TProtoNeutralGenes Class Reference

Prototype class for the TTNeutralGenes trait class. More...

#include <ttneutralgenes.h>

Inheritance diagram for TProtoNeutralGenes:

Collaboration diagram for TProtoNeutralGenes:

Public Member Functions
	TProtoNeutralGenes ()
	TProtoNeutralGenes (const TProtoNeutralGenes &T)
virtual	~TProtoNeutralGenes ()
unsigned int	get_ploidy ()
unsigned int	get_locus_num ()
unsigned int	get_allele_num ()
TTNeutralGenesSH *	get_stater ()
void	inherit_low (sex_t SEX, unsigned char *seq, unsigned char **parent)
void	inherit_free (sex_t SEX, unsigned char *seq, unsigned char **parent)
virtual void	init ()
virtual void	reset ()
virtual TTNeutralGenes *	hatch ()
virtual TProtoNeutralGenes *	clone ()
virtual trait_t	get_type () const
virtual bool	setParameters ()
virtual void	loadFileServices (FileServices *loader)
virtual void	loadStatServices (StatServices *loader)
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
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
unsigned int	_allele_num
unsigned int	_locus_num
unsigned int	_ploidy
double	_mut_rate
int	_mut_model
unsigned short	_init_model
double	_recomb_rate
void(TTNeutralGenes::*	_mutate_func_ptr )(void)
void(TProtoNeutralGenes::*	_inherit_func_ptr )(sex_t, unsigned char *, unsigned char **)
vector< TTNeutralGenesFH * >	_writers
TTNeutralGenesSH *	_stats
const trait_t	_type

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...

Detailed Description

Prototype class for the TTNeutralGenes trait class.

Constructor & Destructor Documentation

TProtoNeutralGenes() [1/2]

TProtoNeutralGenes::TProtoNeutralGenes

(

)

                                        :_allele_num(0), _locus_num(0), _ploidy(2), _mut_rate(0),
_mut_model(0), _init_model(0), _recomb_rate(0), _mutate_func_ptr(0), _inherit_func_ptr(0),
_stats(0), _type(NTRL)
{
  set_paramset("neutralgenes", false, this);
 
  add_parameter("ntrl_loci",              INT, true, false, 0, 0);
  add_parameter("ntrl_init_model",        INT, false, true, 0, 3);
  add_parameter("ntrl_all",               INT, true, true, 2, 256);
  add_parameter("ntrl_mutation_rate",     DBL, true, true, 0, 1);
  add_parameter("ntrl_mutation_model",    INT, true, true, 0, 2);
 
  //genetic map parameters:
  TTProtoWithMap::addGeneticMapParameters("ntrl");
 
  //output
  add_parameter("ntrl_save_genotype",  STR, false, false, 0, 0);
  add_parameter("ntrl_save_fsti",      BOOL, false, false, 0, 0);
  add_parameter("ntrl_save_freq",      STR, false, false, 0, 0);
  add_parameter("ntrl_output_dir",     STR, false, false, 0, 0);
  add_parameter("ntrl_output_logtime", INT, false, false, 0, 0);
}

References SimComponent::add_parameter(), TTProtoWithMap::addGeneticMapParameters(), BOOL, DBL, INT, SimComponent::set_paramset(), and STR.

Referenced by clone().

Here is the caller graph for this function:

TProtoNeutralGenes() [2/2]

TProtoNeutralGenes::TProtoNeutralGenes

(

const TProtoNeutralGenes &

T

)

: _allele_num(T._allele_num), _locus_num(T._locus_num), _ploidy(2), _mut_rate(T._mut_rate),
  _mut_model(T._mut_model), _init_model(T._init_model), _recomb_rate(T._recomb_rate),
  _mutate_func_ptr(T._mutate_func_ptr), _inherit_func_ptr(T._inherit_func_ptr), _stats(0), _type(NTRL)
{
  _paramSet = new ParamSet( *(T._paramSet) ) ;
}  

References SimComponent::_paramSet.

~TProtoNeutralGenes()

TProtoNeutralGenes::~TProtoNeutralGenes ( )

virtual

{
  if(_stats != NULL)      {delete _stats; _stats = NULL;}
  for(unsigned int i = 0; i < _writers.size(); i++)
    delete _writers[i];
  _writers.clear();
 
}

References _stats, and _writers.

Member Function Documentation

clone()

virtual TProtoNeutralGenes * TProtoNeutralGenes::clone ( )

inlinevirtual

Implements TraitPrototype.

