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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnsegments_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/alnmgr/alnsegments.cpp Source File

49

TCalcScoreMethod calc_score)

50

: m_AlnMixSequences(aln_mix_sequences),

51

m_Rows(m_AlnMixSequences->m_Rows),

52

m_ExtraRows(m_AlnMixSequences->m_ExtraRows),

53

x_CalculateScore(calc_score)

60 bool

remove_leading_and_trailing_gaps)

64 #if _DEBUG && _ALNMGR_DEBUG 71

CAlnMixSequences::TSeqs::iterator refseq_it =

m_Rows

.begin();

72 bool

orig_refseq =

true

;

75 while

(refseq_it !=

m_Rows

.end()) {

76

refseq = *(refseq_it++);

87 if

(gapped_segs.size()) {

105 #if _DEBUG && _ALNMGR_TRACE 106

cerr <<

"refseq is on row "

<< refseq->

m_RowIdx 107

" seq "

<< refseq->

m_SeqIdx

"\n"

;

111

stack< CRef<CAlnMixSegment> > seg_stack;

118 #if _DEBUG && _ALNMGR_TRACE 119

cerr <<

" [row "

<< refseq->

m_RowIdx 121

" start "

<< refseq_start

122

" was pushed into stack\n"

;

126 while

( !seg_stack.empty() ) {

128 bool

pop_seg =

true

;

131

seg_stack.top()->m_StartIts) {

135 if

(

row

->GetStarts().current != start_its_i->second) {

137 const TSeqPos

& curr_row_start =

row

->GetStarts().current->first;

138 const TSeqPos

& row_start = start_its_i->second->first;

140 if

(

row

->m_PositiveStrand ?

146 string

(

"CAlnMixSegments::Build():"

)

147

" Internal error: Integrity broken"

157

(

row

->m_PositiveStrand ?

"plus"

"minus"

);

161

seg_stack.push(

row

->GetStarts().current->second);

164 if

(!seg_set.

insert

(

row

->GetStarts().current->second).second) {

166 string

(

"CAlnMixSegments::Build():"

)

167

" Internal error: Infinite loop detected."

;

170 #if _DEBUG && _ALNMGR_TRACE 171

cerr <<

" [row "

row

->m_RowIdx

172

" seq "

row

->m_SeqIdx

173

" start "

<< curr_row_start

174

" (left of start "

<< row_start <<

") " 175

"was pushed into stack\n"

;

186

seg_stack.top()->m_StartIts) {

190 const TSeqPos

& curr_row_start =

row

->GetStarts().current->first;

191 const TSeqPos

& row_start = start_its_i->second->first;

193 if

(

row

->m_PositiveStrand &&

196

row

->m_PositiveStrand &&

200 string

(

"CAlnMixSegments::Build():"

)

201

" Internal error: Integrity broken"

211

(

row

->m_PositiveStrand ?

"plus"

"minus"

);

216 if

(

row

->m_PositiveStrand) {

217 row

->SetStarts().current++;

219 if

(

row

->SetStarts().current ==

row

->GetStarts().begin()) {

220 row

->SetStarts().current =

row

->GetStarts().end();

222 row

->SetStarts().current--;

227 if

(seg_stack.size() > 1) {

229

gapped_segs.push_back(seg_stack.top());

231 #if _DEBUG && _ALNMGR_TRACE 232

cerr <<

" seg popped].\n"

;

236 if

(gapped_segs.size()) {

241

}

else if

(min_gap) {

248

seg_i, gapped_segs) {

258

gapped_segs.push_back(seg_stack.top());

261 #if _DEBUG && _ALNMGR_TRACE 262

cerr <<

" refseq seg popped].\n"

;

268

orig_refseq =

false

;

272 if

(remove_leading_and_trailing_gaps) {

288

vector<TSignedSeqPos> starts;

289

vector<TSeqPos> lens;

290

starts.resize(

m_Rows

.size(), -1);

291

lens.resize(

m_Rows

.size(), 0);

296

TSegments::iterator seg_i =

m_Segments

.begin();

298 len

= (*seg_i)->m_Len;

300

(*seg_i)->m_StartIts) {

302

rowidx =

row

->m_RowIdx;

304 TSeqPos

& prev_len = lens[rowidx];

305 TSeqPos

start = start_its_i->second->first;

