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NCBI C++ ToolKit: src/objects/seq/seqport_util.cpp Source File

68 static const bool kName

=

false

;

119

vector<Uint4>* blast_ambig = 0)

135

vector<TSeqPos>* badIdx,

143

vector<TSeqPos>* out_indices,

230  const string

&

code

);

233  const string

&

code

);

286  for

(

size_t i

=0;

i

<size1;

i

++)

386

vector<Uint4>* blast_ambig = 0)

504

vector<Uint4>* blast_ambig)

524

vector<Uint4>* blast_ambig)

595

vector<TSeqPos>* badIdx,

601

vector<TSeqPos>* badIdx,

607

vector<TSeqPos>* badIdx,

613

vector<TSeqPos>* badIdx,

674

vector<TSeqPos>* out_indices,

686

vector<TSeqPos>* out_indices,

892  const string

**

str

,

893  const

vector<char>** vec)

927

(in_seq, out_seq, to_code, uBeginIdx, uLength, bAmbig,

seed

,

938

vector<Uint4>* blast_ambig)

942

17734276, total_length, out_seq_length, blast_ambig);

960

(in_seq, uBeginIdx, uLength);

966

vector<TSeqPos>* badIdx,

971

(in_seq, badIdx, uBeginIdx, uLength);

978

vector<TSeqPos>* out_indices,

984

(in_seq, out_seq, out_indices, to_code, uBeginIdx, uLength);

995

(in_seq, out_seq, uBeginIdx, uLength);

1006

(in_seq, uBeginIdx, uLength);

1021

in_seq1, uBeginIdx1, uLength1, in_seq2, uBeginIdx2, uLength2);

1031

(in_seq, uBeginIdx, uLength);

1042

(in_seq, out_seq, uBeginIdx, uLength);

1052

(in_seq, uBeginIdx, uLength);

1063

(in_seq, out_seq, uBeginIdx, uLength);

1073

(in_seq, uBeginIdx, uLength);

1084

(in_seq, out_seq, uBeginIdx, uLength);

1145  const string

&

code

)

1152  const string

&

code

)

1307

unique_ptr<CObjectIStream>

1314

*asn_codes_in >> *ptr_seq_code_set;

1317  return

ptr_seq_code_set;

1329

list<CRef<CSeq_code_table> >::const_iterator i_ct;

1330  for

(i_ct = code_list.begin(); i_ct != code_list.end(); ++i_ct)

1331  if

((*i_ct)->GetCode() == code_type)

1335  if

(i_ct == code_list.end())

1336  throw

runtime_error(

"Requested code table not found"

);

1339  const

list<CRef<CSeq_code_table::C_E> >& table_data = (*i_ct)->GetTable();

1341  int

start_at = (*i_ct)->GetStart_at();

1345  for

(

int i

=0;

i

<256;

i

++)

1346

codeTable->m_Table[

i

] =

'\xff'

;

1349  int

nIdx = start_at;

1351  for

(i_td = table_data.begin(); i_td != table_data.end(); ++i_td) {

1352

codeTable->m_Table[nIdx] = *((*i_td)->GetSymbol().c_str());

1353  if

(codeTable->m_Table[nIdx] ==

'\x00'

)

1354

codeTable->m_Table[nIdx++] =

'\xff'

;

1373

list<CRef<CSeq_code_table> >::const_iterator i_ct;

1374  for

(i_ct = code_list.begin(); i_ct != code_list.end(); ++i_ct)

1379  if

(i_ct == code_list.end())

1380  throw

runtime_error(

"Code table for Iupacna not found"

);

1383  if

(!(*i_ct)->IsSetComps())

1384  throw

runtime_error(

"Complement data is not set for iupacna table"

);

1387  const

list<int>& comp_data = (*i_ct)->GetComps();

1388  int

start_at = (*i_ct)->GetStart_at();

1394  for

(

unsigned int i

= 0;

i

<256;

i

++)

1395

compTable->m_Table[

i

] = (

char

) 255;

1398

list<int>::const_iterator i_comp;

1399  unsigned int

nIdx = start_at;

1400  for

(i_comp = comp_data.begin(); i_comp != comp_data.end(); ++i_comp)

1401

compTable->m_Table[nIdx++] = (*i_comp);

1418

list<CRef<CSeq_code_table> >::const_iterator i_ct;

1419  for

(i_ct = code_list.begin(); i_ct != code_list.end(); ++i_ct)

1423  if

(i_ct == code_list.end())

1424  throw

runtime_error(

"Code table for Iupacna not found"

);

1427  if

(!(*i_ct)->IsSetComps())

1428  throw

runtime_error(

"Complement data is not set for ncbi2na table"

);

1431  const

list<int>& comp_data = (*i_ct)->GetComps();

1432  int

start_at = (*i_ct)->GetStart_at();

1439  int

nIdx = start_at;

1440

list<int>::const_iterator i_comp;

1441  for

(i_comp = comp_data.begin(); i_comp != comp_data.end(); ++i_comp)

1442

compArray[nIdx++] = (*i_comp);

1445  for

(

unsigned int i

= 0;

i

< 4;

i

++)

1446  for

(

unsigned int

j = 0; j < 4; j++)

1447  for

(

unsigned int

k = 0; k < 4; k++)

1448  for

(

unsigned int l

= 0;

l

< 4;

l

++)

1450

nIdx =

i

<<6 | j<<4 | k<<2 |

l

;

1451  char

c1 = compArray[

i

] << 6;

1452  char

c2 = compArray[j] << 4;

1453  char

c3 = compArray[k] << 2;

1454  char

c4 = compArray[

l

];

1455

compTable->m_Table[nIdx] = c1 | c2 | c3 | c4;

1473

list<CRef<CSeq_code_table> >::const_iterator i_ct;

1474  for

(i_ct = code_list.begin(); i_ct != code_list.end(); ++i_ct)

1478  if

(i_ct == code_list.end())

1479  throw

runtime_error(

"Code table for Iupacna not found"

);

1482  if

(!(*i_ct)->IsSetComps())

1483  throw

runtime_error(

"Complement data is not set for iupacna table"

);

1486  const

list<int>& comp_data = (*i_ct)->GetComps();

1487  int

start_at = (*i_ct)->GetStart_at();

1495  int

nIdx = start_at;

1496

list<int>::const_iterator i_comp;

1497  for

(i_comp = comp_data.begin(); i_comp != comp_data.end(); ++i_comp)

1498

compArray[nIdx++] = (*i_comp);

1501  for

(

unsigned int i

= 0;

i

<16;

i

++)

1502  for

(

unsigned int

j = 0; j < 16; j++)

1505  char

c1 = compArray[

i

] << 4;

1506  char

c2 = compArray[j];

1507

compTable->m_Table[nIdx] = c1 | c2;

1524  for

(

unsigned int i

= 0;

i

< 4;

i

++)

1525  for

(

unsigned int

j = 0; j < 4; j++)

1526  for

(

unsigned int

k = 0; k < 4; k++)

1527  for

(

unsigned int l

= 0;

l

< 4;

l

++)

1528

revTable->m_Table[64*

i

+ 16*j + 4*k +

l

] =

1529

64*

l

+ 16*k + 4*j +

i

;

1544  for

(

unsigned int i

= 0;

i

< 16;

i

++)

1545  for

(

unsigned int

j = 0; j < 16; j++)

1546

revTable->m_Table[16*

i

+ j] = 16*j +

i

;

1565

list<CRef<CSeq_map_table> >::const_iterator i_mt;

1566  for

(i_mt = map_list.begin(); i_mt != map_list.end(); ++i_mt)

1567  if

((*i_mt)->GetFrom() == from_type && (*i_mt)->GetTo() == to_type)

1570  if

(i_mt == map_list.end())

1571  throw

runtime_error(

"Requested map table not found"

);

1574  const

list<int>& table_data = (*i_mt)->GetTable();

1578  int

start_at = (*i_mt)->GetStart_at();

1582  int

nIdx = start_at;

1583

list<int>::const_iterator i_td;

1584  for

(i_td = table_data.begin(); i_td != table_data.end(); ++i_td)

1586

mapTable->m_Table[nIdx++] = *i_td;

1630  unsigned char i

, j, k,

l

;

1632  for

(

i

= 0;

i

< 4;

i

++)

1633  for

(j = 0; j < 4; j++)

1634  for

(k = 0; k < 4; k++)

1635  for

(

l

= 0;

l

< 4;

l

++) {

1636  unsigned char

aByte = (

i

<<6) | (j<<4) | (k<<2) |

l

;

1643  reinterpret_cast<char

*

>

(&fastTable->m_Table[aByte]);

1644

*(pt++) = (chi << 4) | chj;

1645

*pt = (

chk

<< 4) | chl;

1657  for

(

i

= 0;

i

< 16;

i

++)

1658  for

(j = 0; j < 16; j++) {

1659  unsigned char

aByte = (

i

<<4) | j;

1665  char

*pt =

reinterpret_cast<char

*

>

(&fastTable->m_Table[aByte]);

1680  for

(

int

ch = 0; ch < 256; ch++) {

1681  if

((ch >= start_at) && (ch < (start_at +

size

)))

1685  for

(

unsigned int

pos = 0; pos < 4; pos++)

1686

fastTable->m_Table[pos][ch] =

uch

<< (6-2*pos);

1689  for

(

unsigned int

pos = 0; pos < 4; pos++)

1690

fastTable->m_Table[pos][ch] =

'\x00'

;

1703  for

(

int

ch = 0; ch < 256; ch++) {

1704  if

((ch >= start_at) && (ch < (start_at +

size

)))

1707  for

(

unsigned int

pos = 0; pos < 2; pos++)

1708

fastTable->m_Table[pos][ch] =

uch

<< (4-4*pos);

1712

fastTable->m_Table[0][ch] = 0xF0;

1713

fastTable->m_Table[1][ch] = 0x0F;

1727  for

(

int

n1 = 0; n1 < 16; n1++)

1728  for

(

int

n2 = 0; n2 < 16; n2++) {

1729  int

nIdx = 16*n1 + n2;

1730  unsigned char

u1, u2;

1731  if

((n1 >= start_at) && (n1 < start_at +

size

))

1735  if

((n2 >= start_at) && (n2 < start_at +

size

))

1739

fastTable->m_Table[0][nIdx] = (u1<<6) | (u2<<4);

1740

fastTable->m_Table[1][nIdx] = (u1<<2) | u2;

1757  for

(

unsigned int

ii = 0; ii <

kNumCodes

; ii++) {

1762  if

(!found[

code

-1]) {

1763

found[

code

-1] =

true

;

1765

(*it)->GetStart_at() : 0;

1771

(make_pair((*is)->GetSymbol(),

i

++));

1773  if

( (*it)->IsSetComps() ) {

1774  ITERATE

(list<int>, ic, (*it)->GetComps()) {

1789  unsigned int i

, j, uCnt;

1790  unsigned char

cVal, cRslt;

1795  static const unsigned char mask

[16] = {

1796

0x11, 0x12, 0x14, 0x18,

1797

0x21, 0x22, 0x24, 0x28,

1798

0x41, 0x42, 0x44, 0x48,

1799

0x81, 0x82, 0x84, 0x88

1802  static const unsigned char

maskUpper[4] = { 0x10, 0x20, 0x40, 0x80 };

1803  static const unsigned char

maskLower[4] = { 0x01, 0x02, 0x04, 0x08 };

1807  for

(

i

= 0;

i

< 256;

i

++) {

1812  if

(((cVal &

'\x0f'

) != 0) && ((cVal &

'\xf0'

) != 0))

1813  for

(j = 0; j < 16; j++) {

1814

cRslt = cVal &

mask

[j];

1815  if

(cRslt ==

mask

[j])

1816

aMask->m_Table[

i

].cMask[uCnt++] =

mask

[j];

1820  else if

((cVal &

'\x0f'

) != 0)

1821  for

(j = 0; j < 4; j++)

1823

cRslt = cVal & maskLower[j];

1824  if

(cRslt == maskLower[j])

1825

aMask->m_Table[

i

].cMask[uCnt++] = maskLower[j];

1830  else if

((cVal &

'\xf0'

) != 0)

1831  for

(j = 0; j < 4; j++)

