Interface for all trait types, declares all basic trait operations. More...

#include <ttrait.h>

Inheritance diagram for TTrait:

Collaboration diagram for TTrait:

Public Member Functions
virtual void	init ()=0
	Called to allocate the trait's genotypic sequences. More...

virtual void	init_sequence ()=0
	Called at the start of each replicate, sets the initial genotypes. More...

virtual void	reset ()=0
	Called at the end of each simulation/replicate, deallocates sequence memory. More...

virtual void	inherit (const TTrait mother, const TTrait father)=0
	Inheritance procedure, creates a new trait from mother's and father's traits. More...

virtual void	mutate ()=0
	Mutation procedure, perform mutations on the genes sequence. More...

virtual void *	set_trait (void *value)=0
	Called to set the phenotypic to a particular value or to give context-dependant value(s) to the trait. More...

virtual void	set_sequence (void **seq)=0
	Called to set the sequence pointer to an existing trait. More...

virtual unsigned int	get_allele (int loc, int all) const =0
	Called to read the allele identity at a locus. More...

virtual double	get_allele_value (int loc, int all) const =0
	Called to read the value of the allele at a particular locus. More...

virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)=0
	Called to change the allelic value at a particular locus. More...

virtual void	set_value ()=0
	Tells the trait to set its phenotype from genotype, should be used instead of getValue(). More...

virtual void *	getValue () const =0
	Genotype to phenotype mapper. More...

virtual trait_t	get_type () const =0
	type accessor. More...

virtual void **	get_sequence () const =0
	sequence accessor. More...

virtual void	show_up ()=0
	Writes some info to stdout. More...

virtual TTrait *	clone ()=0
	Returns a copy of itself. More...

virtual	~TTrait ()

Operators
virtual TTrait &	operator= (const TTrait &)=0
	Copies the complete state of the trait from right to left side of the operator, sequence data included. More...

virtual bool	operator== (const TTrait &)=0
	Checks for parameters equivalence, not genetic equivalence. More...

virtual bool	operator!= (const TTrait &)=0

Public Member Functions inherited from StorableComponent
virtual void	store_data (BinaryStorageBuffer *saver)=0
	Interface to store the component data (e.g. gene values) into a binary buffer. More...

virtual bool	retrieve_data (BinaryStorageBuffer *reader)=0
	Interface to retrieve the same data from the binary buffer. More...

virtual	~StorableComponent ()

Detailed Description

Interface for all trait types, declares all basic trait operations.

This pure abstract class declares the traits interface. The precise genetic architecture of the trait is not defined and is up to the designer of the trait. It uses void pointers to allow users to define their own structure. Existing traits use various types for their genes sequence, like char, double or bitset. It is up to the trait's user to know what kind of structure they expect. The trait objects are contained in the Individual class. Their parameters are set by their TraitPrototype.

Constructor & Destructor Documentation

◆ ~TTrait()

virtual TTrait::~TTrait ( )

inlinevirtual

121 { }

Member Function Documentation

◆ clone()

virtual TTrait* TTrait::clone ( )

pure virtual

Returns a copy of itself.

Note: call the copy constructor of the trait which should only copy the parameters values not the complete state of the trait (i.e. shallow copy). The copy of the sequence data is made through the assignement operator!

◆ get_allele()

virtual unsigned int TTrait::get_allele	(	int	loc,
		int	all
	)		const

pure virtual

Called to read the allele identity at a locus.

Identity is 0-based, usually 0 is ancestral, 1+ derived allele (can have more than 2 alleles).

Returns: allele id, integer

Parameters

loc	which locus
allele	from which DNA strand, FEM=1 is maternally inherited, MAL=o is paternally inherited

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by TTNeutralGenesSH::Coancestry(), TTNOhtaStats::FHwrite(), TTNeutralGenesSH::getDxyPerPatch(), GenotyperFH::prepare_data_table(), TTNeutralGenesFH::print_PLINK_PED(), GenotyperFH::print_snp_genotypes(), GenotyperFH::print_snp_id(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setHeteroTable(), TTNeutralGenesSH::setHo(), TTNeutralGenesSH::setHo2(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), and TTNeutralGenesFH::write_patch_TAB().

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◆ get_allele_value()

virtual double TTrait::get_allele_value	(	int	loc,
		int	all
	)		const

pure virtual

Called to read the value of the allele at a particular locus.

It is not the identity of the allele, see get_allele()

Returns: the allelic value at position 'all' at locus 'loc'

Parameters

loc	locus position in the sequence
all	which allele we want to read the value from

Implemented in TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTNeutralGenes, TTWolbachia, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by TProtoQuanti::get_allele_value(), TTDispersal::inherit(), TTQuantiFH::print(), and GenotyperFH::print_genotypes().

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◆ get_sequence()

virtual void** TTrait::get_sequence ( ) const

pure virtual

sequence accessor.

Returns: the sequence pointer

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

◆ get_type()

virtual trait_t TTrait::get_type ( ) const

pure virtual

type accessor.

