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 ()
double	getRecombRate () const
bool	setGeneticMapParameters (string prefix, unsigned int numLoci=0)
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 ()
Implements TraitPrototype
virtual bool	is_mappable ()
	Checks if the trait is mappable, i.e., if the loci can be placed on a genetic map. More...
virtual bool	is_mapped ()
	Checks if the trait's loci are placed on a genetic map. More...
virtual vector< unsigned int >	get_locus_map_positions ()
	Returns the map positions of the loci in vector. More...
Public Member Functions inherited from TraitPrototype
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...
virtual int	get_phenotype_dimension ()=0
	Returns the dimension of the phenotype of the trait (size of the array accessed with TTrait::getValue() More...
virtual int	get_allele_number ()=0
	Returns the number of allele per locus. More...
virtual int	get_locus_number ()=0
	Returns the number of locus. 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 GeneticMap &	getGeneticMapRef ()
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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get_locus_map_positions()

vector< unsigned int > TTProtoWithMap::get_locus_map_positions ( )

virtual

Returns the map positions of the loci in vector.

Implements TraitPrototype.

{
  vector< unsigned int > positions(this->get_locus_number(), 0);
 
  if( is_mapped() ) {
 
    unsigned int * map_pos = _map.getLocusPositionTable(this->get_type());
 
    positions.assign(map_pos, map_pos + this->get_locus_number());
 
  } else if ( is_mappable() ) {
    // trait can be placed on the map but has not been placed because of free recombination
    // generate fake positions:; get a starting position based on the trait index
    // positions are returned in ~Mbase
    unsigned int start = (this->get_index()+1) * 10;
    std::iota(positions.begin(),positions.end(), start);
    std::transform(positions.begin(), positions.end(), positions.begin(), [](unsigned int i) {return i * 100000;});
  }
  // if the trati is non-mappable, then positions remain undefined (all 0)
 
  return positions;
}

References _map, TraitPrototype::get_index(), TraitPrototype::get_locus_number(), TraitPrototype::get_type(), GeneticMap::getLocusPositionTable(), is_mappable(), and is_mapped().

getGeneticMapRef()

static GeneticMap& TTProtoWithMap::getGeneticMapRef ( )

inlinestatic

{return _map;}

References _map.

Referenced by TTNeutralGenes_bitstring::inherit_low().

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getMapIndex()

unsigned int TTProtoWithMap::getMapIndex ( )

inline

{return _mapIndex;}

References _mapIndex.

getRecombRate()

double TTProtoWithMap::getRecombRate ( ) const

inline

{return _recombRate;}

References _recombRate.

is_mappable()

virtual bool TTProtoWithMap::is_mappable ( )

inlinevirtual

Checks if the trait is mappable, i.e., if the loci can be placed on a genetic map.

Implements TraitPrototype.

{return true;}

Referenced by get_locus_map_positions().

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is_mapped()

virtual bool TTProtoWithMap::is_mapped ( )

inlinevirtual

Checks if the trait's loci are placed on a genetic map.

Implements TraitPrototype.

{return _map.checkRegisteredTrait(this->get_type());}

References _map, GeneticMap::checkRegisteredTrait(), and TraitPrototype::get_type().

Referenced by get_locus_map_positions().

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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 TProtoQuanti::setGeneticMapParams(), TProtoBDMI::setParameters(), and TProtoNeutralGenes::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 TProtoQuanti, TProtoNeutralGenes, and TProtoDeletMutations_bitstring.

{ 
  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,
		unsigned int	numLoci = 0
	)

{
  TMatrix tmp_matx;
  bool map_set = false;
 
  _paramPrefix = prefix;
 
  string param_name;
 
  _numLoci = numLoci ? 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\" (%i) different from number of loci (%i) for trait \"%s\"\n",
                       prefix.c_str(), length, _numLoci, 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", prefix.c_str(), 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 TProtoQuanti::setGeneticMapParams(), TProtoBDMI::setParameters(), TProtoDeletMutations_bitstring::setParameters(), and TProtoNeutralGenes::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;
      
//      cout << "chrm "<<i<<" loc "<<j<<" pos: "<<_lociMapPositions[stride + j]<<endl;
    }
    
    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(), GenotyperFH::FHwrite(), get_locus_map_positions(), getGeneticMapRef(), TProtoBDMI::inherit_low(), TProtoDeletMutations_bitstring::inherit_low(), TProtoQuanti::inherit_low(), TProtoNeutralGenes::inherit_low(), is_mapped(), GenotyperFH::print_PLINK(), recombine(), recordRandomMap(), registerGeneticMap(), reset(), TTQuantiFH::setOutputOption(), unregisterFromGeneticMap(), TTNeutralGenesFH::write_PLINK(), and TTQuantiFH::write_PLINK().

_mapIndex

unsigned int TTProtoWithMap::_mapIndex

protected

Referenced by getMapIndex(), TProtoBDMI::inherit_low(), 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 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 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 getRecombRate(), setGeneticMapParameters(), TProtoQuanti::setGeneticMapParams(), TProtoBDMI::setParameters(), and TProtoNeutralGenes::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