{return new TProtoNeutralGenes(*this);}

References TProtoNeutralGenes().

get_allele_num()

unsigned int TProtoNeutralGenes::get_allele_num ( )

inline

{return _allele_num;}

References _allele_num.

Referenced by TTNeutralGenesFH::FHread(), TTNeutralGenesSH::init(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setFreqRecorders(), TTNeutralGenesSH::setFst_li(), TTNeutralGenesSH::setFstat(), TTNeutralGenesSH::setFstat2(), TTNeutralGenesSH::setFstatWeirCockerham(), TTNeutralGenesSH::setFstatWeirCockerham_MS(), TTNeutralGenesSH::setFstMatrix(), TTNeutralGenesSH::setHeteroTable(), TTNeutralGenesSH::setHeterozygosity(), TTNeutralGenesSH::setHs(), TTNeutralGenesSH::setHs2(), TTNeutralGenesSH::setHt(), TTNeutralGenesSH::setHt2(), TTNeutralGenesSH::setLociDivCounter(), TTNeutralGenesSH::setNeiGeneticDistance(), LCE_NtrlInit::setParameters(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), and TTNeutralGenesFH::write_varcompWC().

get_locus_num()

unsigned int TProtoNeutralGenes::get_locus_num ( )

inline

{return _locus_num;}

References _locus_num.

Referenced by TTNeutralGenesFH::FHread(), TTNeutralGenesSH::getDxyPerPatch(), TTNeutralGenesSH::init(), TTNeutralGenesFH::print_PLINK_PED(), TTNeutralGenesSH::setAdults_Theta(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setCoaMatrix(), TTNeutralGenesSH::setFreqRecorders(), TTNeutralGenesSH::setFst_li(), TTNeutralGenesSH::setFstat(), TTNeutralGenesSH::setFstat2(), TTNeutralGenesSH::setFstatWeirCockerham(), TTNeutralGenesSH::setFstatWeirCockerham_MS(), TTNeutralGenesSH::setFstMatrix(), TTNeutralGenesSH::setHeteroTable(), TTNeutralGenesSH::setHeterozygosity(), TTNeutralGenesSH::setHo(), TTNeutralGenesSH::setHo2(), TTNeutralGenesSH::setHs(), TTNeutralGenesSH::setHs2(), TTNeutralGenesSH::setHt(), TTNeutralGenesSH::setHt2(), TTNeutralGenesSH::setLociDivCounter(), TTNeutralGenesSH::setNeiGeneticDistance(), LCE_NtrlInit::setParameters(), TTNeutralGenesSH::setSibCoa(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), TTNeutralGenesFH::write_patch_TAB(), TTNeutralGenesFH::write_PLINK(), TTNeutralGenesFH::write_PLINK_BED(), TTNeutralGenesFH::write_TAB(), and TTNeutralGenesFH::write_varcompWC().

get_ploidy()

unsigned int TProtoNeutralGenes::get_ploidy ( )

inline

{return _ploidy;}

References _ploidy.

Referenced by TTNeutralGenesFH::print_PLINK_PED(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), TTNeutralGenesFH::write_patch_TAB(), TTNeutralGenesFH::write_PLINK(), TTNeutralGenesFH::write_PLINK_BED(), and TTNeutralGenesFH::write_TAB().

Here is the caller graph for this function:

get_stater()

TTNeutralGenesSH * TProtoNeutralGenes::get_stater ( )

inline

{return _stats;}

References _stats.

Referenced by TTNeutralGenesFH::write_Fst_i(), and TTNeutralGenesFH::write_varcompWC().

Here is the caller graph for this function:

get_type()

virtual trait_t TProtoNeutralGenes::get_type ( ) const

inlinevirtual

Implements TraitPrototype.

{return _type;}

References _type.

Referenced by TTNeutralGenesFH::write_PLINK().

Here is the caller graph for this function:

hatch()

TTNeutralGenes * TProtoNeutralGenes::hatch ( )

virtual

Implements TraitPrototype.

