TTProtoWithMap Class Reference

TTProtoWithMap. More...

#include <ttrait_with_map.h>

Inheritance diagram for TTProtoWithMap:

Collaboration diagram for TTProtoWithMap:

Public Member Functions
	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	loadFileServices (FileServices *loader)=0
	Loads the component's FileHandler onto the FileServices. More...
virtual void	loadStatServices (StatServices *loader)=0
	Loads the component's StatHandler onto the StatServices. More...
virtual void	loadUpdaters (UpdaterServices *loader)
	Loads the parameters and component updater onto the updater manager. More...
virtual bool	setParameters ()=0
	Default interface needed to initialize the component's variables from its input parameters value. 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...
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)=0

Static Public Member Functions
static void	recombine (unsigned long indID)

Static Public Attributes
static GeneticMap	_map

Protected Attributes
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...

Private Attributes
string	_paramPrefix
bool	_isRegistered

Friends
class	TTraitWithMap

Detailed Description

TTProtoWithMap.

Constructor & Destructor Documentation

TTProtoWithMap() [1/2]

TTProtoWithMap::TTProtoWithMap ( )

inline

                  :_isRegistered(0), _mapIndex(0), _totRecombEventsMean(0),
  _recombRate(0), _mapResolution(1), _numChromosome(0), _numLoci(0),
  _recombRatePerChrmsm(0), _numLociPerChrmsm(0), _chrsmLength(0),
  _lociMapPositions(0) 
  {}

TTProtoWithMap() [2/2]

TTProtoWithMap::TTProtoWithMap

(

const TTProtoWithMap &

TP

)

                                                      :
_totRecombEventsMean(TP._totRecombEventsMean),_recombRate(TP._recombRate), 
_mapResolution(TP._mapResolution), _mapIndex(TP._mapIndex),
_numChromosome(TP._numChromosome), _numLoci(TP._numLoci)
{
  reset_recombination_pointers();
  
  _recombRatePerChrmsm = new double [_numChromosome];
  for (unsigned int i = 0; i < _numChromosome; ++i)
    _recombRatePerChrmsm[i] = TP._recombRatePerChrmsm[i];
  
  _numLociPerChrmsm = new unsigned int [_numChromosome];
  for (unsigned int i = 0; i < _numChromosome; ++i)
    _numLociPerChrmsm[i] = TP._numLociPerChrmsm[i];
  
  _chrsmLength = new unsigned int [_numChromosome];
  for (unsigned int i = 0; i < _numChromosome; ++i)
    _chrsmLength[i] = TP._chrsmLength[i];
  
  _lociMapPositions = new unsigned int [_numLoci];
  for (unsigned int i = 0; i < _numLoci; ++i)
    _lociMapPositions[i] = TP._lociMapPositions[i];
 
}

References _chrsmLength, _lociMapPositions, _numChromosome, _numLoci, _numLociPerChrmsm, _recombRatePerChrmsm, and reset_recombination_pointers().

~TTProtoWithMap()

TTProtoWithMap::~TTProtoWithMap ( )

virtual

{  
  reset_recombination_pointers(); 
}

References reset_recombination_pointers().

Member Function Documentation

addGeneticMapParameters()

void TTProtoWithMap::addGeneticMapParameters

(

string

prefix

)

{
  add_parameter(prefix + "_recombination_rate",     DBL, false, true,  0, 0.5, 0);
  add_parameter(prefix + "_genetic_map_resolution", DBL, false, false,  0, 0, 0);
  add_parameter(prefix + "_chromosome_num_locus",   MAT, false, false, 0, 0, 0);
  add_parameter(prefix + "_genetic_map",            MAT, false, false, 0, 0, 0);
  add_parameter(prefix + "_random_genetic_map",     MAT, false, false, 0, 0, 0);  
}

References SimComponent::add_parameter(), DBL, and MAT.

Referenced by TProtoBDMI::TProtoBDMI(), TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring(), TProtoNeutralGenes::TProtoNeutralGenes(), and TProtoQuanti::TProtoQuanti().

