TProtoWolbachia Class Reference

Prototype of the Wolbachia trait. More...

#include <ttwolbachia.h>

Inheritance diagram for TProtoWolbachia:

Collaboration diagram for TProtoWolbachia:

Public Member Functions
	TProtoWolbachia ()
	TProtoWolbachia (const TProtoWolbachia &)
	~TProtoWolbachia ()
virtual void	init ()
virtual void	reset ()
virtual bool	setParameters ()
virtual TTWolbachia *	hatch ()
virtual TProtoWolbachia *	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...
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
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	_transmit_rate
TTWolbachiaSH *	_stats

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 Wolbachia trait.

Constructor & Destructor Documentation

TProtoWolbachia() [1/2]

TProtoWolbachia::TProtoWolbachia

(

)

: _transmit_rate(0), _stats(0)
{
  set_paramset("wolbachia", false, this);
  add_parameter("wolbachia_transmission_rate",DBL,true,false,0,1);
}

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

Referenced by clone().

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TProtoWolbachia() [2/2]

TProtoWolbachia::TProtoWolbachia

(

const TProtoWolbachia &

TP

)

: _transmit_rate(TP._transmit_rate), _stats(0)
{
  _paramSet = new ParamSet( *(TP._paramSet) ) ;
}

References SimComponent::_paramSet.

~TProtoWolbachia()

TProtoWolbachia::~TProtoWolbachia

(

)

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

References _stats.

Member Function Documentation

clone()

virtual TProtoWolbachia* TProtoWolbachia::clone ( )

inlinevirtual

Implements TraitPrototype.

{return new TProtoWolbachia(*this);}

References TProtoWolbachia().

get_allele_number()

virtual int TProtoWolbachia::get_allele_number ( )

inlinevirtual

Returns the number of allele per locus.

Implements TraitPrototype.

{return 2;}

get_locus_map_positions()

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

inlinevirtual

Returns the map positions of the loci in vector.

Implements TraitPrototype.

{return vector<unsigned int>(1,0);}

get_locus_number()

virtual int TProtoWolbachia::get_locus_number ( )

inlinevirtual

Returns the number of locus.

Implements TraitPrototype.

{return 1;}

get_phenotype_dimension()

virtual int TProtoWolbachia::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 TProtoWolbachia::get_type ( ) const

inlinevirtual

Implements TraitPrototype.

{return WOLB;}

References WOLB.

hatch()

virtual TTWolbachia* TProtoWolbachia::hatch ( )

inlinevirtual

Implements TraitPrototype.

  {
    TTWolbachia* new_trait = new TTWolbachia();
    new_trait->set_transmit_rate(_transmit_rate);
    return new_trait;
  }

References _transmit_rate, and TTWolbachia::set_transmit_rate().

init()

virtual void TProtoWolbachia::init ( )

inlinevirtual

{}

is_mappable()

virtual bool TProtoWolbachia::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 TProtoWolbachia::is_mapped ( )

inlinevirtual

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

Implements TraitPrototype.

{return false;}

loadFileServices()

virtual void TProtoWolbachia::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{}

loadStatServices()

void TProtoWolbachia::loadStatServices ( StatServices *  loader )

virtual

Implements SimComponent.

{
  if(_stats != NULL)
    delete _stats;
  _stats = new TTWolbachiaSH(this);
  loader->attach(_stats);
}

References _stats, and StatServices::attach().

reset()

virtual void TProtoWolbachia::reset ( )

inlinevirtual

Implements TraitPrototype.

{}

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

retrieve_data()

virtual bool TProtoWolbachia::retrieve_data ( BinaryStorageBuffer *  reader )

inlinevirtual

Implements StorableComponent.

{return true;}

setParameters()

virtual bool TProtoWolbachia::setParameters ( )

inlinevirtual

Implements SimComponent.

  { _transmit_rate =  get_parameter_value("wolbachia_transmission_rate"); return true;}

References _transmit_rate, and SimComponent::get_parameter_value().

store_data()

virtual void TProtoWolbachia::store_data ( BinaryStorageBuffer *  saver )

inlinevirtual

Implements StorableComponent.

{/*we have nothing to save...*/}

Member Data Documentation

_stats

TTWolbachiaSH* TProtoWolbachia::_stats

private

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

_transmit_rate

double TProtoWolbachia::_transmit_rate

private

Referenced by hatch(), and setParameters().

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

• ttwolbachia.h
• ttwolbachia.cc