TProtoDispersal Class Reference

Prototype of the evolving dispersal trait, defines the sex-specific trait type. More...

#include <ttdispersal.h>

Inheritance diagram for TProtoDispersal:

Collaboration diagram for TProtoDispersal:

Public Member Functions
	TProtoDispersal (sex_t sex)
	TProtoDispersal (const TProtoDispersal &TP)
virtual	~TProtoDispersal ()
bool	setNonRandom ()
bool	setRandom ()
bool	get_init_mode ()
TMatrix *	get_init_dist_params ()
string	get_init_dist ()
TraitPrototype implementations
virtual void	init ()
virtual void	reset ()
virtual TTDispersal *	hatch ()
virtual TProtoDispersal *	clone ()
virtual trait_t	get_type () const
virtual int	get_phenotype_dimension ()
	Returns the dimension of the phenotype of the trait (size of the array accessed with TTrait::getValue() More...
virtual int	get_allele_number ()
	Returns the number of allele per locus. More...
virtual int	get_locus_number ()
	Returns the number of locus. More...
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...
StorableComponent implementation
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
SimComponent implementation
virtual bool	setParameters ()
virtual void	loadFileServices (FileServices *loader)
virtual void	loadStatServices (StatServices *loader)
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)
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
double	_mut_rate
	The allelic mutation rate. More...
double	_mut_mean
	Mean mutation step. More...
double	_init_rate_fem
	Initial allele for female dispersal. More...
double	_init_rate_mal
	Initial allele for male dispersal. More...
string	_init_dist
TMatrix	_init_dist_param
bool	_init_random
sex_t	_gender
	The gender of the trait, will determine its type. More...
TTDispersalSH *	_stats
	The trait's type. More...

Additional Inherited Members
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 of the evolving dispersal trait, defines the sex-specific trait type.

Constructor & Destructor Documentation

TProtoDispersal() [1/2]

TProtoDispersal::TProtoDispersal

(

sex_t

sex

)

: _mut_rate(0), _mut_mean(0.2), _init_rate_fem(-1.0), _init_rate_mal(-1.0), _gender(sex), _stats(0)
{
//  _type = (_gender == FEM ? "fdisp" : "mdisp");
 
  set_paramset("dispersal", false, this);
  
  add_parameter("disp_mutation_rate",DBL,true,true,0,1);
  add_parameter("disp_mutation_mean",DBL,true,true,0,1);
  add_parameter("disp_init_rate",DBL,false,true,0,1);
  add_parameter("disp_init_rate_fem",DBL,false,true,0,1);
  add_parameter("disp_init_rate_mal",DBL,false,true,0,1);
  add_parameter("disp_init_distribution", STR, false, false, 0, 0);
  add_parameter("disp_init_dist_params", MAT, false, false, 0, 0);
}

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

Referenced by clone().

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TProtoDispersal() [2/2]

TProtoDispersal::TProtoDispersal

(

const TProtoDispersal &

TP

)

: _mut_rate(TP._mut_rate), _mut_mean(TP._mut_mean), _init_rate_fem(TP._init_rate_fem), 
  _init_rate_mal(TP._init_rate_mal), _gender(TP._gender), _stats(0)
{
  _paramSet = new ParamSet( *(TP._paramSet) ) ;
}

References SimComponent::_paramSet.

~TProtoDispersal()

TProtoDispersal::~TProtoDispersal ( )

virtual

{
  if(_stats != NULL) delete _stats;
}

References _stats.

Member Function Documentation

clone()

virtual TProtoDispersal* TProtoDispersal::clone ( )

inlinevirtual

Implements TraitPrototype.

{return new TProtoDispersal(*this);}

References TProtoDispersal().

get_allele_number()

virtual int TProtoDispersal::get_allele_number ( )

inlinevirtual

Returns the number of allele per locus.

Implements TraitPrototype.

{return 3;} // 3 > 2 means it's not di-allelic

get_init_dist()

string TProtoDispersal::get_init_dist ( )

inline

{return _init_dist;}

References _init_dist.

Referenced by TTDispersal::init_sequence().