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areGeneticMapParamSet()

bool TTProtoWithMap::areGeneticMapParamSet

(

string

prefix

)

{
   if( get_parameter(prefix + "_recombination_rate")->isSet() )  return true;
   else if( get_parameter(prefix + "_genetic_map")->isSet() ) return true;
   else if( get_parameter(prefix + "_random_genetic_map")->isSet() ) return true;
   else return false;
}

References SimComponent::get_parameter().

Referenced by isRecombinationFree().

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getMapIndex()

unsigned int TTProtoWithMap::getMapIndex ( )

inline

{return _mapIndex;}

References _mapIndex.

isRecombinationFree()

bool TTProtoWithMap::isRecombinationFree

(

string

prefix

)

{
  if( ! areGeneticMapParamSet(prefix) ) return true;  //recombination rate is 0.5 by default
 
  string param_name = prefix + "_recombination_rate";
 
  if( get_parameter(param_name)->isSet() ){
 
 
    if( get_parameter(param_name)->isMatrix() ) {
 
      if(get_parameter(param_name)->getArg() == "{{0.5}}")
        return true;
      else
        return false;
 
    } else if( get_parameter_value(param_name) == 0.5)
      return true;
    else
      return false;
  }
 
  return false;
}

References areGeneticMapParamSet(), SimComponent::get_parameter(), and SimComponent::get_parameter_value().

Referenced by TProtoNeutralGenes::setParameters(), and TProtoQuanti::setParameters().

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recombine()

void TTProtoWithMap::recombine ( unsigned long  indID )

static

{
  if(!_map.registerIndForRecombine(indID)) return;
  
  _map.recombine(MAL);
  _map.recombine(FEM);
}

References _map, FEM, MAL, GeneticMap::recombine(), and GeneticMap::registerIndForRecombine().

Referenced by Individual::recombine().

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recordRandomMap()

void TTProtoWithMap::recordRandomMap

(

)

{
  // record positions into genetic_map parameter,
  // will be saved with other params in log file
  ostringstream map;
 
  map<<"{";
 
  for (unsigned int c = 0, l = 0; c < _numChromosome; c++) {
    map<<"{";
 
    for (unsigned int i = 0; i < _numLociPerChrmsm[c]-1 && l < _numLoci; i++) {
      map<<_lociMapPositions[ l++ ]<<", ";
    }
    map<<_lociMapPositions[ l++ ];
    map<<"}";
  }
  map<<"}";
 
  // record the position inthe genetic map parameter
  Param* mapParam = get_parameter( _paramPrefix + "_genetic_map" );
  mapParam->setArg(map.str());
  mapParam->setIsSet(true);
 
  //disable the random map parameter
  mapParam = get_parameter( _paramPrefix + "_random_genetic_map" );
  mapParam->setIsSet(false);
 
  //disable the chromosome num locus parameter
  mapParam = get_parameter( _paramPrefix + "_chromosome_num_locus" );
  mapParam->setIsSet(false);
 
  // set the map resolution right, must be at the same scale as recorded in the map
  mapParam = get_parameter( _paramPrefix + "_genetic_map_resolution" );
  mapParam->setArg(tstring::dble2str( _map.getResolution() ) ); // the local resolution is not updated after registering the trait map, other traits might have changed it
  mapParam->setIsSet(true);
 
}

References _lociMapPositions, _map, _numChromosome, _numLoci, _numLociPerChrmsm, _paramPrefix, tstring::dble2str(), SimComponent::get_parameter(), GeneticMap::getResolution(), Param::setArg(), and Param::setIsSet().

registerGeneticMap()

void TTProtoWithMap::registerGeneticMap

(

)

{
  _mapIndex = _map.addTrait(this->get_type(), _numChromosome, _numLoci, _numLociPerChrmsm,
                            _mapResolution, _lociMapPositions);
  _isRegistered = true;
}

References _isRegistered, _lociMapPositions, _map, _mapIndex, _mapResolution, _numChromosome, _numLoci, _numLociPerChrmsm, GeneticMap::addTrait(), and TraitPrototype::get_type().

Referenced by setGeneticMapParameters().

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reset()

void TTProtoWithMap::reset ( )

virtual

Implements TraitPrototype.

Reimplemented in TProtoDeletMutations_bitstring, TProtoNeutralGenes, and TProtoQuanti.