{
  TTNeutralGenes* kid = new TTNeutralGenes();
 
  kid->set_proto(this);
  kid->set_locus_num(_locus_num);
  kid->set_allele_num(_allele_num);
  kid->set_init_model(_init_model);
  kid->set_mut_model(_mut_model);
  kid->set_mut_rate(_mut_rate);
  kid->set_mut_func_ptr(_mutate_func_ptr);
  kid->set_2L(_ploidy*_locus_num);
 
  if(_recombRate == 0.5) {
 
    _inherit_func_ptr = &TProtoNeutralGenes::inherit_free;
 
  } else {
 
    _inherit_func_ptr = &TProtoNeutralGenes::inherit_low;
 
  }
 
  kid->set_inherit_func_ptr(_inherit_func_ptr);
 
  return kid;
}

References _allele_num, _inherit_func_ptr, _init_model, _locus_num, _mut_model, _mut_rate, _mutate_func_ptr, _ploidy, TTProtoWithMap::_recombRate, inherit_free(), inherit_low(), TTNeutralGenes::set_2L(), TTNeutralGenes::set_allele_num(), TTNeutralGenes::set_inherit_func_ptr(), TTNeutralGenes::set_init_model(), TTNeutralGenes::set_locus_num(), TTNeutralGenes::set_mut_func_ptr(), TTNeutralGenes::set_mut_model(), TTNeutralGenes::set_mut_rate(), and TTNeutralGenes::set_proto().

inherit_free()

void TProtoNeutralGenes::inherit_free ( sex_t  SEX, unsigned char *  seq, unsigned char **  parent  )

inline

{
  //  cout << "TProtoNeutralGenes::inherit_free\n";
 
  for(unsigned int i = 0; i < _locus_num; ++i)
    seq[i] = parent[RAND::RandBool()][i];
}

References _locus_num, and RAND::RandBool().

Referenced by hatch(), and setParameters().

Here is the caller graph for this function:

inherit_low()

void TProtoNeutralGenes::inherit_low ( sex_t  SEX, unsigned char *  seq, unsigned char **  parent  )

inline

{
  register unsigned int prevLoc = 0, chrm_bloc;
  register bool flipper;
 
  vector< unsigned int >& recTable = _map.getRecLoci(SEX, _mapIndex);
  vector< bool > & firstRecPos = _map.getFirstRecPosition(SEX);
 
  unsigned int nbRec = recTable.size();
 
//    cout << "TProtoNeutralGenes::inherit_low; sex="<<SEX<<"\n +++ nb Rec = "
//         << nbRec-1 << "\n    (recLoc[0]=" << recTable[0] << ")" << endl;
 
  //  if (!nbRec) {
  //    memcpy(&seq[0], &parent[flipper][prevLoc], (recTable[rec] - prevLoc));
  //    return;
  //  }
  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
//          cout<<"   --chrm "<<c<<" side="<<firstRecPos[c]<<endl;
 
    for(; rec < nbRec && recTable[rec] < chrm_bloc; rec++) {
 
//                    cout << "   --copy from "<<prevLoc<<" to "<<recTable[rec] //<<" (side="<<flipper<<")"<<endl
//                         <<"    ("<<(recTable[rec] - prevLoc)<<" loc) on side "<<flipper<<endl;
 
      memcpy(&seq[prevLoc], &parent[flipper][prevLoc], (recTable[rec] - prevLoc));
 
      prevLoc = recTable[rec];
 
      flipper = !flipper;
    }
//              cout <<"   --copy end of chrmsm from "<<prevLoc<<" to "<<chrm_bloc
//                   <<"   ("<<(chrm_bloc - prevLoc)<<" loc) on side "<<flipper<<endl;
 
    //copy what's left between the last x-over point and the end of the chrmsme
    memcpy(&seq[prevLoc], &parent[flipper][prevLoc], (chrm_bloc - prevLoc));
 
    stride += _numLociPerChrmsm[c];
 
  }
 
  //  cout << "parent chromosomes:\n --0:";
  //  unsigned int loc = 0;
  //  for (unsigned int c = 0; c < _numChromosome; ++c) {
  //    cout<<" ";
  //    for(unsigned int i = 0; i < _numLociPerChrmsm[c] && loc < _locus_num; ++i)
  //      cout << (int)parent[0][loc++];
  //  }
  //  cout << "\n --1:";
  //  loc = 0;
  //  for (unsigned int c = 0; c < _numChromosome; ++c) {
  //    cout<<" ";
  //    for(unsigned int i = 0; i < _numLociPerChrmsm[c] && loc < _locus_num; ++i)
  //      cout << (int)parent[1][loc++];
  //  }
  //
  //  cout << "\ngamete:\n --0:";
  //  loc = 0;
  //  for (unsigned int c = 0; c < _numChromosome; ++c) {
  //    cout<<" ";
  //    for(unsigned int i = 0; i < _numLociPerChrmsm[c] && loc < _locus_num; ++i)
  //      cout << (int)seq[loc++];
  //  }
  //    cout << "\n\n";
 
}

References TTProtoWithMap::_map, TTProtoWithMap::_mapIndex, TTProtoWithMap::_numChromosome, TTProtoWithMap::_numLociPerChrmsm, GeneticMap::getFirstRecPosition(), and GeneticMap::getRecLoci().