Returns: the trait's type

Implemented in TTWolbachia, TTQuanti, TTNeutralGenes, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by TT_BDMI::operator==(), TTDeletMutations_bitstring::operator==(), TTNeutralGenes::operator==(), TTQuanti_continuous::operator==(), TTQuanti_diallelic::operator==(), TTQuanti_diallelic_bitstring::operator==(), and TTWolbachia::operator==().

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◆ getValue()

virtual void* TTrait::getValue ( ) const

pure virtual

Genotype to phenotype mapper.

Returns: the phenotype computed from the genotype

Implemented in TTWolbachia, TTQuanti, TTNeutralGenes, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by Individual::getTraitValue(), TTWolbachia::inherit(), and TTDeletMutBitstrSH::setViability().

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◆ inherit()

virtual void TTrait::inherit	(	const TTrait *	mother,
		const TTrait *	father
	)

pure virtual

Inheritance procedure, creates a new trait from mother's and father's traits.

Parameters

mother	the mother's trait
father	the father's trait

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by Individual::create(), Individual::createTrait(), and Individual::inheritTrait().

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◆ init()

virtual void TTrait::init ( )

pure virtual

Called to allocate the trait's genotypic sequences.

Called each time a new Individual is created (Individual::init())

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti_diallelic_bitstring_no_pleio, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by TProtoQuanti::setParameters().

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◆ init_sequence()

virtual void TTrait::init_sequence ( )

pure virtual

Called at the start of each replicate, sets the initial genotypes.

Called by Individual::create().

Referenced by LCE_QuantiInit::init_trait_value(), and TProtoQuanti::setParameters().

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◆ mutate()

virtual void TTrait::mutate ( )

pure virtual

Mutation procedure, perform mutations on the genes sequence.

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by Individual::create(), Individual::createTrait(), and Individual::mutateTrait().

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◆ operator!=()

virtual bool TTrait::operator!= ( const TTrait & )

pure virtual

Implemented in TTDispersal, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes, TTDeletMutations_bitstring, and TT_BDMI.

◆ operator=()

virtual TTrait& TTrait::operator= ( const TTrait & )

pure virtual

Copies the complete state of the trait from right to left side of the operator, sequence data included.

Implemented in TTDispersal, TTNeutralGenes, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDeletMutations_bitstring, and TT_BDMI.

◆ operator==()

virtual bool TTrait::operator== ( const TTrait & )

pure virtual

Checks for parameters equivalence, not genetic equivalence.

Implemented in TTDispersal, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes, TTDeletMutations_bitstring, and TT_BDMI.

◆ reset()

virtual void TTrait::reset ( )

pure virtual

Called at the end of each simulation/replicate, deallocates sequence memory.

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

◆ set_allele_value()

virtual void TTrait::set_allele_value	(	unsigned int	locus,
		unsigned int	allele,
		double	value
	)

pure virtual

Called to change the allelic value at a particular locus.

Parameters

locus	the targeted locus
alele	the targeted allele
value	the value of the allele inserted

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by TTNeutralGenesFH::FHread(), and LCE_NtrlInit::init_allele_freq().

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◆ set_sequence()

virtual void TTrait::set_sequence ( void ** seq )

pure virtual

Called to set the sequence pointer to an existing trait.

Parameters

seq	the existing sequence pointer

Implemented in TTNeutralGenes, TTWolbachia, TTQuanti_diallelic_bitstring, TTQuanti_diallelic, TTQuanti_continuous, TTNeutralGenes_bitstring, TTNeutralGenes_byte, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by TTQuantiFH::FHread().

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◆ set_trait()

virtual void* TTrait::set_trait ( void * value )

pure virtual

Called to set the phenotypic to a particular value or to give context-dependant value(s) to the trait.

Parameters

value the value passed to the trait

Returns: the argument passed

Implemented in TTWolbachia, TTQuanti, TTNeutralGenes, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by Individual::setTrait().

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◆ set_value()

virtual void TTrait::set_value ( )

pure virtual

Tells the trait to set its phenotype from genotype, should be used instead of getValue().

Implemented in TTWolbachia, TTQuanti, TTNeutralGenes, TTDispersal, TTDeletMutations_bitstring, and TT_BDMI.

Referenced by Individual::create(), Individual::createTrait(), LCE_QuantiInit::init_trait_value(), and Individual::setTraitValue().

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◆ show_up()

virtual void TTrait::show_up ( )

pure virtual

Writes some info to stdout.

Referenced by TProtoQuanti::setParameters().

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

ttrait.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ~TTrait()

Member Function Documentation

◆ clone()

◆ get_allele()

◆ get_allele_value()

◆ get_sequence()

◆ get_type()

◆ getValue()

◆ inherit()

◆ init()

◆ init_sequence()

◆ mutate()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ reset()

◆ set_allele_value()

◆ set_sequence()

◆ set_trait()

◆ set_value()

◆ show_up()