Individual Class Reference

This class contains traits along with other individual information (sex, pedigree, etc. ). More...

#include <individual.h>

Collaboration diagram for Individual:

Public Types
typedef int	IDX

Public Member Functions
	Individual ()
	~Individual ()
Individual *	init ()
	Inits parameters and traits. More...
void	reset ()
	Resets parameters and traits values. More...
void	show_up ()
	Write some info to stdout. More...
Individual *	clone ()
	Cloning procedure, clones all the traits present in the individual. More...
Setters
void	setID (unsigned long value)
void	setAge (unsigned short value)
void	Aging ()
void	setFatherID (unsigned long value)
void	setMotherID (unsigned long value)
void	setFather (Individual *f)
void	setMother (Individual *m)
void	setHome (unsigned short value)
void	setSex (sex_t sex)
void	setCurrentID (unsigned long value)
void	setIsSelfed (bool s)
void	setPedigreeClass (Individual *mother, Individual *father)
void	setPedigreeClass (unsigned char ped)
Getters
unsigned long	getID ()
unsigned short	getAge ()
unsigned long	getFatherID ()
unsigned long	getMotherID ()
Individual *	getFather ()
Individual *	getMother ()
unsigned short	getHome ()
sex_t	getSex ()
bool	isFemale ()
bool	getIsSelfed ()
unsigned long	getcurrentID ()
double	getFecundity ()
unsigned short	getMatings (unsigned int cat)
	Gives the number of matings that individual had with mates from a given pedigree class. More...
unsigned short	getLocalMatings ()
	Gives the number of times an individual mated with an individual from the same patch. More...
unsigned int	getTotMatings ()
	Gives the total number of matings of an individual. More...
unsigned short	getRealizedFecundity (unsigned int cat)
	Gives the number of surviving offspring for a given pedigree class of mating. More...
unsigned int	getLocalRealizedFecundity ()
	Gives the total number of surviving offspring when mating occures with mates of the same patch. More...
unsigned int	getTotRealizedFecundity ()
	Gives the total number of surviving offspring for all categories of mating. More...
unsigned int	getPedigreeClass ()
	Returns the pedigree class of the individual, as set during offspring creation. More...
unsigned int	getPedigreeClass (Individual *mother, Individual *father)
	Returns the pedigree class of two individuals. More...
implementation
void	store_data (BinaryStorageBuffer *saver)
void	retrieve_data (BinaryStorageBuffer *reader)
Matings and Fecundity
double	setFecundity (double value)
	Sets the fecundity to the value given and returns it. More...
void	reset_counters ()
	Resets the mating and fecundity counters. More...
void	addMating (unsigned int category)
	Increments the mating counter according to the pedigree class of the offspring. More...
void	DidHaveABaby (unsigned int category)
	Increments the mating and realized fecundity counters according to the pedigree class of the offspring. More...
double	getFecWithHomePatchMate ()
	Returns the proportion of succesfull local matings (i.e. More...
double	getFecWithOtherPatchMate ()
	Returns the proportion of successfull remote matings. More...
Trait interface
unsigned int	getTraitNumber ()
	Accessor to the size of the traits table. More...
std::deque< TTrait * > &	getTraits ()
	Accessot to the traits table itself. More...
void *	setTrait (IDX T, void *value)
	Sets the phenotype/value of a trait to a particular value. More...
void	setTraitValue (IDX T)
	Calls the value setting procedure of a particular trait. More...
void	setTraitValue ()
	Calls the value setting procedure of all traits present in an individual. More...
void *	getTraitValue (IDX T)
	Accessor to the value (phenotype) of a particular trait. More...
TTrait *	getTrait (IDX T)
	Trait accessor. More...
void	addTrait (TTrait *theTrait, IDX pos)
	Adds a trait to the table. More...
void	removeTrait (IDX T)
	Removes a trait from the table. More...
void	clearTraits ()
	Clears the traits container. More...
void	inheritTrait (IDX T, Individual *mother, Individual *father)
	Calls the inheritance procedure of a particular trait. More...
void	mutateTrait (IDX T)
	Calls the mutation procedure of a particular trait. More...
void	createTrait (IDX i, Individual *mother, Individual *father)
	Sets a particular trait's genotype and phenotype values from the two parents. More...
Individual *	createTrait (IDX i, bool do_inherit, bool do_mutate)
	Creates an individual's genotypes and phenotypes with optional recombination or mutations on one trait only. More...
Individual *	create_first_gen ()
	Creates an individual's genotypes and phenotypes for first generation. More...
Individual *	create ()
	Creates an individual's genotypes and phenotypes with recombination and mutations. More...
Individual *	create (bool do_inherit, bool do_mutate)
	Creates an individual's genotypes and phenotypes with optional recombination or mutations. More...
Individual *	create (Individual *mother, Individual *father)
	Creates an individual, inherit, mutate and set all its trait's values. More...
void	inherit (Individual *mother, Individual *father)
	Calls the inheritance procedure of all the traits present in the individual. More...
void	mutate ()
	Calls the mutation procedure of all the traits present in the individual. More...
void	recombine (unsigned long ID)
Operators
Individual &	operator= (const Individual &i)
	Assignment, make a deep copy of the parameter values and traits. More...
bool	operator== (const Individual &i)
	Only checks for traits equivalence. More...
bool	operator!= (const Individual &i)

Public Attributes
std::deque< TTrait * >	Traits
	The traits table. More...

Static Public Attributes
static unsigned long	currentID = 0
	The ID counter, reset at the beginning of each simulation. More...

