Interface to all basic components of a simulation (traits, life cycle events, pop, etc. ). More...

#include <simcomponent.h>

Inheritance diagram for SimComponent:

Collaboration diagram for SimComponent:

Public Member Functions
	SimComponent ()
virtual	~SimComponent ()
Services interface
virtual void	loadFileServices (FileServices *loader)=0
	Loads the component's FileHandler onto the FileServices.
virtual void	loadStatServices (StatServices *loader)=0
	Loads the component's StatHandler onto the StatServices.
virtual void	loadUpdaters (UpdaterServices *loader)
	Loads the parameters and component updater onto the updater manager.
Parameters handling
virtual bool	setParameters ()=0
	Default interface needed to initialize the component's variables from its input parameters value.
virtual void	set_paramset (ParamSet *paramset)
	Sets the ParamSet member.
virtual void	set_paramset (std::string name, bool required, SimComponent *owner)
	Sets a new ParamSet and name it.
virtual void	set_paramsetFromCopy (const ParamSet &PSet)
	Reset the set of parameters from a another set.
virtual ParamSet *	get_paramset ()
	ParamSet accessor.
virtual void	add_parameter (Param *param)
	Interface to add a parameter to the set.
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.
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.
virtual Param *	get_parameter (std::string name)
	Param getter.
virtual double	get_parameter_value (std::string name)
	Param value getter.
virtual string	get_name ()
	Returnd the name of the ParamSet, i.e.
Protected Attributes
ParamSet *	_paramSet
	The parameters container.

Detailed Description

Interface to all basic components of a simulation (traits, life cycle events, pop, etc. ).

Implements the interface to handle the files and stats handler, the parameter updaters, and the parameters container. Contains the component's parameters and declares the interface to interact with its parameters.

Definition at line 45 of file simcomponent.h.

Constructor & Destructor Documentation

SimComponent::SimComponent ( ) [inline]

Definition at line 52 of file simcomponent.h.

: _paramSet(0) {}//{ cout << "calling SimComponent()" << endl;}

virtual SimComponent::~SimComponent ( ) [inline, virtual]

Definition at line 54 of file simcomponent.h.

References _paramSet.

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

Member Function Documentation

virtual void SimComponent::add_parameter ( Param * param ) [inline, virtual]

Interface to add a parameter to the set.

Parameters:

param The parameter to add to the set

Definition at line 112 of file simcomponent.h.

References _paramSet, and ParamSet::add_param().

Referenced by BinaryDataSaver::BinaryDataSaver(), LCE_Breed_base::LCE_Breed_base(), LCE_Breed_Disperse::LCE_Breed_Disperse(), LCE_Breed_Selection_Disperse::LCE_Breed_Selection_Disperse(), LCE_Breed_Wolbachia::LCE_Breed_Wolbachia(), LCE_Disperse_base::LCE_Disperse_base(), LCE_Disperse_EvolDisp::LCE_Disperse_EvolDisp(), LCE_QuantiInit::LCE_QuantiInit(), LCE_Resize::LCE_Resize(), LCE_Selection_base::LCE_Selection_base(), LCE_StatServiceNotifier::LCE_StatServiceNotifier(), Metapop::Metapop(), LifeCycleEvent::set_paramset(), TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring(), TProtoNeutralGenes::TProtoNeutralGenes(), and TProtoWolbachia::TProtoWolbachia().

{_paramSet->add_param(param);}

virtual void SimComponent::add_parameter	(	std::string	Name,
		param_t	Type,
		bool	isRequired,
		bool	isBounded,
		double	low_bnd,
		double	up_bnd
	)		`[inline, virtual]`

Interface to add a parameter to the set.

Parameters:

Name	The param string name as read in the init file
Type	The type of the argument (DBL=double, INT=integer, BOOL=boolean, STR=string, etc., see type.h)
isRequired	True if the parameter is mandatory
isBounded	True if the parameter takes bounded values as argument
low_bnd	The lower value the argument can take
up_bnd	The upper value the argument can take

Definition at line 121 of file simcomponent.h.

References _paramSet, and ParamSet::add_param().

  {_paramSet->add_param(Name, Type, isRequired, isBounded, low_bnd, up_bnd, 0);}

virtual void SimComponent::add_parameter	(	std::string	Name,
		param_t	Type,
		bool	isRequired,
		bool	isBounded,
		double	low_bnd,
		double	up_bnd,
		ParamUpdaterBase *	updater
	)		`[inline, virtual]`

Interface to add a parameter and its updater to the set.

Parameters:

Name	The param string name as read in the init file
Type	The type of the argument (DBL=double, INT=integer, BOOL=boolean, STR=string, etc., see type.h)
isRequired	True if the parameter is mandatory
isBounded	True if the parameter takes bounded values as argument
low_bnd	The lower value the argument can take
up_bnd	The upper value the argument can take
updater	a pointer to a ParamUpdaterBase object used to reset its value during a simulation

Definition at line 133 of file simcomponent.h.

