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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sequtil__manip_8cpp_source.html below:

NCBI C++ ToolKit: src/util/sequtil/sequtil_manip.cpp Source File

64 const char

* begin = src + (pos / 4);

65 const char

* end = src + ((pos + length - 1) / 4) + 1;

66 const char

* iter = end;

68 size_t offset

= (pos + length - 1) % 4;

72 for

( ; iter != begin; ++dst ) {

86 if

( length % 4 != 0 ) {

87

*dst =

table

[

static_cast<Uint1>

(*iter) * 2 + 1];

88 if

( iter != begin ) {

90

*dst |= (char)

table

[

static_cast<Uint1>

(*iter) * 2];

96

*dst &= char(0xFF << ((4 - (length % 4)) % 4) * 2);

108 size_t

start_offset = (pos + length - 1) % 2;

112 const char

* begin = src + (pos / 2);

113 const char

* end = src + ((pos + length - 1) / 2) + 1;

114 const char

* iter = end;

116 switch

( start_offset ) {

120 for

( ; iter != begin; ++dst ) {

124 if

( length % 2 != 0 ) {

134

*dst = char((

static_cast<Uint1>

(*iter) & 0xF0) |

135

(

static_cast<Uint1>

(*(iter - 1)) & 0x0F));

138 if

( length % 2 != 0 ) {

140

*dst = char(

static_cast<Uint1>

(*iter) & 0xF0);

150 template

typename

SrcCont,

typename

DstCont>

152

(

const

SrcCont& src,

159 if

( src.empty() || (length == 0) ) {

167

pos, length, &*dst.begin());

172

(

const string

& src,

179 return s_Reverse

(src, src_coding, pos, length, dst);

184

(

const

vector<char>& src,

191 return s_Reverse

(src, coding,pos, length, dst);

202 _ASSERT

((dst != 0) && (src != 0));

204 switch

( src_coding ) {

215

reverse_copy(src + pos, src + pos + length, dst);

227 template

typename

SrcCont,

typename

DstCont>

229

(

const

SrcCont& src,

236 if

( src.empty() || (length == 0) ) {

244

pos, length, &*dst.begin());

249

(

const string

& src,

261

(

const

vector<char>& src,

278 const char

* iter = src + (pos / 4);

279 const char

* end = src + ((pos + length - 1) / 4) + 1;

281 if

( pos % 4 == 0 ) {

282 for

( ; iter != end; ++iter, ++dst ) {

283

*dst = char(~(*iter));

286 if

( length % 4 != 0 ) {

287

*(--dst) &=

char

(0xFF << (8 - (length % 4) * 2));

295 table

[

static_cast<Uint1>

(*(iter + 1)) * 2 + 1] );

299 if

( length % 4 != 0 ) {

300

*dst = (char)

table

[

static_cast<Uint1>

(*iter) * 2];

301 if

( ++iter != end ) {

302

*dst |= (char)

table

[

static_cast<Uint1>

(*iter) * 2 + 1];

307

*dst &= char(0xFF << ((4 - (length % 4)) % 4) * 2);

319 const char

* end = src + pos + length;

320 const char

* iter = src + pos;

322 for

( ; iter != end; ++iter, ++dst ) {

323

*dst = char(3 -

static_cast<Uint1>

(*iter));

336 const char

* iter = src + (pos / 2);

337 const char

* end = src + (pos + length - 1) / 2 + 1;

344 for

( ; iter != end; ++iter, ++dst ) {

345

*dst = (char)

table

[

static_cast<Uint1>

(*iter)];

348 if

( length % 2 != 0 ) {

359 table

[

static_cast<Uint1>

(*(iter + 1)) * 2 + 1] );

362 if

( length % 2 != 0 ) {

363

*dst = (char)

table

[

static_cast<Uint1>

(*iter) * 2];

380 _ASSERT

((dst != 0) && (src != 0));

382 switch

( src_coding ) {

404 "There is no complement for the specified coding."