Private Attributes
unsigned long	_id
	ID tag, unique for one simulation. More...
unsigned short	_age
	Age. More...
sex_t	_sex
	Sex tag. More...
unsigned long	_motherID
	Parents ID tags. More...
unsigned long	_fatherID
Individual *	_mother
	Parents pointers. More...
Individual *	_father
unsigned short	_home
	Natal Patch tag. More...
unsigned char	_pedigreeClass
	Pedigree class of the individual. More...
double	_fecundity
	Assigned fecundity. More...
unsigned short	_matings [5]
	Mating counter. More...
unsigned short	_realizedFecundity [5]
	Number of surviving offspring from the different mating categories (see matings). More...
unsigned int	_trait_nb
	Number of traits in the table. More...

Detailed Description

This class contains traits along with other individual information (sex, pedigree, etc. ).

The Individual class can be view as a trait container. It encapsulates the basic interface to manipulate the traits an individual is carrying like initialization, inheritance, mutation and phenotype getter. It also stores the basic individual info like its sex, pedigree (home Patch, mather and father id, etc.) and its mating and fecundity values. It is not a StorableComponent but declares a similar interface to store and retrieve all the previous info to/from a binary file. All individuals in a simulation are instantiated by a call to the IndFactory class (through its derived class Metapop) which contains the individual and traits prototypes.

Member Typedef Documentation

IDX

typedef int Individual::IDX

Constructor & Destructor Documentation

Individual()

Individual::Individual

(

)

: _age(0), _sex(MAL),_motherID(0),_fatherID(0),_mother(NULL),_father(NULL),
_home(0),_pedigreeClass(0),_fecundity(0),_trait_nb(0)
{
  _id = currentID++;
  for(unsigned int i = 0; i < 5; i++) {
    _matings[i] = 0; _realizedFecundity[i] = 0;
  }
}

References _id, _matings, _realizedFecundity, and currentID.

Referenced by clone().

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~Individual()

Individual::~Individual ( )

inline

{clearTraits();}

References clearTraits().

Member Function Documentation

addMating()

void Individual::addMating ( unsigned int  category )

inline

Increments the mating counter according to the pedigree class of the offspring.

Parameters

category

the pedigree class of the offspring

  { _matings[category]++; }

References _matings.

Referenced by LCE_Breed_Selection::makeOffspringWithSelection().

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addTrait()

void Individual::addTrait ( TTrait *  theTrait, IDX  pos  )

inline

Adds a trait to the table.

Parameters

theTrait	pointer to the trait to add
pos	the position where the trait should be added in the traits table. Used to check that the index of the trait in the table is correctly set.

See also

IndFactory::makePrototype

  { if((int)_trait_nb != pos)
    fatal("Individual::adding a trait to the wrong position (at %i, size %i)!\n",pos,_trait_nb);
    Traits.push_back(theTrait); _trait_nb++;
  }

References _trait_nb, fatal(), and Traits.

Referenced by clone().

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Aging()

void Individual::Aging ( )

inline

{_age++;}

References _age.

clearTraits()

void Individual::clearTraits ( )

inline

Clears the traits container.

  { if(_trait_nb != 0) {for(unsigned int i = 0; i < Traits.size(); ++i) delete Traits[i];
    Traits.clear(); _trait_nb = 0;}
  }

References _trait_nb, and Traits.

Referenced by ~Individual().

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clone()

Individual * Individual::clone

(

)

Cloning procedure, clones all the traits present in the individual.

{
  Individual* myClone = new Individual();
  
  for(unsigned int i = 0; i < _trait_nb; i++)
    myClone->addTrait(Traits[i]->clone(), i);
  
  return myClone;
}

References _trait_nb, addTrait(), Individual(), and Traits.

Referenced by IndFactory::getPrototypeClone(), and IndFactory::makeNewIndividual().

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create() [1/3]

Individual* Individual::create ( )

inline

Creates an individual's genotypes and phenotypes with recombination and mutations.

  { 
    inherit(_mother, _father);
    mutate();
    setTraitValue();
    return this;
  } 

References _father, _mother, inherit(), mutate(), and setTraitValue().

Referenced by LCE_Cross::create_individual_ancestors(), IndFactory::makeOffsprg(), and LCE_Breed_base::makeOffspring().

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create() [2/3]

Individual* Individual::create ( bool  do_inherit, bool  do_mutate  )

inline

Creates an individual's genotypes and phenotypes with optional recombination or mutations.

Parameters

do_inherit	if true, do traits inheritance and recombination
do_mutate	if true, performs mutation of the traits

  { 
    if(do_inherit) inherit(_mother, _father);
    if(do_mutate)  mutate();
    setTraitValue();
    return this;
  } 

References _father, _mother, inherit(), mutate(), and setTraitValue().

create() [3/3]

Individual* Individual::create ( Individual *  mother, Individual *  father  )

inline

Creates an individual, inherit, mutate and set all its trait's values.

Parameters

mother	the mother
father	the father

  { 
    if(!(mother && father))
      fatal("Individual::create::received null parents pointer!!!\n");
    TTrait *TT;
    recombine(_id);
    for(unsigned int i = 0; i < _trait_nb; i++) {
      TT = Traits[i];
      TT->inherit(mother->getTrait(i), father->getTrait(i));
      TT->mutate();
      TT->set_value();
    }
    return this;
  }

References _id, _trait_nb, fatal(), getTrait(), TTrait::inherit(), TTrait::mutate(), recombine(), TTrait::set_value(), and Traits.

create_first_gen()

Individual* Individual::create_first_gen ( )

inline

Creates an individual's genotypes and phenotypes for first generation.

  {
    for(unsigned int i = 0; i < _trait_nb; i++) {
      Traits[i]->init_sequence();
      Traits[i]->set_value();
    }
    //we have to set the parents ids otherwise the first offspring generation will be made of full sibs only.
    static unsigned long ID = std::numeric_limits< unsigned long >::max();
    _motherID = ID--;
    _fatherID = ID--;
    return this;
  }  

References _fatherID, _motherID, _trait_nb, and Traits.