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get_init_dist_params()

TMatrix* TProtoDispersal::get_init_dist_params ( )

inline

{return &_init_dist_param;}

References _init_dist_param.

Referenced by TTDispersal::init_sequence().

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get_init_mode()

bool TProtoDispersal::get_init_mode ( )

inline

{return _init_random;}

References _init_random.

Referenced by TTDispersal::init_sequence().

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get_locus_map_positions()

virtual vector< unsigned int > TProtoDispersal::get_locus_map_positions ( )

inlinevirtual

Returns the map positions of the loci in vector.

Implements TraitPrototype.

{return vector<unsigned int>(2,0);}

get_locus_number()

virtual int TProtoDispersal::get_locus_number ( )

inlinevirtual

Returns the number of locus.

Implements TraitPrototype.

{return 2;}

get_phenotype_dimension()

virtual int TProtoDispersal::get_phenotype_dimension ( )

inlinevirtual

Returns the dimension of the phenotype of the trait (size of the array accessed with TTrait::getValue()

Implements TraitPrototype.

{return 1;}

get_type()

virtual trait_t TProtoDispersal::get_type ( ) const

inlinevirtual

Implements TraitPrototype.

{return (_gender == FEM ? FDISP : MDISP);}

References _gender, FDISP, FEM, and MDISP.

hatch()

TTDispersal * TProtoDispersal::hatch ( )

virtual

Implements TraitPrototype.

{
  TTDispersal* new_trait = new TTDispersal(_gender);
  
  new_trait->set_mut_rate(_mut_rate);
  new_trait->set_mut_mean(_mut_mean);
  new_trait->set_init_rate_fem(_init_rate_fem);
  new_trait->set_init_rate_mal(_init_rate_mal);
  new_trait->set_gender(_gender);
//  new_trait->set_type(_type);
  new_trait->set_proto(this);
  
  return new_trait;
}

References _gender, _init_rate_fem, _init_rate_mal, _mut_mean, _mut_rate, TTDispersal::set_gender(), TTDispersal::set_init_rate_fem(), TTDispersal::set_init_rate_mal(), TTDispersal::set_mut_mean(), TTDispersal::set_mut_rate(), and TTDispersal::set_proto().

init()

virtual void TProtoDispersal::init ( )

inlinevirtual

{}

is_mappable()

virtual bool TProtoDispersal::is_mappable ( )

inlinevirtual

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

Implements TraitPrototype.

{return false;}

is_mapped()

virtual bool TProtoDispersal::is_mapped ( )

inlinevirtual

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

Implements TraitPrototype.

{return false;}

loadFileServices()

virtual void TProtoDispersal::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{}

loadStatServices()

void TProtoDispersal::loadStatServices ( StatServices *  loader )

virtual

Implements SimComponent.

{
  //allocate the stat handler
  if(_stats == NULL)
    _stats = new TTDispersalSH(this);
  if(_stats != NULL) loader->attach(_stats);
}

References _stats, and StatServices::attach().

reset()

virtual void TProtoDispersal::reset ( )

inlinevirtual

Implements TraitPrototype.

{}

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

retrieve_data()

virtual bool TProtoDispersal::retrieve_data ( BinaryStorageBuffer *  reader )

inlinevirtual

Implements StorableComponent.

{reader->read(&_gender, sizeof(sex_t));return true;}

References _gender, and BinaryStorageBuffer::read().

setNonRandom()

bool TProtoDispersal::setNonRandom

(

)

{
  
  Param* init_param = get_parameter("disp_init_rate");
  
  if(init_param->isSet()) {
    
    _init_rate_fem = init_param->getValue();
    
    _init_rate_mal = init_param->getValue();
    
  } else if (get_parameter("disp_init_rate_fem")->isSet() &&
             get_parameter("disp_init_rate_mal")->isSet()) {
    
    _init_rate_fem = get_parameter_value("disp_init_rate_fem");
  
    _init_rate_mal = get_parameter_value("disp_init_rate_mal");
  
  } else {
    error("dispersal trait init parameters not correctly set\n");
    error("note that \"disp_init_rate_fem\" and \"disp_init_rate_mal\" must be set together\n");
    return false;
  }
  
  _init_random = false;
  
  return true;
}

References _init_random, _init_rate_fem, _init_rate_mal, error(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getValue(), and Param::isSet().

