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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/co__fasta_8cpp_source.html below:

NCBI C++ ToolKit: src/app/multireader/co_fasta.cpp Source File

7 using namespace

ncbi::objtools::hugeasn;

15

start_pos = blob.find(

'>'

, start_pos);

16 if

(start_pos == std::string_view::npos || blob[start_pos-1] ==

'\n'

)

24 if

(line.size()>1 && line[0] ==

'>'

&& line[1] ==

'?'

) {

26

ncbi::NStr::StringToNumeric(line.substr(2), &gapsize);

35 size_t

current_pos = 0;

37 bool

is_data_segment =

true

;

38

std::string_view defline;

43 while

(current_pos != std::string_view::npos &&

44

current_pos + 1 <= blob.size() &&

45

blob[current_pos+1] ==

'?'

) {

47

is_data_segment =

false

;

50 if

(current_pos == std::string_view::npos)

53 if

(is_data_segment || !is_delta_seq)

57

is_data_segment =

true

;

63 if

(

buffer

.size() < max_allowed && lit.size()) {

64 size_t

can_add = max_allowed -

buffer

.size();

65

can_add =

std::min

(can_add, lit.size());

66 auto

to_copy = lit.substr(0, can_add);

68

lit = lit.substr(can_add);

71 return buffer

.size() == max_allowed;

81 using

TView = std::string_view;

87 size_t lineno

= start_line;

89 if

(current[0] ==

'\n'

) {

90

co_yield std::make_pair(

lineno

++, TView{});

91

current = current.substr(1);

93 while

(!current.empty()) {

94 auto

next_nl = current.find(

'\n'

);

95 if

(next_nl == TView::npos) {

96

next_nl = current.size();

98 auto

newline_size = (current[next_nl-1] ==

'\r'

) ? next_nl-1 : next_nl;

99 auto

to_yield = current.substr(0, newline_size);

100

co_yield std::make_pair(

lineno

++, to_yield);

101

current = current.substr(next_nl+1);

125 static void

xTrimBlob(TFastaBlob& blob, TView current);

135

m_file.reset(

new

TFile::element_type);

136

m_file->Open(filename,

nullptr

);

138 throw

std::runtime_error(

"Wrong file format used"

);

139

m_blob =

TView

(m_file->m_memory, m_file->m_filesize);

145 throw

std::runtime_error(

"Wrong file format used"

);

152 self

->m_flags =

flags

;

154

std::shared_ptr<TFastaBlob> prev_blob;

156 auto

current =

self

->m_blob;

158 while

(!current.empty()) {

159 if

(current[0] !=

'>'

) {

160 throw

std::runtime_error(

"No defline start found"

);

165 if

(next_nl == TView::npos) {

166 throw

std::runtime_error(

"Defline end was not found"

);

169

current = current.substr(next_nl);

172 auto

next_blob = current.substr(0, next_defline_pos);

173 auto

to_yield = std::make_shared<TFastaBlob> (

self

);

174

to_yield->m_defline = defline;

175

to_yield->m_data = next_blob;

177

current = current.substr(next_defline_pos);

184 auto

it = current.begin();

185 size_t len

= std::distance(blob.

m_data

.begin(), it);

188 len

= std::distance(blob.

m_blob

.begin(), it);

196 self

->m_flags =

flags

;

198

std::shared_ptr<TFastaBlob> prev_blob;

200 auto

current =

self

->m_blob;

205

blob.m_blob = blob.m_data = current;

207 bool

inside_deltaseq =

false

;

209 while

(!current.empty()) {

213 if

(!line.empty() && line[0] ==

'>'

) {

214 if

(line.size()>1 && line[1] ==

'?'

) {

215

inside_deltaseq =

true

;

218 if

(

flags

.test(IsDeltaSeq) && inside_deltaseq) {

219

inside_deltaseq =

false

;

221

inside_deltaseq =

false

;

222 if

(blob.m_numlines>0) {

224

co_yield std::make_shared<TFastaBlob>(blob);

226

blob.m_defline = line;

227

blob.m_blob = current;

228

current = current.substr(nextnl);

229

blob.m_data = current;

230

blob.m_lineno_handicap =

lineno

-1;

231

blob.m_seq_length = 0;

237 if

(line.size()>0 && line[0] !=

'>'

) {

238

blob.m_seq_length += line.size();

241

current = current.substr(nextnl);

243 if

(blob.m_numlines>0) {

245

co_yield std::make_shared<TFastaBlob>(blob);

262 m_impl

= std::make_shared<CFastaSourceImpl>(filename);

267 m_impl

= std::make_shared<CFastaSourceImpl>(

file

);

272 m_impl

= std::make_shared<CFastaSourceImpl>(blob);

CFastaSourceImpl(TView blob)

std::atomic< bool > m_blobs_loaded

ParseFlagsSet Flags() const

static Generator< std::shared_ptr< TFastaBlob > > ReadBlobsQuick(std::shared_ptr< CFastaSourceImpl > self, ParseFlagsSet flags)

std::atomic< bool > m_is_loading

CFastaSource::TFile TFile

CFastaSource::TView TView

static void xTrimBlob(TFastaBlob &blob, TView current)

static Generator< std::shared_ptr< TFastaBlob > > ReadBlobs(std::shared_ptr< CFastaSourceImpl > self, ParseFlagsSet flags)

CFastaSourceImpl(const std::string &filename)

std::shared_ptr< CFastaSourceImpl > m_impl

std::shared_ptr< objects::edit::CHugeFile > TFile

CFastaSource(const std::string &filename)

Generator< std::shared_ptr< TFastaBlob > > ReadBlobs()

Generator< std::shared_ptr< TFastaBlob > > ReadBlobsQuick()

ct::const_bitset< int(ParseFlags::MaxValue), ParseFlags > ParseFlagsSet

@ eFasta

FASTA format sequence record, CFastaReader.

std::optional< size_t > x_CheckGapEstimation(std::string_view line)

size_t x_FindNextDefline(std::string_view blob, size_t start_pos)

Generator< std::pair< size_t, std::string_view > > BasicReadLinesGenerator(size_t start_line, std::string_view blob)

size_t x_FindNextTrueDefline(std::string_view blob, bool is_delta_seq)

bool x_FillLiteralBuffer(size_t max_allowed, std::string &buffer, std::string_view &lit)

size_t SkipLine(std::string_view blob, std::string_view::size_type start_pos, std::string_view &line)

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

ParseFlagsSet Flags() const

std::shared_ptr< CFastaSourceImpl > m_impl

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