LifeCycleEvent Class Reference

Base class of the Life Cycle Events, declares the LCE interface. More...

#include <lifecycleevent.h>

Inheritance diagram for LifeCycleEvent:

Collaboration diagram for LifeCycleEvent:

Public Member Functions
	LifeCycleEvent (const char *name, const char *trait_link)
	Cstor. More...
virtual	~LifeCycleEvent ()
virtual void	init (Metapop *popPtr)
	Sets the pointer to the current Metapop and the trait link if applicable. More...
virtual bool	attach_trait (string trait)
virtual void	set_paramset (std::string name, bool required, SimComponent *owner)
virtual void	set_event_name (std::string &name)
	Set the name of the event (name of the ParamSet) and add the corresponding parameter to the set. More...
virtual void	set_event_name (const char *name)
virtual string &	get_event_name ()
	Accessor to the LCE's name. More...
virtual int	get_rank ()
	Accessor to the LCE rank in the life cycle. More...
virtual void	set_pop_ptr (Metapop *popPtr)
	Accessors for the population pointer. More...
virtual Metapop *	get_pop_ptr ()
LCE interface
virtual void	execute ()=0
	Execute the event on the pop. More...
virtual LifeCycleEvent *	clone ()=0
	Cloning interface. More...
virtual age_t	removeAgeClass ()=0
	Removes the returned age-class flag(s) from the current Metapop age-class flags. More...
virtual age_t	addAgeClass ()=0
	Adds the returned age-class flag(s) to the current Metapop age-class flags. More...
virtual age_t	requiredAgeClass ()=0
	Specifies what age-classes are required by the LCE to execute. More...
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_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

Protected Attributes
std::string	_event_name
	The param name to be read in the init file. More...
Metapop *	_popPtr
	The ptr to the current Metapop. More...
std::string	_LCELinkedTraitType
	The name of the linked trait. More...
int	_LCELinkedTraitIndex
	The index in the individual's trait table of the linked trait. More...
Protected Attributes inherited from SimComponent
ParamSet *	_paramSet
	The parameters container. More...

Detailed Description

Base class of the Life Cycle Events, declares the LCE interface.

A Life Cycle Event (LCE) is a population operator that modifies the state of the population at each iteration of the life cycle. It declares the execute() method that is called during the life cycle loop (Metapop::Cycle()). No interface is given to manage the periodicity of the event, the execute() method is called at each iteration. The periodicity check must thus be implemented in the derived class, within the exectute() method.

Each LCE has a link to the current Metapop instance and a link to a particular trait which are set by LifeCycleEvent::init() at simulation initialization time (called by Metapop::setLifeCycle() through Metapop::init() and SimRunner::setup()). The linked trait can be specified in the constructor by its type identifier (a character string literal) or later, at runtime. In the first case, the trait's index will be set by a call to IndFactory::getTraitIndex() at initialization (see LifeCycleEvent::init()). In the later case, the trait to link with must be specified at initialization time and LifeCycleEvent::init() must be overloaded. The linked trait type (or name) can then be specified by the user in the init file and set in the derived class init() method before explicitly calling LifeCycleEvent::init() which will set the linked trait's index (see LCE_Breed_Selection::init() for an example). That index is then used to easily access the given trait through the Individual interface (see Individual::getTrait()).

Each LCE also has a name by which it is called from the user's defined parameter file to specify when in the life cycle that particular event has to be executed. The position in the life cycle is the LCE's rank (i.e. the value given in input to the parameter "name"). As only one rank value is allowed per LCE, it is executed only once in the life cycle, this is a limitation that might be removed in future versions if need be!

The main action of an LCE is often to move individuals between populations, between age-classes or both. The changes done to the population age structure by a particular LCE are tracked through the removeAgeClass() and addAgeClass() interface methods called after each execution of an LCE. The metapopulation age flag is thus updated by these two functions.

Note: Overloading LifeCycleEvent::init(). If more than one trait is used by your LCE, think about overloading the init() function to allow the registration of several trait links within your derived LCE. The init() method will also be overloaded if you add additional parameters to the LCE's ParamSet. In any cases, LifeCycleEvent::init() MUST be called in your init() function to properly set the metapop pointer (unless you copy the code into your function...).

Note: the LCEs must be inited after a call to IndFactory::makePrototype() has been issued so that the trait links can be set!

Constructor & Destructor Documentation

LifeCycleEvent()

LifeCycleEvent::LifeCycleEvent ( const char *  name, const char *  trait_link  )

inline

Cstor.

Parameters

name	the name of the LCE as it must appear in the parameter input file
trait_link	the name of the linked trait used by this LCE

  : _popPtr(0), _LCELinkedTraitType(trait_link), _LCELinkedTraitIndex(-1)
  {
//    cout << "calling LifeCycleEvent("<<name<<","<<trait_link<<")\n";
    set_event_name(name);
  }

References set_event_name().

