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 ()
double	get_mut_rate ()
unsigned int	get_genome_size ()
unsigned int	get_num_mutations ()
unsigned int	get_init_model ()
TTNeutralGenesSH *	get_stater ()
void	inherit_low (sex_t SEX, unsigned char *seq, const unsigned char **parent)
void	inherit_free (sex_t SEX, unsigned char *seq, const 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 ()
Public Member Functions inherited from TraitPrototype
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	~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 int	_2L
unsigned int	_init_model
double	_recomb_rate
void(TTNeutralGenes::*	_mutate_func_ptr )(void)
void(TProtoNeutralGenes::*	_inherit_func_ptr )(sex_t, unsigned char *, const unsigned char **)
vector< TTNeutralGenesFH * >	_writers
TTNOhtaStats *	_ohtaStats
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), _2L(0), _init_model(0), _recomb_rate(0), _mutate_func_ptr(0), _inherit_func_ptr(0),
 _ohtaStats(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);
  add_parameter("ntrl_ohta_output",    BOOL,false,false,0,0);
  add_parameter("ntrl_ohta_logtime",   INT,false,false,0,0);
}

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

Referenced by clone().

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), _2L(T._2L), _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),
 _ohtaStats(0)
{
  _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();
 
  if(_ohtaStats) delete _ohtaStats;
}

References _ohtaStats, _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(), TTNOhtaStats::FHwrite(), TTNeutralGenesSH::init(), TTNeutralGenes::init_sequence(), TTNeutralGenes::mutate_KAM(), TTNeutralGenes::mutate_SSM(), TTNeutralGenes::operator==(), 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(), TTNeutralGenes::show_up(), TTNeutralGenesFH::write_Fst_i(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), and TTNeutralGenesFH::write_varcompWC().

get_genome_size()

unsigned int TProtoNeutralGenes::get_genome_size ( )

inline

{return _2L;}

References _2L.

get_init_model()

unsigned int TProtoNeutralGenes::get_init_model ( )

inline

{return _init_model;}

References _init_model.

Referenced by TTNeutralGenes::init_sequence().

get_locus_num()

unsigned int TProtoNeutralGenes::get_locus_num ( )

inline

{return _locus_num;}

References _locus_num.

Referenced by TTNeutralGenesFH::FHread(), TTNOhtaStats::FHwrite(), TTNeutralGenes::get_allele_value(), TTNeutralGenesSH::getDxyPerPatch(), TTNeutralGenes::init(), TTNeutralGenesSH::init(), TTNeutralGenes::init_sequence(), TTNeutralGenes::mutate_2all(), TTNeutralGenes::mutate_KAM(), TTNeutralGenes::mutate_SSM(), TTNeutralGenes::operator=(), TTNeutralGenes::operator==(), TTNeutralGenesFH::print_PLINK_PED(), TTNeutralGenes::retrieve_data(), TTNeutralGenes::set_sequence(), TTNeutralGenesSH::setAlleleTables(), 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(), TTNeutralGenes::show_up(), TTNeutralGenes::store_data(), 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_TAB(), and TTNeutralGenesFH::write_varcompWC().

get_mut_rate()

double TProtoNeutralGenes::get_mut_rate ( )

inline

{return _mut_rate;}

References _mut_rate.

get_num_mutations()

unsigned int TProtoNeutralGenes::get_num_mutations ( )

inline

{return RAND::Binomial( _mut_rate, _2L );}

References _2L, _mut_rate, and RAND::Binomial().

Referenced by TTNeutralGenes::mutate_2all(), TTNeutralGenes::mutate_KAM(), and TTNeutralGenes::mutate_SSM().

get_ploidy()

unsigned int TProtoNeutralGenes::get_ploidy ( )

inline

{return _ploidy;}

References _ploidy.

Referenced by TTNeutralGenes::get_allele_value(), TTNeutralGenes::init_sequence(), TTNeutralGenes::operator==(), TTNeutralGenesFH::print_PLINK_PED(), TTNeutralGenes::reset(), TTNeutralGenes::retrieve_data(), TTNeutralGenes::store_data(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), TTNeutralGenesFH::write_patch_TAB(), TTNeutralGenesFH::write_PLINK(), TTNeutralGenesFH::write_TAB(), and TTNeutralGenes::~TTNeutralGenes().

get_stater()

TTNeutralGenesSH* TProtoNeutralGenes::get_stater ( )

inline

{return _stats;}

References _stats.

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

get_type()

virtual trait_t TProtoNeutralGenes::get_type ( ) const

inlinevirtual

Implements TraitPrototype.

{return _type;}

References _type.

Referenced by TTNeutralGenesFH::write_PLINK().

hatch()

TTNeutralGenes * TProtoNeutralGenes::hatch ( )

virtual

Implements TraitPrototype.