1833

cRslt = cVal & maskUpper[j];

1834  if

(cRslt == maskUpper[j])

1835

aMask->m_Table[

i

].cMask[uCnt++] = maskUpper[j];

1840

aMask->m_Table[

i

].cMask[uCnt++] =

'\x00'

;

1843

aMask->m_Table[

i

].nMasks = uCnt;

1847  for

(j = uCnt; j < 16 && uCnt > 0; j++)

1848

aMask->m_Table[

i

].cMask[j] = aMask->m_Table[

i

].cMask[j % uCnt];

1861  unsigned char

low, high,

ambig

;

1871  for

(low = 0; low < 16; low++) {

1873  if

((low == 1) || (low ==2) || (low == 4) || (low == 8))

1879  for

(high = 0; high < 16; high++) {

1882  if

((high != 1) && (high != 2) && (high != 4) && (high != 8))

1886

ambig_detect->m_Table[16*high + low] =

ambig

;

1893  return

ambig_detect;

1907  for

(

unsigned int i

= 0;

i

<256;

i

++)

1908

ambig_detect->m_Table[

i

] = 0;

1912

ambig_detect->m_Table[66] = 1;

1913

ambig_detect->m_Table[68] = 1;

1914

ambig_detect->m_Table[72] = 1;

1915

ambig_detect->m_Table[75] = 1;

1916

ambig_detect->m_Table[77] = 1;

1917

ambig_detect->m_Table[78] = 1;

1918

ambig_detect->m_Table[82] = 1;

1919

ambig_detect->m_Table[83] = 1;

1920

ambig_detect->m_Table[86] = 1;

1921

ambig_detect->m_Table[87] = 1;

1922

ambig_detect->m_Table[89] = 1;

1924  return

ambig_detect;

1977

vector<Uint4>* blast_ambig)

1983  throw

std::runtime_error(

"to_code or from_code not set"

);

1986  throw

std::runtime_error(

"to_code is not Ncbi2na"

);

1989  switch

(from_code) {

1992  seed

, total_length, out_seq_length,

1996  seed

, total_length, out_seq_length,

1999  throw

runtime_error(

"Requested conversion not implemented"

);

2019

vector<Uint4>* blast_ambig)

2025  if

( uLength == 0 ) {

2030  throw

std::runtime_error(

"to_code or from_code not set"

);

2034  throw

runtime_error(

"Requested conversion not implemented"

);

2040  return x_ConvertAmbig

(in_seq, out_seq, to_code, uBeginIdx, uLength,

2041  seed

, total_length, out_seq_length, blast_ambig);

2044  const string

* in_str = 0;

2045  const

vector<char>* in_vec = 0;

2050  if

( in_str != 0 ) {

2057

}

else if

( in_vec != 0 ) {

2065  return static_cast<TSeqPos>

(retval);

2081  throw

runtime_error(

"Unable tp pack requested coding"

);

2086  switch

( from_code ) {

2106  const string

* in_str = 0;

2107  const

vector<char>* in_vec = 0;

2111

vector<char> out_vec;

2115  if

( in_str != 0 ) {

2118

out_vec, coding, uLength);

2119

}

else if

( in_vec != 0 ) {

2122

out_vec, coding, uLength);

2149  switch

(in_seq.

Which

()) {

2163  throw

runtime_error(

"Sequence could not be validated"

);

2173

vector<TSeqPos>* badIdx,

2178  switch

(in_seq.

Which

()) {

2196  throw

runtime_error(

"Sequence could not be validated"

);

2208

vector<TSeqPos>* out_indices,

2216  switch

(in_seq.

Which

()) {

2221

uBeginIdx, uLength);

2229

uBeginIdx, uLength);

2250  switch

(in_seq.

Which

()) {

2265

(

"GetCopy() is not implemented for the requested sequence type"

);

2282  switch

(in_seq->

Which

()) {

2296  throw

runtime_error(

"Cannot perform Keep on in_seq type."

);

2315  throw

runtime_error(

"Append in_seq types do not match."

);

2323  switch

(in_seq1.

Which

()) {

2325  return AppendIupacna

(out_seq, in_seq1, uBeginIdx1, uLength1,

2326

in_seq2, uBeginIdx2, uLength2);

2328  return AppendNcbi2na

(out_seq, in_seq1, uBeginIdx1, uLength1,

2329

in_seq2, uBeginIdx2, uLength2);

2331  return AppendNcbi4na

(out_seq, in_seq1, uBeginIdx1, uLength1,

2332

in_seq2, uBeginIdx2, uLength2);

2334  return AppendNcbieaa

(out_seq, in_seq1, uBeginIdx1, uLength1,

2335

in_seq2, uBeginIdx2, uLength2);

2338

in_seq2, uBeginIdx2, uLength2);

2340  return AppendIupacaa

(out_seq, in_seq1, uBeginIdx1, uLength1,

2341

in_seq2, uBeginIdx2, uLength2);

2343  throw

runtime_error(

"Append for in_seq type not supported."

);

2362

in_seq->

Assign

(complement);

2378  if

( uLength == 0 ) {

2384  const string

* in_str = 0;

2385  const

vector<char>* in_vec = 0;

2394

}

else if

(in_vec != 0) {

2395

vector<char> out_vec;

2400  return static_cast<TSeqPos>

(retval);

2432  if

( uLength == 0 ) {

2439  const string

* in_str = 0;

2440  const

vector<char>* in_vec = 0;

2449

}

else if

(in_vec !=

NULL

) {

2450

vector<char> out_vec;

2455  return static_cast<TSeqPos>

(retval);

2475  string

* in_str = 0;

2476

vector<char>* in_vec = 0;

2482

}

else if

(in_vec !=

NULL

) {

2485  return static_cast<TSeqPos>

(retval);

2499  if

( uLength == 0 ) {

2506  const string

* in_str = 0;

2507  const

vector<char>* in_vec = 0;

2516

}

else if

(in_vec !=

NULL

) {

2517

vector<char> out_vec;

2523  return static_cast<TSeqPos>

(retval);

2770

{ 0, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1 };

2791

: m_vAmbBuf(amb_buff)

2835

res[0] = (in_byte >> 4) & 0x0f;

2836

res[1] = in_byte & 0x0f;

2838  for

(

int i

= 0;

i

< 2; ++

i

, ++seq_pos) {

2879

vector<Uint4>* blast_ambig)

2884  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

2887  if

(out_seq_length !=

nullptr

&& *out_seq_length == 0)

2890

vector<char>& out_seq_data = out_seq->

SetNcbi2na

().

Set

();

2893  if

(uBeginIdx >= in_seq_data.size())

2898  if

((uLenSav == 0) || ((uLenSav + uBeginIdx)) > in_seq_data.size())

2899

uLenSav = in_seq_length - uBeginIdx;

2904  Adjust

(&uBeginIdx, &uLength, in_seq_length, 1, 4);

2910  if

(out_seq_length) {

2911

out_seq_pos = *out_seq_length;

2912

*out_seq_length += uLenSav;

2914  TSeqPos

rbit = 2*(out_seq_pos % 4);

2919

vector<char>::size_type nBytes = (out_seq_pos + uLenSav + 3) / 4;

2920

out_seq_data.resize(nBytes);

2924

unique_ptr<CAmbiguityContext> amb_context;

2930

vector<char>::iterator i_out;

2931

vector<char>::iterator i_out_begin = out_seq_data.begin() + out_seq_pos/4;

2932

vector<char>::iterator i_out_end = i_out_begin + uLength/4;

2935

string::const_iterator i_in = in_seq_data.begin() + uBeginIdx;

2938  const int

kOneByteMask = 0xff;

2943  unsigned char

c1, c2;

2957  for

(i_out = i_out_begin; i_out != i_out_end; )

2962

[0][

static_cast<unsigned char>

(*i_in)] |

2964

[1][

static_cast<unsigned char>

(*(i_in+1))];

2969

[0][

static_cast<unsigned char>

(*(i_in+2))]|

2971

[1][

static_cast<unsigned char>

(*(i_in+3))];

2974

amb_context->AddAmbiguity(c1, out_seq_pos);

2975

amb_context->AddAmbiguity(c2, out_seq_pos);

2980

c1 &=

m_Masks

->m_Table[c1].cMask[rv];

2982

c2 &=

m_Masks

->m_Table[c2].cMask[rv];

2991

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

2996

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3003  switch

(uOverhang) {

3007

[0][

static_cast<unsigned char>

(*i_in)];

3009

amb_context->AddAmbiguity(c1, out_seq_pos);

3011

c1 &=

m_Masks

->m_Table[c1].cMask[rv];

3017

[0][

static_cast<unsigned char>

(*i_in)] |

3019

[1][

static_cast<unsigned char>

(*(i_in+1))];

3021

amb_context->AddAmbiguity(c1, out_seq_pos);

3023

c1 &=

m_Masks

->m_Table[c1].cMask[rv];

3029

[0][

static_cast<unsigned char>

(*i_in)] |

3031

[1][

static_cast<unsigned char>

(*(i_in+1))];

3034

[0][

static_cast<unsigned char>

(*(i_in+2))];

3036

amb_context->AddAmbiguity(c1, out_seq_pos);

3037

amb_context->AddAmbiguity(c2, out_seq_pos);

3040

c1 &=

m_Masks

->m_Table[c1].cMask[rv];

3042

c2 &=

m_Masks

->m_Table[c2].cMask[rv];

3058  if

(uOverhang > 0) {

3059

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

3060  if

(2*uOverhang > lbit) {

3062

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3067

amb_context->Finish();

3072  for

(i_out = i_out_begin; i_out != i_out_end; )

3076

[0][

static_cast<unsigned char>

(*(i_in))] |

3078

[1][

static_cast<unsigned char>

(*(i_in+1))] |

3080

[2][

static_cast<unsigned char>

(*(i_in+2))] |

3082

[3][

static_cast<unsigned char>

(*(i_in+3))];

3083

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

3088

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3093  if

(uOverhang > 0) {

3098

[

i

][

static_cast<unsigned char>

(*(i_in+

i

))];

3100

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

3101  if

(2*uOverhang > lbit) {

3103

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3182  TSeqPos

* out_seq_length, vector<Uint4>* blast_ambig)

3186  const

vector<char>& in_seq_data = in_seq.

GetNcbi4na

().

Get

();

3187  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

3190  if

(out_seq_length !=

nullptr

&& *out_seq_length == 0)

3193

vector<char>& out_seq_data = out_seq->

SetNcbi2na

().