{ 
  if(_isRegistered) _map.unregisterTrait( this->get_type() );
  _isRegistered = false;
}

References _isRegistered, _map, TraitPrototype::get_type(), and GeneticMap::unregisterTrait().

Referenced by TProtoDeletMutations_bitstring::reset(), TProtoNeutralGenes::reset(), and TProtoQuanti::reset().

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reset_recombination_pointers()

void TTProtoWithMap::reset_recombination_pointers

(

)

{
  if(_recombRatePerChrmsm) {delete [] _recombRatePerChrmsm; _recombRatePerChrmsm = NULL;}
  if(_numLociPerChrmsm) {delete [] _numLociPerChrmsm; _numLociPerChrmsm = NULL;}
  if(_chrsmLength) {delete [] _chrsmLength; _chrsmLength = NULL;}
  if(_lociMapPositions) {delete [] _lociMapPositions; _lociMapPositions = NULL;}
}

References _chrsmLength, _lociMapPositions, _numLociPerChrmsm, and _recombRatePerChrmsm.

Referenced by setGeneticMapParameters(), TTProtoWithMap(), and ~TTProtoWithMap().

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setGeneticMapParameters()

bool TTProtoWithMap::setGeneticMapParameters

(

string

prefix

)

{
  TMatrix tmp_matx;
  bool map_set = false;
  
  _paramPrefix = prefix;
  
  string param_name;
  
  _numLoci = (unsigned int)get_parameter_value(prefix + "_loci");
  
//map resolution:
  param_name = prefix + "_genetic_map_resolution";
 
  _mapResolution = (get_parameter(param_name)->isSet() ? get_parameter_value(param_name) : 1);
 
  _recombRate = 0;
  
  reset_recombination_pointers();
 
// ---------------------------------------------------------------------------
//recombination rates --> "fixed" map  
  param_name = prefix + "_recombination_rate";
  if( get_parameter(param_name)->isSet() ) {
    
    if(!get_parameter(param_name)->isMatrix()) {
      
      _numChromosome = 1;
      
      _recombRate = get_parameter_value(param_name);
      
      _numLociPerChrmsm = new unsigned int[1];
      _numLociPerChrmsm[0] = _numLoci;
      
      _recombRatePerChrmsm = new double[1];
      _recombRatePerChrmsm[0] = _recombRate;
      
    } else { 
      //is a matrix parameter
      
      get_parameter(param_name)->getMatrix(&tmp_matx);
      
      if(tmp_matx.getNbRows() != 1) {
        return error("\"%s_recombination_rate\" must be one-dimensional, with chromosome-specific recombination rates as elements.\n", prefix.c_str());
      }
      
      _numChromosome = tmp_matx.getNbCols();
      
      if( !setNumLociPerChromosome(prefix) ) return false;
 
      //store the chromosome recombination rates:
      _recombRatePerChrmsm = new double [_numChromosome];
      
      for (unsigned int i = 0; i < _numChromosome; ++i)
        _recombRatePerChrmsm[i] = tmp_matx.get(0, i);
    }     
    
    if(_numChromosome == 1 && _recombRatePerChrmsm[0] == 0.5) {  // in case "{{0.5}}" was passed as argument
 
      _recombRate = 0.5;
 
    }
 
    if( !setRecombinationMapFixed() ) return false;
    
    map_set = true;
  }
  
//---------------------------------------------------------------------------------------------
//non random map:
  param_name = prefix + "_genetic_map";
  if ( get_parameter(param_name)->isSet() ) {
    
    if(map_set) {
      return error("A genetic map is already specified for trait \"%s\" while parameter \"%s\" is set.\n",prefix.c_str(), param_name.c_str());
    }
    //the genetic map gives the position of each locus on the map
    vector< vector<double> > tmp_varmatx;
 
    get_parameter(param_name)->getVariableMatrix(&tmp_varmatx);
    
    _numChromosome = tmp_varmatx.size();
     
    param_name = prefix + "_chromosome_num_locus";
    
    if ( get_parameter(param_name)->isSet() ) {
      warning("\"%s_chromosome_num_locus\" is not used with \"%s_genetic_map\", ignoring it.\n", prefix.c_str(), prefix.c_str());
    }
    
    assert(_numLociPerChrmsm == NULL);
 