Referenced by hatch(), and setParameters().

Here is the caller graph for this function:

init()

virtual void TProtoNeutralGenes::init ( )

inlinevirtual

{}

loadFileServices()

void TProtoNeutralGenes::loadFileServices ( FileServices *  loader )

virtual

Implements SimComponent.

{ 
  TTNeutralGenesFH* writer;
 
  if(_writers.size() != 0) {
    for(unsigned int i = 0; i < _writers.size(); i++)
      delete _writers[i];
    _writers.clear();
  }
 
  // --- THE READER ---
  // note that this reader only reads in FSTAT format
  //always add the reader:
  //NOTE: the default extension is ".txt", will not accept ".dat" FSTAT files in input
  writer = new TTNeutralGenesFH(this);
 
  //set to read mode:
  writer->set_isInputHandler(true);
 
  //attach to file manager:
  loader->attach_reader(writer);
 
  //add to list of FileHandlers, will be deleted upon destruction
  _writers.push_back( writer );
 
  // Add a reader for ".dat" FSTAT files:
  writer = new TTNeutralGenesFH(this);
  writer->set_isInputHandler(true);
  writer->set_extension(".dat");
  loader->attach_reader(writer);
 
  _writers.push_back( writer );
 
  // --- WRITERS ---
  Param* param = get_parameter("ntrl_output_logtime");
  TMatrix temp;
  bool isMatrix = 0;
 
  if(param->isMatrix()) {
    param->getMatrix(&temp);
    isMatrix = 1;
  }
 
  if( get_parameter("ntrl_save_genotype")->isSet() ) {
 
    writer = new TTNeutralGenesFH(this);
 
    if(isMatrix)
      writer->set_multi(true, true, 1, &temp, get_parameter("ntrl_output_dir")->getArg());
 
    else
      writer->set(true, param->isSet(), 1, (param->isSet() ? (int)param->getValue() : 0), 0, get_parameter("ntrl_output_dir")->getArg(), this);
    //                 rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
 
    if(get_parameter("ntrl_save_genotype")->getArg().length() == 0 || //default mode is tabular
        get_parameter("ntrl_save_genotype")->getArg() == "TAB" ||
        get_parameter("ntrl_save_genotype")->getArg() == "tab"
    )
    {
      writer->setOutputOption("allele");
      writer->set_write_fct( &TTNeutralGenesFH::write_TAB );
 
    }
    else if(get_parameter("ntrl_save_genotype")->getArg() == "snp_tab" ||
            get_parameter("ntrl_save_genotype")->getArg() == "SNP_TAB")
    {
      writer->setOutputOption("snp");
      writer->set_write_fct( &TTNeutralGenesFH::write_TAB );
    }
    else if(get_parameter("ntrl_save_genotype")->getArg() == "FSTAT" ||
        get_parameter("ntrl_save_genotype")->getArg() == "fstat")
    {
 
      writer->set_write_fct( &TTNeutralGenesFH::write_FSTAT );
      writer->set_extension(".dat");
 
    }
    else if(get_parameter("ntrl_save_genotype")->getArg() == "GENEPOP" ||
        get_parameter("ntrl_save_genotype")->getArg() == "genepop")
    {
 
      writer->set_write_fct( &TTNeutralGenesFH::write_GENEPOP );
 
    }
    else if(get_parameter("ntrl_save_genotype")->getArg() == "PLINK" ||
        get_parameter("ntrl_save_genotype")->getArg() == "plink")
    {
      writer->set_write_fct( &TTNeutralGenesFH::write_PLINK );
    }
    else
      fatal("parameter \"ntrl_save_genotype\" options are \"TAB\", \"SNP_TAB\", \"FSTAT\", \"GENEPOP\" or \"PLINK\".\n");
 
    loader->attach(writer);
 