Set

();

3196  TSeqPos

uBeginSav = uBeginIdx;

3201  if

(uBeginSav >= 2*in_seq_data.size())

3205  if

((uLenSav == 0) || ((uBeginSav + uLenSav) > 2*in_seq_data.size()))

3206

uLenSav = 2*in_seq_length - uBeginSav;

3210  Adjust

(&uBeginIdx, &uLength, in_seq_length, 2, 4);

3216  if

(out_seq_length) {

3217

out_seq_pos = *out_seq_length;

3218

*out_seq_length += uLenSav;

3220  TSeqPos

rbit = 2*(out_seq_pos % 4);

3225

vector<char>::size_type nBytes = (out_seq_pos + uLenSav + 3) / 4;

3226

out_seq_data.resize(nBytes);

3230

unique_ptr<CAmbiguityContext> amb_context;

3236

vector<char>::iterator i_out;

3237

vector<char>::iterator i_out_begin = out_seq_data.begin() + out_seq_pos/4;

3238

vector<char>::iterator i_out_end = i_out_begin + uLength/4;

3242

*i_out_begin &= (0xff << lbit);

3245

vector<char>::const_iterator i_in = in_seq_data.begin() + uBeginIdx/2;

3248  const int

kOneByteMask = 0xff;

3256  for

(i_out = i_out_begin; i_out != i_out_end; ) {

3258  unsigned char

c1 =

static_cast<unsigned char>

(*i_in);

3259  unsigned char

c2 =

static_cast<unsigned char>

(*(i_in+1));

3262

amb_context->AddAmbiguity(c1, out_seq_pos);

3263

amb_context->AddAmbiguity(c2, out_seq_pos);

3266

c1 &=

m_Masks

->m_Table[c1].cMask[rv];

3268

c2 &=

m_Masks

->m_Table[c2].cMask[rv];

3273

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

3278

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3285  if

(uOverhang > 0) {

3287  unsigned char

c1 =

static_cast<unsigned char>

(*i_in);

3293

amb_context->AddAmbiguity(c1, out_seq_pos);

3295

c1 &=

m_Masks

->m_Table[c1].cMask[rv];

3301  if

(uOverhang == 3) {

3304  unsigned char

c1 =

static_cast<unsigned char>

(*(++i_in)) & 0xf0;

3306

amb_context->AddAmbiguity(c1, out_seq_pos);

3308

c1 &=

m_Masks

->m_Table[c1].cMask[rv];

3314  if

(uOverhang > 0) {

3315

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

3316  if

(2*uOverhang > lbit) {

3318

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3323

amb_context->Finish();

3327  for

(i_out = i_out_begin; i_out != i_out_end; ) {

3330

[0][

static_cast<unsigned char>

(*i_in)] |

3332

[1][

static_cast<unsigned char>

(*(i_in+1))];

3333

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

3338

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3343  if

(uOverhang > 0) {

3346

[0][

static_cast<unsigned char>

(*i_in)];

3350

[1][

static_cast<unsigned char>

(*(++i_in))];

3352

(*i_out) |= ((new_byte & kOneByteMask) >> rbit);

3353  if

(2*uOverhang > lbit) {

3355

(*i_out) = ((new_byte & kOneByteMask) << lbit);

3360  TSeqPos

keepidx = uBeginSav - uBeginIdx;

3633  if

(uBeginIdx >= in_seq_data.size())

3637  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3641

string::const_iterator itor;

3642

string::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3643

string::const_iterator e_itor = b_itor + uLength;

3646  unsigned char

ch =

'\x00'

;

3647  for

(itor = b_itor; itor != e_itor; ++itor)

3648

ch |=

m_Iupacna

->m_Table[

static_cast<unsigned char>

(*itor)];

3665  if

(uBeginIdx >= in_seq_data.size())

3669  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3673

string::const_iterator itor;

3674

string::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3675

string::const_iterator e_itor = b_itor + uLength;

3678  unsigned char

ch =

'\x00'

;

3679  for

(itor = b_itor; itor != e_itor; ++itor)

3680

ch |=

m_Ncbieaa

->m_Table[

static_cast<unsigned char>

(*itor)];

3698  if

(uBeginIdx >= in_seq_data.size())

3702  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3706

vector<char>::const_iterator itor;

3707

vector<char>::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3708

vector<char>::const_iterator e_itor = b_itor + uLength;

3711  unsigned char

ch =

'\x00'

;

3712  for

(itor = b_itor; itor != e_itor; ++itor)

3713

ch |=

m_Ncbistdaa

->m_Table[

static_cast<unsigned char>

(*itor)];

3731  if

(uBeginIdx >= in_seq_data.size())

3735  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3739

string::const_iterator itor;

3740

string::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3741

string::const_iterator e_itor = b_itor + uLength;

3744  unsigned char

ch =

'\x00'

;

3745  for

(itor=b_itor; itor!=e_itor; ++itor)

3746

ch |=

m_Iupacaa

->m_Table[

static_cast<unsigned char>

(*itor)];

3755

vector<TSeqPos>* badIdx,

3767  if

(uBeginIdx >= in_seq_data.size())

3771  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3775

string::const_iterator itor;

3776

string::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3777

string::const_iterator e_itor = b_itor + uLength;

3781  for

(itor = b_itor; itor != e_itor; ++itor)

3782  if

(

m_Iupacna

->m_Table[

static_cast<unsigned char>

(*itor)] ==

char

(255))

3783

badIdx->push_back(nIdx++);

3794

vector<TSeqPos>* badIdx,

3806  if

(uBeginIdx >= in_seq_data.size())

3810  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3814

string::const_iterator itor;

3815

string::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3816

string::const_iterator e_itor = b_itor + uLength;

3820  for

(itor = b_itor; itor != e_itor; ++itor)

3821  if

(

m_Ncbieaa

->m_Table[

static_cast<unsigned char>

(*itor)] ==

char

(255))

3822

badIdx->push_back(nIdx++);

3833

vector<TSeqPos>* badIdx,

3845  if

(uBeginIdx >= in_seq_data.size())

3849  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3853

vector<char>::const_iterator itor;

3854

vector<char>::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3855

vector<char>::const_iterator e_itor = b_itor + uLength;

3859  for

(itor=b_itor; itor!=e_itor; ++itor)

3860  if

(

m_Ncbistdaa

->m_Table[

static_cast<unsigned char>

(*itor)]==

char

(255))

3861

badIdx->push_back(nIdx++);

3872

vector<TSeqPos>* badIdx,

3884  if

(uBeginIdx >= in_seq_data.size())

3888  Adjust

(&uBeginIdx, &uLength,

static_cast<TSeqPos>

(in_seq_data.size()),

3892

string::const_iterator itor;

3893

string::const_iterator b_itor = in_seq_data.begin() + uBeginIdx;

3894

string::const_iterator e_itor = b_itor + uLength;

3898  for

(itor=b_itor; itor!=e_itor; ++itor)

3899  if

(

m_Iupacaa

->m_Table[

static_cast<unsigned char>

(*itor)] ==

char

(255))

3900

badIdx->push_back(nIdx++);

3919

vector<char>& out_seq_data = out_seq->

SetNcbi2na

().

Set

();

3922  const

vector<char>& in_seq_data = in_seq.

GetNcbi2na

().

Get

();

3925  if

(uBeginIdx >= 4 * in_seq_data.size())

3929  if

( (uLength ==0) || ((uBeginIdx + uLength) > (4*in_seq_data.size() )) )

3930

uLength = 4 *

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

3933  if

((uLength % 4) == 0)

3934

out_seq_data.resize(uLength/4);

3936

out_seq_data.resize(uLength/4 + 1);

3939

vector<char>::iterator i_out = out_seq_data.begin() - 1;

3942  unsigned int

lShift, rShift;

3943

lShift = 2*(uBeginIdx % 4);

3944

rShift = 8 - lShift;

3947

vector<char>::const_iterator i_in;

3948

vector<char>::const_iterator i_in_begin =

3949

in_seq_data.begin() + uBeginIdx/4;

3953  if

((uLength % 4) != 0)

3957  bool

bDoLastByte =

false

;

3958  if

((uBeginIdx/4 + uNumBytes) >= in_seq_data.size())

3960

uNumBytes = in_seq_data.size() - uBeginIdx/4 - 1;

3961

bDoLastByte =

true

;

3963

vector<char>::const_iterator i_in_end = i_in_begin + uNumBytes;

3967  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

3969

((*i_in) << lShift) | (((*(i_in+1)) & 255) >> rShift);

3971  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

3972

(*(++i_out)) = (*i_in);

3976

(*(++i_out)) = (*i_in) << lShift;

3992

vector<char>& out_seq_data = out_seq->

SetNcbi4na

().

Set

();

3995  const

vector<char>& in_seq_data = in_seq.

GetNcbi4na

().

Get

();

3998  if

(uBeginIdx >= 2 * in_seq_data.size())

4002  if

( (uLength ==0) || ((uBeginIdx + uLength) > (2*in_seq_data.size() )) )

4003

uLength = 2 *

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

4006  if

((uLength % 2) == 0)

4007

out_seq_data.resize(uLength/2);

4009

out_seq_data.resize(uLength/2 + 1);

4013

vector<char>::iterator i_out = out_seq_data.begin() - 1;

4016  unsigned int

lShift, rShift;

4017

lShift = 4*(uBeginIdx % 2);

4018

rShift = 8 - lShift;

4021

vector<char>::const_iterator i_in;

4022

vector<char>::const_iterator i_in_begin =

4023

in_seq_data.begin() + uBeginIdx/2;

4027  if

((uLength % 2) != 0)

4031  bool

bDoLastByte =

false

;

4032  if

((uBeginIdx/2 + uNumBytes) >= in_seq_data.size())

4034

uNumBytes = in_seq_data.size() - uBeginIdx/2 - 1;

4035

bDoLastByte =

true

;

4037

vector<char>::const_iterator i_in_end = i_in_begin + uNumBytes;

4041  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

4043

((*i_in) << lShift) | (((*(i_in+1)) & 255) >> rShift);

4045  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

4046

(*(++i_out)) = (*i_in);

4050

(*(++i_out)) = (*i_in) << lShift;

4072  if

(uBeginIdx >= in_seq_data.size())

4076  if

( (uLength ==0) || ((uBeginIdx + uLength) > (in_seq_data.size() )) )

4077

uLength =

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

4080

out_seq_data.resize(uLength);

4083

string::iterator i_out = out_seq_data.begin() - 1;

4086

string::const_iterator i_in;

4087

string::const_iterator i_in_begin = in_seq_data.begin() + uBeginIdx;

4088

string::const_iterator i_in_end = i_in_begin + uLength;

4091  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

4092

(*(++i_out)) = (*i_in);

4114  if

(uBeginIdx >= in_seq_data.size())

4118  if

( (uLength ==0) || ((uBeginIdx + uLength) > (in_seq_data.size() )) )

4119

uLength =

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

4122

out_seq_data.resize(uLength);

4125

string::iterator i_out = out_seq_data.begin() - 1;

4128

string::const_iterator i_in;

4129

string::const_iterator i_in_begin = in_seq_data.begin() + uBeginIdx;

4130

string::const_iterator i_in_end = i_in_begin + uLength;

4133  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

4134

(*(++i_out)) = (*i_in);

4156  if

(uBeginIdx >= in_seq_data.size())

4160  if

( (uLength ==0) || ((uBeginIdx + uLength) > (in_seq_data.size() )) )

4161

uLength =

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

4164

out_seq_data.resize(uLength);

4167

vector<char>::iterator i_out = out_seq_data.begin() - 1;

4170

vector<char>::const_iterator i_in;

4171

vector<char>::const_iterator i_in_begin = in_seq_data.begin() + uBeginIdx;

4172

vector<char>::const_iterator i_in_end = i_in_begin + uLength;

4175  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

4176

(*(++i_out)) = (*i_in);

4198  if

(uBeginIdx >= in_seq_data.size())

4202  if

( (uLength ==0) || ((uBeginIdx + uLength) > (in_seq_data.size() )) )

4203

uLength =

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

4206

out_seq_data.resize(uLength);

4209

string::iterator i_out = out_seq_data.begin() - 1;

4212

string::const_iterator i_in;

4213

string::const_iterator i_in_begin = in_seq_data.begin() + uBeginIdx;

4214

string::const_iterator i_in_end = i_in_begin + uLength;

4217  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

4218

(*(++i_out)) = (*i_in);

4239

*uLength = uInSeqsPerByte * uInSeqBytes;

4242  if

(*uBeginIdx >= uInSeqsPerByte * uInSeqBytes)

4243

*uBeginIdx = uInSeqsPerByte * uInSeqBytes - uInSeqsPerByte;

4246

*uLength += *uBeginIdx % uInSeqsPerByte;

4247

*uBeginIdx = uInSeqsPerByte * (*uBeginIdx/uInSeqsPerByte);

4250  if

(*uLength > uInSeqsPerByte * uInSeqBytes - *uBeginIdx)

4251

*uLength = uInSeqsPerByte * uInSeqBytes - *uBeginIdx;

4255  TSeqPos

uOverhang = *uLength % uOutSeqsPerByte;

4256

*uLength = uOutSeqsPerByte * (*uLength / uOutSeqsPerByte);

4270

vector<TSeqPos>* out_indices,

4276  const

vector<char>& in_seq_data = in_seq.

GetNcbi4na

().

Get

();

4280

vector<char>& out_seq_data = out_seq->

SetNcbi4na

().