    _numLociPerChrmsm = new unsigned int[_numChromosome];
 
    unsigned int length = 0;
 
    for (unsigned int i = 0; i < _numChromosome; ++i) {
      _numLociPerChrmsm[i] = tmp_varmatx[i].size();
      length += _numLociPerChrmsm[i];
    }
    
    if(length != _numLoci) {
      return error("Number of loci in \"%s_genetic_map\" different from number of loci for trait \"%s\"\n",
                       prefix.c_str(), prefix.c_str());
    }
 
    if( !setRecombinationMapNonRandom(&tmp_varmatx) ) return false;
    
    map_set = true;
  }
  
//---------------------------------------------------------------------------------------------
//random map:
  param_name = prefix + "_random_genetic_map";
  if ( get_parameter(param_name)->isSet() ) {
    
    if(map_set) {
      return error("A genetic map is already specified for trait \"%s\" while parameter \"%s\" is set.\n",param_name.c_str());
    }
    
    get_parameter(param_name)->getMatrix(&tmp_matx);
    
    if(tmp_matx.getNbRows() != 1) {
      error("\"%s_random_genetic_map\" must have one row, with chromosome lengths as elements.\n",get_type().c_str());
      return false;
    }
    
    _numChromosome = tmp_matx.getNbCols();
    
    _chrsmLength = new unsigned int [_numChromosome];
    
    for (unsigned int i = 0; i < _numChromosome; ++i)
      _chrsmLength[i] = tmp_matx.get(0, i);
    
    if( !setNumLociPerChromosome(prefix) ) return false;
 
    if( !setRecombinationMapRandom() ) return false;
    
    map_set = true;
  }
  
//---------------------------------------------------------------------------------------------
//the map/recombination parameters are missing in the config file, setting default map
  if( !map_set ) {
 
    _recombRate = 0.5;
    _numChromosome = 1;
    
    _numLociPerChrmsm = new unsigned int[1];
    _numLociPerChrmsm[0] = _numLoci;
    
    _recombRatePerChrmsm = new double[1];
    _recombRatePerChrmsm[0] = _recombRate;
 
    if( !setRecombinationMapFixed() ) return false;
  }
  
//---------------------------------------------------------------------------------------------
  
  // transmit positions to the map!!
  registerGeneticMap();
  
//  // record the random loci positions into the trait parameter for saving in log file
//  if (get_parameter(prefix + "_random_genetic_map")->isSet()) {
//
//    recordRandomMap();
//  }
 
  return true;
}

References _chrsmLength, _mapResolution, _numChromosome, _numLoci, _numLociPerChrmsm, _paramPrefix, _recombRate, _recombRatePerChrmsm, error(), TMatrix::get(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), TraitPrototype::get_type(), Param::getMatrix(), TMatrix::getNbCols(), TMatrix::getNbRows(), Param::getVariableMatrix(), Param::isSet(), registerGeneticMap(), reset_recombination_pointers(), setNumLociPerChromosome(), setRecombinationMapFixed(), setRecombinationMapNonRandom(), setRecombinationMapRandom(), and warning().

Referenced by TProtoBDMI::setParameters(), TProtoDeletMutations_bitstring::setParameters(), TProtoNeutralGenes::setParameters(), and TProtoQuanti::setParameters().

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setMapIndex()

void TTProtoWithMap::setMapIndex ( unsigned int  idx )

inline

{_mapIndex = idx;}

References _mapIndex.

setNumLociPerChromosome()

bool TTProtoWithMap::setNumLociPerChromosome

(

string

param_name

)

{
  assert(_numLociPerChrmsm == NULL);
  
  _numLociPerChrmsm = new unsigned int[_numChromosome];
 
  //fill the table:
 
  string param_name = prefix + "_chromosome_num_locus";
 
  if ( !get_parameter(param_name)->isSet()) {
    
    if(_numLoci % _numChromosome != 0) {
      
      return error("Loci cannot be evenly distributed on chromosome map for trait %s\n", prefix.c_str());
      
    } else {
 
      for (unsigned int i = 0; i < _numChromosome; ++i){
        _numLociPerChrmsm[i] = _numLoci / _numChromosome;
      }
    }
    
