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NCBI C++ ToolKit: src/algo/align/nw/nw_formatter.cpp Source File

54  const char

id_not_set[] =

"ID_not_set"

;

91

score->SetId().SetStr(

"global_score"

);

93

seqalign->

SetScore

().push_back(score);

100  ITERATE

(

string

, ii, transcript) {

109  Int8

endi = transcript.size() - 1;

113  for

( ;ind < endi; ++ind) {

118

length = endi + 1 - ind;

122

length = transcript.size();

130

idty = double(matches) / length;

133

score->SetId().SetStr(

"identity"

);

134

score->SetValue().SetReal(idty);

135

seqalign->

SetScore

().push_back(score);

139

subj_start, subj_strand,

flags

);

142

seqalign->

SetSegs

().SetDenseg(*rds);

144

seqalign->

SetSegs

().SetDendiag();

160  if

(transcript.size() == 0) {

171

vector<CNWAligner::ETranscriptSymbol>::const_iterator

172

ib = stranscript.begin(),

173

ie = stranscript.end();

174  while

( ( ie != ib ) &&

187

subj_start, subj_strand,

195

ids.push_back(id_query);

199

ids.push_back(id_subj);

227  const size_t

min_query_size = 4;

228  if

(

int

(m_box[1] - m_box[0] + 1) <

int

(min_query_size)) {

234  int

len_total = (

int

)m_details.size();

236

string::iterator irs0 = m_details.begin(),

237

irs1 = m_details.end(), irs;

239  for

(irs = irs0; irs != irs1; ++irs) {

246

string::reverse_iterator rirs0 = m_details.rbegin(),

247

rirs1 = m_details.rend(), rirs = rirs0;

248  int cnt

= 0, max_cnt = 20;

251  for

( ; ( rirs != rirs1 ) && (

cnt

!= max_cnt) ; ++rirs, ++

cnt

) {

257  double

ident =

match

/(double)

len

;

260  int

i0_max = 0, i1_max = 0;

261

string::iterator irs_max;

268  const double

dropoff_diff = .19;

271  for

(irs = irs0; irs != irs1; ++irs) {

305

match_total -=

match

;

316  while

(i0_max > 0 && i1_max > 0) {

317  if

(

toupper

(seq1[m_box[0]+i0_max-1]) !=

'N'

&& seq1[m_box[0]+i0_max-1] == seq2[m_box[2]+i1_max-1] ) {

328  if

(i0_max == 0 && i1_max == 0)

return

;

331  if

(m_box[1] - m_box[0] + 1 - i0_max >= min_query_size )

336  const size_t

L = irs_max - irs0 + 1;

337

m_details.erase(0, L);

338

m_details.insert(m_details.begin(),

head

,

'M'

);

342  if

(m_annot.size() > 2 && m_annot[2] ==

'<'

) {

343  int

j1 =

int

(m_box[2]) - 2;

344  char

c1 = j1 >= 0? seq2[j1]:

' '

;

346  int

j2 =

int

(m_box[2]) - 1;

347  char

c2 = j2 >= 0? seq2[j2]:

' '

;

360  const size_t

min_query_size = 4;

362  int

i0 =

int

(m_box[1] - m_box[0] + 1), i0_max = i0;

363  if

(i0 <

int

(min_query_size)) {

369  int

i1 =

int

(m_box[3] - m_box[2] + 1), i1_max = i1;

378

string::reverse_iterator irs0 = m_details.rbegin(),

379

irs1 = m_details.rend(), irs = irs0, irs_max = irs0;

381  for

( ; irs != irs1; ++irs) {

401  if

(irs > irs0 && *(irs-1)!=

'I'

) s += wg;

408  if

(irs > irs0 && *(irs-1)!=

'D'

) s += wg;

413  if

(s >= score_max) {

425  while

(i0_max > 0 && i1_max > 0) {

426  if

(

toupper

(seq1[m_box[0]+i0_max-1]) !=

'N'

&& seq1[m_box[0]+i0_max-1] == seq2[m_box[2]+i1_max-1]) {

435  if

(i0_max == 0 && i1_max == 0)

return

;

438  if

(m_box[1] - m_box[0] + 1 - i0_max >= min_query_size )

443  const size_t

L = m_details.size() - (irs_max - irs0 + 1);