Set

();

4283  if

(uBeginIdx >= 2*in_seq_data.size())

4286  if

((uLength == 0) || (((uBeginIdx + uLength) > 2*in_seq_data.size())))

4287

uLength = 2 *

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

4290  TSeqPos

uBeginSav = uBeginIdx;

4292

uLength += uBeginIdx % 2;

4293

uBeginIdx = 2*(uBeginIdx/2);

4300

out_seq_data.resize(uLength/2 + (uLength % 2));

4301

out_indices->resize(uLength);

4307

vector<char>::const_iterator i_in;

4308

vector<char>::const_iterator i_in_begin =

4309

in_seq_data.begin() + uBeginIdx/2;

4310

vector<char>::const_iterator i_in_end =

4311

i_in_begin + uLength/2 + (uLength % 2);

4314

vector<char>::iterator i_out_seq = out_seq_data.begin();

4315

vector<TSeqPos>::iterator i_out_idx = out_indices->begin();

4321  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in) {

4323

[

static_cast<unsigned char>

(*i_in)]) {

4330

(*i_out_seq) |= (*i_in) &

'\x0f'

;

4336

(*i_out_seq) = (*i_in) << 4;

4339

(*i_out_idx) = uIdx + 1;

4351

(*i_out_seq) |= ((*i_in) >> 4) &

'\x0f'

;

4357

(*i_out_seq) = (*i_in) &

'\xf0'

;

4360

(*i_out_idx) = uIdx;

4375

(*i_out_seq) |= ((*i_in) >> 4) &

'\x0f'

;

4376

(*(++i_out_seq)) = (*i_in) << 4;

4385

(*i_out_seq) = (*i_in);

4390

(*i_out_idx) = uIdx;

4391

(*(++i_out_idx)) = uIdx + 1;

4404

out_indices->resize(uNumAmbigs);

4405

out_seq_data.resize(uNumAmbigs/2 + uNumAmbigs % 2);

4410  if

((*out_indices)[0] < uBeginSav)

4413

out_indices->erase(out_indices->begin(), out_indices->begin() + 1);

4416  if

((*out_indices)[out_indices->size()-1] >= uBeginSav + uLenSav)

4418

out_indices->pop_back();

4419

uKeepLen =

static_cast<TSeqPos>

(out_indices->size());

4422  if

((uKeepBeg != 0) || (uKeepLen != 0))

4423

uNumAmbigs =

KeepNcbi4na

(out_seq, uKeepBeg, uKeepLen);

4437

vector<TSeqPos>* out_indices,

4450  if

(uBeginIdx >= in_seq_data.size())

4453  if

((uLength == 0) || ((uBeginIdx + uLength) > in_seq_data.size()))

4454

uLength =

static_cast<TSeqPos>

(in_seq_data.size()) - uBeginIdx;

4459

out_seq_data.resize(uLength);

4460

out_indices->resize(uLength);

4466

string::const_iterator i_in;

4467

string::const_iterator i_in_begin = in_seq_data.begin() + uBeginIdx;

4468

string::const_iterator i_in_end = i_in_begin + uLength;

4471

string::iterator i_out_seq = out_seq_data.begin();

4472

vector<TSeqPos>::iterator i_out_idx = out_indices->begin();

4478  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

4481

[

static_cast<unsigned char>

(*i_in)] == 1)

4483

(*i_out_seq) = (*i_in);

4485

(*i_out_idx) = uIdx;

4493

out_seq_data.resize(uNumAmbigs);

4494

out_indices->resize(uNumAmbigs);

4510  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

4513  if

(uBeginIdx >= in_seq_data.size()*4)

4515

in_seq_data.clear();

4521

uLength = 4 * in_seq_length - uBeginIdx;

4526  if

(uLength > (4*in_seq_data.size() - uBeginIdx))

4527

uLength = 4 * in_seq_length - uBeginIdx;

4530  if

((uBeginIdx == 0) && (uLength >= 4*in_seq_data.size()))

4537  TSeqPos

uStartInByte = 2 * (uBeginIdx % 4);

4540  unsigned char

rightMask = 0xff << uStartInByte;

4541  unsigned char

leftMask = ~rightMask;

4545  TSeqPos

uEnd = (uBeginIdx + uLength - 1)/4;

4548

vector<char>::iterator i_write;

4551

vector<char>::iterator i_read = in_seq_data.begin() + uStart;

4552

vector<char>::iterator i_read_end = in_seq_data.begin() + uEnd;

4556  for

(i_write = in_seq_data.begin(); i_read != i_read_end; ++i_write) {

4557

(*i_write) = (((*i_read) << uStartInByte) | leftMask) &

4558

(((*(i_read+1)) >> (8-uStartInByte)) | rightMask);

4563

(*i_write) = (*i_read) << uStartInByte;

4567  if

((uLength % 4) != 0)

4569

in_seq_data.resize(uSize);

4585  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

4588  if

(uBeginIdx >= in_seq_data.size()*2)

4590

in_seq_data.clear();

4596

uLength = 2 * in_seq_length - uBeginIdx;

4601  if

(uLength > (2*in_seq_data.size() - uBeginIdx))

4602

uLength = 2 * in_seq_length - uBeginIdx;

4605  if

((uBeginIdx == 0) && (uLength >= 2*in_seq_data.size()))

4612  unsigned int

uStartInByte = 4 * (uBeginIdx % 2);

4615  unsigned char

rightMask = 0xff << uStartInByte;

4616  unsigned char

leftMask = ~rightMask;

4620  TSeqPos

uEnd = (uBeginIdx + uLength - 1)/2;

4623

vector<char>::iterator i_write;

4626

vector<char>::iterator i_read = in_seq_data.begin() + uStart;

4627

vector<char>::iterator i_read_end = in_seq_data.begin() + uEnd;

4631  for

(i_write = in_seq_data.begin(); i_read != i_read_end; ++i_write) {

4632

(*i_write) = (((*i_read) << uStartInByte) | leftMask) &

4633

(((*(i_read+1)) >> (8-uStartInByte)) | rightMask);

4638

(*i_write) = (*i_read) << uStartInByte;

4642  if

((uLength % 2) != 0)

4644

in_seq_data.resize(uSize);

4660  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

4664  if

(uBeginIdx >= in_seq_data.size())

4666

in_seq_data.erase();

4672

uLength = in_seq_length - uBeginIdx;

4675  if

((uBeginIdx + uLength) > in_seq_data.size())

4676

uLength = in_seq_length - uBeginIdx;

4680  if

((uBeginIdx == 0) && (uLength >= in_seq_data.size()))

4684

string::iterator i_read;

4685

string::iterator i_write;

4688

i_read = in_seq_data.begin() + uBeginIdx;

4689

string::iterator i_read_end = i_read + uLength;

4693  for

(i_write = in_seq_data.begin(); i_read != i_read_end; ++i_write)

4695

(*i_write) = (*i_read);

4700

in_seq_data.resize(uLength);

4715  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

4719  if

(uBeginIdx >= in_seq_data.size())

4721

in_seq_data.erase();

4727

uLength = in_seq_length - uBeginIdx;

4730  if

((uBeginIdx + uLength) > in_seq_data.size())

4731

uLength = in_seq_length - uBeginIdx;

4735  if

((uBeginIdx == 0) && (uLength >= in_seq_data.size()))

4739

string::iterator i_read;

4740

string::iterator i_write;

4743

i_read = in_seq_data.begin() + uBeginIdx;

4744

string::iterator i_read_end = i_read + uLength;

4748  for

(i_write = in_seq_data.begin(); i_read != i_read_end; ++i_write) {

4749

(*i_write) = (*i_read);

4754

in_seq_data.resize(uLength);

4769  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

4772  if

(uBeginIdx >= in_seq_data.size())

4774

in_seq_data.clear();

4780

uLength = in_seq_length - uBeginIdx;

4783  if

((uBeginIdx + uLength) > in_seq_data.size())

4784

uLength = in_seq_length - uBeginIdx;

4788  if

((uBeginIdx == 0) && (uLength >= in_seq_data.size()))

4792

vector<char>::iterator i_read;

4793

vector<char>::iterator i_write;

4796

i_read = in_seq_data.begin() + uBeginIdx;

4797

vector<char>::iterator i_read_end = i_read + uLength;

4801  for

(i_write = in_seq_data.begin(); i_read != i_read_end; ++i_write) {

4802

(*i_write) = (*i_read);

4807

in_seq_data.resize(uLength);

4822  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

4826  if

(uBeginIdx >= in_seq_data.size()) {

4827

in_seq_data.erase();

4833

uLength = in_seq_length - uBeginIdx;

4836  if

((uBeginIdx + uLength) > in_seq_data.size())

4837

uLength = in_seq_length - uBeginIdx;

4841  if

((uBeginIdx == 0) && (uLength >= in_seq_data.size()))

4845

string::iterator i_read;

4846

string::iterator i_write;

4849

i_read = in_seq_data.begin() + uBeginIdx;

4850

string::iterator i_read_end = i_read + uLength;

4854  for

(i_write = in_seq_data.begin(); i_read != i_read_end; ++i_write) {

4855

(*i_write) = (*i_read);

4860

in_seq_data.resize(uLength);

4883

string::iterator i_data;

4886

string::iterator i_data_end = in_seq_data.end();

4889  for

(i_data = in_seq_data.begin(); i_data != i_data_end; ++i_data)

4910

vector<char>::iterator i_data;

4913

vector<char>::iterator i_data_end = in_seq_data.end();

4916  for

(i_data = in_seq_data.begin(); i_data != i_data_end; ++i_data)

4937

vector<char>::iterator i_data;

4940

vector<char>::iterator i_data_end = in_seq_data.end();

4943  for

(i_data = in_seq_data.begin(); i_data != i_data_end; ++i_data)

5010

reverse(in_seq_data.begin(), in_seq_data.end());

5024  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

5027  if

(uBeginIdx >= 4*in_seq_data.size())

5029

in_seq_data.erase(in_seq_data.begin(), in_seq_data.end());

5035

uLength = 4 * in_seq_length - uBeginIdx;

5038  if

((uBeginIdx + uLength) > (4 * in_seq_data.size()))

5039

uLength = 4 * in_seq_length - uBeginIdx;

5043  TSeqPos

uEnd = uStart + (uLength - 1 +(uBeginIdx % 4))/4 + 1;

5046

vector<char>::iterator i_in;

5047

vector<char>::iterator i_in_begin = in_seq_data.begin() + uStart;

5048

vector<char>::iterator i_in_end = in_seq_data.begin() + uEnd;

5051  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

5052

(*i_in) =

m_Ncbi2naRev

->m_Table[

static_cast<unsigned char>

(*i_in)];

5055

reverse(i_in_begin, i_in_end);

5058  TSeqPos

uJagged = 3 - ((uBeginIdx + uLength - 1) % 4) + 4*uStart;

5071  TSeqPos

in_seq_length =

static_cast<TSeqPos>

(in_seq_data.size());

5074  if

(uBeginIdx >= 2*in_seq_data.size())

5076

in_seq_data.erase(in_seq_data.begin(), in_seq_data.end());

5082

uLength = 2 * in_seq_length - uBeginIdx;

5085  if

((uBeginIdx + uLength) > (2 * in_seq_data.size()))

5086

uLength = 2 * in_seq_length - uBeginIdx;

5090  TSeqPos

uEnd = uStart + (uLength - 1 +(uBeginIdx % 2))/2 + 1;

5093

vector<char>::iterator i_in;

5094

vector<char>::iterator i_in_begin = in_seq_data.begin() + uStart;

5095

vector<char>::iterator i_in_end = in_seq_data.begin() + uEnd;

5098  for

(i_in = i_in_begin; i_in != i_in_end; ++i_in)

5099

(*i_in) =

m_Ncbi4naRev

->m_Table[

static_cast<unsigned char>

(*i_in)];

5102

reverse(i_in_begin, i_in_end);

5105  TSeqPos

uJagged = 1 - ((uBeginIdx + uLength - 1) % 2) + 2*uStart;

5120  TSeqPos

uIdx1 = 0, uIdx2 = uLength;

5134  TSeqPos

uIdx1 = 0, uIdx2 = uLength;

5148  TSeqPos

uIdx1 = 0, uIdx2 = uLength;

5250  const string

& in_seq1_data = in_seq1.

GetIupacna

().

Get

();

5251  const string

& in_seq2_data = in_seq2.

GetIupacna

().