  } else { //chromosome num locus provided in input
    
    TMatrix numlocmat;
    
    get_parameter(param_name)->getMatrix(&numlocmat);
    
    if(numlocmat.getNbRows() != 1) {
 
      return error("\"%s_chromosome_num_locus\" must be one-dimensional, with num. loci per chromosome as elements.\n", prefix.c_str());
 
    }
    
    if(numlocmat.getNbCols() > _numChromosome) {
 
      return error("\"%s_chromosome_num_locus\" must have same number of elements (chromosomes) as genetic map parameters.\n", prefix.c_str());
 
    }
    
    unsigned int cntr=0;
 
    for (unsigned int i = 0; i < _numChromosome; ++i) {
 
      if(numlocmat.get(0, i) == 0){
 
        return error("the genetic map doesn't accept empty chromosomes with 0 loci\n");
 
      }
      _numLociPerChrmsm[i] = numlocmat.get(0, i);
      cntr += numlocmat.get(0, i);
    }
 
    if (cntr != _numLoci) {
 
      return error("\"%s_chromosome_num_locus\" has more loci than \"%s_loci\"\n", prefix.c_str(), prefix.c_str());
 
    }
 
  } //else chromosom num locus provided in input
  
  return true;
}

References _numChromosome, _numLoci, _numLociPerChrmsm, error(), TMatrix::get(), SimComponent::get_parameter(), Param::getMatrix(), TMatrix::getNbCols(), and TMatrix::getNbRows().

Referenced by setGeneticMapParameters().

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setRecombinationMapFixed()

bool TTProtoWithMap::setRecombinationMapFixed

(

)

{
  assert(_lociMapPositions == NULL);
 
  _lociMapPositions = new unsigned int [_numLoci];
 
//  cout << "TTProtoWithMap::setRecombinationMapFixed\n";
  
  double interval_scale;
  
  //find the minimum recombination rate, this will give the resolution of the map.
  
//  cout << "   map resolution (start): "<<_mapResolution<<endl;
 
  interval_scale = 0.01 * _mapResolution;  // reminder: map resolution is relative to cM = 0.01 rec rate, we rescale
 
  for(unsigned int i = 0; i < _numChromosome; i++){
    interval_scale = std::min(_recombRatePerChrmsm[i], interval_scale);
  }
 
  _mapResolution = interval_scale / 0.01;  // rescale back from rec rate to cM
 
//  cout << "   map resolution (min): "<<_mapResolution<<endl;
//  cout << "   interval scale = "<<interval_scale<<endl;
  
  //recombination rates are distance *between* loci!
  double step;
  for(unsigned int i = 0, stride = 0; i < _numChromosome; i++) {
 
    step = round(_recombRatePerChrmsm[i] / interval_scale);  //positions are integers!
    
//    cout << "   chrm "<<i<<" [step="<<step<<"] \n";
 
    _lociMapPositions[stride] = 0;
    
    for(unsigned int j = 1, k = 0; j < _numLociPerChrmsm[i]; ++j, ++k){
      
      _lociMapPositions[stride + j] = _lociMapPositions[stride + k] + step;
      
    }
    
    stride += _numLociPerChrmsm[i];
  }
  
  return true;
}

References _lociMapPositions, _mapResolution, _numChromosome, _numLoci, _numLociPerChrmsm, and _recombRatePerChrmsm.

Referenced by setGeneticMapParameters().

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setRecombinationMapNonRandom()

bool TTProtoWithMap::setRecombinationMapNonRandom

(

vector< vector< double > > *

lociPositions

)

{
  assert(_lociMapPositions == NULL);
 
  _lociMapPositions = new unsigned int [_numLoci];
 
//    cout << "TTProtoWithMap::setRecombinationMapNonRandom\n";
 
  //set loci position in absolute size
  for(unsigned int i = 0, stride = 0; i < _numChromosome; i++) {
 
    for(unsigned int j = 0; j < _numLociPerChrmsm[i]; j++){
      _lociMapPositions[stride + j] = (unsigned int)(*lociPositions)[i][j];
//          cout << _lociMapPositions[stride + j]<<" ";
    }
    stride += _numLociPerChrmsm[i];
//    cout << endl;
  }
  
  return true;
}

References _lociMapPositions, _numChromosome, _numLoci, and _numLociPerChrmsm.