Referenced by LCE_Cross::create_individual_ancestors(), and Patch::setNewGeneration().

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createTrait() [1/2]

Individual* Individual::createTrait ( IDX  i, bool  do_inherit, bool  do_mutate  )

inline

Creates an individual's genotypes and phenotypes with optional recombination or mutations on one trait only.

Parameters

i	the index of the trait in the traits' table
do_inherit	if true, does inheritance and recombination of the trait
do_mutate	if true, performs mutation of the trait

  {
    if(do_inherit) inheritTrait(i, _mother, _father);
    if(do_mutate)  mutateTrait(i);
    setTraitValue(i);
    return this;
  } 

References _father, _mother, inheritTrait(), mutateTrait(), and setTraitValue().

createTrait() [2/2]

void Individual::createTrait ( IDX  i, Individual *  mother, Individual *  father  )

inline

Sets a particular trait's genotype and phenotype values from the two parents.

Includes its inheritance, mutation and value setting.

Parameters

i	the index of the trait to create in the traits table
mother	the mother
father	the father

  { if(!(mother && father)) 
      fatal("Individual::create::received null pointer!!!\n");
    TTrait* T = Traits[i];
    recombine(_id);
    T->inherit(mother->getTrait(i),father->getTrait(i));
    T->mutate();  
    T->set_value();
  }

References _id, fatal(), getTrait(), TTrait::inherit(), TTrait::mutate(), recombine(), TTrait::set_value(), and Traits.

Referenced by LCE_Breed_Selection::makeOffspringWithSelection().

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DidHaveABaby()

void Individual::DidHaveABaby ( unsigned int  category )

inline

Increments the mating and realized fecundity counters according to the pedigree class of the offspring.

Parameters

category

the pedigree class of the offspring

  { _matings[category]++; _realizedFecundity[category]++; }

References _matings, and _realizedFecundity.

Referenced by IndFactory::makeOffsprg(), LCE_Breed_base::makeOffspring(), and LCE_Breed_Selection::makeOffspringWithSelection().

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getAge()

unsigned short Individual::getAge ( )

inline

{return _age;}

References _age.

Referenced by LCE_SelectionFH::print(), GenotyperFH::print_genotypes(), GenotyperFH::print_snp_genotypes(), and GenotyperFH::print_snp_id().

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getcurrentID()

unsigned long Individual::getcurrentID ( )

inline

{return currentID;}

References currentID.

getFather()

Individual* Individual::getFather ( )

inline

{return _father;}

References _father.

Referenced by LCE_Cross::create_individual_ancestors(), TTDeletMutBitstrFH::FHwrite(), LCE_Breed_base::makeOffspring(), LCE_Breed_Selection::makeOffspringWithSelection(), TTQuantiFH::print(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), and TTNeutralGenesFH::write_patch_TAB().

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getFatherID()

unsigned long Individual::getFatherID ( )

inline

{return _fatherID;}

References _fatherID.

Referenced by LCE_Cross::create_individual_ancestors(), MPFileHandler::createAndPrintSample(), TTDeletMutBitstrFH::FHwrite(), getPedigreeClass(), TTQuantiFH::print(), TTQuantiFH::print_PLINK_FAM(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), MPFileHandler::printNoSample(), MPStatHandler::setKinClassCounter(), TTNeutralGenesSH::setSibCoa(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), and TTNeutralGenesFH::write_patch_TAB().

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getFecundity()

double Individual::getFecundity ( )

inline

{return _fecundity;}

References _fecundity.

Referenced by MPStatHandler::getMeanAssignedFecundity().

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getFecWithHomePatchMate()

double Individual::getFecWithHomePatchMate ( )

inline

Returns the proportion of succesfull local matings (i.e.

those that survived selection).

  { 
    unsigned short mate = getLocalMatings();
    return (mate != 0 ? (double) getLocalRealizedFecundity()/mate : 0.0);
  }

References getLocalMatings(), and getLocalRealizedFecundity().

Referenced by TTDeletMutBitstrSH::getMeanFecWithPatchMate().

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getFecWithOtherPatchMate()

double Individual::getFecWithOtherPatchMate ( )

inline

Returns the proportion of successfull remote matings.

Returns

_realizedFecundity[0]/_matings[0]

  {
    return (_matings[0] != 0 ? (double) _realizedFecundity[0]/_matings[0] : 0.0);
  }

References _matings, and _realizedFecundity.

Referenced by TTDeletMutBitstrSH::getMeanFecWithPatchMate().

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getHome()

unsigned short Individual::getHome ( )

inline

{return _home;}

References _home.

Referenced by MPFileHandler::createAndPrintSample(), TTDeletMutBitstrFH::FHwrite(), getPedigreeClass(), TTQuantiFH::print(), LCE_SelectionFH::print(), TTQuantiFH::print_PLINK_FAM(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), MPFileHandler::printNoSample(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), and TTNeutralGenesFH::write_patch_TAB().

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getID()

unsigned long Individual::getID ( )

inline

{return _id;}

References _id.

Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), MPFileHandler::createAndPrintSample(), IndFactory::decorateNewIndividual(), TTDeletMutBitstrFH::FHwrite(), IndFactory::makeNewIndividual(), TTQuantiFH::print(), GenotyperFH::print_genotypes(), TTQuantiFH::print_PLINK_FAM(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), GenotyperFH::print_snp_genotypes(), GenotyperFH::print_snp_id(), MPFileHandler::printNoSample(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), and TTNeutralGenesFH::write_patch_TAB().

