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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/LargeInt1_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/gnomon/debruijn/LargeInt1.hpp Source File

25 template

<>

class

LargeInt<1>

33  int

sizeKmer = kmer.size();

34  for

(

int i

= 0;

i

< sizeKmer;

i

++) {

40  template

<

typename

T>

42  for

(

T i

=

a

;

i

<

b

; ++

i

) {

50  static const char

*

getName

() {

return "LargeInt<1>"

; }

52  static const size_t getSize

() {

return

8*

sizeof

(u_int64_t); }

62

u_int32_t

operator%

(

const

u_int32_t& divisor)

const

{

return value

[0] % divisor; }

77  LargeInt<1>

& operator<<= (

const int

& coeff) {

value

[0] <<= coeff;

return

*

this

; }

78  LargeInt<1>

& operator>>= (

const int

& coeff) {

value

[0] >>= coeff;

return

*

this

; }

80

u_int8_t operator[] (

size_t

idx)

const

{

return

(

value

[0] >> (2*idx)) & 3; }

85

s <<

std::hex

<<

l

.value[0] << std::dec;

return

s;

95

u_int64_t temp =

value

[0];

98  for

(

i

=sizeKmer-1;

i

>=0;

i

--)

112  inline static

u_int64_t

revcomp64

(

const

u_int64_t& x,

size_t

sizeKmer)

121

res = ((res>> 2 & 0x3333333333333333) | (res & 0x3333333333333333) << 2);

122

res = ((res>> 4 & 0x0F0F0F0F0F0F0F0F) | (res & 0x0F0F0F0F0F0F0F0F) << 4);

123

res = ((res>> 8 & 0x00FF00FF00FF00FF) | (res & 0x00FF00FF00FF00FF) << 8);

124

res = ((res>>16 & 0x0000FFFF0000FFFF) | (res & 0x0000FFFF0000FFFF) << 16);

125

res = ((res>>32 & 0x00000000FFFFFFFF) | (res & 0x00000000FFFFFFFF) << 32);

126

res = res ^ 0xAAAAAAAAAAAAAAAA;

128  return

(res >> (2*(32-sizeKmer))) ;

132  template

<

typename

Map>

LargeInt< 1 > revcomp(const LargeInt< 1 > &x, size_t sizeKmer)

std::array< const char, 4 > bin2NT

static u_int64_t revcomp64(const u_int64_t &x, size_t sizeKmer)

static const size_t getSize()

static const char * getName()

friend std::ostream & operator<<(std::ostream &s, const LargeInt< 1 > &l)

u_int64_t toInt() const

Returns lower 64 bits.

std::string toString(size_t sizeKmer) const

Print corresponding kmer in ASCII.

static LargeInt< 1 > polynom(const char *data, size_t size, Map fct)

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

CNcbiOstream & operator<<(CNcbiOstream &out, const CEquivRange &range)

CNcbiIstream & operator>>(CNcbiIstream &s, const getcontig &c)

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

CSafeFlags< E > operator&(E a, CSafeFlags< E > b)

CSafeFlags< E > operator^(E a, CSafeFlags< E > b)

string operator+(const CCgiEntry &e, const string &s)

CVect2< T > operator-(const CVect2< T > &v)

CVect2< NCBI_PROMOTE(T, U) > operator/(const CVect2< T > &v1, U v2)

CVect2< NCBI_PROMOTE(int,U) > operator*(int v1, const CVect2< U > &v2)

CFields operator|(CFields, CFields)

CExpression operator<=(time_point, CREATED)

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

CNcbiMatrix< T > & operator+=(CNcbiMatrix< T > &, const CNcbiMatrix< U > &)

global addition: matrix += matrix

static void hex(unsigned char c)

static u_int64_t oahash64(u_int64_t elem)

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

CObject operator%(const CObject &a, const CObject &b)

const GenericPointer< typename T::ValueType > T2 value

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

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