    _writers.push_back( writer );
  }
 
  // new writer
  if( get_parameter("ntrl_save_fsti")->isSet() ) {
 
    writer = new TTNeutralGenesFH(this);
 
    if(isMatrix) writer->set_multi(true, true, 1, &temp, get_parameter("ntrl_output_dir")->getArg());
    //           rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
    else writer->set(true, param->isSet(), 1, (param->isSet() ? (int)param->getValue() : 0), 0, get_parameter("ntrl_output_dir")->getArg(), this);
 
    writer->set_write_fct( &TTNeutralGenesFH::write_Fst_i );
 
    writer->set_extension(".fsti");
 
    loader->attach(writer);
 
    _writers.push_back( writer );
  }
 
  // new writer
  if( get_parameter("ntrl_save_freq")->isSet() ) {
 
    writer = new TTNeutralGenesFH(this);
 
    writer->set_extension(".freq");
 
    if (isMatrix) writer->set_multi(true, true, 1, &temp, get_parameter("ntrl_output_dir")->getArg());
    //           rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
    else writer->set(true, param->isSet(), 1, (param->isSet() ? (int)param->getValue() : 0), 0, get_parameter("ntrl_output_dir")->getArg(), this);
 
    //check validity of output option:
 
    if(get_parameter("ntrl_save_freq")->getArg() == "allfreq") {
 
      warning("option \"allfreq\" to \"ntrl_save_freq\" is deprecated, using \"locus\" instead\n");
 
      writer->setOutputOption("locus");
 
    } else if(get_parameter("ntrl_save_freq")->getArg() == "vcomp") {
 
      warning("option \"vcomp\" to \"ntrl_save_freq\" is deprecated, using \"allele\" instead\n");
 
      writer->setOutputOption("allele");
 
    } else if( get_parameter("ntrl_save_freq")->getArg() != "1" &&
        get_parameter("ntrl_save_freq")->getArg() != "locus" &&
        get_parameter("ntrl_save_freq")->getArg() != "allele") {
 
      fatal("parameter \"ntrl_save_freq\" options are \"locus\" or \"allele\".\n");
 
    } else
      writer->setOutputOption(get_parameter("ntrl_save_freq")->getArg());
 
    writer->set_write_fct( &TTNeutralGenesFH::write_varcompWC );
 
    loader->attach(writer);
 
    _writers.push_back( writer );
  }
 
}

References _writers, FileServices::attach(), FileServices::attach_reader(), fatal(), SimComponent::get_parameter(), Param::getMatrix(), Param::getValue(), Param::isMatrix(), Param::isSet(), TraitFileHandler< TP >::set(), FileHandler::set_extension(), FileHandler::set_isInputHandler(), FileHandler::set_multi(), TTNeutralGenesFH::set_write_fct(), TTNeutralGenesFH::setOutputOption(), warning(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), TTNeutralGenesFH::write_TAB(), and TTNeutralGenesFH::write_varcompWC().

loadStatServices()

void TProtoNeutralGenes::loadStatServices ( StatServices *  loader )

virtual

Implements SimComponent.

{
  //allocate the stat handler
  if(_stats) delete _stats;
 
  // this makes sure that the trait index is reset correctly between simulations
  _stats = new TTNeutralGenesSH(this);
 
  loader->attach(_stats);
 
}

References _stats, and StatServices::attach().

reset()

virtual void TProtoNeutralGenes::reset ( )

inlinevirtual

Reimplemented from TTProtoWithMap.

{TTProtoWithMap::reset();}

References TTProtoWithMap::reset().

resetParameterFromSource()

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

virtual

Implements SimComponent.

{
  TProtoNeutralGenes *srcProto = dynamic_cast< TProtoNeutralGenes* >(cmpt);
 
  if( param != "ntrl_genetic_map" ) return false;
 
  Param *srcMap = srcProto->get_parameter(param);
 
  if(!srcMap->isSet()) return error("parameter \"ntrl_genetic_map\" not set in source.\n");
 
 
  //@TODO need to implement a way to update the genetic map of a trait in GeneticMap
  return false;
}

References error(), SimComponent::get_parameter(), and Param::isSet().

retrieve_data()

bool TProtoNeutralGenes::retrieve_data ( BinaryStorageBuffer *  reader )

virtual

Implements StorableComponent.

{
  unsigned int dummy;
  reader->read(&dummy, sizeof(int));
  if(dummy != _locus_num ){
    warning("Neutral 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", _locus_num, dummy);
    _locus_num = dummy;
  }
  return true;
}

References _locus_num, BinaryStorageBuffer::read(), and warning().

setParameters()

bool TProtoNeutralGenes::setParameters ( )

virtual

Implements SimComponent.