306 const bool plus

row

->m_PositiveStrand;

307 const int

& width =

row

->m_Width;

308 TSeqPos

prev_start_plus_len = prev_start + prev_len * width;

310 if

(prev_start >= 0) {

311 if

(

plus

&& prev_start_plus_len < start ||

312

plus

&& start_plus_len < (

TSeqPos

) prev_start) {

316 if

(

row

->m_PositiveStrand) {

317

new_start = prev_start + prev_len * width;

318

seg->

m_Len

= (start - new_start) / width;

320

new_start = start_plus_len;

321

seg->

m_Len

= (prev_start - new_start) / width;

323 row

->SetStarts()[new_start] = seg;

327 row

->m_PositiveStrand ?

346

TSegmentsContainer::iterator seg1_i, seg2_i;

348

seg2_i = seg1_i = gapped_segs.begin();

349 if

(seg2_i != gapped_segs.end()) {

359 while

(seg2_i != gapped_segs.end()) {

375

(*seg1_i)->m_StartIts) {

376 if

(st_it->first == seq2) {

409 if

(score2 < 75 * score1 / 100) {

427

seg2_i = gapped_segs.erase(seg2_i);

440

TSegmentsContainer::iterator seg_i, seg_i_end, seg_i_begin;

446

seg_i_begin = seg_i_end = seg_i = gapped_segs.begin();

451 while

(seg_i_end != gapped_segs.end()) {

453

len_map[(*seg_i_end)->m_Len];

459 while

(seg_i != seg_i_end) {

480 if

( !

possible

|| seg_i_end == gapped_segs.end()) {

485

TLenMap::iterator len_i = len_map.begin();

486 while

(len_i != len_map.end()) {

488

len_i->second->m_Len = len_i->first - len_so_far;

489

len_so_far += len_i->second->m_Len;

495

TLenMap::iterator len_i_end;

497 while

(seg_i != seg_i_end) {

498 TSeqPos

orig_len = (*seg_i)->m_Len;

501

len_i_end = len_map.find(orig_len);

507

(*seg_i)->m_StartIts) {

510 TSeqPos

orig_start = st_it->second->first;

512

len_i = len_map.begin();

515 while

(len_i != len_i_end) {

519 TSeqPos

this_start = orig_start +

522

orig_len - len_so_far - seg->

m_Len

) *

529

len_so_far += seg->

m_Len

;

535

new_segs.push_back(len_it->second);

538

seg_i_begin = seg_i_end;

543

gapped_segs.push_back(*new_seg_i);

551 size_t

match_idx)

const 555 if

((*st_it_i).second->second !=

this

) {

557 string

(

"CAlnMixSegment::StartItsConsistencyCheck"

)

559

" The internal consistency check failed for" 560

" the segment containing [" 564

((*st_it_i).first->m_PositiveStrand ?

"plus"

"minus"

)

void StartItsConsistencyCheck(const CAlnMixSeq &seq, const TSeqPos &start, size_t match_idx) const

void SetStartIterator(CAlnMixSeq *seq, CAlnMixStarts::iterator iter)

TStartIterators m_StartIts

void Build(bool gap_join=false, bool min_gap=false, bool remove_leading_and_trailing_gaps=false)

list< CRef< CAlnMixSegment > > TSegmentsContainer

void x_MinimizeGaps(TSegmentsContainer &gapped_segs)

CAlnMixSegments(CRef< CAlnMixSequences > &aln_mix_sequences, TCalcScoreMethod calc_score=0)

CRef< CAlnMixSequences > m_AlnMixSequences

TCalcScoreMethod x_CalculateScore

void FillUnalignedRegions(void)

void x_ConsolidateGaps(TSegmentsContainer &gapped_segs)

vector< CRef< CAlnMixSeq > > & m_Rows

CAlnMixStarts & SetStarts()

const CAlnMixStarts & GetStarts() const

void GetSeqString(string &s, TSeqPos start, TSeqPos len, bool positive_strand=true)

void RowsStartItsContsistencyCheck(size_t match_idx)

void InitExtraRowsStartIts()

CAlnMixStarts::const_iterator current

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

use n only the LMDB cache</td > n</tr > n< tr > n< td ></td > n< td > use the LMDB cache if at all possible

#define row(bind, expected)

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