Referenced by setParameters().

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setParameters()

bool TProtoDispersal::setParameters ( )

virtual

Implements SimComponent.

{
  _mut_rate = get_parameter_value("disp_mutation_rate");
  _mut_mean = get_parameter_value("disp_mutation_mean");
  
  if (( get_parameter("disp_init_rate")->isSet() || 
       get_parameter("disp_init_rate_fem")->isSet() || 
       get_parameter("disp_init_rate_mal")->isSet() ) )
  {
    
    if(get_parameter("disp_init_distribution")->isSet()) {
          warning("both \"disp_init_rate[...]\" and \"disp_init_distribution\" are set\n");
          warning("discarding \"disp_init_rate[...]\" parameters\n");
          return setRandom();
        }
    
    return setNonRandom();
    
  } else if (get_parameter("disp_init_distribution")->isSet()) {
  
    return setRandom();
    
  } else { //no init parameter specified
    
    Param* init_param = get_parameter("disp_init_distribution");
    
    init_param->setArg("uniform");
    init_param->setIsSet(true);
    
    init_param = get_parameter("disp_init_dist_params");
    
    init_param->setArg("{{0,0}}");
    init_param->setIsSet(true);
    
    return setRandom();
    
  }
  return true;
}

References _mut_mean, _mut_rate, SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::setArg(), Param::setIsSet(), setNonRandom(), setRandom(), and warning().

setRandom()

bool TProtoDispersal::setRandom

(

)

{
  
  Param *init_param = get_parameter("disp_init_distribution");
  
  if (init_param->isSet()) {
 
    if (!get_parameter("disp_init_dist_params")->isSet()) {
      error("parameter \"disp_init_distribution\" requires \"disp_init_dist_params\" to be set as well.\n");
      return false;
    } else {
      get_parameter("disp_init_dist_params")->getMatrix(&_init_dist_param);
    }
 
    _init_dist = init_param->getArg();
    
    
  } else { //this should not happen...
    error("something got wrong with the dispersal trait init distribution parameters\n");
    return false;
  }
  
  _init_random = true;
  
  return true;
}

References _init_dist, _init_dist_param, _init_random, error(), SimComponent::get_parameter(), Param::getArg(), Param::getMatrix(), and Param::isSet().

Referenced by setParameters().

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store_data()

virtual void TProtoDispersal::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

{saver->store(&_gender, sizeof(sex_t));}

References _gender, and BinaryStorageBuffer::store().

Member Data Documentation

_gender

sex_t TProtoDispersal::_gender

private

The gender of the trait, will determine its type.

Referenced by get_type(), hatch(), retrieve_data(), and store_data().

_init_dist

string TProtoDispersal::_init_dist

private

Referenced by get_init_dist(), and setRandom().

_init_dist_param

TMatrix TProtoDispersal::_init_dist_param

private

Referenced by get_init_dist_params(), and setRandom().

_init_random

bool TProtoDispersal::_init_random

private

Referenced by get_init_mode(), setNonRandom(), and setRandom().

_init_rate_fem

double TProtoDispersal::_init_rate_fem

private

Initial allele for female dispersal.

Referenced by hatch(), and setNonRandom().

_init_rate_mal

double TProtoDispersal::_init_rate_mal

private

Initial allele for male dispersal.

Referenced by hatch(), and setNonRandom().

_mut_mean

double TProtoDispersal::_mut_mean

private

Mean mutation step.

Referenced by hatch(), and setParameters().

_mut_rate

double TProtoDispersal::_mut_rate

private

The allelic mutation rate.

Referenced by hatch(), and setParameters().

_stats

TTDispersalSH* TProtoDispersal::_stats

private

The trait's type.

The trait's StatHandler.

Referenced by loadStatServices(), and ~TProtoDispersal().

---

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

• ttdispersal.h
• ttdispersal.cc