{
  _locus_num =  (unsigned int)get_parameter_value("ntrl_loci");
  _allele_num = (unsigned int)get_parameter_value("ntrl_all");
  _ploidy = 2;
  _mut_rate =  get_parameter_value("ntrl_mutation_rate");
  _mut_model = (unsigned int)get_parameter_value("ntrl_mutation_model");
 
  if(get_parameter("ntrl_init_model")->isSet())
    _init_model = (unsigned short)get_parameter_value("ntrl_init_model");
  else
    _init_model = 1; //maximum variance
 
  switch(_mut_model) {
  case 0:
  {
    _mutate_func_ptr = &TTNeutralGenes::mutate_NULL;
    break;
  }
  case 1:
  {
    _mutate_func_ptr = &TTNeutralGenes::mutate_SSM;
    break;
  }
  case 2:
  {
    _mutate_func_ptr = &TTNeutralGenes::mutate_KAM;
    break;
  }
  default:
  {
    error("wrong parameter value for parameter \"ntrl_mutation_model\", max is 2\n");
    break; //should return false
  }
  }
  //special case:
  if(_allele_num==2) _mutate_func_ptr = &TTNeutralGenes::mutate_2all;
 
  // we want to bypass the genetic map if loci are not linked
  if( TTProtoWithMap::isRecombinationFree("ntrl")) { //test all possible options to set recomb rate = 0.5
 
    TTProtoWithMap::_recombRate = 0.5;
 
    _inherit_func_ptr = &TProtoNeutralGenes::inherit_free;
 
  } else {
 
    // register the locus positions on the genetic map
    if( ! TTProtoWithMap::setGeneticMapParameters ("ntrl") ) return false;
 
    _inherit_func_ptr = &TProtoNeutralGenes::inherit_low;
 
  }
 
  return true;
}

References _allele_num, _inherit_func_ptr, _init_model, _locus_num, _mut_model, _mut_rate, _mutate_func_ptr, _ploidy, TTProtoWithMap::_recombRate, error(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), inherit_free(), inherit_low(), TTProtoWithMap::isRecombinationFree(), Param::isSet(), TTNeutralGenes::mutate_2all(), TTNeutralGenes::mutate_KAM(), TTNeutralGenes::mutate_NULL(), TTNeutralGenes::mutate_SSM(), and TTProtoWithMap::setGeneticMapParameters().

store_data()

virtual void TProtoNeutralGenes::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

{saver->store(&_locus_num,sizeof(int));}

References _locus_num, and BinaryStorageBuffer::store().

Member Data Documentation

_allele_num

unsigned int TProtoNeutralGenes::_allele_num

private

Referenced by get_allele_num(), hatch(), and setParameters().

_inherit_func_ptr

void(TProtoNeutralGenes::* TProtoNeutralGenes::_inherit_func_ptr) (sex_t, unsigned char *, unsigned char **)

private

Referenced by hatch(), and setParameters().

_init_model

unsigned short TProtoNeutralGenes::_init_model

private

Referenced by hatch(), and setParameters().

_locus_num

unsigned int TProtoNeutralGenes::_locus_num

private

Referenced by get_locus_num(), hatch(), inherit_free(), retrieve_data(), setParameters(), and store_data().

_mut_model

int TProtoNeutralGenes::_mut_model

private

Referenced by hatch(), and setParameters().

_mut_rate

double TProtoNeutralGenes::_mut_rate

private

Referenced by hatch(), and setParameters().

_mutate_func_ptr

void(TTNeutralGenes::* TProtoNeutralGenes::_mutate_func_ptr) (void)

private

Referenced by hatch(), and setParameters().

_ploidy

unsigned int TProtoNeutralGenes::_ploidy

private

Referenced by get_ploidy(), hatch(), and setParameters().

_recomb_rate

double TProtoNeutralGenes::_recomb_rate

private

_stats

TTNeutralGenesSH* TProtoNeutralGenes::_stats

private

Referenced by get_stater(), loadStatServices(), and ~TProtoNeutralGenes().

_type

const trait_t TProtoNeutralGenes::_type

private

Referenced by get_type().

_writers

vector< TTNeutralGenesFH* > TProtoNeutralGenes::_writers

private

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

---

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

• ttneutralgenes.h
• ttneutralgenes.cc