TTrait Class Reference

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

#include <ttrait.h>

Inheritance diagram for TTrait:

Collaboration diagram for TTrait:

List of all members.

Public Member Functions
virtual void	init ()=0
	Called to allocate the trait's genotypic sequences.
virtual void	init_sequence ()=0
	Called at the start of each replicate, sets the initial genotypes.
virtual void	reset ()=0
	Called at the end of each simulation/replicate, deallocates sequence memory.
virtual void	inherit (TTrait *mother, TTrait *father)=0
	Inheritance procedure, creates a new trait from mother's and father's traits.
virtual void	mutate ()=0
	Mutation procedure, perform mutations on the genes sequence.
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.
virtual void	set_sequence (void **seq)=0
	Called to set the sequence pointer to an existing trait.
virtual void	set_value ()=0
	Tells the trait to set its phenotype from genotype, should be used instead of getValue().
virtual void *	getValue ()=0
	Genotype to phenotype mapper.
virtual trait_t	get_type () const =0
	type accessor.
virtual void **	get_sequence () const =0
	sequence accessor.
virtual void *	get_allele (int loc, int all) const =0
	Called to read one allele value at a particular locus.
virtual void	show_up ()=0
	Writes some info to stdout.
virtual TTrait *	clone ()=0
	Returns a copy of itself.
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.
virtual bool	operator== (const TTrait &)=0
	Checks for parameters equivalence, not genetic equivalence.
virtual bool	operator!= (const TTrait &)=0

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Detailed Description

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

This pure abstract class declares the traits intreface. 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.

Definition at line 46 of file ttrait.h.

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Constructor & Destructor Documentation

virtual TTrait::~TTrait

(

)

[inline, virtual]

Definition at line 109 of file ttrait.h.

{ }

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Member Function Documentation

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!

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

virtual void* TTrait::get_allele	(	int	loc,
		int	all
	)		const [pure virtual]

Called to read one allele value at a particular locus.

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 TTDeletMutations_bitstring, TTNeutralGenes, TTDispersal, TTQuanti, and TTWolbachia.

virtual void** TTrait::get_sequence

(

)

const [pure virtual]

sequence accessor.

Returns:

the sequence pointer

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

Referenced by TTDeletMutBitstrFH::FHwrite(), TTDeletMutations_bitstring::inherit_0(), TTNeutralGenes::inherit_free(), TTDeletMutations_bitstring::inherit_free(), TTNeutralGenes::inherit_low(), TTDeletMutations_bitstring::inherit_low(), TTNeutralGenesFH::write_FSTAT(), and TTNeutralGenesFH::write_varcompWC().

virtual trait_t TTrait::get_type

(

)

const [pure virtual]

type accessor.

Returns:

the trait's type

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

Referenced by TTWolbachia::operator==(), TTNeutralGenes::operator==(), and TTDeletMutations_bitstring::operator==().

virtual void* TTrait::getValue

(

)

[pure virtual]

Genotype to phenotype mapper.

Returns:

the phenotype computed from the genotype

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

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

virtual void TTrait::inherit	(	TTrait *	mother,
		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 TTDeletMutations_bitstring, TTNeutralGenes, TTDispersal, TTQuanti, and TTWolbachia.

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

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 TTDeletMutations_bitstring, TTNeutralGenes, TTDispersal, TTQuanti, and TTWolbachia.

virtual void TTrait::init_sequence

(

)

[pure virtual]

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

Called by Individual::create().

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

virtual void TTrait::mutate

(

)

[pure virtual]

Mutation procedure, perform mutations on the genes sequence.

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

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

virtual bool TTrait::operator!=

(

const TTrait &

)

[pure virtual]

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

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 TTDeletMutations_bitstring, TTNeutralGenes, TTDispersal, TTQuanti, and TTWolbachia.

virtual bool TTrait::operator==

(

const TTrait &

)

[pure virtual]

Checks for parameters equivalence, not genetic equivalence.

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

virtual void TTrait::reset

(

)

[pure virtual]

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

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

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 TTDeletMutations_bitstring, TTNeutralGenes, TTDispersal, TTQuanti, and TTWolbachia.

Referenced by TTNeutralGenesFH::FHread().

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 TTDeletMutations_bitstring, TTNeutralGenes, TTDispersal, TTQuanti, and TTWolbachia.

Referenced by Individual::setTrait().

virtual void TTrait::set_value

(

)

[pure virtual]

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

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

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

virtual void TTrait::show_up

(

)

[pure virtual]

Writes some info to stdout.

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

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

• ttrait.h