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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Integer_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/gnomon/debruijn/Integer.hpp Source File

25 #ifndef _GATB_CORE_TOOLS_MATH_INTEGER_HPP_ 26 #define _GATB_CORE_TOOLS_MATH_INTEGER_HPP_ 31 #include <boost/variant.hpp> 59 template

typename

T1,

typename

T2,

typename

T3,

typename

T4,

typename

T5>

64 typedef

boost::variant<T1,T2,T3,T4,T5>

Type

;

77 int

p = (kmer_len+31)/32;

83 else

{ std::cerr <<

"Not supported kmer length in Integer initialization"

;

exit

(1); }

87 int

p = (kmer.size()+31)/32;

89 else if

(p <=

PREC_2

)

= T2(kmer);

90 else if

(p <=

PREC_3

)

= T3(kmer);

91 else if

(p <=

PREC_4

)

= T4(kmer);

92 else if

(p <=

PREC_5

)

= T5(kmer);

93 else

{ std::cerr <<

"Not supported kmer length in Integer initialization"

;

exit

(1); }

96 IntegerTemplate

(

const

std::string::const_iterator&

const

std::string::const_iterator&

) {

97 int

p = (

+31)/32;

103 else

{ std::cerr <<

"Not supported kmer length in Integer initialization"

;

exit

(1); }

124 template

typename

134 const char

getName

()

const

{

return

boost::apply_visitor (Integer_name(), *(*

this

)); }

139 const size_t getSize

()

const

{

return

boost::apply_visitor (Integer_size(), *(*

this

)); }

262

u_int8_t

operator[]

(

size_t

idx)

const

{

return

boost::apply_visitor (Integer_value_at(idx), *(*

this

)); }

275 std::string toString

(

size_t

sizeKmer)

const

{

return

boost::apply_visitor (Integer_toString(sizeKmer), *(*

this

)); }

289 template

typename

290 const U

get

()

const

{

return

* boost::get<U>(&

); }

299

u_int64_t

oahash

()

const

{

return

boost::apply_visitor (Integer_oahash(), *(*

this

)); }

305 template

typename

void operator()

(

& newl,

& origl)

const

{

306 int

orig_precision = origl.getSize()/64;

307 uint64_t

* orig_guts = origl.GetGuts();

309 int

new_precision = newl.getSize()/64;

310 uint64_t

* new_guts = newl.GetGuts();

312 std::copy

(orig_guts, orig_guts+

std::min

(orig_precision, new_precision), new_guts);

313 int

partial_part_bits = 2*(

kmer_len

%32);

314 if

(partial_part_bits > 0) {

316

new_guts[new_precision-1] &=

mask

;

322 template

typename

T> u_int64_t

operator()

(

const T

)

const

{

return a

.oahash(); }};

324 struct Pointer

public

boost::static_visitor<void*> {

328 template

typename

const char

operator()

(

const T

)

const

{

return a

.getName(); }};

331 template

typename

const size_t operator()

(

const T

)

const

{

return a

.getSize(); }};

343 struct Integer_or

public

boost::static_visitor<IntegerTemplate> {

348 struct Integer_xor

public

boost::static_visitor<IntegerTemplate> {

353 struct Integer_and

public

boost::static_visitor<IntegerTemplate> {

359 template

typename

bool operator()

(

const T

)

const

{

return a

; }

360 template

typename

bool operator()

(

const T

const U

)

const

{

return false

; }

364 template

typename

bool operator()

(

const T

)

const

{

return a

; }

365 template

typename

bool operator()

(

const T

const U

)

const

{

return false

; }

369 template

typename

bool operator()

(

const T

)

const

{

return a

; }

370 template

typename

bool operator()

(

const T

const U

)

const

{

return false

; }

375 template

typename

void operator()

(

const U

)

const

{ }

380 template

typename

void operator()

(

const U

)

const

{ }

386 template

typename

Result,

typename

Arg>

387 struct Visitor

public

boost::static_visitor<Result>

403 template

typename

T> u_int32_t

operator()

(

const T

)

const

{

return

(

%this->

arg

); }};

419 template

typename

T> u_int8_t

operator()

(

const T

)

const

{

return a

[this->

arg

]; }};

428 #define INTEGER_TYPES LargeInt<PREC_1>,LargeInt<PREC_2>,LargeInt<PREC_3>,LargeInt<PREC_4>,LargeInt<PREC_5>

Class that manages large integers.

ncbi::TMaskedQueryRegions mask

Class for large integers calculus.

const char * getName() const

Get the name of the class used by the variant (ie.

const U & get() const

Get the value of the IntegerTemplate object as a U type, U being one of the T1,T2,...

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

Output stream operator for the IntegerTemplate class.

u_int8_t operator[](size_t idx) const

Operator[] access the ith nucleotide in the given integer.

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

Operator <.

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

Operator !=.

friend IntegerTemplate revcomp(const IntegerTemplate &a, size_t sizeKmer)

Get the reverse complement of a kmer encoded as an IntegerTemplate object.

void operator^=(const IntegerTemplate &a)

Operator ^=.

IntegerTemplate(const T &t)

Construct from a different size IntegerTemplate Will clip (or add) extra nucs on the LEFT of the stri...

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

Operator &.

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

Operator ^.

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

Operator ==.

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

Operator +.

const size_t getSize() const

Get the size of an instance of the class used by the variant (ie.

IntegerTemplate(int kmer_len, uint64_t n)

void operator+=(const IntegerTemplate &a)

Operator +=.

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

Operator /.

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

Operator <<.

IntegerTemplate(const std::string::const_iterator &a, const std::string::const_iterator &b)

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

Operator -.

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

Operator <=.

IntegerTemplate(const std::string &kmer)

IntegerTemplate & operator=(const T &t)

Affectation operator.

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

Operator |.

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

Operator %.

friend IntegerTemplate operator~(const IntegerTemplate &a)

Operator ~.

boost::variant< T1, T2, T3, T4, T5 > Type

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

Operator >>

std::string toString(size_t sizeKmer) const

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

void * getPointer()

Get pointer to the actual data - used for EMPHF.

u_int64_t oahash() const

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

unsigned int

A callback function used to compare two keys in a database.

IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > > TKmer

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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

IntegerTemplate operator()(const T &a)