444

m_details.erase(0, L);

445

m_details.insert(m_details.begin(),

head

,

'M'

);

449  if

(m_annot.size() > 2 && m_annot[2] ==

'<'

) {

450  int

j1 =

int

(m_box[2]) - 2;

451  char

c1 = j1 >= 0? seq2[j1]:

' '

;

453  int

j2 =

int

(m_box[2]) - 1;

454  char

c2 = j2 >= 0? seq2[j2]:

' '

;

464  size_t

gap_count = 0;

465  ITERATE

(

string

, irs, m_details) {

482  for

(

size_t i

= m_box[0];

i

<=m_box[1]; ++

i

) {

485  size_t

gap_len = GapLength();

487  if

( m_len * 70 <= 100 * (

i

->second + gap_len) ) {

499  const size_t

min_query_size = 4;

501  if

(m_box[1] - m_box[0] + 1 < min_query_size) {

507  int

len_total = (

int

)m_details.size();

509

string::iterator irs0 = m_details.begin(),

510

irs1 = m_details.end(), irs;

512  for

(irs = irs0; irs != irs1; ++irs) {

519  int cnt

= 0, max_cnt = 20;

521  for

( irs = irs0; ( irs != irs1 ) && (

cnt

!= max_cnt) ; ++irs, ++

cnt

) {

527  double

ident =

match

/(double)

len

;

530  const double

dropoff_diff = .19;

532  int

i0 =

int

(m_box[1] - m_box[0] + 1), i0_max = i0;

533  int

i1 =

int

(m_box[3] - m_box[2] + 1), i1_max = i1;

536

string::reverse_iterator rirs0 = m_details.rbegin(),

537

rirs1 = m_details.rend(), rirs = rirs0, rirs_max;

540  for

( ; rirs != rirs1; ++rirs) {

574

match_total -=

match

;

581  int

dimq =

int

(m_box[1] - m_box[0] + 1);

582  int

dims =

int

(m_box[3] - m_box[2] + 1);

588  while

(i0_max < dimq && i1_max < dims ) {

589  if

(

toupper

(seq1[m_box[0]+i0_max]) !=

'N'

&& seq1[m_box[0]+i0_max] == seq2[m_box[2]+i1_max]) {

598  if

( i0_max >= dimq && i1_max >= dims )

return

;

601  if

(i0_max - 1 >=

int

(min_query_size) ) {

603

m_box[1] = m_box[0] + i0_max - 1;

604

m_box[3] = m_box[2] + i1_max - 1;

606

m_details.resize(m_details.size() - (rirs_max - rirs0 + 1));

607

m_details.insert(m_details.end(), tail,

'M'

);

611  const size_t

adim = m_annot.size();

612  if

(adim > 2 && m_annot[adim - 3] ==

'>'

) {

615  const char

c3 (m_box[3] + 1 < len2? seq2[m_box[3] + 1]:

' '

);

616  const char

c4 (m_box[3] + 2 < len2? seq2[m_box[3] + 2]:

' '

);

617

m_annot[adim-2] = c3;

618

m_annot[adim-1] = c4;

631  const size_t

min_query_size = 4;

633  if

(m_box[1] - m_box[0] + 1 < min_query_size) {

639  int

i0 = -1, i0_max = i0;

640  int

i1 = -1, i1_max = i1;

649

string::iterator irs0 = m_details.begin(),

650

irs1 = m_details.end(), irs = irs0, irs_max = irs0;

652  for

( ; irs != irs1; ++irs) {

672  if

(irs > irs0 && *(irs-1) !=

'I'

) s += wg;

679  if

(irs > irs0 && *(irs-1) !=

'D'

) s += wg;

684  if

(s >= score_max) {

692  int

dimq =

int

(m_box[1] - m_box[0] + 1);

693  int

dims =

int

(m_box[3] - m_box[2] + 1);

699  while

(i0_max < dimq - 1 && i1_max < dims - 1) {

700  if

(

toupper

(seq1[m_box[0]+i0_max+1]) !=

'N'

&& seq1[m_box[0]+i0_max+1] == seq2[m_box[2]+i1_max+1] ) {

712  if

(i0_max >= dimq - 1 && i1_max >= dims - 1)

return

;

715  if

(i0_max >=

int

(min_query_size) ) {

717

m_box[1] = m_box[0] + i0_max;