);

411 template

typename

SrcCont,

typename

DstCont>

413

(

const

SrcCont& src,

420 if

( src.empty() || (length == 0) ) {

428

pos, length, &*dst.begin());

433

(

const string

& src,

445

(

const

vector<char>& src,

462 size_t offset

= (pos + length - 1) % 4;

465 const char

* begin = src + (pos / 4);

466 const char

* iter = src + (pos + length - 1) / 4 + 1;

475 table

[

static_cast<Uint1>

(*(iter - 1)) * 2 + 1];

479 if

( length % 4 != 0 ) {

480

*dst =

table

[

static_cast<Uint1>

(*iter) * 2];

481 if

( iter != begin ) {

483

*dst |= (char)

table

[

static_cast<Uint1>

(*iter) * 2 + 1];

490 for

( ; iter != begin; ++dst ) {

497

*dst &= char(0xFF << ((4 - (length % 4)) % 4) * 2);

509 const char

* begin = src + pos;

510 const char

* iter = src + pos + length;

512 for

( ; iter != begin; ++dst ) {

513

*dst = char(3 -

static_cast<Uint1>

(*--iter));

526 const char

* begin = src + (pos / 2);

527 const char

* iter = src + ((pos + length - 1) / 2) + 1;

529 size_t offset

= (pos + length - 1) % 2;

539 table

[

static_cast<Uint1>

(*(iter - 1)) * 2 + 1];

542 if

( length % 2 != 0 ) {

543

*dst =

table

[

static_cast<Uint1>

(*iter) * 2];

550 for

( ; iter != begin; ++dst ) {

554 if

( length % 2 != 0 ) {

572 _ASSERT

((dst != 0) && (src != 0));

574 switch

( src_coding ) {

597 "There is no complement for the specified coding."

);

603 template

typename

SrcCont>

611 if

( src.empty() || (length == 0) ) {

649 char

first

= src + pos;

654

temp = char(3 - *

first

);

660 copy

(src + pos, src + pos + length, src);

672 char

buf

new char

[length];

689 char

buf

new char

[length];

709 switch

( src_coding ) {

731 "There is no complement for the specified coding."

);

static const Uint1 * GetTable(size_t offset)

static const Uint1 * GetTable(void)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

static SIZE_TYPE Reverse(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

static SIZE_TYPE Complement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

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

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

uint8_t Uint1

1-byte (8-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

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

static SIZE_TYPE s_Ncbi2naRevCmp(const char *src, TSeqPos pos, TSeqPos length, char *dst)

static SIZE_TYPE s_Ncbi2naExpandRevCmp(const char *src, TSeqPos pos, TSeqPos length, char *dst)

static SIZE_TYPE s_4naReverse(const char *src, TSeqPos pos, TSeqPos length, char *dst)

static SIZE_TYPE s_Ncbi4naRevCmp(const char *src, TSeqPos pos, TSeqPos length, char *dst)

SIZE_TYPE s_ReverseComplement(const SrcCont &src, CSeqUtil::TCoding src_coding, TSeqPos pos, TSeqPos length, DstCont &dst)

static SIZE_TYPE s_Ncbi2naComplement(const char *src, TSeqPos pos, TSeqPos length, char *dst)

static SIZE_TYPE s_2naReverse(const char *src, TSeqPos pos, TSeqPos length, char *dst)

SIZE_TYPE s_Complement(const SrcCont &src, CSeqUtil::TCoding src_coding, TSeqPos pos, TSeqPos length, DstCont &dst)

static SIZE_TYPE s_Ncbi2naExpandComplement(const char *src, TSeqPos pos, TSeqPos length, char *dst)

SIZE_TYPE s_Reverse(const SrcCont &src, CSeqUtil::TCoding src_coding, TSeqPos pos, TSeqPos length, DstCont &dst)

static SIZE_TYPE s_Ncbi4naComplement(const char *src, TSeqPos pos, TSeqPos length, char *dst)

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