Get

();

5258  if

((uBeginIdx1 >= in_seq1_data.size()) &&

5259

(uBeginIdx2 >= in_seq2_data.size()))

5262  if

(((uBeginIdx1 + uLength1) > in_seq1_data.size()) || uLength1 == 0)

5263

uLength1 =

static_cast<TSeqPos>

(in_seq1_data.size()) - uBeginIdx1;

5265  if

(((uBeginIdx2 + uLength2) > in_seq2_data.size()) || uLength2 == 0)

5266

uLength2 =

static_cast<TSeqPos>

(in_seq2_data.size()) - uBeginIdx2;

5269

out_seq_data.append(in_seq1_data.substr(uBeginIdx1,uLength1));

5270

out_seq_data.append(in_seq2_data.substr(uBeginIdx2,uLength2));

5272  return

uLength1 + uLength2;

5287  const

vector<char>& in_seq1_data = in_seq1.

GetNcbi2na

().

Get

();

5288  const

vector<char>& in_seq2_data = in_seq2.

GetNcbi2na

().

Get

();

5292

vector<char>& out_seq_data = out_seq->

SetNcbi2na

().

Set

();

5295  if

((uBeginIdx1 >= 4*in_seq1_data.size()) &&

5296

(uBeginIdx2 >= 4*in_seq2_data.size()))

5300  if

(uBeginIdx1 >= 4*in_seq1_data.size())

5304  if

(uBeginIdx2 >= 4*in_seq2_data.size())

5308  if

(((uBeginIdx1 + uLength1) > 4*in_seq1_data.size()) || uLength1 == 0)

5309

uLength1 = 4 *

static_cast<TSeqPos>

(in_seq1_data.size()) - uBeginIdx1;

5311  if

(((uBeginIdx2 + uLength2) > 4*in_seq2_data.size()) || uLength2 == 0)

5312

uLength2 = 4 *

static_cast<TSeqPos>

(in_seq2_data.size()) - uBeginIdx2;

5316  TSeqPos

uTotalLength = uLength1 + uLength2;

5317  if

((uTotalLength % 4) == 0)

5318

out_seq_data.resize(uTotalLength/4);

5320

out_seq_data.resize(uTotalLength/4 + 1);

5323  unsigned int

lShift1 = 2*(uBeginIdx1 % 4);

5324  unsigned int

rShift1 = 8 - lShift1;

5327  unsigned int

lShift2, rShift2, uCase;

5328  unsigned int

uVacantIdx = 2*(uLength1 % 4);

5329  unsigned int

uStartIdx = 2*(uBeginIdx2 % 4);

5330  if

((uVacantIdx < uStartIdx) && (uVacantIdx > 0))

5333

lShift2 = uStartIdx - uVacantIdx;

5334

rShift2 = 8 - lShift2;

5336  else if

((uVacantIdx < uStartIdx) && (uVacantIdx == 0))

5339

lShift2 = uStartIdx;

5340

rShift2 = 8 - lShift2;

5342  else if

((uVacantIdx == uStartIdx) && (uVacantIdx > 0))

5348  else if

((uVacantIdx == uStartIdx) && (uVacantIdx == 0))

5357

rShift2 = uVacantIdx - uStartIdx;

5358

lShift2 = 8 - rShift2;

5363  TSeqPos

uStart1 = uBeginIdx1/4;

5365  if

(((uBeginIdx1 + uLength1) % 4) == 0)

5366

uEnd1 = (uBeginIdx1 + uLength1)/4;

5368

uEnd1 = (uBeginIdx1 + uLength1)/4 + 1;

5370  TSeqPos

uStart2 = uBeginIdx2/4;

5372  if

(((uBeginIdx2 + uLength2) % 4) == 0)

5373

uEnd2 = (uBeginIdx2 + uLength2)/4;

5375

uEnd2 = (uBeginIdx2 + uLength2)/4 + 1;

5378

vector<char>::const_iterator i_in1_begin = in_seq1_data.begin() + uStart1;

5379

vector<char>::const_iterator i_in1_end = in_seq1_data.begin() + uEnd1 - 1;

5380

vector<char>::const_iterator i_in2_begin = in_seq2_data.begin() + uStart2;

5381

vector<char>::const_iterator i_in2_end = in_seq2_data.begin() + uEnd2;

5384

vector<char>::iterator i_out = out_seq_data.begin() - 1;

5385

vector<char>::const_iterator i_in1;

5386

vector<char>::const_iterator i_in2;

5389  for

(i_in1 = i_in1_begin; i_in1 != i_in1_end; ++i_in1)

5390

(*(++i_out)) = ((*i_in1) << lShift1) | ((*(i_in1+1) & 255) >> rShift1);

5394  if

((uLength1 % 4) == 0)

5395

uEndOutByte = uLength1/4 - 1;

5397

uEndOutByte = uLength1/4;

5398  if

(i_out != (out_seq_data.begin() + uEndOutByte))

5399

(*(++i_out)) = (*i_in1) << lShift1;

5402  unsigned char

uMask1 = 255 << (8 - 2*(uLength1 % 4));

5403  unsigned char

uMask2 = 255 >> (2*(uBeginIdx2 % 4));

5408  if

((i_in2_begin + 1) == i_in2_end)

5411

(*i_out) |= ((*i_in2_begin) & uMask2) << lShift2;

5412  return

uTotalLength;

5418

(((*i_in2_begin) & uMask2) << lShift2) |

5419

(((*(i_in2_begin+1)) & 255) >> rShift2);

5423  if

((i_in2_begin + 1) == i_in2_end)

5425

(*(++i_out)) = (*i_in2_begin) << lShift2;

5426  return

uTotalLength;

5431

((*i_in2_begin) << lShift2) |

5432

(((*(i_in2_begin+1)) & 255) >> rShift2);

5437

(*i_out) |= (*i_in2_begin) & uMask2;

5438  if

((i_in2_begin + 1) == i_in2_end)

5439  return

uTotalLength;

5442

(*(++i_out)) = (*i_in2_begin);

5443  if

((i_in2_begin + 1) == i_in2_end)

5444  return

uTotalLength;

5447  if

((i_in2_begin + 1) == i_in2_end)

5450

(*i_out) |= ((*i_in2_begin) & uMask2) >> rShift2;

5451  if

(++i_out != out_seq_data.end())

5452

(*i_out) = (*i_in2_begin) << lShift2;

5453  return

uTotalLength;

5459

(((*i_in2_begin) & uMask2) >> rShift2) |

5460

((*(i_in2_begin+1) & ~uMask2) << lShift2);

5467  for

(i_in2 = i_in2_begin+uSeq2Inc; (i_in2 != i_in2_end) &&

5468

((i_in2+1) != i_in2_end); ++i_in2) {

5469

(*(++i_out)) = ((*i_in2) << lShift2) | ((*(i_in2+1) & 255) >> rShift2);

5473  if

((++i_out != out_seq_data.end()) && (i_in2 != i_in2_end))

5474

(*i_out) = (*i_in2) << lShift2;

5476  return

uLength1 + uLength2;

5491  const

vector<char>& in_seq1_data = in_seq1.

GetNcbi4na

().

Get

();

5492  const

vector<char>& in_seq2_data = in_seq2.

GetNcbi4na

().

Get

();

5496

vector<char>& out_seq_data = out_seq->

SetNcbi4na

().

Set

();

5499  if

((uBeginIdx1 >= 4*in_seq1_data.size()) &&

5500

(uBeginIdx2 >= 4*in_seq2_data.size()))

5504  if

(uBeginIdx1 >= 4*in_seq1_data.size())

5508  if

(uBeginIdx2 >= 4*in_seq2_data.size())

5512  if

(((uBeginIdx1 + uLength1) > 2*in_seq1_data.size()) || uLength1 == 0)

5513

uLength1 = 2 *

static_cast<TSeqPos>

(in_seq1_data.size()) - uBeginIdx1;

5515  if

(((uBeginIdx2 + uLength2) > 2*in_seq2_data.size()) || uLength2 == 0)

5516

uLength2 = 2 *

static_cast<TSeqPos>

(in_seq2_data.size()) - uBeginIdx2;

5519  TSeqPos

uTotalLength = uLength1 + uLength2;

5520  if

((uTotalLength % 2) == 0)

5521

out_seq_data.resize(uTotalLength/2);

5523

out_seq_data.resize(uTotalLength/2 + 1);

5526  unsigned int

lShift1 = 4*(uBeginIdx1 % 2);

5527  unsigned int

rShift1 = 8 - lShift1;

5530  unsigned int

lShift2, rShift2, uCase;

5531  unsigned int

uVacantIdx = 4*(uLength1 % 2);

5532  unsigned int

uStartIdx = 4*(uBeginIdx2 % 2);

5533  if

((uVacantIdx < uStartIdx))

5536

lShift2 = uStartIdx;

5537

rShift2 = 8 - lShift2;

5539  else if

((uVacantIdx == uStartIdx) && (uVacantIdx > 0))

5545  else if

((uVacantIdx == uStartIdx) && (uVacantIdx == 0))

5554

rShift2 = uVacantIdx - uStartIdx;

5555

lShift2 = 8 - rShift2;

5560  TSeqPos

uStart1 = uBeginIdx1/2;

5562  if

(((uBeginIdx1 + uLength1) % 2) == 0)

5563

uEnd1 = (uBeginIdx1 + uLength1)/2;

5565

uEnd1 = (uBeginIdx1 + uLength1)/2 + 1;

5567  TSeqPos

uStart2 = uBeginIdx2/2;

5569  if

(((uBeginIdx2 + uLength2) % 2) == 0)

5570

uEnd2 = (uBeginIdx2 + uLength2)/2;

5572

uEnd2 = (uBeginIdx2 + uLength2)/2 + 1;

5575

vector<char>::const_iterator i_in1_begin = in_seq1_data.begin() + uStart1;

5576

vector<char>::const_iterator i_in1_end = in_seq1_data.begin() + uEnd1 - 1;

5577

vector<char>::const_iterator i_in2_begin = in_seq2_data.begin() + uStart2;

5578

vector<char>::const_iterator i_in2_end = in_seq2_data.begin() + uEnd2;

5581

vector<char>::iterator i_out = out_seq_data.begin() - 1;

5582

vector<char>::const_iterator i_in1;

5583

vector<char>::const_iterator i_in2;

5586  for

(i_in1 = i_in1_begin; i_in1 != i_in1_end; ++i_in1)

5587

(*(++i_out)) = ((*i_in1) << lShift1) | ((*(i_in1+1) & 255) >> rShift1);

5591  if

((uLength1 % 2) == 0)

5592

uEndOutByte = uLength1/2 - 1;

5594

uEndOutByte = uLength1/2;

5595  if

(i_out != (out_seq_data.begin() + uEndOutByte))

5596

(*(++i_out)) = (*i_in1) << lShift1;

5599  unsigned char

uMask1 = 255 << (8 - 4*(uLength1 % 2));

5600  unsigned char

uMask2 = 255 >> (4*(uBeginIdx2 % 2));

5605  if

((i_in2_begin+1) == i_in2_end)

5607

(*(++i_out)) = (*i_in2_begin) << lShift2;

5608  return

uTotalLength;

5613

((*i_in2_begin) << lShift2) |

5614

(((*(i_in2_begin+1)) & 255) >> rShift2);

5619

(*i_out) |= (*i_in2_begin) & uMask2;

5620  if

((i_in2_begin+1) == i_in2_end)

5621  return

uTotalLength;

5624

(*(++i_out)) = (*i_in2_begin);

5625  if

((i_in2_begin+1) == i_in2_end)

5626  return

uTotalLength;

5629  if

((i_in2_begin+1) == i_in2_end)

5632

(*i_out) |= ((*i_in2_begin) & uMask2) >> rShift2;

5633  if

(++i_out != out_seq_data.end())

5634

(*i_out) = (*i_in2_begin) << lShift2;

5635  return

uTotalLength;

5641

(((*i_in2_begin) & uMask2) >> rShift2) |

5642

((*(i_in2_begin+1) & ~uMask2) << lShift2);

5649  for

(i_in2 = i_in2_begin+uSeq2Inc; (i_in2 != i_in2_end) &&

5650

((i_in2+1) != i_in2_end); ++i_in2) {

5652

((*i_in2) << lShift2) | ((*(i_in2+1) & 255) >> rShift2);

5656  if

((++i_out != out_seq_data.end()) && (i_in2 != i_in2_end))

5657

(*i_out) = (*i_in2) << lShift2;

5659  return

uTotalLength;

5674  const string

& in_seq1_data = in_seq1.

