IndFactory Class Reference

Factory of Individual, stores the individual prototype and the trait prototypes, manages the individual garbage collector. More...

#include <indfactory.h>

Inheritance diagram for IndFactory:

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Collaboration diagram for IndFactory:

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List of all members.

Public Member Functions
	IndFactory ()
virtual	~IndFactory ()
void	recycle (Individual *ind)
	Put an individual in the recycling pool.
void	purgeRecyclingPOOL ()
	Empty the recycling pool.
void	makePrototype (map< trait_t, TraitPrototype * > TTlist)
	Creates the individuals prototype from the selected trait prototypes.
Individual *	getNewIndividual ()
	Creates a blank individual which has to be "decorated" later.
Individual *	makeNewIndividual (Individual *mother, Individual *father, sex_t sex, unsigned short homepatch)
	Creates an individual with pointers to parents, sex and home ID set but no genetic data.
Individual *	makeOffsprg (Individual *mother, Individual *father, sex_t sex, unsigned short homepatch)
	Completely creates an individual with inheritance and mutations on all traits.
Individual *	getIndividualProtoype ()
	Individual prototype accessor.
TraitPrototype *	getTraitPrototype (trait_t type)
	Accessor to a TraitPrototype.
std::map< trait_t, TraitPrototype * > &	getTraitPrototypes ()
	Accessor to the list of TraitPrototype's.
int	getTraitIndex (trait_t type)
	Gives the index of trait with type.
Protected Attributes
std::map< trait_t, TraitPrototype * >	_protoTraits
	Map of the trait prototypes.
std::map< trait_t, int >	_TraitsIndex
	Table containing the index of each trait.
Individual	_protoIndividual
	The individuals prototype used to create any new individual in a simulation.
std::deque< Individual * >	RecyclingPOOL
	Garbage collector for unused Individual's.

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Detailed Description

Factory of Individual, stores the individual prototype and the trait prototypes, manages the individual garbage collector.

Provides methods to generate new individuals within the Metapop. Each new individual is created by cloning a prototype itself created at the simulation setup. New individuals are decorated with the appropriate traits as set by the trait prototypes and receives a unique ID (unique within a simulation).

Definition at line 43 of file indfactory.h.

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Constructor & Destructor Documentation

IndFactory::IndFactory

(

)

[inline]

Definition at line 58 of file indfactory.h.

{ }; 

IndFactory::~IndFactory

(

)

[virtual]

Definition at line 36 of file indfactory.cc.

{
  purgeRecyclingPOOL(); 
  
  _protoIndividual.clearTraits(); 

// for(map< trait_t, TraitPrototype* >::iterator trait = _protoTraits.begin(); trait != _protoTraits.end();
//      trait++)
//    delete trait->second;
    
  _protoTraits.clear();
  
  _TraitsIndex.clear();
  
}

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Member Function Documentation

Individual* IndFactory::getIndividualProtoype

(

)

[inline]

Individual prototype accessor.

Definition at line 99 of file indfactory.h.

Referenced by LCE_Selection_base::setParameters().

{return &_protoIndividual;}

Individual* IndFactory::getNewIndividual

(

)

[inline]

Creates a blank individual which has to be "decorated" later.

ID is set and new traits are allocated but no genetic data is created (i.e. TTrait::init_sequence() is not called). Sex has to be set later too.

Definition at line 78 of file indfactory.h.

Referenced by LCE_Breed_base::breed_cloning(), Metapop::fillPatchFromSource(), Metapop::fillPopulationFromSource(), Metapop::loadPopFromBinarySource(), and Metapop::retrieve_data().

{return makeNewIndividual(NULL,NULL,MAL,0);}

int IndFactory::getTraitIndex

(

trait_t

type

)

Gives the index of trait with type.

Parameters:

type

the type of the trait (i.e. its "name")

Definition at line 91 of file indfactory.cc.