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getIsSelfed()

bool Individual::getIsSelfed ( )

inline

{return (_pedigreeClass == 4);}

References _pedigreeClass.

Referenced by MPStatHandler::setKinship().

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getLocalMatings()

unsigned short Individual::getLocalMatings ( )

inline

Gives the number of times an individual mated with an individual from the same patch.

  {
    return _matings[1]+_matings[2]+_matings[3]+_matings[4];
  }

References _matings.

Referenced by getFecWithHomePatchMate(), TTDeletMutBitstrSH::getMeanFecWithPatchMate(), and getTotMatings().

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getLocalRealizedFecundity()

unsigned int Individual::getLocalRealizedFecundity ( )

inline

Gives the total number of surviving offspring when mating occures with mates of the same patch.

  {
    return _realizedFecundity[1]+_realizedFecundity[2]+_realizedFecundity[3]+_realizedFecundity[4];
  }

References _realizedFecundity.

Referenced by getFecWithHomePatchMate(), and getTotRealizedFecundity().

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getMatings()

unsigned short Individual::getMatings ( unsigned int  cat )

inline

Gives the number of matings that individual had with mates from a given pedigree class.

Parameters

cat	the mating category (= the pedigree class of the offspring): 0 = mates are from different patches 1 = mates are from the same patch 2 = mates are half sib 3 = mates are full sib 4 = selfed mating

  {
    return _matings[cat];
  }

References _matings.

Referenced by TTDeletMutBitstrSH::getMeanFecWithPatchMate().

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getMother()

Individual* Individual::getMother ( )

inline

{return _mother;}

References _mother.

Referenced by LCE_Cross::create_individual_ancestors(), TTDeletMutBitstrFH::FHwrite(), LCE_Breed_base::makeOffspring(), LCE_Breed_Selection::makeOffspringWithSelection(), TTQuantiFH::print(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), and TTNeutralGenesFH::write_patch_TAB().

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getMotherID()

unsigned long Individual::getMotherID ( )

inline

{return _motherID;}

References _motherID.

Referenced by LCE_Cross::create_individual_ancestors(), MPFileHandler::createAndPrintSample(), TTDeletMutBitstrFH::FHwrite(), getPedigreeClass(), TTQuantiFH::print(), TTQuantiFH::print_PLINK_FAM(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), MPFileHandler::printNoSample(), MPStatHandler::setKinClassCounter(), TTNeutralGenesSH::setSibCoa(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), and TTNeutralGenesFH::write_patch_TAB().

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getPedigreeClass() [1/2]

unsigned int Individual::getPedigreeClass ( )

inline

Returns the pedigree class of the individual, as set during offspring creation.

  {
    return _pedigreeClass;
  }

References _pedigreeClass.

Referenced by LCE_Breed_Selection::do_breed_selection_FecFitness(), LCE_Selection_base::doViabilitySelection(), TTDeletMutBitstrFH::FHwrite(), LCE_Selection_base::getFitnessFixedEffect(), IndFactory::makeOffsprg(), LCE_Breed_base::makeOffspring(), LCE_Breed_Selection::makeOffspringWithSelection(), TTQuantiFH::print(), MPStatHandler::setPedegreeCount(), setPedigreeClass(), TTDeletMutBitstrSH::setViability(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), and TTNeutralGenesFH::write_patch_TAB().

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getPedigreeClass() [2/2]

unsigned int Individual::getPedigreeClass	(	Individual *	mother,
		Individual *	father
	)

Returns the pedigree class of two individuals.

Parameters

mother	the first individual (e.g.the mother of this individual)
father	the second individual (e.g. the father of this individual)

Returns

• 0 = mother and father are from different patches
• 1 = mother and father are from the same patch
• 2 = mother and father are half sib
• 3 = mother and father are full sib
• 4 = mother and father are the same individual (selfed offspring)

{
  if(mother == father) return 4; //selfed
 
  if(mother->getHome() != father->getHome()) return 0; //outbred between patch
  
  unsigned int mm,mf,fm,ff;
  //mother's parents:
  mm = mother->getMotherID();
  mf = mother->getFatherID();
  //father's parents:
  fm = father->getMotherID();
  ff = father->getFatherID();
 
  if(mm != fm && mf != ff) return 1; //outbred within patch
    
  else if((mm == fm && mf != ff) || (mm != fm && mf == ff)) return 2; //half sibs
    
  else return 3; //full sibs
}

References getFatherID(), getHome(), and getMotherID().

getRealizedFecundity()

unsigned short Individual::getRealizedFecundity ( unsigned int  cat )

inline

Gives the number of surviving offspring for a given pedigree class of mating.

Parameters

cat	the mating category: 0 = mates are from different patches 1 = mates are from the same patch 2 = mates are half sib 3 = mates are full sib 4 = selfed mating

  {
    return _realizedFecundity[cat];
  }

References _realizedFecundity.

getSex()

sex_t Individual::getSex ( )

inline

{return _sex;}

References _sex.

Referenced by LCE_Breed_Selection::do_breed_selection_FecFitness(), LCE_Breed_Selection::do_breed_selection_OffSurvival(), TTDeletMutBitstrFH::FHwrite(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), TTQuantiFH::print(), GenotyperFH::print_genotypes(), GenotyperFH::print_snp_genotypes(), GenotyperFH::print_snp_id(), Metapop::retrieve_data(), LCE_Breed_Wolbachia::wolbachia_model_1(), LCE_Breed_Wolbachia::wolbachia_model_2(), TTBDMI_FH::write_diplo(), and TTBDMI_FH::write_haplo().

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getTotMatings()

unsigned int Individual::getTotMatings ( )

inline

Gives the total number of matings of an individual.