GetNcbieaa

().

Get

();

5675  const string

& in_seq2_data = in_seq2.

GetNcbieaa

().

Get

();

5682  if

((uBeginIdx1 >= in_seq1_data.size()) &&

5683

(uBeginIdx2 >= in_seq2_data.size()))

5688  if

(((uBeginIdx1 + uLength1) > in_seq1_data.size()) || uLength1 == 0)

5689

uLength1 =

static_cast<TSeqPos>

(in_seq1_data.size()) - uBeginIdx1;

5691  if

(((uBeginIdx2 + uLength2) > in_seq2_data.size()) || uLength2 == 0)

5692

uLength2 =

static_cast<TSeqPos>

(in_seq2_data.size()) - uBeginIdx2;

5695

out_seq_data.append(in_seq1_data.substr(uBeginIdx1,uLength1));

5696

out_seq_data.append(in_seq2_data.substr(uBeginIdx2,uLength2));

5698  return

uLength1 + uLength2;

5721  if

((uBeginIdx1 >= in_seq1_data.size()) &&

5722

(uBeginIdx2 >= in_seq2_data.size()))

5725  if

(((uBeginIdx1 + uLength1) > in_seq1_data.size()) || uLength1 == 0)

5726

uLength1 =

static_cast<TSeqPos>

(in_seq1_data.size()) - uBeginIdx1;

5728  if

(((uBeginIdx2 + uLength2) > in_seq2_data.size()) || uLength2 == 0)

5729

uLength2 =

static_cast<TSeqPos>

(in_seq2_data.size()) - uBeginIdx2;

5732

vector<char>::const_iterator i_in1_begin =

5733

in_seq1_data.begin() + uBeginIdx1;

5734

vector<char>::const_iterator i_in1_end = i_in1_begin + uLength1;

5735

vector<char>::const_iterator i_in2_begin =

5736

in_seq2_data.begin() + uBeginIdx2;

5737

vector<char>::const_iterator i_in2_end = i_in2_begin + uLength2;

5740

out_seq_data.insert(out_seq_data.end(), i_in1_begin, i_in1_end);

5741

out_seq_data.insert(out_seq_data.end(), i_in2_begin, i_in2_end);

5743  return

uLength1 + uLength2;

5758  const string

& in_seq1_data = in_seq1.

GetIupacaa

().

Get

();

5759  const string

& in_seq2_data = in_seq2.

GetIupacaa

().

Get

();

5766  if

((uBeginIdx1 >= in_seq1_data.size()) &&

5767

(uBeginIdx2 >= in_seq2_data.size()))

5772  if

(((uBeginIdx1 + uLength1) > in_seq1_data.size()) || uLength1 == 0)

5773

uLength1 =

static_cast<TSeqPos>

(in_seq1_data.size()) - uBeginIdx1;

5775  if

(((uBeginIdx2 + uLength2) > in_seq2_data.size()) || uLength2 == 0)

5776

uLength2 =

static_cast<TSeqPos>

(in_seq2_data.size()) - uBeginIdx2;

5779

out_seq_data.append(in_seq1_data.substr(uBeginIdx1,uLength1));

5780

out_seq_data.append(in_seq2_data.substr(uBeginIdx2,uLength2));

5782  return

uLength1 + uLength2;

5808  if

((*i_ct)->GetCode() == code_type) {

5831  if

((*i_ct)->GetCode() == code_type) {

5832  if

( (*i_ct)->IsSetStart_at() ) {

5833

p.first =

static_cast<TIndex>

((*i_ct)->GetStart_at());

5837

p.second = p.first +

static_cast<TIndex>

((*i_ct)->GetNum() - 1);

5875  const string

&

code

)

5883  const string

&

code

)

5993  if

(from_idx - (*Map).m_StartAt >= (

TIndex

)(*Map).m_Size) {

5995

from_idx -

static_cast<TIndex>

((*Map).m_StartAt),

6000  return

(*Map).m_Table[from_idx];

6008  const string

**

str

,

6009  const

vector<char>** vec)

6015  switch

(

data

.Which() ) {

6017

*

str

= &(

data

.GetIupacna().Get());

6021

*vec = &(

data

.GetNcbi2na().Get());

6025

*vec = &(

data

.GetNcbi4na().Get());

6029

*vec = &(

data

.GetNcbi8na().Get());

6033

*

str

= &(

data

.GetIupacaa().Get());

6037

*vec = &(

data

.GetNcbi8aa().Get());

6041

*

str

= &(

data

.GetNcbieaa().Get());

6045

*vec = &(

data

.GetNcbistdaa().Get());

6067  switch

(

data

.Which() ) {

6069

*

str

= &(

data

.SetIupacna().Set());

6073

*vec = &(

data

.SetNcbi2na().Set());

6077

*vec = &(

data

.SetNcbi4na().Set());

6081

*vec = &(

data

.SetNcbi8na().Set());

6085

*

str

= &(

data

.SetIupacaa().Set());

6089

*vec = &(

data

.SetNcbi8aa().Set());

6093

*

str

= &(

data

.SetNcbieaa().Set());

6097

*vec = &(

data

.SetNcbistdaa().Set());

6116  "-- This is the set of NCBI sequence code tables\n"

,

6117  "-- J.Ostell 10/18/91\n"

,

6120  "Seq-code-set ::= {\n"

,

6121  " codes { -- codes\n"

,

6123  " code iupacna ,\n"

,

6124  " num 25 , -- continuous 65-89\n"

,

6125  " one-letter TRUE , -- all one letter codes\n"

,

6126  " start-at 65 , -- starts with A, ASCII 65\n"

,

6128  " { symbol \"A\", name \"Adenine\" },\n"

,

6129  " { symbol \"B\" , name \"G or T or C\" },\n"

,

6130  " { symbol \"C\", name \"Cytosine\" },\n"

,

6131  " { symbol \"D\", name \"G or A or T\" },\n"

,

6132  " { symbol \"\", name \"\" },\n"

,

6133  " { symbol \"\", name \"\" },\n"

,

6134  " { symbol \"G\", name \"Guanine\" },\n"

,

6135  " { symbol \"H\", name \"A or C or T\" } ,\n"

,

6136  " { symbol \"\", name \"\" },\n"

,

6137  " { symbol \"\", name \"\" },\n"

,

6138  " { symbol \"K\", name \"G or T\" },\n"

,

6139  " { symbol \"\", name \"\"},\n"

,

6140  " { symbol \"M\", name \"A or C\" },\n"

,

6141  " { symbol \"N\", name \"A or G or C or T\" } ,\n"

,

6142  " { symbol \"\", name \"\" },\n"

,

6143  " { symbol \"\", name \"\" },\n"

,

6144  " { symbol \"\", name \"\"},\n"

,

6145  " { symbol \"R\", name \"G or A\"},\n"

,

6146  " { symbol \"S\", name \"G or C\"},\n"

,

6147  " { symbol \"T\", name \"Thymine\"},\n"

,

6148  " { symbol \"\", name \"\"},\n"

,

6149  " { symbol \"V\", name \"G or C or A\"},\n"

,

6150  " { symbol \"W\", name \"A or T\" },\n"

,

6151  " { symbol \"\", name \"\"},\n"

,

6152  " { symbol \"Y\", name \"T or C\"}\n"

,

6153  " } , -- end of table\n"

,

6154  " comps { -- complements\n"

,

6183  " code iupacaa ,\n"

,

6184  " num 26 , -- continuous 65-90\n"

,

6185  " one-letter TRUE , -- all one letter codes\n"

,

6186  " start-at 65 , -- starts with A, ASCII 65\n"

,

6188  " { symbol \"A\", name \"Alanine\" },\n"

,

6189  " { symbol \"B\" , name \"Asp or Asn\" },\n"

,

6190  " { symbol \"C\", name \"Cysteine\" },\n"

,

6191  " { symbol \"D\", name \"Aspartic Acid\" },\n"

,

6192  " { symbol \"E\", name \"Glutamic Acid\" },\n"

,

6193  " { symbol \"F\", name \"Phenylalanine\" },\n"

,

6194  " { symbol \"G\", name \"Glycine\" },\n"

,

6195  " { symbol \"H\", name \"Histidine\" } ,\n"

,

6196  " { symbol \"I\", name \"Isoleucine\" },\n"

,

6197  " { symbol \"J\", name \"Leu or Ile\" },\n"

,

6198  " { symbol \"K\", name \"Lysine\" },\n"

,

6199  " { symbol \"L\", name \"Leucine\" },\n"

,

6200  " { symbol \"M\", name \"Methionine\" },\n"

,

6201  " { symbol \"N\", name \"Asparagine\" } ,\n"

,

6202  " { symbol \"O\", name \"Pyrrolysine\" },\n"

,

6203  " { symbol \"P\", name \"Proline\" },\n"

,

6204  " { symbol \"Q\", name \"Glutamine\"},\n"

,

6205  " { symbol \"R\", name \"Arginine\"},\n"

,

6206  " { symbol \"S\", name \"Serine\"},\n"

,

6207  " { symbol \"T\", name \"Threonine\"},\n"

,

6208  " { symbol \"U\", name \"Selenocysteine\"}, -- was empty\n"

,

6209  " { symbol \"V\", name \"Valine\"},\n"

,

6210  " { symbol \"W\", name \"Tryptophan\" },\n"

,

6211  " { symbol \"X\", name \"Undetermined or atypical\"},\n"

,

6212  " { symbol \"Y\", name \"Tyrosine\"},\n"

,

6213  " { symbol \"Z\", name \"Glu or Gln\" }\n"

,

6214  " } -- end of table \n"

,

6216  " { -- IUPACeaa\n"

,

6217  " code ncbieaa ,\n"

,

6218  " num 49 , -- continuous 42-90\n"

,

6219  " one-letter TRUE , -- all one letter codes\n"

,

6220  " start-at 42 , -- starts with *, ASCII 42\n"

,

6222  " { symbol \"*\", name \"Termination\" } ,\n"

,

6223  " { symbol \"\", name \"\" } ,\n"

,

6224  " { symbol \"\", name \"\" } ,\n"

,

6225  " { symbol \"-\", name \"Gap\" } ,\n"

,

6226  " { symbol \"\", name \"\" } ,\n"

,

6227  " { symbol \"\", name \"\" } ,\n"

,

6228  " { symbol \"\", name \"\" } ,\n"

,

6229  " { symbol \"\", name \"\" } ,\n"

,

6230  " { symbol \"\", name \"\" } ,\n"

,

6231  " { symbol \"\", name \"\" } ,\n"

,

6232  " { symbol \"\", name \"\" } ,\n"

,

6233  " { symbol \"\", name \"\" } ,\n"

,

6234  " { symbol \"\", name \"\" } ,\n"

,

6235  " { symbol \"\", name \"\" } ,\n"

,

6236  " { symbol \"\", name \"\" } ,\n"

,

6237  " { symbol \"\", name \"\" } ,\n"

,

6238  " { symbol \"\", name \"\" } ,\n"

,

6239  " { symbol \"\", name \"\" } ,\n"

,

6240  " { symbol \"\", name \"\" } ,\n"

,

6241  " { symbol \"\", name \"\" } ,\n"

,

6242  " { symbol \"\", name \"\" } ,\n"

,

6243  " { symbol \"\", name \"\" } ,\n"

,

6244  " { symbol \"\", name \"\" } ,\n"

,

6245  " { symbol \"A\", name \"Alanine\" },\n"

,

6246  " { symbol \"B\" , name \"Asp or Asn\" },\n"

,

6247  " { symbol \"C\", name \"Cysteine\" },\n"

,

6248  " { symbol \"D\", name \"Aspartic Acid\" },\n"

,

6249  " { symbol \"E\", name \"Glutamic Acid\" },\n"

,

6250  " { symbol \"F\", name \"Phenylalanine\" },\n"

,

6251  " { symbol \"G\", name \"Glycine\" },\n"

,

6252  " { symbol \"H\", name \"Histidine\" } ,\n"