Referenced by LifeCycleEvent::attach_trait(), TTDispersalSH::init(), and LCE_Disperse_EvolDisp::setParameters().

{
  map< trait_t, int >::iterator trait = _TraitsIndex.find(type);
  
  if(trait == _TraitsIndex.end())
    return -1;
  
  return trait->second;
}

TraitPrototype * IndFactory::getTraitPrototype

(

trait_t

type

)

Accessor to a TraitPrototype.

Parameters:

type

the trait name

Definition at line 103 of file indfactory.cc.

{
  map< trait_t, TraitPrototype* >::iterator trait = _protoTraits.find(type);
  
  if(trait == _protoTraits.end())
    return NULL;
  
  return trait->second;
  
}

std::map< trait_t,TraitPrototype* >& IndFactory::getTraitPrototypes

(

)

[inline]

Accessor to the list of TraitPrototype's.

Definition at line 105 of file indfactory.h.

Referenced by Metapop::loadPopFromTraitFile(), and Metapop::store_data().

{return _protoTraits;}

Individual * IndFactory::makeNewIndividual	(	Individual *	mother,
		Individual *	father,
		sex_t	sex,
		unsigned short	homepatch
	)

Creates an individual with pointers to parents, sex and home ID set but no genetic data.

No inheritance or mutations on the trait sequences are done. Sets the pedigree class of the individual. Calls Individual::init() to allocate traits' sequences memory if individual is cloned from the prototype. Otherwise, calls Individual::reset() if the new individual is coming from the recycling pool.

Parameters:

	mother	ptr to the mother
	father	ptr to the father
	sex	gender of the individual
	homepatch	ID of the Patch where this individual is born, usually the current position in the Metapop::vPatch array.

Definition at line 116 of file indfactory.cc.

Referenced by LCE_Breed_base::breed(), LCE_Breed_base::breed_cloning(), TTNeutralGenesFH::FHread(), TTDeletMutBitstrFH::FHread(), LCE_Resize::fillPatchNoBackup(), getNewIndividual(), makeOffsprg(), LCE_Breed_Disperse::mate_full_selfing(), LCE_Breed_Disperse::mate_random(), LCE_Breed_Disperse::mate_random_hermaphrodite(), LCE_Breed_Disperse::mate_selfing(), and Patch::setNewGeneration().

{
  Individual* newind;

  if(RecyclingPOOL.empty()) {
        //create new Individual by cloning the proto-individual
        newind = _protoIndividual.clone();
        //allocate memory for the traits' sequences:
        newind->init();
  } else {
        //recycle an Individual from the POOL
        newind = RecyclingPOOL[0];
        RecyclingPOOL.pop_front();
        newind->reset();
        newind->setID(Individual::currentID++);
  }
  
  newind->setSex(sex);
  newind->setHome(homepatch);
  if(mother != NULL && father != NULL) {
        newind->setFatherID(father->getID());
        newind->setMotherID(mother->getID());
        newind->setFather(father);
        newind->setMother(mother);
    newind->setPedigreeClass(mother, father);
  }
  
  return newind;
}

Individual * IndFactory::makeOffsprg	(	Individual *	mother,
		Individual *	father,
		sex_t	sex,
		unsigned short	homepatch
	)

Completely creates an individual with inheritance and mutations on all traits.

Calls makeNewIndividual() to get the new offspring.

Parameters:

	mother	ptr to the mother
	father	ptr to the father
	sex	gender of the individual
	homepatch	ID of the Patch where this individual is born, usually the current position in the Patch array

Definition at line 148 of file indfactory.cc.

Referenced by LCE_Cross::execute(), and LCE_Breed_Wolbachia::execute().

{  
  Individual* offspring = makeNewIndividual(mother,father,sex,homepatch);
  unsigned int cat = offspring->getPedigreeClass();
  mother->DidHaveABaby(cat);
  if(cat!=4) father->DidHaveABaby(cat);
  return offspring->create(mother, father);
}

void IndFactory::makePrototype

(

map< trait_t, TraitPrototype * >

TTlist

)

Creates the individuals prototype from the selected trait prototypes.