  {
    return _matings[0] + getLocalMatings();
  }

References _matings, and getLocalMatings().

Referenced by LCE_BreedAssortativeMating::assortative_mating(), MPStatHandler::getMeanMatings(), TTDeletMutBitstrSH::getPatchLoad(), and LCE_BreedAssortativeMating::non_assortative_mating().

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getTotRealizedFecundity()

unsigned int Individual::getTotRealizedFecundity ( )

inline

Gives the total number of surviving offspring for all categories of mating.

{return _realizedFecundity[0] + getLocalRealizedFecundity( );}

References _realizedFecundity, and getLocalRealizedFecundity().

Referenced by TTDeletMutBitstrSH::getPatchLoad(), and MPStatHandler::setReproductiveStats().

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getTrait()

TTrait* Individual::getTrait ( IDX  T )

inline

Trait accessor.

Parameters

T	the trait's index in the traits table

Returns

the pointer to the trait

  { if( T == -1 || !(T < (int)_trait_nb) )
    fatal("Individual::Trying to access a trait not present in the traits table (at %i, size %i)\n",T,_trait_nb);
    return Traits[T]; 
  }

References _trait_nb, fatal(), and Traits.

Referenced by TTBDMI_SH::countAllele_diplo(), TTBDMI_SH::countAllele_haplo(), create(), createTrait(), TTDeletMutBitstrFH::FHread(), TTNeutralGenesFH::FHread(), TTQuantiFH::FHread(), TTDeletMutBitstrFH::FHwrite(), TTNOhtaStats::FHwrite(), TTQFreqExtractor::FHwrite(), TTQOhtaStats::FHwrite(), TTNeutralGenesSH::getDxyPerPatch(), TTQuantiSH::getSNPalleleFreqInPatch(), getTraitValue(), TTQuantiSH::getVaNoDominance(), TTQuantiSH::getVaWithDominance(), inherit(), inheritTrait(), LCE_NtrlInit::init_allele_freq(), LCE_QuantiInit::init_allele_freq(), LCE_QuantiInit::init_trait_value(), LCE_Init_BDMI::init_value(), mutateTrait(), GenotyperFH::prepare_data_table(), TTQuantiFH::print(), GenotyperFH::print_genotypes(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), GenotyperFH::print_snp_genotypes(), GenotyperFH::print_snp_id(), Metapop::read_trait(), TTNeutralGenesSH::setAdults_Theta(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setCoaMatrix(), TTDeletMutBitstrSH::setDeletStats(), TTNeutralGenesSH::setFstat_bitstring(), TTNeutralGenesSH::setFstatWeirCockerham_bitstring(), TTNeutralGenesSH::setHo(), TTNeutralGenesSH::setHo2(), LCE_PhenotypeExpression::setIndLiability(), LCE_PhenotypeExpression::setIndLiability_evolving(), LCE_PhenotypeExpression::setIndLiability_evolving_sigmoid(), LCE_PhenotypeExpression::setIndLiability_sigmoid(), LCE_PhenotypeExpression::setIndPhenotype(), LCE_PhenotypeExpression::setIndPhenotype_labile(), TTNeutralGenesSH::setSibCoa(), setTrait(), setTraitValue(), TTDeletMutBitstrSH::setViability(), store_quanti_trait_values(), Metapop::store_trait(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), and TTNeutralGenesFH::write_patch_TAB().

getTraitNumber()

unsigned int Individual::getTraitNumber ( )

inline

Accessor to the size of the traits table.

{ return _trait_nb;}

References _trait_nb.

Referenced by LCE_Breed_Selection::setNonSelectedTraitTable().

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getTraits()

std::deque<TTrait *>& Individual::getTraits ( )

inline

Accessot to the traits table itself.

Returns

the traits table (a deque)

{return Traits;}

References Traits.

getTraitValue()

void* Individual::getTraitValue ( IDX  T )

inline

Accessor to the value (phenotype) of a particular trait.

Parameters

T	the trait's index in the traits table

Returns

the trait's value, using the TTrait interface

  { return getTrait(T)->getValue(); }

References getTrait(), and TTrait::getValue().

Referenced by LCE_Selection_base::addPhenotypicSD(), LCE_BreedAssortativeMating::assortative_mating(), LCE_Disperse_EvolDisp::evoldisp(), LCE_Selection_base::getFitnessDirect(), LCE_Selection_base::getFitnessMultivariateDisruptive(), LCE_Selection_base::getFitnessMultivariateGaussian(), LCE_Selection_base::getFitnessMultivariateGaussian_VE(), LCE_Selection_base::getFitnessTruncation(), LCE_Selection_base::getFitnessUnivariateDisruptive(), LCE_Selection_base::getFitnessUnivariateGaussian(), LCE_Selection_base::getFitnessUnivariateGaussian_VE(), LCE_Selection_base::getFitnessUnivariateLinear(), LCE_Selection_base::getFitnessUnivariateQuadratic(), TTDispersalSH::getMeanDispRate(), TTDispersalSH::getMeanDispRateInPatch(), TTWolbachiaSH::getMeanFemaleInfection_perPatch(), TTDispersalSH::getMeanFemDispRate(), TTDispersalSH::getMeanMalDispRate(), TTWolbachiaSH::getMeanMaleInfection_perPatch(), TTWolbachiaSH::getMeanOffsprgFemaleInfection_perPatch(), TTWolbachiaSH::getMeanOffsprgInfection(), TTWolbachiaSH::getMeanOffsprgMaleInfection_perPatch(), TTDispersalSH::getOffsprgMeanDispRate(), LCE_Breed_Wolbachia::hasInfectedFemale(), TTQuantiFH::print_PLINK_FAM(), TTQuantiFH::print_PLINK_PED(), TTWolbachiaSH::setInfectionStats(), TTDeletMutBitstrSH::setMeanViability(), LCE_Selection_base::setScalingFactorForLinearSelection(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().

inherit()

void Individual::inherit ( Individual *  mother, Individual *  father  )

inline

Calls the inheritance procedure of all the traits present in the individual.

Parameters

mother	the mother
father	the father

  { 
    recombine(_id);
    for(unsigned int i = 0; i < _trait_nb; i++) 
      Traits[i]->inherit(mother->getTrait(i), father->getTrait(i)); 
  }

References _id, _trait_nb, getTrait(), recombine(), and Traits.

Referenced by create().

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inheritTrait()

void Individual::inheritTrait ( IDX  T, Individual *  mother, Individual *  father  )

inline

Calls the inheritance procedure of a particular trait.

Parameters

T	the trait's index in the traits table
mother	the mother
father	the father

  {  
    recombine(_id);
    getTrait(T)->inherit(mother->getTrait(T), father->getTrait(T)); 
  }

References _id, getTrait(), TTrait::inherit(), and recombine().

Referenced by createTrait().

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init()

Individual * Individual::init

(

)

Inits parameters and traits.

Called by IndFactory::makeNewIndividual() to allocate the traits' sequences memory.

{
  _age = 0;
  _pedigreeClass = 0;
  _motherID = 0;
  _fatherID = 0;
  _mother = NULL;
  _father = NULL;
  _home = 0;
 
  memset(&_matings[0],0, 5*sizeof(unsigned short));
  memset(&_realizedFecundity[0], 0, 5*sizeof(unsigned short));
  
  if(_trait_nb != Traits.size()){
    error("Individual::init: trait counter and table size differ, resetting\n");
    _trait_nb = Traits.size();
  }
  
  for(unsigned int i = 0; i < _trait_nb; i++)
    Traits[i]->init();
 
  return this;
}

References _age, _father, _fatherID, _home, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _trait_nb, error(), and Traits.

Referenced by LCE_Cross::generatePedigree(), and IndFactory::makeNewIndividual().

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isFemale()

bool Individual::isFemale ( )

inline

{return (_sex == FEM);}

References _sex, and FEM.

mutate()

void Individual::mutate ( )

inline

Calls the mutation procedure of all the traits present in the individual.

  { for(unsigned int i = 0; i < _trait_nb; i++) Traits[i]->mutate(); }

References _trait_nb, and Traits.

Referenced by create().

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mutateTrait()

void Individual::mutateTrait ( IDX  T )

inline

Calls the mutation procedure of a particular trait.

Parameters

T	trait's index in the traits table

  {  getTrait(T)->mutate(); }

References getTrait(), and TTrait::mutate().

Referenced by createTrait().

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operator!=()

bool Individual::operator!=

(

const Individual &

i

)

{
  if(!((*this) == i))
    return true;
  else
    return false;
}

operator=()

Individual & Individual::operator=

(

const Individual &

i

)

Assignment, make a deep copy of the parameter values and traits.

{
  if(this != &i) {  
    
    if(Traits.size() != i.Traits.size())
      fatal("Individual::operator=:not same number of traits in left and right sides of assignment\n");
 
    if(_trait_nb != i._trait_nb) {
      error("Individual::operator=:trait counters differ, resetting\n");
      _trait_nb = i._trait_nb;
    }
 
    _sex = i._sex;
    _age = i._age;
    _motherID = i._motherID;
    _fatherID = i._fatherID;
    _mother = i._mother;
    _father = i._father;
    _home = i._home;
    _pedigreeClass = i._pedigreeClass;
    _fecundity = i._fecundity;
 
    for(unsigned int j = 0; j < 5; j++) {
      _matings[j] = i._matings[j];
      _realizedFecundity[j] = i._realizedFecundity[j];
    }
 
    for(unsigned int t = 0; t < _trait_nb; t++){ 
 
      if(Traits[t]->get_type() != i.Traits[t]->get_type()) {
 
        fatal("Individual::operator=: not same kinds of traits on left and right sides of assignment\n");
 
      }
 
      (*Traits[t]) = (*i.Traits[t]);
    }
  }
  return *this;
}

References _age, _father, _fatherID, _fecundity, _home, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _sex, _trait_nb, error(), fatal(), and Traits.

operator==()

bool Individual::operator==

(

const Individual &

i

)

Only checks for traits equivalence.

{
  if(this != &i) {
    if(Traits.size() != i.Traits.size()) return false;
 
    for(unsigned int t = 0; t < Traits.size(); t++) {
      if((*Traits[t]) != (*i.Traits[t])) {
        return false;
      }
    }
 
  //if(_sex != i._sex) return false;
  }
  return true;
}

References Traits.

recombine()

void Individual::recombine ( unsigned long  ID )

inline

  {  TTProtoWithMap::recombine(ID); }

References TTProtoWithMap::recombine().

Referenced by create(), createTrait(), inherit(), and inheritTrait().

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removeTrait()

void Individual::removeTrait ( IDX  T )

inline

Removes a trait from the table.

Parameters

T	the trait's index in the traits table

  { delete Traits[T]; Traits.erase(Traits.begin() + T); _trait_nb--;}

References _trait_nb, and Traits.

reset()

void Individual::reset

(

)

Resets parameters and traits values.

Does not de-allocate the traits' sequences memory (i.e. is not calling TTrait::reset() on each trait).

{
  _id = 0;
  _age = 0;
  _sex = MAL;
  _pedigreeClass = 0;
  _motherID = 0;
  _fatherID = 0;
  _mother = NULL;
  _father = NULL;
  _home = 0;
 
  memset(&_matings[0],0, 5*sizeof(unsigned short));
  memset(&_realizedFecundity[0], 0, 5*sizeof(unsigned short));
   
//  if(_trait_nb != Traits.size()){
//    warning("Individual::reset: trait counter and table size differ, resetting\n");
//    _trait_nb = Traits.size();
//  }
}

References _age, _father, _fatherID, _home, _id, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _sex, and MAL.

Referenced by IndFactory::makeNewIndividual().

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reset_counters()

void Individual::reset_counters ( )

inline

Resets the mating and fecundity counters.

  { 
    for(unsigned int i = 0; i < 5; i++) {
      _matings[i] = 0; _realizedFecundity[i] = 0;
    } }

References _matings, and _realizedFecundity.

Referenced by LCE_Breed_base::breed_cloning().

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retrieve_data()

void Individual::retrieve_data

(

BinaryStorageBuffer *

reader

)

{
  reader->read(&_id, sizeof(unsigned long));
  reader->read(&_motherID, sizeof(unsigned long));
  reader->read(&_fatherID, sizeof(unsigned long));
  reader->read(&_sex, sizeof(sex_t));
  reader->read(&_home, sizeof(unsigned short));
  reader->read(&_matings, 2*sizeof(unsigned short));
  reader->read(&_realizedFecundity, 2*sizeof(unsigned short));
//reader->read(&_pedigreeClass, 1);
//reader->read(&_age, sizeof(unsigned short));
}

References _fatherID, _home, _id, _matings, _motherID, _realizedFecundity, _sex, and BinaryStorageBuffer::read().

Referenced by Metapop::retrieve_data().

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setAge()

void Individual::setAge ( unsigned short  value )

inline

{_age = value;}

References _age.

Referenced by LCE_Breed_base::breed_cloning(), IndFactory::decorateNewIndividual(), TTDeletMutBitstrFH::FHread(), and TTQuantiFH::FHread().

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setCurrentID()

void Individual::setCurrentID ( unsigned long  value )

inline

{currentID = value;}

References currentID.

setFather()

void Individual::setFather ( Individual *  f )

inline

{_father = f;}

References _father.

Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), IndFactory::decorateNewIndividual(), and IndFactory::makeNewIndividual().

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setFatherID()

void Individual::setFatherID ( unsigned long  value )

inline

{_fatherID = value;}

References _fatherID.

Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), IndFactory::decorateNewIndividual(), LCE_Cross::generatePedigree(), and IndFactory::makeNewIndividual().

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setFecundity()

double Individual::setFecundity ( double  value )

inline

Sets the fecundity to the value given and returns it.

Parameters

value

the fecundity

{_fecundity = value; return value;}

References _fecundity.

Referenced by LCE_Breed_Selection::do_breed_selection_FecFitness(), LCE_Breed_Selection::do_breed_selection_OffSurvival(), LCE_BreedAssortativeMating::execute(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().

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setHome()

void Individual::setHome ( unsigned short  value )

inline

{_home = value;}

References _home.

Referenced by LCE_Breed_base::breed_cloning(), IndFactory::decorateNewIndividual(), TTDeletMutBitstrFH::FHread(), and IndFactory::makeNewIndividual().

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setID()

void Individual::setID ( unsigned long  value )

inline

{_id = value;}

References _id.

Referenced by LCE_Cross::generatePedigree(), and IndFactory::makeNewIndividual().

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setIsSelfed()

void Individual::setIsSelfed ( bool  s )

inline

{_pedigreeClass = (s ? 4 : 0);}

References _pedigreeClass.

Referenced by LCE_Breed_base::breed_cloning().

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setMother()

void Individual::setMother ( Individual *  m )

inline

{_mother = m;}

References _mother.

Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), IndFactory::decorateNewIndividual(), and IndFactory::makeNewIndividual().

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setMotherID()

void Individual::setMotherID ( unsigned long  value )

inline

{_motherID = value;}

References _motherID.

Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), IndFactory::decorateNewIndividual(), LCE_Cross::generatePedigree(), and IndFactory::makeNewIndividual().

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setPedigreeClass() [1/2]

void Individual::setPedigreeClass ( Individual *  mother, Individual *  father  )

inline

{_pedigreeClass = getPedigreeClass(mother,father);}

References _pedigreeClass, and getPedigreeClass().

Referenced by IndFactory::decorateNewIndividual(), TTDeletMutBitstrFH::FHread(), TTNeutralGenesFH::FHread(), TTQuantiFH::FHread(), and IndFactory::makeNewIndividual().

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setPedigreeClass() [2/2]

void Individual::setPedigreeClass ( unsigned char  ped )

inline

{_pedigreeClass = ped;}

References _pedigreeClass.

setSex()

void Individual::setSex ( sex_t  sex )

inline

{_sex = sex;}

References _sex.

Referenced by IndFactory::decorateNewIndividual(), LCE_Breed_Selection::do_breed_selection_WrightFisher_1sex(), LCE_Breed_Selection::do_breed_selection_WrightFisher_2sex(), IndFactory::makeNewIndividual(), LCE_Breed_base::WrightFisherPopulation(), and LCE_Breed_Quanti::WrightFisherPopulation().

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setTrait()

void* Individual::setTrait ( IDX  T, void *  value  )

inline

Sets the phenotype/value of a trait to a particular value.

Parameters

T	the trait's index in the traits table
value	the value passed to the trait (using the TTrait interface)

  { return getTrait(T)->set_trait(value); }

References getTrait(), and TTrait::set_trait().

Referenced by LCE_Breed_Wolbachia::inoculate_wolbachia().

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setTraitValue() [1/2]

void Individual::setTraitValue ( )

inline

Calls the value setting procedure of all traits present in an individual.

  { for(unsigned int i = 0; i < _trait_nb; i++) Traits[i]->set_value(); }

References _trait_nb, and Traits.

Referenced by create(), and createTrait().

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setTraitValue() [2/2]

void Individual::setTraitValue ( IDX  T )

inline

Calls the value setting procedure of a particular trait.

Parameters

T	the trait's index in the traits table

  {  getTrait(T)->set_value(); }

References getTrait(), and TTrait::set_value().

Referenced by LCE_QuantiInit::init_allele_freq(), LCE_QuantiModifier::setIndPhenotype(), and LCE_Breed_Quanti::setIndPhenotype().

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show_up()

void Individual::show_up

(

)

Write some info to stdout.

{
  message("\n Individual ID: %i\n\
           age: %i\n\
           sex: %i\n\
        mother: %i\n\
        father: %i\n\
pedigree class: %i\n\
          home: %i\n\
trait in table: %i\n\
 traits values: \n",_id,_age,_sex,_motherID,_fatherID, _pedigreeClass,_home, Traits.size());
 
for(unsigned int i = 0; i < _trait_nb; i++)
  Traits[i]->show_up();
}

References _age, _fatherID, _home, _id, _motherID, _pedigreeClass, _sex, _trait_nb, message(), and Traits.

store_data()

void Individual::store_data

(

BinaryStorageBuffer *

saver

)

{
  saver->store(&_id, sizeof(unsigned long));
  saver->store(&_motherID, sizeof(unsigned long));
  saver->store(&_fatherID, sizeof(unsigned long));
  saver->store(&_sex, sizeof(sex_t));
  saver->store(&_home, sizeof(unsigned short));
  saver->store(&_matings, 2*sizeof(unsigned short));
  saver->store(&_realizedFecundity, 2*sizeof(unsigned short));
  //saver->store(&_pedigreeClass, 1);
  //saver->store(&_age, sizeof(unsigned short));
}

References _fatherID, _home, _id, _matings, _motherID, _realizedFecundity, _sex, and BinaryStorageBuffer::store().

Referenced by Metapop::store_data().

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Member Data Documentation

_age

unsigned short Individual::_age

private

Age.

Referenced by Aging(), getAge(), init(), operator=(), reset(), setAge(), and show_up().

_father

Individual * Individual::_father

private

Referenced by create(), createTrait(), getFather(), init(), operator=(), reset(), and setFather().

_fatherID

unsigned long Individual::_fatherID

private

Referenced by create_first_gen(), getFatherID(), init(), operator=(), reset(), retrieve_data(), setFatherID(), show_up(), and store_data().

_fecundity

double Individual::_fecundity

private

Assigned fecundity.

Referenced by getFecundity(), operator=(), and setFecundity().

_home

unsigned short Individual::_home

private

Natal Patch tag.

Referenced by getHome(), init(), operator=(), reset(), retrieve_data(), setHome(), show_up(), and store_data().

_id

unsigned long Individual::_id

private

ID tag, unique for one simulation.

Referenced by create(), createTrait(), getID(), Individual(), inherit(), inheritTrait(), reset(), retrieve_data(), setID(), show_up(), and store_data().

_matings

unsigned short Individual::_matings[5]

private

Mating counter.

The relationship

Referenced by addMating(), DidHaveABaby(), getFecWithOtherPatchMate(), getLocalMatings(), getMatings(), getTotMatings(), Individual(), init(), operator=(), reset(), reset_counters(), retrieve_data(), and store_data().

_mother

Individual* Individual::_mother

private

Parents pointers.

Referenced by create(), createTrait(), getMother(), init(), operator=(), reset(), and setMother().

_motherID

unsigned long Individual::_motherID

private

Parents ID tags.

Referenced by create_first_gen(), getMotherID(), init(), operator=(), reset(), retrieve_data(), setMotherID(), show_up(), and store_data().

_pedigreeClass

unsigned char Individual::_pedigreeClass

private

Pedigree class of the individual.

• 0: parents are from different demes.\
• 1: parents are from the same deme but unrelated.\
• 2: parents are half-sib\
• 3: parents are full-sib\
• 4: parents are the same individual (i.e. selfing).\

Referenced by getIsSelfed(), getPedigreeClass(), init(), operator=(), reset(), setIsSelfed(), setPedigreeClass(), and show_up().

_realizedFecundity

unsigned short Individual::_realizedFecundity[5]

private

Number of surviving offspring from the different mating categories (see matings).

Referenced by DidHaveABaby(), getFecWithOtherPatchMate(), getLocalRealizedFecundity(), getRealizedFecundity(), getTotRealizedFecundity(), Individual(), init(), operator=(), reset(), reset_counters(), retrieve_data(), and store_data().

_sex

sex_t Individual::_sex

private

Sex tag.

Referenced by getSex(), isFemale(), operator=(), reset(), retrieve_data(), setSex(), show_up(), and store_data().

_trait_nb

unsigned int Individual::_trait_nb

private

Number of traits in the table.

Referenced by addTrait(), clearTraits(), clone(), create(), create_first_gen(), getTrait(), getTraitNumber(), inherit(), init(), mutate(), operator=(), removeTrait(), setTraitValue(), and show_up().

currentID

unsigned long Individual::currentID = 0

static

The ID counter, reset at the beginning of each simulation.

Referenced by getcurrentID(), Individual(), IndFactory::makeNewIndividual(), and setCurrentID().

Traits

std::deque<TTrait*> Individual::Traits

The traits table.

Referenced by addTrait(), clearTraits(), clone(), create(), create_first_gen(), createTrait(), getTrait(), getTraits(), inherit(), init(), mutate(), operator=(), operator==(), removeTrait(), setTraitValue(), and show_up().

---

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

• individual.h
• individual.cc