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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/LargeInt_8hpp_source.html below:

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

std::array<const unsigned char, 256>

;

std::array<const char, 4>

;

u_int64_t

(u_int64_t elem)

u_int64_t

= elem;

=

;

sizeKmer = kmer.size();

(

= 0;

< sizeKmer;

++) {

<

T>

(

=

;

<

; ++

) {

(coeff == 2 || coeff == 4)

printf(

,coeff);

(

j = 1; j >= 0; --j)

u_int64_t

= (

<< 32) | ((this->

[

] >> (32*j)) & mask32bits );

.value[

] =

.value[

] | (((

/ divisor) & mask32bits) << (32*j));

(

j = 1; j >= 0; --j)

u_int64_t

= (

<< 32) | ((this->

[

] >> (32*j)) & mask32bits );

.value[

] = ~this->value[

];

large_shift = coeff / 64;

small_shift = coeff % 64;

(small_shift == 0)

.value[

+1] = this->

[

-large_shift] >> (64 - small_shift);

large_shift = coeff / 64;

small_shift = coeff % 64;

.value[0] = (this->

[large_shift] >> small_shift);

.value[

] = (this->

[

+large_shift] >> small_shift);

(small_shift == 0)

.value[

-1] =

.value[

-1] | (this->

[

+large_shift] << (64 - small_shift));

*

= *

+ other;

*(

) = (*

) << coeff;

*

;

*(

) = (*

) >> coeff;

*

;

( ;

>=0 ;

--) { s <<

.value[

];

(

>=1) { s <<

; } }

<

Map>

(

=0;

<

; ++

) { res = res * 4 + fct(

[

]); }

(

=0;

<sizeKmer;

++) { seq[sizeKmer-

-1] =

[(*this)[

]]; }

u_int8_t

(

idx)

{

(this->

[idx/32] >> (2*idx%64)) & 3; }

chunk = (intermediate &

).

[0];

intermediate = intermediate >> 64;

* kmerrev = (

*) (&(res.

[0]));

* kmer = (

*) (&(x.

[0]));

(res >> (2*( 32*

- sizeKmer)) ) ;

std::array< const unsigned char, 256 > revcomp_4NT

std::array< const char, 4 > bin2NT

ncbi::TMaskedQueryRegions mask

LargeInt & operator+=(const LargeInt &other)

Operator +=.

LargeInt operator-(const LargeInt &other) const

Operator -.

LargeInt operator|(const LargeInt &other) const

Operator |.

LargeInt(const std::string &kmer)

LargeInt operator/(const uint32_t &divisor) const

Operator /.

LargeInt & operator>>=(const int &coeff)

Operator >>=.

friend std::ostream & operator<<(std::ostream &s, const LargeInt< precision > &l)

Output stream operator for the IntegerTemplate class.

LargeInt operator&(const char &other) const

Operator &.

LargeInt & operator|=(const LargeInt &other)

Operator |=.

bool operator<(const LargeInt &c) const

Operator <.

u_int64_t value[precision]

bool operator==(const LargeInt &c) const

Operator ==.

LargeInt & operator&=(const LargeInt &other)

Operator &=.

LargeInt(const T &a, const T &b)

LargeInt operator&(const LargeInt &other) const

Operator &.

u_int64_t getVal() const

Get the 64 less significant bits of the LargeInt object as a native integer type.

std::string toString(size_t sizeKmer) const

Print corresponding kmer in ASCII.

bool operator<=(const LargeInt &c) const

Operator <=.

static const size_t getSize()

Get the size of an instance of the class.

LargeInt(const u_int64_t &val=0)

Constructor.

LargeInt operator>>(const int &coeff) const

Operator >>.

bool operator!=(const LargeInt &c) const

Operator !=.

LargeInt operator~() const

Operator ~.

static const char * getName()

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

LargeInt & operator<<=(const int &coeff)

Operator <<=.

LargeInt & operator^=(const LargeInt &other)

Operator ^=.

uint32_t operator%(const uint32_t &divisor) const

Operator %.

LargeInt operator^(const LargeInt &other) const

Operator ^.

u_int8_t operator[](size_t idx) const

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

friend LargeInt< T > revcomp(const LargeInt< T > &i, size_t sizeKmer)

static LargeInt polynom(const char *data, size_t size, Map fct)

Computes a kmer value as polynom.

LargeInt operator<<(const int &coeff) const

Operator <<.

LargeInt operator+(const LargeInt &other) const

Operator +.

LargeInt operator*(const int &coeff) const

Operator *.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

CRange< Position > Map(const CRange< Position > &target, const CRange< Position > &range)

static void hex(unsigned char c)

static u_int64_t oahash64(u_int64_t elem)

LargeInt< precision > revcomp(const LargeInt< precision > &x, size_t sizeKmer)

const struct ncbi::grid::netcache::search::fields::SIZE size

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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