718

m_box[3] = m_box[2] + i1_max;

720

m_details.resize(irs_max - irs0 + 1);

721

m_details.insert(m_details.end(), tail,

'M'

);

725  const size_t

adim = m_annot.size();

726  if

(adim > 2 && m_annot[adim - 3] ==

'>'

) {

729  const char

c3 (m_box[3] + 1 < len2? seq2[m_box[3] + 1]:

' '

);

730  const char

c4 (m_box[3] + 2 < len2? seq2[m_box[3] + 2]:

' '

);

731

m_annot[adim-2] = c3;

732

m_annot[adim-1] = c4;

742  Int8

mind0 = m_box[1] + 1;

744  Int8

gind = m_box[3] + 1;

745  for

(; mind < (

int

)mrna.size() && gind < (

int

)genomic.size(); ++gind, ++mind) {

746  if

(

toupper

(mrna[mind]) ==

'N'

|| mrna[mind] != genomic[gind] )

break

;

755  int

mind0 = (

int

)m_box[0] - 1;

757  int

gind = (

int

)m_box[2] - 1;

758  for

(; mind >= 0 && gind >= 0; --mind, --gind) {

759  if

(

toupper

(mrna[mind]) ==

'N'

|| mrna[mind] != genomic[gind] )

break

;

770

m_details.append(ext_len,

'M'

);

773  const size_t

ann_dim = m_annot.size();

774  if

(ann_dim > 2 && m_annot[ann_dim - 3] ==

'>'

) {

775

m_annot[ann_dim - 2] = (m_box[3] + 1) < genomic.size() ? genomic[m_box[3] + 1] :

' '

;

776

m_annot[ann_dim - 1] = (m_box[3] + 2) < genomic.size() ? genomic[m_box[3] + 2] :

' '

;

787

m_details.insert(m_details.begin(), ext_len,

'M'

);

790  if

( ( m_annot.size() > 2 ) && ( m_annot[2] ==

'<'

) ) {

791

m_annot[1] = m_box[2] >= 1 ? genomic[m_box[2] - 1] :

' '

;

792

m_annot[0] = m_box[2] >= 2 ? genomic[m_box[2] - 2] :

' '

;

801

m_len = m_details.size();

803

string::const_iterator ib = m_details.begin(), ie = m_details.end();

805  for

(string::const_iterator ii = ib; ii != ie; ++ii) {

806  if

(*ii ==

'M'

) ++

count

;

808

m_idty = double(

count

) / m_len;

810  const size_t

xcript_dim (m_details.size());

812  for

(

size_t i

(0);

i

< xcript_dim; ++

i

) {

816

m_score = float(paligner->CNWAligner::ScoreFromTranscript(transcript)) /

823  const size_t

adim = m_annot.size();

825

(adim > 2 && m_annot[adim - 3] ==

'>'

)? (m_annot.c_str() + adim - 2): 0;

831  const size_t

adim = m_annot.size();

832  return

(adim > 3 && m_annot[2] ==

'<'

)? m_annot.c_str(): 0;

837  const char

* acceptor,

840  if

(!donor || !acceptor)

return false

;

845  if

(acceptor[0] ==

'A'

) {

846  if

(donor[0] ==

'G'

&& acceptor[1] ==

'G'

) {

847

rv = donor[1] ==

'T'

|| donor[1] ==

'C'

;

850

rv = donor[0] ==

'A'

&& donor[1] ==

'T'

&& acceptor[1] ==

'C'

;

858

rv = donor[0] ==

'G'

&& donor[1] ==

'T' 859

&& acceptor[0] ==

'A'

&& acceptor[1] ==

'G'

;

869  copy

(v.begin(), v.end(), psegments->begin());

875  if

(transcript.size() == 0) {

879

vector<SSegment>& segments(*psegments);

882  bool

esfL1, esfR1, esfL2, esfR2;

887  const char

* p1 (start1);

888  const char

* p2 (start2);

889  Int8

tr_idx_hi0 (transcript.size() - 1), tr_idx_hi (tr_idx_hi0);

890  Int8

tr_idx_lo0 (0), tr_idx_lo (tr_idx_lo0);

930

vector<char> trans_ex (tr_idx_hi - tr_idx_lo + 1);

