delete [] patchIcmpTable;
}

References _freq, _freqIcomp, _patchFreq, _patchIcmp, StatHandlerBase::_pop, TraitStatHandler< TProtoBDMI, TTBDMI_SH >::_SHLinkedTrait, FEM, TProtoBDMI::get_nb_locus(), Metapop::getPatch(), Metapop::getPatchNbr(), TProtoBDMI::isHaploid(), MAL, and Patch::size().

Referenced by setAdultStats(), and setOffsprgStats().

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Member Data Documentation

_freq

double TTBDMI_SH::_freq

private

Referenced by getFreq(), and setStats().

_freqIcomp

double TTBDMI_SH::_freqIcomp

private

Referenced by getFreqIcmp(), and setStats().

_patchFreq

double* TTBDMI_SH::_patchFreq

private

Referenced by getPatchFreq(), setStats(), and ~TTBDMI_SH().

_patchIcmp

double * TTBDMI_SH::_patchIcmp

private

Referenced by getPatchIcmp(), setStats(), and ~TTBDMI_SH().

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

• ttbdmi.h
• ttbdmi.cc