Resets the individual's ID counter to 0 and sets the traits index table.

Parameters:

TTlist

the list of the current trait prototype selected from the current simulation parameters.

Definition at line 54 of file indfactory.cc.

Referenced by BinaryDataLoader::extractPop(), SimRunner::init_components(), and Metapop::loadPopFromTraitFile().

{
#ifdef _DEBUG_
  message("IndFactory::makePrototype\n");
#endif
  //first, reset the ID counter:
  _protoIndividual.setCurrentID(0);
  //and clear the ttraits:
  _protoIndividual.clearTraits();
  //store the traits list for future use:
  _protoTraits = TTlist;
  //then add the traits from the trait prototypes:
  map< trait_t, TraitPrototype* >::iterator trait = TTlist.begin();

  _TraitsIndex.clear();
  int i = 0;
  
  while(trait != TTlist.end()) {
#ifdef _DEBUG_
    message("IndFactory::makePrototype::addTrait: %s\n",trait->first.c_str());
#endif
    //init the trait prototype, set attribute from input file parameters value
//    trait->second->init();
    if(!trait->second->setParameters()) fatal("bailing out from trait initialization\n");
    //set the prototype's index value
    trait->second->set_index(i);
    //create the trait and add it to the proto-individual
        _protoIndividual.addTrait(trait->second->hatch(),i);
    //store the trait's index into the index map
    _TraitsIndex[trait->first] = i++;
    trait++;
  }
  
}

void IndFactory::purgeRecyclingPOOL

(

)

[inline]

Empty the recycling pool.

Definition at line 66 of file indfactory.h.

Referenced by Metapop::init(), Metapop::setPopulation(), and ~IndFactory().

  { for(unsigned int i=0; i < RecyclingPOOL.size(); ++i) delete RecyclingPOOL[i]; RecyclingPOOL.clear(); }

void IndFactory::recycle

(

Individual *

ind

)

[inline]

Put an individual in the recycling pool.

Definition at line 62 of file indfactory.h.

Referenced by LCE_Selection_base::doViabilitySelection(), LCE_Disperse_EvolDisp::evoldisp(), LCE_Breed_Wolbachia::execute(), LCE_Disperse_EvolDisp::fixdisp(), Patch::flush(), LCE_Breed_Selection::makeOffspringWithSelection(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), LCE_Resize::regulateAgeClassNoBackup(), and LCE_Regulation::regulatePatch().

  { if(ind == NULL) error("IndFactory::recycle:ind is NULL!!\n"); else RecyclingPOOL.push_back(ind); }

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Member Data Documentation

Individual IndFactory::_protoIndividual [protected]

The individuals prototype used to create any new individual in a simulation.

Definition at line 51 of file indfactory.h.

Referenced by getIndividualProtoype(), makeNewIndividual(), makePrototype(), and ~IndFactory().

std::map< trait_t,TraitPrototype* > IndFactory::_protoTraits [protected]

Map of the trait prototypes.

Definition at line 46 of file indfactory.h.

Referenced by getTraitPrototype(), getTraitPrototypes(), makePrototype(), Metapop::retrieve_data(), and ~IndFactory().

std::map< trait_t, int > IndFactory::_TraitsIndex [protected]

Table containing the index of each trait.

Definition at line 48 of file indfactory.h.

Referenced by getTraitIndex(), makePrototype(), and ~IndFactory().

std::deque<Individual*> IndFactory::RecyclingPOOL [protected]

Garbage collector for unused Individual's.

Definition at line 54 of file indfactory.h.

Referenced by makeNewIndividual(), purgeRecyclingPOOL(), and recycle().

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

• indfactory.h
• indfactory.cc