itk::bio::Gene Class Reference

#include <itkBioGene.h>

Collaboration diagram for itk::bio::Gene:

List of all members.

Classes
struct	ControlDomainType

Public Types
typedef double	AffinityType
typedef std::string	DomainType
typedef std::vector < ControlDomainType >	GeneControlDomainsType
typedef std::string	NameType
typedef std::map< DomainType, AffinityType >	ProteinDomainsType

Public Member Functions
void	AddGeneControlDomain (const DomainType &domain, bool type)
void	AddProteinDomain (const DomainType &domain, AffinityType affinity)
void	Copy (const Gene &genome)
	Gene ()
const char *	GetName () const
void	SetName (const NameType &name)
void	SetName (const char *name)
virtual	~Gene ()

Private Attributes
GeneControlDomainsType	m_ControlDomains
NameType	m_Name
ProteinDomainsType	m_ProteinDomains

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Detailed Description

This class implements the abstraction of a biological gene.

The gene has a name and a specification of promoter and represor binding sites. Promoters and represors encode a boolean expression that controls the expression of the gene. These boolean expressions will result in a polynome in a finite different equation determining the rate at which protein is syntethizied by this gene.

Definition at line 42 of file itkBioGene.h.

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Member Typedef Documentation

typedef double itk::bio::Gene::AffinityType

Definition at line 47 of file itkBioGene.h.

typedef std::string itk::bio::Gene::DomainType

Definition at line 46 of file itkBioGene.h.

typedef std::vector< ControlDomainType > itk::bio::Gene::GeneControlDomainsType

Definition at line 55 of file itkBioGene.h.

typedef std::string itk::bio::Gene::NameType

Definition at line 45 of file itkBioGene.h.

typedef std::map< DomainType, AffinityType > itk::bio::Gene::ProteinDomainsType

Definition at line 48 of file itkBioGene.h.

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Constructor & Destructor Documentation

itk::bio::Gene::Gene

(

)

virtual itk::bio::Gene::~Gene ( )

virtual

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Member Function Documentation

void itk::bio::Gene::AddGeneControlDomain	(	const DomainType &	domain,
		bool	type
	)

Add a control domain to the gene. A control domain is an enhancer or silencer. A gene can have any number of them. The type will indicate if they are enhancers or silencers.

void itk::bio::Gene::AddProteinDomain	(	const DomainType &	domain,
		AffinityType	affinity
	)

Add a protein domain along with an affinity. The name of the domain here actually refers to the one for which this protein will have binding affinity. For example, adding "SH2" with affinity 0.05 will mean that this gene will synthetize a proteing with a domain that has 0.05 affinity for a standard SH2 domain.

void itk::bio::Gene::Copy

(

const Gene &

genome

)

const char* itk::bio::Gene::GetName

(

)

const

void itk::bio::Gene::SetName

(

const NameType &

name

)

Set/Get the name of the gene. This uses a std::string type.

void itk::bio::Gene::SetName

(

const char *

name

)

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Member Data Documentation

GeneControlDomainsType itk::bio::Gene::m_ControlDomains

private

Definition at line 83 of file itkBioGene.h.

NameType itk::bio::Gene::m_Name

private

Definition at line 82 of file itkBioGene.h.

ProteinDomainsType itk::bio::Gene::m_ProteinDomains

private

Definition at line 84 of file itkBioGene.h.

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

• itkBioGene.h