932  for

(

int

tr_idx (

static_cast<int>

(tr_idx_hi)); tr_idx >= tr_idx_lo; ) {

934  const char

* p1_beg (p1), * p1_x (0);

935  const char

* p2_beg (p2);

936  size_t

matches (0), exon_aln_size (0), exon_aln_size_x(0);

939

vector<char>::iterator ii_ex (trans_ex.begin()), ii_ex_x;

940  size_t

cons_dels (0);

941  const size_t

max_cons_dels (25);

946  if

(noins && nodel) {

948  if

(cons_dels > max_cons_dels) {

954  if

(

toupper

(*p1) !=

'N'

&& *p1 == *p2) {

965  if

(cons_dels == 0) {

968

exon_aln_size_x = exon_aln_size;

985  if

(cons_dels > max_cons_dels) {

987  swap

(ii_ex, ii_ex_x);

988  swap

(exon_aln_size, exon_aln_size_x);

989  swap

(tr_idx, tr_idx_x);

992  if

(exon_aln_size > 0) {

998

s.

m_idty

= float(matches) / exon_aln_size;

999

s.

m_len

= exon_aln_size;

1001  size_t

beg1 (p1_beg - start1), end1 (p1 - start1 - 1);

1002  size_t

beg2 (p2_beg - start2), end2 (p2 - start2 - 1);

1004

s.

m_box

[0] = beg1;

1005

s.

m_box

[1] = end1;

1006

s.

m_box

[2] = beg2;

1007

s.

m_box

[3] = end2;

1009  char

c1 ((p2_beg >= start2 + 2)? *(p2_beg - 2):

' '

);

1010  char

c2 ((p2_beg >= start2 + 1)? *(p2_beg - 1):

' '

);

1011  char

c3 ((p2 < start2 + len2)? *(p2):

' '

);

1012  char

c4 ((p2 < start2 + len2 - 1)? *(p2+1):

' '

);

1017  const string

s_exontag (

"<exon>"

);

1018  copy

(s_exontag.begin(), s_exontag.end(), s.

m_annot

.begin() + 2);

1021

s.

m_details

.resize(ii_ex - trans_ex.begin());

1026  if

(cons_dels > max_cons_dels) {

1033

s.

m_len

= exon_aln_size_x - exon_aln_size;

1035  size_t

beg1 (p1 - start1), end1 (p1_x - start1 - 1);

1036  size_t

beg2 (0), end2 (0);

1038

s.

m_box

[0] = beg1;

1039

s.

m_box

[1] = end1;

1040

s.

m_box

[2] = beg2;

1041

s.

m_box

[3] = end2;

1048  swap

(ii_ex, ii_ex_x);

1049  swap

(exon_aln_size, exon_aln_size_x);

1050  swap

(tr_idx, tr_idx_x);

1074  if

(transcript.size() == 0) {

1080  const string

strid_query =

m_Seq1Id

->GetSeqIdString(

true

);

1081  const string

strid_subj =

m_Seq2Id

->GetSeqIdString(

true

);

1087

ss << '>

' << strid_query << '\t' << strid_subj << endl; 1089  vector<char> v1, v2; 1090  unsigned i1 (0), i2 (0); 1091  size_t aln_size (x_ApplyTranscript(&v1, &v2)); 1092  for (size_t i = 0; i < aln_size; ) { 1094  ss << i << '\t' << i1 << '

:

' << i2 << endl; 1096  for (size_t jPos = 0; i < aln_size && jPos < line_width; ++i, ++jPos) { 1097  char c1 (v1[i0 + jPos]); 1099  if(c1 != '

-

' && c1 != '

x

' && c1 != '

+

') ++i1; 1103  string marker_line(line_width, ' '); 1105  for (size_t jPos = 0; i < aln_size && jPos < line_width; ++i, ++jPos) { 1106  char c1 (v1[i0 + jPos]); 1107  char c2 (v2[i0 + jPos]); 1109  if(c2 != '

-

' && c2 != '

+

' && c2 != '

x

') 1111  if( c2 != '

-

' && c1 != '

-

' && c1 != '

+

' && c1 != '

x

' && ( toupper(c2) != toupper(c1) || m_aligner->GetScoreMatrix().s[(size_t)c1][(size_t)c2] <= 0 )) 1112  marker_line[jPos] = '