References _paramSet, and ParamSet::add_param().

  {_paramSet->add_param(Name, Type, isRequired, isBounded, low_bnd, up_bnd, updater);}

virtual string SimComponent::get_name ( ) [inline, virtual]

Returnd the name of the ParamSet, i.e.

the name of the component.

Definition at line 146 of file simcomponent.h.

References _paramSet, and ParamSet::getName().

{return _paramSet->getName();}

virtual Param* SimComponent::get_parameter ( std::string name ) [inline, virtual]

Param getter.

Asks the ParamSet to return a pointer to Param name.

See also:: ParamSet::get_param

Definition at line 139 of file simcomponent.h.

References _paramSet, and ParamSet::get_param().

Referenced by LCE_Resize::execute(), TProtoNeutralGenes::loadFileServices(), TProtoDeletMutations_bitstring::loadFileServices(), LCE_Breed_Wolbachia::loadFileServices(), LCE_Selection_base::set_sel_model(), LCE_Breed_base::setFecundity(), LCE_Breed_base::setMatingSystem(), BinaryDataSaver::setParameters(), LCE_Breed_Selection_Disperse::setParameters(), TProtoNeutralGenes::setParameters(), TProtoDeletMutations_bitstring::setParameters(), LCE_Selection_base::setParameters(), LCE_Breed_Wolbachia::setParameters(), LCE_Selection_base::setSelectionMatrix(), TProtoDeletMutations_bitstring::setSelectionParameters(), LCE_Breed_base::setSexRatio(), and LCE_Resize::updateParameters().

{return _paramSet->get_param(name);}

virtual double SimComponent::get_parameter_value ( std::string name ) [inline, virtual]

Param value getter.

Asks the ParamSet to return the value of Param name.

See also:: ParamSet::getValue

Definition at line 143 of file simcomponent.h.

References _paramSet, and ParamSet::getValue().

Referenced by LifeCycleEvent::get_rank(), LCE_Selection_base::set_sel_model(), LCE_Disperse_base::setBasicLatticeMatrix(), LCE_Breed_base::setFecundity(), LCE_Disperse_base::setLatticeMatrix(), LCE_Disperse_base::setLatticeReflectingMatrix(), LCE_Disperse_base::setLatticeTorrusMatrix(), LCE_Breed_base::setMatingSystem(), BinaryDataSaver::setParameters(), LCE_Breed_Disperse::setParameters(), TProtoWolbachia::setParameters(), LCE_Disperse_ConstDisp::setParameters(), LCE_Breed_Selection_Disperse::setParameters(), TProtoNeutralGenes::setParameters(), TProtoDeletMutations_bitstring::setParameters(), LCE_Resize::setParameters(), LCE_Breed_Wolbachia::setParameters(), LCE_Selection_base::setSelectionMatrix(), TProtoDeletMutations_bitstring::setSelectionParameters(), and LCE_Disperse_base::setSteppingStone1DMatrix().

{return _paramSet->getValue(name);}

virtual ParamSet* SimComponent::get_paramset ( ) [inline, virtual]

ParamSet accessor.

Definition at line 108 of file simcomponent.h.

References _paramSet.

Referenced by LCE_Resize::execute(), BinaryDataLoader::extractPop(), Metapop::loadPopFromTraitFile(), and LCE_StatServiceNotifier::loadStatServices().

{return _paramSet;}

virtual void SimComponent::loadFileServices ( FileServices * loader ) [pure virtual]

Loads the component's FileHandler onto the FileServices.

Parameters:

loader the file service

Implemented in LCE_Breed_Wolbachia, LCE_Breed, LCE_Resize, LCE_Selection_base, Metapop, TProtoDeletMutations_bitstring, TProtoNeutralGenes, LCE_Breed_Selection_Disperse, LCE_Cross, TProtoQuanti, LCE_StatServiceNotifier, LCE_Patch_Extinction, LCE_Breed_Selection, TProtoWolbachia, TProtoDispersal, LCE_Breed_Disperse, LCE_Disperse_base, LCE_Aging, LCE_FileServicesNotifier, BinaryDataSaver, LCE_Regulation, LCE_QuantiInit, and LCE_ParamUpdaterNotifier.

Referenced by FileServices::load().

virtual void SimComponent::loadStatServices ( StatServices * loader ) [pure virtual]

Loads the component's StatHandler onto the StatServices.

Parameters:

loader the stat service

Implemented in LCE_Breed_Wolbachia, LCE_Breed, LCE_Resize, LCE_Selection_base, Metapop, TProtoDeletMutations_bitstring, TProtoNeutralGenes, LCE_Breed_Selection_Disperse, LCE_Cross, TProtoQuanti, LCE_StatServiceNotifier, LCE_Patch_Extinction, LCE_Breed_Selection, TProtoWolbachia, TProtoDispersal, LCE_Breed_Disperse, LCE_Disperse_base, LCE_Aging, LCE_FileServicesNotifier, BinaryDataSaver, LCE_Regulation, LCE_QuantiInit, and LCE_ParamUpdaterNotifier.

