Nemo
2.3.56
Simulate forward-in-time genetic evolution in a spatially explicit, individual-based stochastic simulator
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This class contains traits along with other individual information (sex, pedigree, etc. ). More...
#include <individual.h>
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... | |
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.
typedef int Individual::IDX |
Individual::Individual | ( | ) |
References _id, _matings, _realizedFecundity, and currentID.
Referenced by clone().
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References clearTraits().
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Increments the mating counter according to the pedigree class of the offspring.
category | the pedigree class of the offspring |
References _matings.
Referenced by LCE_Breed_Selection::makeOffspringWithSelection().
Adds a trait to the table.
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. |
References _trait_nb, fatal(), and Traits.
Referenced by clone(), and IndFactory::makePrototype().
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Clears the traits container.
References _trait_nb, and Traits.
Referenced by IndFactory::clearPrototype(), IndFactory::~IndFactory(), and ~Individual().
Individual * Individual::clone | ( | ) |
Cloning procedure, clones all the traits present in the individual.
References _trait_nb, addTrait(), Individual(), and Traits.
Referenced by IndFactory::getPrototypeClone(), and IndFactory::makeNewIndividual().
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Creates an individual's genotypes and phenotypes with recombination and mutations.
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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Creates an individual's genotypes and phenotypes with optional recombination or mutations.
do_inherit | if true, do traits inheritance and recombination |
do_mutate | if true, performs mutation of the traits |
References _father, _mother, inherit(), mutate(), and setTraitValue().
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Creates an individual, inherit, mutate and set all its trait's values.
mother | the mother |
father | the father |
References _id, _trait_nb, fatal(), getTrait(), TTrait::inherit(), TTrait::mutate(), recombine(), TTrait::set_value(), and Traits.
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Creates an individual's genotypes and phenotypes for first generation.
References _fatherID, _motherID, _trait_nb, and Traits.
Referenced by LCE_Cross::create_individual_ancestors(), and Patch::setNewGeneration().
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Creates an individual's genotypes and phenotypes with optional recombination or mutations on one trait only.
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 |
References _father, _mother, inheritTrait(), mutateTrait(), and setTraitValue().
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Sets a particular trait's genotype and phenotype values from the two parents.
Includes its inheritance, mutation and value setting.
i | the index of the trait to create in the traits table |
mother | the mother |
father | the father |
References _id, fatal(), getTrait(), TTrait::inherit(), TTrait::mutate(), recombine(), TTrait::set_value(), and Traits.
Referenced by LCE_Breed_Selection::makeOffspringWithSelection().
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Increments the mating and realized fecundity counters according to the pedigree class of the offspring.
category | the pedigree class of the offspring |
References _matings, and _realizedFecundity.
Referenced by IndFactory::makeOffsprg(), LCE_Breed_base::makeOffspring(), and LCE_Breed_Selection::makeOffspringWithSelection().
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References _age.
Referenced by LCE_SelectionFH::print().
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References _father.
Referenced by LCE_Cross::create_individual_ancestors(), LCE_Breed_base::makeOffspring(), LCE_Breed_Selection::makeOffspringWithSelection(), TTQuantiFH::print(), and TTNeutralGenesFH::write_patch_TAB().
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References _fatherID.
Referenced by LCE_Cross::create_individual_ancestors(), MPFileHandler::createAndPrintSample(), getPedigreeClass(), TTQuantiFH::print(), MPFileHandler::printNoSample(), MPStatHandler::setKinClassCounter(), TTNeutralGenesSH::setSibCoa(), and TTNeutralGenesFH::write_patch_TAB().
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References _fecundity.
Referenced by MPStatHandler::getMeanAssignedFecundity().
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Returns the proportion of succesfull local matings (i.e.
those that survived selection).
References getLocalMatings(), and getLocalRealizedFecundity().
Referenced by TTDeletMutBitstrSH::getMeanFecWithPatchMate().
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Returns the proportion of successfull remote matings.
References _matings, and _realizedFecundity.
Referenced by TTDeletMutBitstrSH::getMeanFecWithPatchMate().
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References _home.
Referenced by MPFileHandler::createAndPrintSample(), TTDeletMutBitstrFH::FHwrite(), getPedigreeClass(), LCE_SelectionFH::print(), TTQuantiFH::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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References _id.
Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), MPFileHandler::createAndPrintSample(), TTDeletMutBitstrFH::FHwrite(), IndFactory::makeNewIndividual(), TTQuantiFH::print(), TTQuantiFH::print_PLINK_FAM(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), MPFileHandler::printNoSample(), and TTNeutralGenesFH::write_patch_TAB().
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References _pedigreeClass.
Referenced by MPStatHandler::setKinship().
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Gives the number of times an individual mated with an individual from the same patch.
References _matings.
Referenced by getFecWithHomePatchMate(), TTDeletMutBitstrSH::getMeanFecWithPatchMate(), and getTotMatings().
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Gives the total number of surviving offspring when mating occures with mates of the same patch.
References _realizedFecundity.
Referenced by getFecWithHomePatchMate(), and getTotRealizedFecundity().
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Gives the number of matings that individual had with mates from a given pedigree class.
cat | the mating category (= the pedigree class of the offspring):
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References _matings.
Referenced by TTDeletMutBitstrSH::getMeanFecWithPatchMate().
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References _mother.
Referenced by LCE_Cross::create_individual_ancestors(), LCE_Breed_base::makeOffspring(), LCE_Breed_Selection::makeOffspringWithSelection(), TTQuantiFH::print(), and TTNeutralGenesFH::write_patch_TAB().
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References _motherID.
Referenced by LCE_Cross::create_individual_ancestors(), MPFileHandler::createAndPrintSample(), getPedigreeClass(), TTQuantiFH::print(), MPFileHandler::printNoSample(), MPStatHandler::setKinClassCounter(), TTNeutralGenesSH::setSibCoa(), and TTNeutralGenesFH::write_patch_TAB().
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Returns the pedigree class of the individual, as set during offspring creation.
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().
unsigned int Individual::getPedigreeClass | ( | Individual * | mother, |
Individual * | father | ||
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Returns the pedigree class of two individuals.
mother | the first individual (e.g.the mother of this individual) |
father | the second individual (e.g. the father of this individual) |
References getFatherID(), getHome(), and getMotherID().
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Gives the number of surviving offspring for a given pedigree class of mating.
cat | the mating category:
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References _realizedFecundity.
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References _sex.
Referenced by LCE_Breed_Selection::do_breed_selection_FecFitness(), LCE_Breed_Selection::do_breed_selection_OffSurvival(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), TTQuantiFH::print(), Metapop::retrieve_data(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().
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Gives the total number of matings of an individual.
References _matings, and getLocalMatings().
Referenced by MPStatHandler::getMeanMatings(), and TTDeletMutBitstrSH::getPatchLoad().
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Gives the total number of surviving offspring for all categories of mating.
References _realizedFecundity, and getLocalRealizedFecundity().
Referenced by TTDeletMutBitstrSH::getPatchLoad(), and MPStatHandler::setReproductiveStats().
Trait accessor.
T | the trait's index in the traits table |
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(), TTQFreqExtractor::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(), TTQuantiFH::print(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), Metapop::read_trait(), TTNeutralGenesSH::setAdults_Theta(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setCoaMatrix(), TTDeletMutBitstrSH::setDeletStats(), TTNeutralGenesSH::setHeteroTable(), TTNeutralGenesSH::setHo(), TTNeutralGenesSH::setHo2(), 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().
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Accessor to the size of the traits table.
References _trait_nb.
Referenced by SimRunner::run(), and LCE_Breed_Selection::setNonSelectedTraitTable().
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Accessor to the value (phenotype) of a particular trait.
T | the trait's index in the traits table |
References getTrait(), and TTrait::getValue().
Referenced by LCE_Selection_base::addPhenotypicSD(), LCE_Disperse_EvolDisp::evoldisp(), LCE_Selection_base::getFitnessDirect(), LCE_Selection_base::getFitnessMultivariateGaussian(), LCE_Selection_base::getFitnessMultivariateGaussian_VE(), LCE_Selection_base::getFitnessUnivariateGaussian(), LCE_Selection_base::getFitnessUnivariateGaussian_VE(), 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_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().
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Calls the inheritance procedure of all the traits present in the individual.
mother | the mother |
father | the father |
References _id, _trait_nb, getTrait(), inherit(), recombine(), and Traits.
Referenced by create(), and inherit().
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Calls the inheritance procedure of a particular trait.
T | the trait's index in the traits table |
mother | the mother |
father | the father |
References _id, getTrait(), TTrait::inherit(), and recombine().
Referenced by createTrait().
Individual * Individual::init | ( | ) |
Inits parameters and traits.
Called by IndFactory::makeNewIndividual() to allocate the traits' sequences memory.
References _age, _father, _fatherID, _home, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _trait_nb, error(), init(), and Traits.
Referenced by LCE_Cross::generatePedigree(), init(), and IndFactory::makeNewIndividual().
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Calls the mutation procedure of a particular trait.
T | trait's index in the traits table |
References getTrait(), and TTrait::mutate().
Referenced by createTrait().
bool Individual::operator!= | ( | const Individual & | i | ) |
Individual & Individual::operator= | ( | const Individual & | i | ) |
Assignment, make a deep copy of the parameter values and traits.
References _age, _father, _fatherID, _fecundity, _home, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _sex, _trait_nb, error(), fatal(), and Traits.
bool Individual::operator== | ( | const Individual & | i | ) |
Only checks for traits equivalence.
References Traits.
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References TTProtoWithMap::recombine().
Referenced by create(), createTrait(), inherit(), and inheritTrait().
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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).