,

6253  " { symbol \"I\", name \"Isoleucine\" },\n"

,

6254  " { symbol \"J\", name \"Leu or Ile\" },\n"

,

6255  " { symbol \"K\", name \"Lysine\" },\n"

,

6256  " { symbol \"L\", name \"Leucine\" },\n"

,

6257  " { symbol \"M\", name \"Methionine\" },\n"

,

6258  " { symbol \"N\", name \"Asparagine\" } ,\n"

,

6259  " { symbol \"O\", name \"Pyrrolysine\" },\n"

,

6260  " { symbol \"P\", name \"Proline\" },\n"

,

6261  " { symbol \"Q\", name \"Glutamine\"},\n"

,

6262  " { symbol \"R\", name \"Arginine\"},\n"

,

6263  " { symbol \"S\", name \"Serine\"},\n"

,

6264  " { symbol \"T\", name \"Threonine\"},\n"

,

6265  " { symbol \"U\", name \"Selenocysteine\"},\n"

,

6266  " { symbol \"V\", name \"Valine\"},\n"

,

6267  " { symbol \"W\", name \"Tryptophan\" },\n"

,

6268  " { symbol \"X\", name \"Undetermined or atypical\"},\n"

,

6269  " { symbol \"Y\", name \"Tyrosine\"},\n"

,

6270  " { symbol \"Z\", name \"Glu or Gln\" }\n"

,

6271  " } -- end of table \n"

,

6273  " { -- IUPACaa3\n"

,

6274  " code iupacaa3 ,\n"

,

6275  " num 28 , -- continuous 0-27\n"

,

6276  " one-letter FALSE , -- all 3 letter codes\n"

,

6278  " { symbol \"---\", name \"Gap\" } ,\n"

,

6279  " { symbol \"Ala\", name \"Alanine\" },\n"

,

6280  " { symbol \"Asx\" , name \"Asp or Asn\" },\n"

,

6281  " { symbol \"Cys\", name \"Cysteine\" },\n"

,

6282  " { symbol \"Asp\", name \"Aspartic Acid\" },\n"

,

6283  " { symbol \"Glu\", name \"Glutamic Acid\" },\n"

,

6284  " { symbol \"Phe\", name \"Phenylalanine\" },\n"

,

6285  " { symbol \"Gly\", name \"Glycine\" },\n"

,

6286  " { symbol \"His\", name \"Histidine\" } ,\n"

,

6287  " { symbol \"Ile\", name \"Isoleucine\" },\n"

,

6288  " { symbol \"Lys\", name \"Lysine\" },\n"

,

6289  " { symbol \"Leu\", name \"Leucine\" },\n"

,

6290  " { symbol \"Met\", name \"Methionine\" },\n"

,

6291  " { symbol \"Asn\", name \"Asparagine\" } ,\n"

,

6292  " { symbol \"Pro\", name \"Proline\" },\n"

,

6293  " { symbol \"Gln\", name \"Glutamine\"},\n"

,

6294  " { symbol \"Arg\", name \"Arginine\"},\n"

,

6295  " { symbol \"Ser\", name \"Serine\"},\n"

,

6296  " { symbol \"Thr\", name \"Threonine\"},\n"

,

6297  " { symbol \"Val\", name \"Valine\"},\n"

,

6298  " { symbol \"Trp\", name \"Tryptophan\" },\n"

,

6299  " { symbol \"Xxx\", name \"Undetermined or atypical\"},\n"

,

6300  " { symbol \"Tyr\", name \"Tyrosine\"},\n"

,

6301  " { symbol \"Glx\", name \"Glu or Gln\" },\n"

,

6302  " { symbol \"Sec\", name \"Selenocysteine\"},\n"

,

6303  " { symbol \"Ter\", name \"Termination\" },\n"

,

6304  " { symbol \"Pyl\", name \"Pyrrolysine\"},\n"

,

6305  " { symbol \"Xle\", name \"Leu or Ile\"}\n"

,

6306  " } -- end of table \n"

,

6308  " { -- NCBIstdaa\n"

,

6309  " code ncbistdaa ,\n"

,

6310  " num 28 , -- continuous 0-27\n"

,

6311  " one-letter TRUE , -- all one letter codes\n"

,

6313  " { symbol \"-\", name \"Gap\" } , -- 0\n"

,

6314  " { symbol \"A\", name \"Alanine\" }, -- 1\n"

,

6315  " { symbol \"B\" , name \"Asp or Asn\" }, -- 2\n"

,

6316  " { symbol \"C\", name \"Cysteine\" }, -- 3\n"

,

6317  " { symbol \"D\", name \"Aspartic Acid\" }, -- 4\n"

,

6318  " { symbol \"E\", name \"Glutamic Acid\" }, -- 5\n"

,

6319  " { symbol \"F\", name \"Phenylalanine\" }, -- 6\n"

,

6320  " { symbol \"G\", name \"Glycine\" }, -- 7\n"

,

6321  " { symbol \"H\", name \"Histidine\" } , -- 8\n"

,

6322  " { symbol \"I\", name \"Isoleucine\" }, -- 9\n"

,

6323  " { symbol \"K\", name \"Lysine\" }, -- 10\n"

,

6324  " { symbol \"L\", name \"Leucine\" }, -- 11\n"

,

6325  " { symbol \"M\", name \"Methionine\" }, -- 12\n"

,

6326  " { symbol \"N\", name \"Asparagine\" } , -- 13\n"

,

6327  " { symbol \"P\", name \"Proline\" }, -- 14\n"

,

6328  " { symbol \"Q\", name \"Glutamine\"}, -- 15\n"

,

6329  " { symbol \"R\", name \"Arginine\"}, -- 16\n"

,

6330  " { symbol \"S\", name \"Serine\"}, -- 17\n"

,

6331  " { symbol \"T\", name \"Threoine\"}, -- 18\n"

,

6332  " { symbol \"V\", name \"Valine\"}, -- 19\n"

,

6333  " { symbol \"W\", name \"Tryptophan\" }, -- 20\n"

,

6334  " { symbol \"X\", name \"Undetermined or atypical\"}, -- 21\n"

,

6335  " { symbol \"Y\", name \"Tyrosine\"}, -- 22\n"

,

6336  " { symbol \"Z\", name \"Glu or Gln\" }, -- 23\n"

,

6337  " { symbol \"U\", name \"Selenocysteine\"}, -- 24 \n"

,

6338  " { symbol \"*\", name \"Termination\" }, -- 25\n"

,

6339  " { symbol \"O\", name \"Pyrrolysine\" }, -- 26\n"

,

6340  " { symbol \"J\", name \"Leu or Ile\" } -- 27\n"

,

6341  " } -- end of table \n"

,

6344  " code ncbi2na ,\n"

,

6345  " num 4 , -- continuous 0-3\n"

,

6346  " one-letter TRUE , -- all one letter codes\n"

,

6348  " { symbol \"A\", name \"Adenine\" },\n"

,

6349  " { symbol \"C\", name \"Cytosine\" },\n"

,

6350  " { symbol \"G\", name \"Guanine\" },\n"

,

6351  " { symbol \"T\", name \"Thymine/Uracil\"}\n"

,

6352  " } , -- end of table \n"

,

6353  " comps { -- complements\n"

,

6361  " code ncbi4na ,\n"

,

6362  " num 16 , -- continuous 0-15\n"

,

6363  " one-letter TRUE , -- all one letter codes\n"

,

6365  " { symbol \"-\", name \"Gap\" } ,\n"

,

6366  " { symbol \"A\", name \"Adenine\" },\n"

,

6367  " { symbol \"C\", name \"Cytosine\" },\n"

,

6368  " { symbol \"M\", name \"A or C\" },\n"

,

6369  " { symbol \"G\", name \"Guanine\" },\n"

,

6370  " { symbol \"R\", name \"G or A\"},\n"

,

6371  " { symbol \"S\", name \"G or C\"},\n"

,

6372  " { symbol \"V\", name \"G or C or A\"},\n"

,

6373  " { symbol \"T\", name \"Thymine/Uracil\"},\n"

,

6374  " { symbol \"W\", name \"A or T\" },\n"

,

6375  " { symbol \"Y\", name \"T or C\"} ,\n"

,

6376  " { symbol \"H\", name \"A or C or T\" } ,\n"

,

6377  " { symbol \"K\", name \"G or T\" },\n"

,

6378  " { symbol \"D\", name \"G or A or T\" },\n"

,

6379  " { symbol \"B\" , name \"G or T or C\" },\n"

,

6380  " { symbol \"N\", name \"A or G or C or T\" }\n"

,

6381  " } , -- end of table \n"

,

6382  " comps { -- complements\n"

,

6401  " } , -- end of codes\n"

,

6404  " from iupacna ,\n"

,

6407  " start-at 65 ,\n"

,

6433  " 3 } -- Y -> T\n"

,

6436  " from iupacna ,\n"

,

6439  " start-at 64 ,\n"

,

6441  " 0, -- @ used by FastaToSeqEntry to convert hyphen to gap\n"

,

6469  " from ncbi2na ,\n"

,

6479  " from ncbi2na ,\n"

,

6489  " from ncbi4na ,\n"

,

6493  " 78, -- gap -> N\n"

,

6511  " from ncbi4na ,\n"

,

6515  " 3, -- gap -> T\n"

,

6530  " 0 } -- N -> A\n"

,

6533  " from iupacaa ,\n"

,

6536  " start-at 65 ,\n"

,

6538  " 65 , -- they map directly\n"

,

6547  " 74, -- J - was 255\n"

,

6552  " 79, -- O - was 255\n"

,

6558  " 85, -- U - was 255\n"

,

6566  " from ncbieaa ,\n"

,

6569  " start-at 42 ,\n"

,

6571  " 88 , -- termination -> X\n"

,

6574  " 88, -- Gap -> X\n"

,

6594  " 65 , -- from here they map directly\n"

,

6603  " 74, -- J - was 255\n"

,

6608  " 79, -- O - was 255\n"

,

6614  " 85, -- U was -> X 88\n"

,

6622  " from iupacaa ,\n"

,

6623  " to ncbistdaa ,\n"

,

6625  " start-at 65 ,\n"

,

6627  " 1 , -- they map directly\n"

,

6636  " 27, -- J - was 255\n"

,

6641  " 26, -- O - was 255\n"

,

6647  " 24, -- U - was 255\n"

,

6655  " from ncbieaa ,\n"

,

6656  " to ncbistdaa ,\n"

,

6658  " start-at 42 ,\n"

,

6660  " 25, -- termination\n"

,

6683  " 1 , -- they map directly\n"

,

6692  " 27, -- J - was 255\n"

,

6697  " 26, -- O - was 255\n"

,

6711  " from ncbistdaa ,\n"

,

6715  " 45 , -- \"-\"\n"

,

6716  " 65 , -- they map directly with holes for O and J\n"

,

6741  " 79, -- O - new\n"

,

6742  " 74} -- J - new\n"

,

6745  " from ncbistdaa ,\n"

,

6749  " 255 , -- \"-\"\n"

,

6750  " 65 , -- they map directly with holes for O and J\n"

,

6773  " 85, -- U - was 88\n"

,

6775  " 79, -- O - new\n"

,

6776  " 74} -- J - new\n"

,

6779  "-- end of seq-code-set -- }"

,

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

ncbi::TMaskedQueryRegions mask

void AddAmbiguity(char in_byte, TSeqPos &seq_pos)

char m_LastAmbChar

Last previous ambiguity character.