{
  TTNeutralGenes* kid = new TTNeutralGenes();
 
  kid->set_proto(this);
  kid->set_mut_func_ptr(_mutate_func_ptr);
  kid->set_inherit_func_ptr(_inherit_func_ptr);
 
  return kid;
}

References _inherit_func_ptr, _mutate_func_ptr, TTNeutralGenes::set_inherit_func_ptr(), TTNeutralGenes::set_mut_func_ptr(), and TTNeutralGenes::set_proto().

inherit_free()

void TProtoNeutralGenes::inherit_free ( sex_t  SEX, unsigned char *  seq, const 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 setParameters().

inherit_low()

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

inline

{
  unsigned int prevLoc = 0, cEnd;
  //  bool flipper;
 
  vector< pair<unsigned int, unsigned int> > recTable = _map.reduceJunctions(SEX, _mapIndex);
 
  //the table containing which homologous chromosome copy we start with, for each chromosome
  //  vector< bool > & firstRecPos = _map.getFirstRecPosition(SEX);
 
  //number of x-overs
  unsigned int nbRec = recTable.size();
 
#ifdef _REC_DEBUG_
  cout << "TProtoNeutralGenes::inherit_low; nb Rec = "<<nbRec - 1<<endl;
  cout << "   --sex = "<<SEX<<"\n";
#endif
 
 
  vector< pair<unsigned int, unsigned int> >::const_iterator xover = recTable.begin();
 
  while(xover != recTable.end()) {
 
#ifdef _REC_DEBUG_
    cout<< "   copy seq from "<<prevLoc<<" to "<<xover->first
        <<" ("<<(xover->first - prevLoc)<<" loc) ("
        <<(xover->first - prevLoc)<<"B) on side "<<xover->second<<std::endl;
#endif
 
    memcpy(&seq[prevLoc], &parent[xover->second][prevLoc], (xover->first - prevLoc));
 
    prevLoc = xover->first;
 
    xover++;
  }
 
//
//#ifdef _REC_DEBUG_
//  cout << "TProtoNeutralGenes::inherit_low; nb Rec = "<< nbRec-1 << endl;
//  cout << "   --sex = "<<SEX<<"\n ";
//#endif
//
//  for(unsigned int c = 0, cStart = 0, rec = 0; c < _numChromosome; ++c) {
//
//    flipper = firstRecPos[c];
//
//    cEnd = cStart + _numLociPerChrmsm[c]; //last locus of focal chromosome
//
//    prevLoc = cStart; //cStart = first locus of focal chromosome
//
//#ifdef _REC_DEBUG_
//    //do recombination chromosome-wise
//    cout<<"   --chrm "<<c<<" side="<<firstRecPos[c]<<endl;
//#endif
//
//    // check if we have to process x-over on focal chromosome
//    for(; rec < nbRec && recTable[rec] < cEnd; ++rec) {
//
//#ifdef _REC_DEBUG_
//      cout << "   ["<<rec<<"] copy from "<<prevLoc<<" to "<<recTable[rec]
//           << "    ("<<(recTable[rec] - prevLoc)<<" loc) on side "<<flipper<<endl;
//#endif
//      //skip recombination events that would lead to copying 0 byte
//
//      memcpy(&seq[prevLoc], &parent[flipper][prevLoc], (recTable[rec] - prevLoc));
//
//      prevLoc = recTable[rec];
//
//      flipper = !flipper;
//    }
//
//#ifdef _REC_DEBUG_
//    cout <<"   --copy end of chrmsm from "<<prevLoc<<" to "<<cEnd
//        <<"   ("<<(cEnd - prevLoc)<<" loc) on side "<<flipper<<endl;
//#endif
//
//    //copy what's left between the last x-over point and the end of the chrmsme
//    memcpy(&seq[prevLoc], &parent[flipper][prevLoc], (cEnd - prevLoc));
//
//    cStart += _numLociPerChrmsm[c];
//
//  }
 
#ifdef _REC_DEBUG_
  //  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";
#endif
 
}

References TTProtoWithMap::_map, TTProtoWithMap::_mapIndex, and GeneticMap::reduceJunctions().

Referenced by setParameters().