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~LifeCycleEvent()

virtual LifeCycleEvent::~LifeCycleEvent ( )

inlinevirtual

{ }

Member Function Documentation

addAgeClass()

virtual age_t LifeCycleEvent::addAgeClass ( )

pure virtual

Adds the returned age-class flag(s) to the current Metapop age-class flags.

Implemented in BinaryDataSaver, LCE_Breed, LCE_Breed_Disperse, LCE_Breed_Selection, LCE_Breed_Selection_Disperse, LCE_Disperse_base, LCE_Regulation, LCE_Aging, LCE_Patch_Extinction, LCE_Cross, LCE_Resize, LCE_QuantiInit, LCE_QuantiModifier, LCE_Breed_Quanti, LCE_Selection_base, LCE_ParamUpdaterNotifier, LCE_FileServicesNotifier, LCE_StatServiceNotifier, LCE_Init_BDMI, LCE_NtrlInit, and LCE_Breed_Wolbachia.

Referenced by Metapop::setCurrentAge().

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attach_trait()

virtual bool LifeCycleEvent::attach_trait ( string  trait )

inlinevirtual

  {
    _LCELinkedTraitType = trait;
    
    if(_LCELinkedTraitType.size() != 0) {
      
      _LCELinkedTraitIndex = _popPtr->getTraitIndex(_LCELinkedTraitType.c_str());
  
      if(_LCELinkedTraitIndex == -1) {
        return error("cannot attach trait \"%s\" to life cycle event \"%s\", trait has not been initiated.\n",
              _LCELinkedTraitType.c_str(), _event_name.c_str()); 
      }
    
    }
    
    return true;
  }

References _event_name, _LCELinkedTraitIndex, _LCELinkedTraitType, _popPtr, error(), and IndFactory::getTraitIndex().

Referenced by init().

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clone()

virtual LifeCycleEvent * LifeCycleEvent::clone ( )

pure virtual

Cloning interface.

Implemented in BinaryDataSaver, LCE_Breed, LCE_Breed_Disperse, LCE_Breed_Selection, LCE_Breed_Selection_Disperse, LCE_Disperse_ConstDisp, LCE_SeedDisp, LCE_Disperse_EvolDisp, LCE_Regulation, LCE_Aging, LCE_Patch_Extinction, LCE_Cross, LCE_Resize, LCE_QuantiInit, LCE_QuantiModifier, LCE_Breed_Quanti, LCE_Selection_base, LCE_ParamUpdaterNotifier, LCE_FileServicesNotifier, LCE_StatServiceNotifier, LCE_Init_BDMI, LCE_NtrlInit, and LCE_Breed_Wolbachia.

execute()

virtual void LifeCycleEvent::execute ( )

pure virtual

Execute the event on the pop.

Implemented in BinaryDataSaver, LCE_Breed, LCE_Breed_Disperse, LCE_Breed_Selection, LCE_Breed_Selection_Disperse, LCE_Disperse_ConstDisp, LCE_Disperse_EvolDisp, LCE_Regulation, LCE_Aging, LCE_Patch_Extinction, LCE_Cross, LCE_Resize, LCE_QuantiInit, LCE_QuantiModifier, LCE_Breed_Quanti, LCE_Selection_base, LCE_ParamUpdaterNotifier, LCE_FileServicesNotifier, LCE_StatServiceNotifier, LCE_Init_BDMI, LCE_NtrlInit, and LCE_Breed_Wolbachia.

get_event_name()

virtual string & LifeCycleEvent::get_event_name ( )

inlinevirtual

Accessor to the LCE's name.

  { return _event_name; }

References _event_name.

get_pop_ptr()

virtual Metapop * LifeCycleEvent::get_pop_ptr ( )

inlinevirtual

  { return _popPtr; }

References _popPtr.

Referenced by LCE_ParamUpdaterNotifier::execute(), and LCE_FileServicesNotifier::execute().

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get_rank()

virtual int LifeCycleEvent::get_rank ( )

inlinevirtual

Accessor to the LCE rank in the life cycle.

  { return (int)get_parameter_value(_event_name.c_str()); }

References _event_name, and SimComponent::get_parameter_value().

Referenced by BinaryDataSaver::FHwrite(), BinaryDataSaver::setParameters(), and LCE_StatServiceNotifier::setParameters().

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init()

virtual void LifeCycleEvent::init ( Metapop *  popPtr )

inlinevirtual

Sets the pointer to the current Metapop and the trait link if applicable.

DEV: Don't forget to explicitly call this function (LifeCycleEvent::init()) when you overload it!