CAmbiguityContext(vector< Uint4 > &amb_buff, int seq_length)

vector< Uint4 > & m_vAmbBuf

Ambiguity buffer to fill.

static SIZE_TYPE Pack(const string &src, TCoding src_coding, vector< char > &dst, TCoding &dst_coding, TSeqPos length=ncbi::numeric_limits< TSeqPos >::max())

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)

CWrapper_2D(size_t size1, int start1, size_t size2, int start2)

CWrapper_table(size_t size, size_t start)

const string & GetIupacaa3(TIndex ncbistdaa)

CRef< CMap_table > m_Ncbi2naNcbi4na

CRef< CFast_table2 > InitFastNcbi4naIupacna()

TSeqPos GetNcbistdaaCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos AppendNcbi4na(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2) const

TSeqPos GetIupacnaCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos Reverse(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CCode_comp > m_Ncbi4naComplement

CRef< CCode_table > m_Ncbieaa

TSeqPos AppendIupacaa(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2) const

CRef< CMap_table > m_IupacaaNcbistdaa

CRef< CMap_table > InitMaps(ESeq_code_type from_type, ESeq_code_type to_type)

TSeqPos KeepNcbi4na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CCode_comp > InitIupacnaComplement()

CRef< CFast_4_1 > InitFastIupacnaNcbi2na()

CRef< CCode_comp > InitNcbi2naComplement()

TSeqPos GetNcbi2naCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos GetCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos KeepIupacna(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos ComplementIupacna(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CCode_table > m_Ncbistdaa

CRef< CMap_table > m_NcbistdaaIupacaa

CRef< CFast_2_1 > InitFastNcbi4naNcbi2na()

CRef< CAmbig_detect > InitAmbigNcbi4naNcbi2na()

TSeqPos ReverseNcbi4na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CWrapper_table< char > CCode_table

TSeqPos KeepNcbi2na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

bool FastValidateNcbieaa(const CSeq_data &in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos AppendNcbieaa(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2) const

CSeqportUtil::TPair TPair

TSeqPos ReverseComplement(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CMap_table > m_IupacnaNcbi2na

vector< map< string, TIndex > > m_StringIndex

CRef< CMap_table > m_Ncbi2naIupacna

bool IsCodeAvailable(CSeq_data::E_Choice code_type)

CRef< CCode_comp > m_Ncbi2naComplement

CRef< CCode_table > m_Iupacna

TSeqPos GetNcbieaaCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos ReverseComplementNcbi4na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CMap_table > m_NcbieaaNcbistdaa

vector< TIndex > m_StartAt

vector< vector< TIndex > > m_IndexComplement

CWrapper_2D< unsigned char > CFast_4_1

CRef< CMap_table > m_IupacaaNcbieaa

TSeqPos GetAmbigs(const CSeq_data &in_seq, CSeq_data *out_seq, vector< TSeqPos > *out_indices, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx, TSeqPos uLength) const

const string & GetCodeOrName(CSeq_data::E_Choice code_type, TIndex idx, bool get_code)

TPair GetCodeIndexFromTo(CSeq_data::E_Choice code_type)

CRef< CSeq_code_set > m_SeqCodeSet

vector< vector< string > > m_IndexString[2]

CWrapper_2D< unsigned char > CFast_2_1

CRef< CCode_comp > InitNcbi4naComplement()

CWrapper_table< int > CMap_table

CRef< CCode_rev > InitNcbi2naRev()

CRef< CSeq_code_set > Init()

TSeqPos KeepIupacaa(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CWrapper_table< char > CCode_rev

CRef< CAmbig_detect > m_DetectAmbigNcbi4naNcbi2na

CRef< SMasksArray > m_Masks

TSeqPos ComplementNcbi4na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

size_t Pack(CSeq_data *in_seq, TSeqPos uLength) const

bool FastValidateIupacaa(const CSeq_data &in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

void ValidateIupacna(const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CMap_table > m_Ncbi4naNcbi2na

CRef< CCode_rev > InitNcbi4naRev()

TIndex GetIndexComplement(CSeq_data::E_Choice code_type, TIndex idx)

TSeqPos ReverseNcbi2na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CCode_comp > m_Iupacna_complement

CSeqportUtil::TIndex TIndex

CSeqportUtil_implementation()

TSeqPos ReverseIupacna(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CWrapper_table< unsigned short > CFast_table2

TIndex GetMapToIndex(CSeq_data::E_Choice from_type, CSeq_data::E_Choice to_type, TIndex from_idx)

CRef< CFast_2_1 > m_FastNcbi4naNcbi2na

CRef< CCode_table > InitCodes(ESeq_code_type code_type)

CRef< CFast_4_1 > m_FastIupacnaNcbi2na

CRef< CFast_2_1 > m_FastIupacnaNcbi4na

CRef< CMap_table > m_Ncbi4naIupacna

TSeqPos Keep(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CAmbig_detect > InitAmbigIupacnaNcbi2na()

TSeqPos GetAmbigs_iupacna_ncbi2na(const CSeq_data &in_seq, CSeq_data *out_seq, vector< TSeqPos > *out_indices, TSeqPos uBeginIdx, TSeqPos uLength) const

void Validate(const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx, TSeqPos uLength) const

void ValidateNcbieaa(const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos GetAmbigs_ncbi4na_ncbi2na(const CSeq_data &in_seq, CSeq_data *out_seq, vector< TSeqPos > *out_indices, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos ReverseComplementIupacna(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos Adjust(TSeqPos *uBeginIdx, TSeqPos *uLength, TSeqPos uInSeqBytes, TSeqPos uInSeqsPerByte, TSeqPos uOutSeqsPerByte) const

TIndex GetIndex(CSeq_data::E_Choice code_type, const string &code)

CRef< CMap_table > m_NcbistdaaNcbieaa

TSeqPos Complement(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CWrapper_table< string > CCode_table_str

static const char * sm_StrAsnData[]

CRef< CCode_table > m_Iupacaa

CRef< CCode_rev > m_Ncbi2naRev

TSeqPos AppendNcbi2na(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2) const

TSeqPos AppendNcbistdaa(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2) const

bool FastValidateNcbistdaa(const CSeq_data &in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos Append(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2) const

CWrapper_table< unsigned int > CFast_table4

TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx, TSeqPos uLength, bool bAmbig, CRandom::TValue seed, TSeqPos total_length=0, TSeqPos *out_seq_length=0, vector< Uint4 > *blast_ambig=0) const

TSeqPos KeepNcbieaa(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CWrapper_table< unsigned char > CAmbig_detect

bool FastValidateIupacna(const CSeq_data &in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos ComplementNcbi2na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos AppendIupacna(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2) const

void ValidateIupacaa(const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos x_ConvertAmbig(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx, TSeqPos uLength, CRandom::TValue seed, TSeqPos total_length=0, TSeqPos *out_seq_length=0, vector< Uint4 > *blast_ambig=0) const

CRef< CMap_table > m_IupacnaNcbi4na

CRef< CFast_2_1 > InitFastIupacnaNcbi4na()

CWrapper_table< char > CCode_comp

void x_GetSeqFromSeqData(const CSeq_data &data, const string **str, const vector< char > **vec) const

bool FastValidate(const CSeq_data &in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos GetNcbi4naCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

TSeqPos MapIupacnaToNcbi2na(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength, bool bAmbig, CRandom::TValue seed, TSeqPos total_length, TSeqPos *out_seq_length, vector< Uint4 > *blast_ambig) const

CRef< CMap_table > m_NcbieaaIupacaa

TSeqPos ReverseComplementNcbi2na(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CAmbig_detect > m_DetectAmbigIupacnaNcbi2na

~CSeqportUtil_implementation()

TSeqPos GetIupacaaCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

void ValidateNcbistdaa(const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< SMasksArray > InitMasks()

TSeqPos MapNcbi4naToNcbi2na(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength, bool bAmbig, CRandom::TValue seed, TSeqPos total_length, TSeqPos *out_seq_length, vector< Uint4 > *blast_ambig) const

CRef< CFast_table2 > InitFastNcbi2naNcbi4na()

TSeqPos KeepNcbistdaa(CSeq_data *in_seq, TSeqPos uBeginIdx, TSeqPos uLength) const

CRef< CCode_rev > m_Ncbi4naRev

static CSeqportUtil_implementation & x_GetImplementation(void)

static TPair GetCodeIndexFromTo(CSeq_data::E_Choice code_type)

static TSeqPos Reverse(CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static const string & GetName(CSeq_data::E_Choice code_type, TIndex idx)

static bool IsCodeAvailable(CSeq_data::E_Choice code_type)

static bool FastValidate(const CSeq_data &in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

static TIndex GetIndex(CSeq_data::E_Choice code_type, const string &code)

static TIndex GetIndexComplement(CSeq_data::E_Choice code_type, TIndex idx)

static TSeqPos ConvertWithBlastAmbig(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength, TSeqPos total_length, TSeqPos *out_seq_length, vector< Uint4 > *blast_ambig)

static TSeqPos GetAmbigs(const CSeq_data &in_seq, CSeq_data *out_seq, vector< TSeqPos > *out_indices, CSeq_data::E_Choice to_code=CSeq_data::e_Ncbi2na, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static TIndex GetMapToIndex(CSeq_data::E_Choice from_type, CSeq_data::E_Choice to_type, TIndex from_idx)

static TSeqPos GetCopy(const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static TSeqPos Complement(CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static TSeqPos Keep(CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static TSeqPos ReverseComplement(CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static const string & GetCode(CSeq_data::E_Choice code_type, TIndex idx)

pair< TIndex, TIndex > TPair

static void Validate(const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx=0, TSeqPos uLength=0)

static const string & GetIupacaa3(TIndex ncbistdaa)

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

static TSeqPos Append(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2)

container_type::const_iterator const_iterator

static void chk(int check, const char *fmt,...)

static const char * str(char *buf, int n)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

const TPrim & Get(void) const

@ eSerial_AsnText

ASN.1 text.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

uint32_t Uint4

4-byte (32-bit) unsigned integer

Uint4 TValue

Type of the generated integer value and/or the seed value.

TValue GetRand(void)

Get the next random number in the interval [0..GetMax()] (inclusive)

void SetSeed(TValue seed)

Seed the random number generator with "seed".

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

list< CRef< C_E_Table > > TTable

list< CRef< CSeq_code_table > > TCodes

const TMaps & GetMaps(void) const

Get the Maps member data.

ESeq_code_type

sequence representations

const TCodes & GetCodes(void) const

Get the Codes member data.

@ eSeq_code_type_ncbi2na

2 bit nucleic acid code

@ eSeq_code_type_ncbistdaa

consecutive codes for std aas, 0-25

@ eSeq_code_type_ncbi4na

4 bit nucleic acid code

@ eSeq_code_type_ncbieaa

extended ASCII 1 letter aa codes

@ eSeq_code_type_ncbipaa

amino acid probabilities

@ eSeq_code_type_ncbi8aa

8 bit extended amino acid codes

@ eSeq_code_type_ncbi8na

8 bit extended nucleic acid code

@ eSeq_code_type_ncbipna

nucleic acid probabilities

@ eSeq_code_type_iupacaa3

3 letter code only for display

@ eSeq_code_type_iupacaa

IUPAC 1 letter amino acid code.

@ eSeq_code_type_iupacna

IUPAC 1 letter nuc acid code.

const TIupacaa & GetIupacaa(void) const

Get the variant data.

const TIupacna & GetIupacna(void) const

Get the variant data.

const TNcbipaa & GetNcbipaa(void) const

Get the variant data.

const TNcbi8aa & GetNcbi8aa(void) const

Get the variant data.

TNcbieaa & SetNcbieaa(void)

Select the variant.

E_Choice

Choice variants.

TIupacna & SetIupacna(void)

Select the variant.

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

const TNcbistdaa & GetNcbistdaa(void) const

Get the variant data.

TNcbistdaa & SetNcbistdaa(void)

Select the variant.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

TNcbi2na & SetNcbi2na(void)

Select the variant.

const TNcbi2na & GetNcbi2na(void) const

Get the variant data.

TNcbi4na & SetNcbi4na(void)

Select the variant.

TIupacaa & SetIupacaa(void)

Select the variant.

virtual void Reset(void)

Reset the whole object.

E_Choice Which(void) const

Which variant is currently selected.

@ e_not_set

No variant selected.

@ e_Ncbipna

nucleic acid probabilities

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbipaa

amino acid probabilities

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ e_Ncbi8aa

8 bit extended amino acid codes

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

Static variables safety - create on demand, destroy on application termination.

static const unsigned int kNumCodes

static ESeq_code_type EChoiceToESeq(CSeq_data::E_Choice from_type)

static const char kAmbig4na[16]

static CSafeStatic< CSeqportUtil_implementation > sx_Implementation

static const bool kSymbol

static CSeqUtil::TCoding s_SeqDataToSeqUtil[]

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

static bool ambig(char c)

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