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_logtime = get_parameter("ntrl_output_logtime");
  TMatrix logtime_matrix;
  bool logtime_isMatrix = 0;
 
  if(param_logtime->isMatrix()) {
    param_logtime->getMatrix(&logtime_matrix);
    logtime_isMatrix = 1;
  }
 
  if( get_parameter("ntrl_save_genotype")->isSet() ) {
 
    writer = new TTNeutralGenesFH(this);
 
    if(logtime_isMatrix)
      writer->set_multi(true, true, 1, &logtime_matrix, get_parameter("ntrl_output_dir")->getArg(), this);
 
    else
      writer->set(true, param_logtime->isSet(), 1, (param_logtime->isSet() ? (int)param_logtime->getValue() : 0), 0, get_parameter("ntrl_output_dir")->getArg(), this);
    //                 rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
 
    // check the output file type
    string file_type = get_parameter("ntrl_save_genotype")->getArg();
 
    // lowercase the arg string:
    std::for_each(file_type.begin(), file_type.end(), [](char& c){c = ::tolower(c);});
 
    if(file_type.length() == 0 || //default mode is tabular
        file_type == "tab")
    {
      writer->setOutputOption("allele");
      writer->set_write_fct( &TTNeutralGenesFH::write_TAB );
    }
    else if(file_type == "snp_tab")
    {
      writer->setOutputOption("snp");
      writer->set_write_fct( &TTNeutralGenesFH::write_TAB );
    }
    else if(file_type == "fstat")
    {
 
      writer->set_write_fct( &TTNeutralGenesFH::write_FSTAT );
      writer->set_extension(".dat");
 
    }
    else if(file_type == "genepop")
    {
      writer->set_write_fct( &TTNeutralGenesFH::write_GENEPOP );
    }
    else if(file_type == "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(logtime_isMatrix)
      writer->set_multi(true, true, 1, &logtime_matrix, get_parameter("ntrl_output_dir")->getArg(), this);
    //           rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
    else writer->set(true, param_logtime->isSet(), 1, (param_logtime->isSet() ? (int)param_logtime->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 (logtime_isMatrix)
      writer->set_multi(true, true, 1, &logtime_matrix, get_parameter("ntrl_output_dir")->getArg(), this);
    //           rpl_per, gen_per, rpl_occ, gen_occ, rank, path, self-ref
    else writer->set(true, param_logtime->isSet(), 1, (param_logtime->isSet() ? (int)param_logtime->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 );
  }
 
 
  // Ohta's (1982) D statistics
  if(get_parameter("ntrl_ohta_output")->isSet()) {
 
    //  Output Ohta stats :
    //    Only if pop alive
    //    Only for diallelic mutation models
    //    Only for multi-population scenarios
    if ((_allele_num > 2) || (SIMenv::MainSim->get_pop()->getPatchNbr() < 2)) {
      fatal("output option \"ntrl_ohta_output\" is only valid for diallelic neutral markers and multiple patches!\n");
    }
 
    if(_ohtaStats == NULL) _ohtaStats = new TTNOhtaStats(this);
 
    Param* param = get_parameter("ntrl_ohta_logtime");
 
    if(param->isMatrix()) {
 
      TMatrix temp;
      param->getMatrix(&temp);
      _ohtaStats->set_multi(true, true, 1, &temp, get_parameter("ntrl_output_dir")->getArg(), this);
 
    } else   //  rpl_per, gen_per, rpl_occ, gen_occ, rank (0), path, self-ref
      _ohtaStats->set(true, true, 1, (param->isSet() ? (int)param->getValue() : 0),
                   0, get_parameter("ntrl_output_dir")->getArg(),this);
 
    loader->attach(_ohtaStats);
  }
  else if(_ohtaStats != NULL) {
    delete _ohtaStats;
    _ohtaStats = NULL;
  }
 
}

References _allele_num, _ohtaStats, _writers, FileServices::attach(), FileServices::attach_reader(), fatal(), SimComponent::get_parameter(), Param::getArg(), Param::getMatrix(), Param::getValue(), Param::isMatrix(), Param::isSet(), SIMenv::MainSim, TraitFileHandler< TP >::set(), FileHandler::set_extension(), FileHandler::set_isInputHandler(), TraitFileHandler< TP >::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");
  _2L = _ploidy * _locus_num; // genome size
 
  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 _2L, _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

_2L

unsigned int TProtoNeutralGenes::_2L

private

Referenced by get_genome_size(), get_num_mutations(), and setParameters().

_allele_num

unsigned int TProtoNeutralGenes::_allele_num

private

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

_inherit_func_ptr

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

private

Referenced by hatch(), and setParameters().

_init_model

unsigned int TProtoNeutralGenes::_init_model

private

Referenced by get_init_model(), and setParameters().

_locus_num

unsigned int TProtoNeutralGenes::_locus_num

private

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

_mut_model

int TProtoNeutralGenes::_mut_model

private

Referenced by setParameters().

_mut_rate

double TProtoNeutralGenes::_mut_rate

private

Referenced by get_mut_rate(), get_num_mutations(), and setParameters().

_mutate_func_ptr

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

private

Referenced by hatch(), and setParameters().

_ohtaStats

TTNOhtaStats* TProtoNeutralGenes::_ohtaStats

private

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

_ploidy

unsigned int TProtoNeutralGenes::_ploidy

private

Referenced by get_ploidy(), 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