References _age, _father, _fatherID, _home, _id, _matings, _mother, _motherID, _pedigreeClass, _realizedFecundity, _sex, and MAL.
Referenced by IndFactory::makeNewIndividual().
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Resets the mating and fecundity counters.
References _matings, and _realizedFecundity.
Referenced by LCE_Breed_base::breed_cloning().
void Individual::retrieve_data | ( | BinaryStorageBuffer * | reader | ) |
References _fatherID, _home, _id, _matings, _motherID, _realizedFecundity, _sex, and BinaryStorageBuffer::read().
Referenced by Metapop::retrieve_data().
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References _age.
Referenced by LCE_Breed_base::breed_cloning(), TTDeletMutBitstrFH::FHread(), and TTQuantiFH::FHread().
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References currentID.
Referenced by IndFactory::makePrototype().
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References _father.
Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), and IndFactory::makeNewIndividual().
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References _fatherID.
Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), LCE_Cross::generatePedigree(), and IndFactory::makeNewIndividual().
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Sets the fecundity to the value given and returns it.
value | the fecundity |
References _fecundity.
Referenced by LCE_Breed_Selection::do_breed_selection_FecFitness(), LCE_Breed_Selection::do_breed_selection_OffSurvival(), 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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References _home.
Referenced by LCE_Breed_base::breed_cloning(), TTDeletMutBitstrFH::FHread(), and IndFactory::makeNewIndividual().
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References _id.
Referenced by LCE_Cross::generatePedigree(), and IndFactory::makeNewIndividual().
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References _pedigreeClass.
Referenced by LCE_Breed_base::breed_cloning().
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References _mother.
Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), and IndFactory::makeNewIndividual().
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References _motherID.
Referenced by LCE_Breed_base::breed_cloning(), LCE_Cross::create_individual_ancestors(), LCE_Cross::generatePedigree(), and IndFactory::makeNewIndividual().
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References _pedigreeClass, and getPedigreeClass().
Referenced by TTDeletMutBitstrFH::FHread(), TTNeutralGenesFH::FHread(), TTQuantiFH::FHread(), and IndFactory::makeNewIndividual().
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References _pedigreeClass.
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References _sex.
Referenced by 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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Sets the phenotype/value of a trait to a particular value.
T | the trait's index in the traits table |
value | the value passed to the trait (using the TTrait interface) |
References getTrait(), and TTrait::set_trait().
Referenced by LCE_Breed_Wolbachia::inoculate_wolbachia().
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Calls the value setting procedure of a particular trait.
T | the trait's index in the traits table |
References getTrait(), and TTrait::set_value().
Referenced by LCE_QuantiModifier::setIndPhenotype(), and LCE_Breed_Quanti::setIndPhenotype().
void Individual::show_up | ( | ) |
Write some info to stdout.
References _age, _fatherID, _home, _id, _motherID, _pedigreeClass, _sex, _trait_nb, message(), show_up(), and Traits.
Referenced by show_up().
void Individual::store_data | ( | BinaryStorageBuffer * | saver | ) |
References _fatherID, _home, _id, _matings, _motherID, _realizedFecundity, _sex, and BinaryStorageBuffer::store().
Referenced by Metapop::store_data().
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Referenced by create(), createTrait(), getFather(), init(), operator=(), reset(), and setFather().
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Referenced by create_first_gen(), getFatherID(), init(), operator=(), reset(), retrieve_data(), setFatherID(), show_up(), and store_data().
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Assigned fecundity.
Referenced by getFecundity(), operator=(), and setFecundity().
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Natal Patch tag.
Referenced by getHome(), init(), operator=(), reset(), retrieve_data(), setHome(), show_up(), and store_data().
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ID tag, unique for one simulation.
Referenced by create(), createTrait(), getID(), Individual(), inherit(), inheritTrait(), reset(), retrieve_data(), setID(), show_up(), and store_data().
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Mating counter.
The relationship
Referenced by addMating(), DidHaveABaby(), getFecWithOtherPatchMate(), getLocalMatings(), getMatings(), getTotMatings(), Individual(), init(), operator=(), reset(), reset_counters(), retrieve_data(), and store_data().
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Parents pointers.
Referenced by create(), createTrait(), getMother(), init(), operator=(), reset(), and setMother().
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Parents ID tags.
Referenced by create_first_gen(), getMotherID(), init(), operator=(), reset(), retrieve_data(), setMotherID(), show_up(), and store_data().
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Pedigree class of the individual.
Referenced by getIsSelfed(), getPedigreeClass(), init(), operator=(), reset(), setIsSelfed(), setPedigreeClass(), and show_up().
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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().
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Sex tag.
Referenced by getSex(), isFemale(), operator=(), reset(), retrieve_data(), setSex(), show_up(), and store_data().
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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().
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The ID counter, reset at the beginning of each simulation.
Referenced by getcurrentID(), Individual(), IndFactory::makeNewIndividual(), and setCurrentID().
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().