Referenced by StatServices::load().

virtual void SimComponent::loadUpdaters ( UpdaterServices * loader ) [inline, virtual]

Loads the parameters and component updater onto the updater manager.

Parameters:

loader the updater manager

Reimplemented in LCE_ParamUpdaterNotifier.

Definition at line 68 of file simcomponent.h.

References _paramSet, UpdaterServices::attach(), and ParamSet::getUpdaters().

Referenced by UpdaterServices::load().

                                                         {
    list<ParamUpdaterBase*> updaters = _paramSet->getUpdaters();
    //remove duplicates:
    updaters.unique();
    for (list<ParamUpdaterBase*>::iterator u = updaters.begin(); u != updaters.end(); u++) {
      loader->attach( (*u) );
    }
  }

virtual void SimComponent::set_paramset ( ParamSet * paramset ) [inline, virtual]

Sets the ParamSet member.

Parameters:

paramset a pointer to a ParamSet object

Definition at line 86 of file simcomponent.h.

References _paramSet.

Referenced by LCE_Resize::execute(), Metapop::Metapop(), TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring(), TProtoNeutralGenes::TProtoNeutralGenes(), and TProtoWolbachia::TProtoWolbachia().

  { _paramSet = paramset; }

virtual void SimComponent::set_paramset	(	std::string	name,
		bool	required,
		SimComponent *	owner
	)		`[inline, virtual]`

Sets a new ParamSet and name it.

Parameters:

name	the name of the parameters container
required	tag whether the component is required to run a simulation
owner	a reference to the owner of the ParamSet (should be this).

Reimplemented in LifeCycleEvent.

Definition at line 93 of file simcomponent.h.

References _paramSet, ParamSet::setIsRequired(), ParamSet::setName(), and ParamSet::setOwner().

                                                                                  {
    if(_paramSet != NULL) delete _paramSet;
    _paramSet = new ParamSet(); 
    _paramSet->setName(name);
    _paramSet->setIsRequired(required);
    _paramSet->setOwner(owner);
  }

virtual void SimComponent::set_paramsetFromCopy ( const ParamSet & PSet ) [inline, virtual]

Reset the set of parameters from a another set.

Parameters:

PSet	the parameter set to copy parameters from

Definition at line 103 of file simcomponent.h.

References _paramSet.

Referenced by Metapop::loadPopFromTraitFile().

                                                           {
    if(_paramSet != NULL) delete _paramSet;
    _paramSet = new ParamSet(PSet); 
  }

virtual bool SimComponent::setParameters ( ) [pure virtual]

Default interface needed to initialize the component's variables from its input parameters value.

Formerly called 'init'.

Implemented in LCE_Breed_Wolbachia, LCE_Breed, LCE_Resize, LCE_Selection_base, TProtoDeletMutations_bitstring, TProtoNeutralGenes, LCE_Breed_Selection_Disperse, LCE_Cross, LCE_Disperse_EvolDisp, TProtoQuanti, LCE_StatServiceNotifier, Metapop, LCE_Patch_Extinction, LCE_Breed_Selection, LCE_Disperse_ConstDisp, TProtoDispersal, TProtoWolbachia, LCE_Breed_Disperse, LCE_Disperse_base, LCE_Aging, LCE_Breed_base, LCE_FileServicesNotifier, BinaryDataSaver, LCE_Regulation, LCE_QuantiInit, and LCE_ParamUpdaterNotifier.

Referenced by LifeCycleEvent::init().

Member Data Documentation

ParamSet* SimComponent::_paramSet [protected]

The parameters container.

Definition at line 48 of file simcomponent.h.

Referenced by add_parameter(), LCE_Resize::execute(), get_name(), get_parameter(), get_parameter_value(), get_paramset(), Metapop::init(), loadUpdaters(), LCE_Selection_base::set_fit_model(), set_paramset(), set_paramsetFromCopy(), LCE_Selection_base::set_sel_model(), LCE_Disperse_base::setIsland_PropagulePool_Matrix(), LCE_Disperse_base::setLatticeMatrix(), LCE_Breed_base::setMatingSystem(), LCE_Disperse_base::setParameters(), LCE_StatServiceNotifier::setParameters(), LCE_Disperse_EvolDisp::setParameters(), LCE_Resize::setParameters(), Metapop::setPatchCapacities(), Metapop::setPopulationParameters(), LCE_Selection_base::setSelectionMatrix(), TProtoDeletMutations_bitstring::setSelectionParameters(), Metapop::setSourceParameters(), LCE_Selection_base::setSpatialMatrix(), TProtoDeletMutations_bitstring::TProtoDeletMutations_bitstring(), TProtoNeutralGenes::TProtoNeutralGenes(), TProtoWolbachia::TProtoWolbachia(), LCE_Resize::updateParameters(), and ~SimComponent().

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

simcomponent.h

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation