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itk::bio::Gene Class Reference

This class implements the abstraction of a biological gene. More...

#include <itkBioGene.h>

+ Collaboration diagram for itk::bio::Gene:

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

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

Private Attributes

GeneControlDomainsType m_ControlDomains
 
NameType m_Name
 
ProteinDomainsType m_ProteinDomains
 

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.

Member Typedef Documentation

Definition at line 47 of file itkBioGene.h.

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

Definition at line 46 of file itkBioGene.h.

Definition at line 55 of file itkBioGene.h.

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

Definition at line 45 of file itkBioGene.h.

Definition at line 48 of file itkBioGene.h.

Constructor & Destructor Documentation

itk::bio::Gene::Gene ( )

Constructor

Definition at line 28 of file itkBioGene.cxx.

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

Destructor

Definition at line 37 of file itkBioGene.cxx.

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.

Add a protein domain

Definition at line 112 of file itkBioGene.cxx.

References itk::bio::Gene::ControlDomainType::m_Domain, and itk::bio::Gene::ControlDomainType::m_Type.

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.

Add a protein domain

Definition at line 102 of file itkBioGene.cxx.

void itk::bio::Gene::Copy ( const Gene gene)

Copy from another genome

Definition at line 45 of file itkBioGene.cxx.

References m_ControlDomains, m_Name, and m_ProteinDomains.

const char * itk::bio::Gene::GetName ( void  ) const

Get the name of the gene

Definition at line 92 of file itkBioGene.cxx.

void itk::bio::Gene::SetName ( const NameType name)

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

Set the name of the gene

Definition at line 72 of file itkBioGene.cxx.

void itk::bio::Gene::SetName ( const char *  name)

Set the name of the gene

Definition at line 82 of file itkBioGene.cxx.

Member Data Documentation

GeneControlDomainsType itk::bio::Gene::m_ControlDomains
private

Definition at line 84 of file itkBioGene.h.

Referenced by Copy().

NameType itk::bio::Gene::m_Name
private

Definition at line 83 of file itkBioGene.h.

Referenced by Copy().

ProteinDomainsType itk::bio::Gene::m_ProteinDomains
private

Definition at line 85 of file itkBioGene.h.

Referenced by Copy().


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

Generated at Sat Mar 8 2014 18:02:22 for Orfeo Toolbox with doxygen 1.8.3.1