Genotype Class Reference

Genotype is a data type derived from Data. More...

#include <Genotype.h>

Inheritance diagram for Genotype:

List of all members.

Public Types
enum	{ SNP_A_ORDINAL = 1, SNP_C_ORDINAL = 2, SNP_G_ORDINAL = 3, SNP_T_ORDINAL = 4 }
Public Member Functions
	Genotype ()
	Genotype (const char *g)
	Genotype (const std::string &g)
	Genotype (const int allele1, const int allele2)
bool	isMissing (void) const
void	setMissing (void)
void	set (const char *genotype)
void	set (const std::string &genotype)
const std::string	get (void) const
void	set (const int allele1, const int allele2)
void	setAllele1 (const int allele1)
void	setAllele2 (const int allele2)
void	setAllele1 (const char *allele1)
void	setAllele2 (const char *allele2)
void	setAllele1 (const std::string &allele1)
void	setAllele2 (const std::string &allele2)
const Number	getAllele1 (void) const
const Number	getAllele2 (void) const
Genotype &	operator+= (const int allele)
Genotype &	operator-= (const int allele)
Genotype &	operator+= (const Number &allele)
Genotype &	operator-= (const Number &allele)
bool	operator< (const Data &b) const
bool	operator== (const Data &b) const
const DATATYPE	getDataType (void) const
virtual Genotype *	clone () const
Static Public Member Functions
static void	addGenotypeMissingValue (std::string &value)
static bool	isMissingValue (std::string value)
static bool	isA (const std::string &s)
	Determines whether a string is a valid Genotype string.
Private Member Functions
void	_orderAlleles (void)
void	_setNormalizedStringRepresentation (void)
const char *	_itoa (unsigned int i) const
const char *	_snpOrdinalToCString (unsigned int allele)
const char *	_setAllele (const char *input, unsigned &value, bool &snp)
Private Attributes
bool	_isMissing
bool	_isSNP
std::string	_genotype
unsigned int	_allele1
unsigned int	_allele2
Static Private Attributes
static std::set< std::string >	_genotypeMissingValue
static const char	_normalDelimiter = '/'
static const char	_alternateDelimiter = '|'

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Detailed Description

Genotype is a data type derived from Data.

Genotype deals with both microsatellite marker alleles and SNP alleles.

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Member Enumeration Documentation

anonymous enum

Enumerator: SNP_A_ORDINAL  SNP_C_ORDINAL  SNP_G_ORDINAL  SNP_T_ORDINAL

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Constructor & Destructor Documentation

Genotype::Genotype (   )  [inline]

Genotype::Genotype (  const char *  g  )  [inline]

Genotype::Genotype (  const std::string &  g  )  [inline]

Genotype::Genotype (  const int  allele1, const int  allele2 )  [inline]

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Member Function Documentation

const char * Genotype::_itoa (  unsigned int  i  )  const [private]

void Genotype::_orderAlleles (  void   )  [private]

_orderAlleles(): The normal convention is to have the lesser allele shown first:

const char * Genotype::_setAllele (  const char *  s, unsigned &  value, bool &  snp )  [private]

_setAllele(): set an allele from a char* input

void Genotype::_setNormalizedStringRepresentation (  void   )  [private]

_setNormalizedStringRepresentation(): Convert genotype to the normalized form d{1,}/d{1,} or [ACGT]/[ACGT]

const char * Genotype::_snpOrdinalToCString (  unsigned int  allele  )  [private]

_snpOrdinalToCString(): Convert unsigned int to a SNP ordinal.

static void Genotype::addGenotypeMissingValue (  std::string &  value  )  [inline, static]

Genotype * Genotype::clone (   )  const [virtual]

Implements Data.

const std::string Genotype::get (  void   )  const [virtual]

Implements Data.

const Number Genotype::getAllele1 (  void   )  const [inline]

const Number Genotype::getAllele2 (  void   )  const [inline]

const DATATYPE Genotype::getDataType (  void   )  const [inline, virtual]

Implements Data.

bool Genotype::isA (  const std::string &  s  )  [static]

Determines whether a string is a valid Genotype string. isA(): Determines whether a string is a valid Genotype string

bool Genotype::isMissing (  void   )  const [inline, virtual]

Implements Data.

bool Genotype::isMissingValue (  std::string  value  )  [static]

Genotype & Genotype::operator+= (  const Number &  allele  )

Genotype & Genotype::operator+= (  const int  allele  )

Genotype & Genotype::operator-= (  const Number &  allele  )

Genotype & Genotype::operator-= (  const int  allele  )

bool Genotype::operator< (  const Data &  b  )  const [virtual]

operator < NOTA BENE: This is used for SORTING ONLY Implements Data.

bool Genotype::operator== (  const Data &  b  )  const [virtual]

Implements Data.

void Genotype::set (  const int  allele1, const int  allele2 )

void Genotype::set (  const std::string &  genotype  )  [virtual]

Implements Data.

void Genotype::set (  const char *  genotype  )  [virtual]

Implements Data.

void Genotype::setAllele1 (  const std::string &  allele1  )

void Genotype::setAllele1 (  const char *  allele1  )

void Genotype::setAllele1 (  const int  allele1  )

void Genotype::setAllele2 (  const std::string &  allele2  )

void Genotype::setAllele2 (  const char *  allele2  )

void Genotype::setAllele2 (  const int  allele2  )

void Genotype::setMissing (  void   )  [inline, virtual]

Implements Data.

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Member Data Documentation

unsigned int Genotype::_allele1 [private]

unsigned int Genotype::_allele2 [private]

const char Genotype::_alternateDelimiter = '|' [static, private]

std::string Genotype::_genotype [private]

String representation of the genotype alleles

std::set< std::string > Genotype::_genotypeMissingValue [static, private]

bool Genotype::_isMissing [private]

bool Genotype::_isSNP [private]

Is the genotype for a SNP?

const char Genotype::_normalDelimiter = '/' [static, private]

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

• Genotype.h
• Genotype.cpp

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