gatb.core-API-0.0.0: IntegerTemplate< IntegerList

Class for large integers calculus. More...

#include <Integer.hpp>

Public Types
typedef boost::make_variant_over< transfolist >::type	Type

Public Member Functions
	IntegerTemplate (int64_t n=0)

template<typename T >
	IntegerTemplate (const T &t)

template<typename T >
IntegerTemplate &	operator= (const T &t)

const char *	getName ()

size_t	getSize ()

hid_t	hdf5 (bool &isCompound)

void	operator+= (const IntegerTemplate &a)

void	operator^= (const IntegerTemplate &a)

u_int8_t	operator[] (size_t idx) const

std::string	toString (size_t sizeKmer) const

template<typename U >
const U &	get () const

Static Public Member Functions
template<template< size_t > class Functor, typename Parameter >
static void	apply (size_t kmerSize, Parameter params)

Friends
IntegerTemplate	operator+ (const IntegerTemplate &a, const IntegerTemplate &b)

IntegerTemplate	operator- (const IntegerTemplate &a, const IntegerTemplate &b)

IntegerTemplate	operator\| (const IntegerTemplate &a, const IntegerTemplate &b)

IntegerTemplate	operator^ (const IntegerTemplate &a, const IntegerTemplate &b)

IntegerTemplate	operator& (const IntegerTemplate &a, const IntegerTemplate &b)

IntegerTemplate	operator~ (const IntegerTemplate &a)

bool	operator== (const IntegerTemplate &a, const IntegerTemplate &b)

bool	operator!= (const IntegerTemplate &a, const IntegerTemplate &b)

bool	operator< (const IntegerTemplate &a, const IntegerTemplate &b)

bool	operator<= (const IntegerTemplate &a, const IntegerTemplate &b)

IntegerTemplate	operator* (const IntegerTemplate &a, const int &c)

IntegerTemplate	operator/ (const IntegerTemplate &a, const u_int32_t &c)

u_int32_t	operator% (const IntegerTemplate &a, const u_int32_t &c)

IntegerTemplate	operator>> (const IntegerTemplate &a, const int &c)

IntegerTemplate	operator<< (const IntegerTemplate &a, const int &c)

IntegerTemplate	revcomp (const IntegerTemplate &a, size_t sizeKmer)

u_int64_t	hash1 (const IntegerTemplate &a, u_int64_t seed)

u_int64_t	oahash (const IntegerTemplate &a)

u_int64_t	simplehash16 (const IntegerTemplate &a, int shift)

u_int32_t	fastLexiMinimizer (const IntegerTemplate &a, int _nbMinimizers, bool &validResult)

std::ostream &	operator<< (std::ostream &s, const IntegerTemplate &a)

Detailed Description

template<typename IntegerList>
class gatb::core::tools::math::IntegerTemplate< IntegerList >

Class for large integers calculus.

The IntegerTemplate is implemented as a boost variant, which means that it can act like T1, T2, T3 or T4, etc.. type according to the configuration.

All the methods are implemented through a boost variant visitor.

Note that we have 2 possible native implementations (NativeInt64 and NativeInt128) that rely on native types uint64_t and __uint128_t.

For larger integer, a multi-precision LargeInt is used.

From the user point of view, [s]he has just to include this file and use the Integer class.

Member Typedef Documentation

typedef boost::make_variant_over<transfolist>::type Type

We define a boost variant from this type list.

Constructor & Destructor Documentation

IntegerTemplate ( int64_t n = 0 )

inline

Constructor. Note that the type (see getType and setType) has to be first initialized otherwise no instance can be created (exception thrown).

Parameters

[in] n : value for initialization of the integer.

IntegerTemplate ( const T & t )

inlineexplicit

Copy constructor. Relies on the copy constructor of boost variant

Parameters

[in] t : the object to be used for initialization

Member Function Documentation

static void apply	(	size_t	kmerSize,
		Parameter	params
	)

inlinestatic

Apply a functor with the best template specialization according to the provided kmer size.

const U& get ( ) const

inline

Get the value of the IntegerTemplate object as a U type, U being one of the T1,T2,T3,T4 template class parameters. This method can be seen as a converter from the IntegerTemplate class to a specific U type (given as a template parameter of this method).

Returns: the converted value as a U type.

const char* getName ( )

inline

Get the name of the class used by the variant (ie. one of the Ti template class parameters)

Returns: the class name.

size_t getSize ( )

inline

Get the size of an instance of the class used by the variant (ie. one of the Ti template class parameters)

Returns: the size of an object (in bits).

hid_t hdf5 ( bool & isCompound )

inline

Get the HDF5 type for the the class used by the variant (ie. one of the Ti template class parameters)

Parameters

[in] isCompound : tells whether the type is composed or not

Returns: a HDF5 identifier for the type.

void operator+= ( const IntegerTemplate< IntegerList > & a )

inline

Operator +=

Parameters

[in] a : first operand

Returns: addition and affectation.

IntegerTemplate& operator= ( const T & t )

inline

Affectation operator. Relies on the affectation operator of boost variant

Parameters

[in] t : object to be copied

Returns: the current object.

u_int8_t operator[] ( size_t idx ) const

inline

Operator[] access the ith nucleotide in the given integer. For instance a[4] get the 5th nucleotide of a kmer encoded as an Integer object.