^

'; 1114  ss << endl << marker_line << endl; 1119  case eFormatType2: { 1121  ss << '

>

' << strid_query << '\t' << strid_subj << endl; 1123  vector<char> v1, v2; 1124  unsigned i1 (0), i2 (0); 1125  size_t aln_size (x_ApplyTranscript(&v1, &v2)); 1126  for (size_t i = 0; i < aln_size; ) { 1127  ss << i << '\t' << i1 << '

:

' << i2 << endl; 1129  for (size_t jPos = 0; i < aln_size && jPos < line_width; ++i, ++jPos) { 1130  char c (v1[i0 + jPos]); 1132  if(c != '

-

' && c != '

+

' && c != '

x

') ++i1; 1136  string line2 (line_width, ' '); 1137  string line3 (line_width, ' '); 1139  for (size_t jPos = 0; i < aln_size && jPos < line_width; ++i, ++jPos) { 1140  char c1 (v1[i0 + jPos]); 1141  char c2 (v2[i0 + jPos]); 1142  if(c2 != '

-

' && c2 != '

+

' && c2 != '

x

') i2++; 1143  if( toupper(c2) == toupper(c1) && m_aligner-> GetScoreMatrix().s[(size_t)c1][(size_t)c2] > 0 ) line2[jPos] = '

|

'; 1146  ss << line2 << endl << line3 << endl << endl; 1153  CRef<CSeq_align> sa = AsSeqAlign(); 1154  CObjectOStreamAsn asn_stream (ss); 1156  asn_stream << Separator; 1160  case eFormatDenseSeg: { 1162  CRef<CDense_seg> ds = AsDenseSeg(); 1163  CObjectOStreamAsn asn_stream (ss); 1165  asn_stream << Separator; 1169  case eFormatFastA: { 1170  vector<char> v1, v2; 1171  size_t aln_size (x_ApplyTranscript(&v1, &v2)); 1173  ss << '

>

' << strid_query << endl; 1174  const vector<char>* pv = &v1; 1175  for(size_t i = 0; i < aln_size; ) { 1176  for(size_t j = 0; j < line_width && i < aln_size; ++j, ++i) { 1182  ss << '

>

' << strid_subj << endl; 1184  for(size_t i = 0; i < aln_size; ) { 1185  for(size_t j = 0; j < line_width && i < aln_size; ++j, ++i) { 1193  case eFormatExonTable: 1194  case eFormatExonTableEx: { 1198  typedef deque<SSegment> TSegments; 1200  MakeSegments(&segments); 1201  ITERATE(TSegments, ii, segments) { 1203  ss << strid_query << '\t' << strid_subj << '\t'; 1204  ss << ii->m_idty << '\t' << ii->m_len << '\t'; 1205  copy(ii->m_box, ii->m_box + 4, 1206  ostream_iterator<size_t>(ss,"\t")); 1207  ss << '\t' << ii->m_annot; 1208  if(type == eFormatExonTableEx) { 1209  ss << '\t' << ii->m_details; 1217  NCBI_THROW(CAlgoAlignException, eBadParameter, "Incorrect format specified"); 1220  *output = CNcbiOstrstreamToString(ss); 1225 // Transform source sequences according to the transcript. 1226 // cut flank gaps for Smith-Waterman 1227 // Write the results to v1 and v2 leaving source sequences intact. 1228 // Return alignment size. 1229 size_t CNWFormatter::x_ApplyTranscript(vector<char>* pv1, vector<char>* pv2) 1232  const CNWAligner::TTranscript transcript = m_aligner->GetTranscript(); 1234  vector<char>& v1 (*pv1); 1235  vector<char>& v2 (*pv2); 1240  if(transcript.size() == 0) { 1245  vector<CNWAligner::ETranscriptSymbol>::const_reverse_iterator 1246  ib = transcript.rbegin(), 1247  ie = transcript.rend(), 1250  if( m_aligner->IsSmithWaterman() ) { 1252  while( ( ie != ib ) && 1253  ( *ie == CNWAligner::eTS_Insert || *ie == CNWAligner::eTS_Delete || *ie == CNWAligner::eTS_Intron || 1254  *ie == CNWAligner::eTS_SlackInsert || *ie == CNWAligner::eTS_SlackDelete ) ) { 1259  const char* iv1 (m_aligner->GetSeq1()); 1260  const char* iv2 (m_aligner->GetSeq2()); 1262  bool sw_ini_gap = false; 1263  if( m_aligner->IsSmithWaterman() ) { 1267  for (ii = ib; ii != ie; ii++) { 1269  CNWAligner::ETranscriptSymbol ts (*ii); 1273  case CNWAligner::eTS_Insert: 1278  case CNWAligner::eTS_SlackInsert: 1283  case CNWAligner::eTS_Delete: 1289  case CNWAligner::eTS_SlackDelete: 1294  case CNWAligner::eTS_Match: 1295  case CNWAligner::eTS_Replace: 1301  case CNWAligner::eTS_Intron:

User-defined methods of the data storage class.

void TrimEndGaps()

Trim leading/training gaps if possible.

void FromTranscript(TSeqPos query_start, ENa_strand query_strand, TSeqPos subj_start, ENa_strand subj_strand, const string &transcript)

Initialize from pairwise alignment transcript (a string representation produced by CNWAligner)

container_type::iterator iterator

static SQLCHAR output[256]

void ImproveFromLeft(const char *seq1, const char *seq2, CConstRef< CSplicedAligner > aligner)

void ExtendRight(const vector< char > &mrna, const vector< char > &genomic, Int8 ext_len, const CNWAligner *aligner)

CRef< objects::CDense_seg > AsDenseSeg(TSeqPos query_start=0, objects::ENa_strand query_strand=objects::eNa_strand_plus, TSeqPos subj_start=0, objects::ENa_strand subj_strand=objects::eNa_strand_plus, int SAFF_flags=eSAFF_None) const

void ImproveFromRight(const char *seq1, const char *seq2, CConstRef< CSplicedAligner > aligner)

CNWFormatter(const CNWAligner &aligner)

void AsText(string *output, ETextFormatType type, size_t line_width=100) const

void MakeSegments(vector< SSegment > *psegments) const

const CNWAligner * m_aligner

int CanExtendRight(const vector< char > &mrna, const vector< char > &genomic) const

const char * GetDonor(void) const

void ImproveFromLeft1(const char *seq1, const char *seq2, CConstRef< CSplicedAligner > aligner)

CRef< objects::CSeq_align > AsSeqAlign(TSeqPos query_start=0, objects::ENa_strand query_strand=objects::eNa_strand_plus, TSeqPos subj_start=0, objects::ENa_strand subj_strand=objects::eNa_strand_plus, int SAFF_flags=eSAFF_None) const

void ImproveFromRight1(const char *seq1, const char *seq2, CConstRef< CSplicedAligner > aligner)

CConstRef< objects::CSeq_id > m_Seq2Id

static bool s_IsConsensusSplice(const char *donor, const char *acceptor, bool semi_as_cons=false)

const char * GetAcceptor(void) const

int CanExtendLeft(const vector< char > &mrna, const vector< char > &genomic) const

CConstRef< objects::CSeq_id > m_Seq1Id

void SetSeqIds(CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)

void Update(const CNWAligner *aligner)

void ExtendLeft(const vector< char > &mrna, const vector< char > &genomic, Int8 ext_len, const CNWAligner *aligner)

bool IsLowComplexityExon(const char *rna_seq)

const char * GetSeq2(void) const

TTranscript GetTranscript(bool reversed=true) const

const char * GetSeq1(void) const

bool IsSmithWaterman() const

size_t GetSeqLen2(void) const

TScore GetScore(void) const

string GetTranscriptString(void) const

vector< ETranscriptSymbol > TTranscript

void GetEndSpaceFree(bool *L1, bool *R1, bool *L2, bool *R2) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

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

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void Reset(void)

Reset reference object.

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

int64_t Int8

8-byte (64-bit) signed integer

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TStr & SetStr(void)

Select the variant.

TScore & SetScore(void)

Assign a value to Score data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

vector< CRef< CSeq_id > > TIds

TIds & SetIds(void)

Assign a value to Ids data member.

@ eType_partial

mapping pieces together

ENa_strand

strand of nucleic acid

TLocal & SetLocal(void)

Select the variant.

unsigned int

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

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

static const char s_kGap[]

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

const char g_msg_NoAlignment[]

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