Parameters

popPtr

the pointer to the current instance of Metapop

  { 
    _popPtr = popPtr;
    if(!attach_trait(_LCELinkedTraitType)) fatal("bailing out\n");
    if(!setParameters()) fatal("bailing out\n");
  }

References _LCELinkedTraitType, _popPtr, attach_trait(), fatal(), and SimComponent::setParameters().

Referenced by SimRunner::init_components().

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removeAgeClass()

virtual age_t LifeCycleEvent::removeAgeClass ( )

pure virtual

Removes the returned age-class flag(s) from the current Metapop age-class flags.

Implemented in BinaryDataSaver, LCE_Breed, LCE_Breed_Disperse, LCE_Breed_Selection, LCE_Breed_Selection_Disperse, LCE_Disperse_base, LCE_Regulation, LCE_Aging, LCE_Patch_Extinction, LCE_Cross, LCE_Resize, LCE_QuantiInit, LCE_QuantiModifier, LCE_Breed_Quanti, LCE_Selection_base, LCE_ParamUpdaterNotifier, LCE_FileServicesNotifier, LCE_StatServiceNotifier, LCE_Init_BDMI, LCE_NtrlInit, and LCE_Breed_Wolbachia.

Referenced by Metapop::setCurrentAge().

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requiredAgeClass()

virtual age_t LifeCycleEvent::requiredAgeClass ( )

pure virtual

Specifies what age-classes are required by the LCE to execute.

Implemented in BinaryDataSaver, LCE_Breed, LCE_Breed_Disperse, LCE_Breed_Selection, LCE_Breed_Selection_Disperse, LCE_Disperse_base, LCE_Regulation, LCE_Aging, LCE_Patch_Extinction, LCE_Cross, LCE_Resize, LCE_QuantiInit, LCE_QuantiModifier, LCE_Breed_Quanti, LCE_Selection_base, LCE_ParamUpdaterNotifier, LCE_FileServicesNotifier, LCE_StatServiceNotifier, LCE_Init_BDMI, LCE_NtrlInit, and LCE_Breed_Wolbachia.

set_event_name() [1/2]

virtual void LifeCycleEvent::set_event_name ( const char *  name )

inlinevirtual

  {
    _event_name = name;
    set_paramset(name, 0, this); 
  }

References _event_name, and set_paramset().

set_event_name() [2/2]

virtual void LifeCycleEvent::set_event_name ( std::string &  name )

inlinevirtual

Set the name of the event (name of the ParamSet) and add the corresponding parameter to the set.

  {
    _event_name = name;
    set_paramset(name, 0, this);
  }

References _event_name, and set_paramset().

Referenced by LCE_SeedDisp::LCE_SeedDisp(), and LifeCycleEvent().

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set_paramset()

virtual void LifeCycleEvent::set_paramset ( std::string  name, bool  required, SimComponent *  owner  )

inlinevirtual

Reimplemented from SimComponent.

  {
    SimComponent::set_paramset(name, required, owner);
    add_parameter(name.c_str(),INT,1,0,0,0,0);
  }

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

Referenced by set_event_name().

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set_pop_ptr()

virtual void LifeCycleEvent::set_pop_ptr ( Metapop *  popPtr )

inlinevirtual

Accessors for the population pointer.

Parameters

popPtr

The pointer to the current Metapop

  {_popPtr = popPtr;}

References _popPtr.

Member Data Documentation

_event_name

std::string LifeCycleEvent::_event_name

protected

The param name to be read in the init file.

Referenced by attach_trait(), get_event_name(), get_rank(), set_event_name(), and LCE_Selection_base::setParameters().

_LCELinkedTraitIndex

int LifeCycleEvent::_LCELinkedTraitIndex

protected

The index in the individual's trait table of the linked trait.

A value of -1 means the link is broken.

Referenced by LCE_Selection_base::addPhenotypicSD(), attach_trait(), LCE_Breed_Wolbachia::hasInfectedFemale(), LCE_NtrlInit::init_allele_freq(), LCE_QuantiInit::init_allele_freq(), LCE_QuantiInit::init_trait_value(), LCE_Init_BDMI::init_value(), LCE_Breed_Wolbachia::inoculate_wolbachia(), LCE_QuantiModifier::setIndPhenotype(), LCE_Breed_Quanti::setIndPhenotype(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().

_LCELinkedTraitType

std::string LifeCycleEvent::_LCELinkedTraitType

protected

The name of the linked trait.

Referenced by attach_trait(), and init().

_popPtr

Metapop* LifeCycleEvent::_popPtr

protected

The ptr to the current Metapop.