Referenced by setGeneticMapParameters().

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setRecombinationMapRandom()

bool TTProtoWithMap::setRecombinationMapRandom

(

)

!there might be duplicates, we don't deal with those

{
  assert(_lociMapPositions == NULL);
 
  _lociMapPositions = new unsigned int [_numLoci];
 
//  cout << "TTProtoWithMap::setRecombinationMapRandom\n";
    
  vector<unsigned int> chr_length(_numChromosome, 0);
 
  for(unsigned int i = 0; i < _numChromosome; i++)
    chr_length[i] = (unsigned int)(_chrsmLength[i] / _mapResolution);
  
  //draw the positions:
  vector< unsigned int > tmp_map;
  unsigned int **chrm_map;
  
  chrm_map = new unsigned int* [_numChromosome];
  
  for (unsigned int i = 0; i < _numChromosome; ++i) {
    chrm_map[i] = new unsigned int [ _numLociPerChrmsm[i] ];
  }
  
  for(unsigned int i = 0; i < _numChromosome; i++) {
    
    tmp_map.assign(_numLociPerChrmsm[i], 0);
    
    for(unsigned int j = 0; j < _numLociPerChrmsm[i]; ++j)
      tmp_map[j] = RAND::Uniform( chr_length[i] );
    
    vector<unsigned int>::iterator vec_first = tmp_map.begin(), vec_last = tmp_map.end();
    //sort the vector
    std::sort(vec_first, vec_last);
    
    
    for(unsigned int j = 0; j < _numLociPerChrmsm[i]; ++j)
      chrm_map[i][j] = tmp_map[j];
  }
  
//  cout << "   loci positions:\n";
  for(unsigned int i = 0, stride = 0; i < _numChromosome; i++) {
    //offset = 0,
    for(unsigned int j = 0; j < _numLociPerChrmsm[i]; j++){
      _lociMapPositions[stride + j] = chrm_map[i][j];// + offset;
//      cout << _lociMapPositions[stride + j]<<" ";
    }
    //total size of chrmsm, to add to pos of next chrmsm loci
//    offset += chr_length[i];
//    cout << endl;
    
    stride += _numLociPerChrmsm[i];
  }
  
//  unsigned int totLength = _lociMapPositions[numLoci -1];
  
  for (unsigned int i = 0; i < _numChromosome; ++i) {
    delete [] chrm_map[i];
  }
  delete [] chrm_map; 
  
  // record positions into genetic_map parameter,
  // will be saved with other params in log file
  ostringstream map;
  
  map<<"{";
  
  for (unsigned int c = 0, l = 0; c < _numChromosome; c++) {
    map<<"{";
    
    for (unsigned int i = 0; i < _numLociPerChrmsm[c]-1 && l < _numLoci; i++) {
      map<<_lociMapPositions[ l++ ]<<", ";
    }
    map<<_lociMapPositions[ l++ ];
    map<<"}";
  }
  map<<"}";
  
  Param* mapParam = get_parameter( _paramPrefix + "_genetic_map" );
 
  mapParam->setArg(map.str());
  mapParam->setIsSet(true);
  mapParam = get_parameter( _paramPrefix + "_random_genetic_map" );
  mapParam->setIsSet(false);
  mapParam = get_parameter( _paramPrefix + "_chromosome_num_locus" );
  mapParam->setIsSet(false);
  mapParam = get_parameter( _paramPrefix + "_genetic_map_resolution" );
  mapParam->setArg(tstring::dble2str( _mapResolution )); // the local resolution is not updated after registering the trait map, other traits might have changed it
  mapParam->setIsSet(true);
  
  return true;
}

References _chrsmLength, _lociMapPositions, _mapResolution, _numChromosome, _numLoci, _numLociPerChrmsm, _paramPrefix, tstring::dble2str(), SimComponent::get_parameter(), Param::setArg(), Param::setIsSet(), and RAND::Uniform().

Referenced by setGeneticMapParameters().

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unregisterFromGeneticMap()

void TTProtoWithMap::unregisterFromGeneticMap

(

)

{
  _map.unregisterTrait(this->get_type());
  _isRegistered = false;
}

References _isRegistered, _map, TraitPrototype::get_type(), and GeneticMap::unregisterTrait().