Parameters

[in] idx : index of the nucleotide to be retrieved

Returns: the nucleotide value as follow: A=0, C=1, T=2 and G=3

void operator^= ( const IntegerTemplate< IntegerList > & a )

inline

Operator ^=

Parameters

[in] a : first operand

Returns: xor and affectation.

std::string toString ( size_t sizeKmer ) const

inline

Get an ASCII string representation of a kmer encoded as a IntegerTemplate object

Parameters

[in] sizeKmer : size of the kmer

Returns: the ASCII representation of the kmer.

Friends And Related Function Documentation

u_int32_t fastLexiMinimizer	(	const IntegerTemplate< IntegerList > &	a,
		int	_nbMinimizers,
		bool &	validResult
	)

friend

Get the lexicographical minimizer of the k-mer, quickly, using bit tricks. minimizers containing 'AA' are forbidden. might not return a valid result sometimes.

Parameters

[in]	nbminimizers	number of minimizers inside this kmer
[in]	&validResult	whether the returned result should be considered valid (if not, compute minimizer with another approach please)

Returns: the reverse complement kmer as a IntegerTemplate value

u_int64_t hash1	(	const IntegerTemplate< IntegerList > &	a,
		u_int64_t	seed
	)

friend

Get a hash value on 64 bits for a given IntegerTemplate object.

Parameters

[in]	a	: the integer value
[in]	seed	: some seed value used for the hash computation.

Returns: the hash value on 64 bits.

u_int64_t oahash ( const IntegerTemplate< IntegerList > & a )

friend

Get a hash value on 64 bits for a given IntegerTemplate object.

Parameters

[in] a : the integer value

Returns: the hash value on 64 bits.

bool operator!=	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator !=

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: inequality of the two operands.

u_int32_t operator%	(	const IntegerTemplate< IntegerList > &	a,
		const u_int32_t &	c
	)

friend

Operator %

Parameters

[in]	a	: first operand
[in]	c	: second operand

Returns: modulo of the two operands.

IntegerTemplate operator&	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator &

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: 'and' of the two operands.

IntegerTemplate operator*	(	const IntegerTemplate< IntegerList > &	a,
		const int &	c
	)

friend

Operator *

Parameters

[in]	a	: first operand
[in]	c	: second operand

Returns: multiplication of the two operands.

IntegerTemplate operator+	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator +

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: sum of the two operands.

IntegerTemplate operator-	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator -

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: substraction of the two operands.

IntegerTemplate operator/	(	const IntegerTemplate< IntegerList > &	a,
		const u_int32_t &	c
	)

friend

Operator /

Parameters

[in]	a	: first operand
[in]	c	: second operand

Returns: division of the two operands.

bool operator<	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator <

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: '<' of the two operands.

IntegerTemplate operator<<	(	const IntegerTemplate< IntegerList > &	a,
		const int &	c
	)

friend

Operator <<

Parameters

[in]	a	: first operand
[in]	c	: second operand

Returns: left shift of the two operands.

std::ostream& operator<<	(	std::ostream &	s,
		const IntegerTemplate< IntegerList > &	a
	)

friend

Output stream operator for the IntegerTemplate class

Parameters

[in]	s	: the output stream to be used.
[in]	a	: the object to output

Returns: the modified output stream.

bool operator<=	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator <=

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: '<=' of the two operands.

bool operator==	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator ==

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: equality of the two operands.

IntegerTemplate operator>>	(	const IntegerTemplate< IntegerList > &	a,
		const int &	c
	)

friend

Operator >>

Parameters

[in]	a	: first operand
[in]	c	: second operand

Returns: right shift of the two operands.

IntegerTemplate operator^	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator ^

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: 'xor' of the two operands.

IntegerTemplate operator\|	(	const IntegerTemplate< IntegerList > &	a,
		const IntegerTemplate< IntegerList > &	b
	)

friend

Operator |

Parameters

[in]	a	: first operand
[in]	b	: second operand

Returns: 'or' of the two operands.

IntegerTemplate operator~ ( const IntegerTemplate< IntegerList > & a )

friend

Operator ~

Parameters

[in] a : operand

Returns: negation of the operand

IntegerTemplate revcomp	(	const IntegerTemplate< IntegerList > &	a,
		size_t	sizeKmer
	)

friend

Get the reverse complement of a kmer encoded as an IntegerTemplate object. Note that the kmer size must be known.

Parameters

[in]	a	: kmer value to be reversed-complemented
[in]	sizeKmer	: size of the kmer

Returns: the reverse complement kmer as a IntegerTemplate value

u_int64_t simplehash16	(	const IntegerTemplate< IntegerList > &	a,
		int	shift
	)

friend

Get a hash value on 64 bits for a given IntegerTemplate object. Note: although we return 64 bits, only the first 16 bits are set

Parameters

[in]	a	: the integer value
[in]	shift	: some value used for the hash computation.

Returns: the hash value on 64 bits.

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

/builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/tools/math/Integer.hpp

Public Types

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

template<typename IntegerList> class gatb::core::tools::math::IntegerTemplate< IntegerList >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

template<typename IntegerList>
class gatb::core::tools::math::IntegerTemplate< IntegerList >