Referenced by LCE_Selection_base::addPhenotypicSD(), attach_trait(), LCE_Breed_base::breed(), LCE_Breed_base::breed_cloning(), LCE_Breed_Selection_Disperse::breed_selection_disperse(), LCE_Resize::buildNewPatchArrayNoBackup(), LCE_Resize::buildNewPatchArrayWithBackup(), LCE_Breed_base::checkCloning(), LCE_Breed_base::checkSelfing(), LCE_Cross::create_individual_ancestors(), LCE_Breed_Disperse::do_breed_disperse(), LCE_Patch_Extinction::do_flush(), LCE_Patch_Extinction::do_remove(), LCE_Selection_base::doViabilitySelection(), LCE_Disperse_EvolDisp::evoldisp(), BinaryDataSaver::execute(), LCE_Breed::execute(), LCE_Breed_Disperse::execute(), LCE_Breed_Selection::execute(), LCE_Breed_Selection_Disperse::execute(), LCE_Disperse_ConstDisp::execute(), LCE_Disperse_EvolDisp::execute(), LCE_Regulation::execute(), LCE_Aging::execute(), LCE_Patch_Extinction::execute(), LCE_Cross::execute(), LCE_Resize::execute(), LCE_QuantiInit::execute(), LCE_QuantiModifier::execute(), LCE_Breed_Quanti::execute(), LCE_Selection_base::execute(), LCE_ParamUpdaterNotifier::execute(), LCE_Init_BDMI::execute(), LCE_NtrlInit::execute(), LCE_Breed_Wolbachia::execute(), LCE_Resize::fillPatchNoBackup(), LCE_Resize::fillPatchWithBackup(), LCE_Resize::fillPop(), BinaryDataSaver::finish(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Cross::generatePedigree(), LCE_Breed_Disperse::get_parent(), get_pop_ptr(), LCE_Selection_base::getMaxFitness(), LCE_Selection_base::getMaxPatchFitness(), LCE_Selection_base::getMeanFitness(), LCE_Selection_base::getMeanPatchFitness(), LCE_Breed_Wolbachia::hasInfectedFemale(), init(), LCE_NtrlInit::init_allele_freq(), LCE_QuantiInit::init_allele_freq(), LCE_QuantiInit::init_trait_value(), LCE_Init_BDMI::init_value(), LCE_Breed_Wolbachia::inoculate_wolbachia(), LCE_FileServicesNotifier::loadFileServices(), LCE_Breed_Selection::makeOffspringWithSelection(), LCE_Breed_Disperse::mate_full_selfing(), LCE_Breed_Disperse::mate_random(), LCE_Breed_Disperse::mate_random_hermaphrodite(), LCE_Breed_Disperse::mate_selfing(), LCE_Disperse_ConstDisp::Migrate(), LCE_Disperse_ConstDisp::MigratePatch(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), LCE_Disperse_ConstDisp::MigratePatchByNumber(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), BinaryDataSaver::printOffsetTable(), LCE_Resize::regulate(), LCE_Resize::regulateAgeClassNoBackup(), LCE_Regulation::regulatePatch(), LCE_Resize::removeDesignatedPatch(), LCE_Disperse_base::reset_counters(), LCE_Cross::sampleAmongPop(), LCE_Cross::sampleWithinPop(), LCE_Selection_base::set_local_optima(), LCE_Patch_Extinction::set_matrix_param(), LCE_Selection_base::set_param_rate_of_change(), set_pop_ptr(), LCE_Selection_base::set_sel_model(), LCE_Selection_base::set_std_rate_of_change(), LCE_Disperse_base::setBaseParameters(), LCE_Breed_base::setFecundity(), LCE_Breed_base::setMatingSystem(), LCE_Breed_Selection::setNonSelectedTraitTable(), BinaryDataSaver::setParameters(), LCE_Breed_Disperse::setParameters(), LCE_Disperse_EvolDisp::setParameters(), LCE_QuantiInit::setParameters(), LCE_QuantiModifier::setParameters(), LCE_Breed_Quanti::setParameters(), LCE_Selection_base::setParameters(), LCE_Init_BDMI::setParameters(), LCE_NtrlInit::setParameters(), LCE_Breed_Wolbachia::setParameters(), LCE_Disperse_base::setPropaguleTargets(), LCE_Selection_base::setSelectionMatrix(), LCE_Breed_Quanti::setVefromVa(), BinaryDataSaver::storeData(), LCE_Disperse_base::swapPostDisp(), LCE_Resize::updateParameters(), LCE_Resize::updatePatchCapacities(), LCE_Breed_Wolbachia::wolbachia_model_1(), LCE_Breed_Wolbachia::wolbachia_model_2(), LCE_Breed_base::WrightFisherPopulation(), and LCE_Breed_Quanti::WrightFisherPopulation().

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

• lifecycleevent.h