Friends And Related Function Documentation

TTraitWithMap

friend class TTraitWithMap

friend

Member Data Documentation

_chrsmLength

unsigned int* TTProtoWithMap::_chrsmLength

protected

Referenced by reset_recombination_pointers(), setGeneticMapParameters(), setRecombinationMapRandom(), and TTProtoWithMap().

_isRegistered

bool TTProtoWithMap::_isRegistered

private

Referenced by registerGeneticMap(), reset(), and unregisterFromGeneticMap().

_lociMapPositions

unsigned int* TTProtoWithMap::_lociMapPositions

protected

Referenced by recordRandomMap(), registerGeneticMap(), reset_recombination_pointers(), setRecombinationMapFixed(), setRecombinationMapNonRandom(), setRecombinationMapRandom(), and TTProtoWithMap().

_map

GeneticMap TTProtoWithMap::_map

static

Referenced by IndFactory::clearPrototype(), TProtoBDMI::inherit(), TProtoDeletMutations_bitstring::inherit_low(), TProtoQuanti::inherit_low(), TProtoNeutralGenes::inherit_low(), recombine(), recordRandomMap(), registerGeneticMap(), reset(), unregisterFromGeneticMap(), TTNeutralGenesFH::write_PLINK(), and TTQuantiFH::write_PLINK().

_mapIndex

unsigned int TTProtoWithMap::_mapIndex

protected

Referenced by getMapIndex(), TProtoBDMI::inherit(), TProtoDeletMutations_bitstring::inherit_low(), TProtoQuanti::inherit_low(), TProtoNeutralGenes::inherit_low(), registerGeneticMap(), and setMapIndex().

_mapResolution

double TTProtoWithMap::_mapResolution

protected

Referenced by registerGeneticMap(), setGeneticMapParameters(), setRecombinationMapFixed(), and setRecombinationMapRandom().

_numChromosome

unsigned int TTProtoWithMap::_numChromosome

protected

Referenced by TProtoBDMI::inherit(), TProtoDeletMutations_bitstring::inherit_low(), TProtoQuanti::inherit_low(), TProtoNeutralGenes::inherit_low(), recordRandomMap(), registerGeneticMap(), setGeneticMapParameters(), setNumLociPerChromosome(), setRecombinationMapFixed(), setRecombinationMapNonRandom(), setRecombinationMapRandom(), and TTProtoWithMap().

_numLoci

unsigned int TTProtoWithMap::_numLoci

protected

Referenced by recordRandomMap(), registerGeneticMap(), setGeneticMapParameters(), setNumLociPerChromosome(), setRecombinationMapFixed(), setRecombinationMapNonRandom(), setRecombinationMapRandom(), and TTProtoWithMap().

_numLociPerChrmsm

unsigned int* TTProtoWithMap::_numLociPerChrmsm

protected

Referenced by TProtoBDMI::inherit(), TProtoDeletMutations_bitstring::inherit_low(), TProtoQuanti::inherit_low(), TProtoNeutralGenes::inherit_low(), recordRandomMap(), registerGeneticMap(), reset_recombination_pointers(), setGeneticMapParameters(), setNumLociPerChromosome(), setRecombinationMapFixed(), setRecombinationMapNonRandom(), setRecombinationMapRandom(), and TTProtoWithMap().

_paramPrefix

string TTProtoWithMap::_paramPrefix

private

Referenced by recordRandomMap(), setGeneticMapParameters(), and setRecombinationMapRandom().

_recombRate

double TTProtoWithMap::_recombRate

protected

Referenced by TProtoNeutralGenes::hatch(), setGeneticMapParameters(), TProtoNeutralGenes::setParameters(), and TProtoQuanti::setParameters().

_recombRatePerChrmsm

double* TTProtoWithMap::_recombRatePerChrmsm

protected

Referenced by reset_recombination_pointers(), setGeneticMapParameters(), setRecombinationMapFixed(), and TTProtoWithMap().

_totRecombEventsMean

double TTProtoWithMap::_totRecombEventsMean

protected

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

• ttrait_with_map.h
• ttrait_with_map.cc