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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/annot__match__5col_8cpp_source.html below:

NCBI C++ ToolKit: src/app/table2asn/annot_match_5col.cpp Source File

CFast5colReaderIndexer

m_current_pos = 0;

std::string_view m_whole_file;

m_current_lineno = 0;

m_prev_line_pos = 0;

ncbi::CFast5colReader::CMemBlockInfo m_current_block;

std::list<ncbi::CFast5colReader::CMemBlockInfo>* m_blocks =

;

GetNextLine(std::string_view&

);

MakeNewBlock(

pos, std::string_view seqid);

CFast5colReaderIndexer::MakeNewBlock(

pos, std::string_view seqid)

(m_current_block.line_no) {

m_current_block.size = pos - m_current_block.start_pos;

m_blocks->push_back(m_current_block);

m_current_block.index++;

m_current_block.start_pos = pos;

m_current_block.seqid = seqid;

m_current_block.line_no = m_current_lineno;

CFast5colReaderIndexer::GetNextLine(std::string_view& next_line)

(m_current_pos>=m_whole_file.size())

std::string_view::npos;

nl_pos = m_whole_file.find(

, m_current_pos);

(nl_pos == m_whole_file.npos)

nl_pos = m_whole_file.size()-1;

(cr_pos>0 && m_whole_file[cr_pos-1]==

)

next_line = m_whole_file.substr(m_current_pos, cr_pos-m_current_pos);

start = m_current_pos;

m_current_pos = nl_pos + 1;

m_reader_flags = reader_flags;

(genome_center_id.empty())

m_seqid_prefix.clear();

m_seqid_prefix =

+ genome_center_id +

;

= std::make_unique<TFile>();

->Open(filename,

);

Open(std::move(

));

m_hugefile = std::move(

);

x_IndexFile(std::string_view(m_hugefile->m_memory, m_hugefile->m_filesize));

std::list<CRef<CSeq_annot>> annots;

range = m_blocks_map.equal_range(label_with_ver);

(range.first == range.second) {

(label_nover != label_with_ver)

range = m_blocks_map.equal_range(label_nover);

std::list<CRef<CSeq_annot>> annots;

range = x_FindAnnots(seqid);

(

it = range.first; it != range.second; ++it)

(m_used_annots.reset(it->second->index)) {

line_reader(m_memory.data()+it->second->start_pos, it->second->size);

line_reader, m_reader_flags, m_logger);

(annot && annot->IsFtable() && annot->GetData().GetFtable().size() > 0) {

annots.push_back(annot);

std::list<CRef<CSeq_id>> seqids;

range = x_FindAnnots(seqid);

(

it = range.first; it != range.second; ++it)

seqids.splice(seqids.end(), ids);

CFast5colReaderIndexer

;

.m_blocks = &m_blocks;

.m_whole_file = memory;

std::string_view next_line;

((start =

.GetNextLine(next_line)) != std::string_view::npos)

(next_line[0]==

) {

.MakeNewBlock(start, seqid);

.MakeNewBlock(memory.size(), {});

(

& rec: m_blocks)

(

: ids) {

label_nover, label_with_ver, label_only;

m_blocks_map.emplace(std::make_pair(label_with_ver, &rec));

(label_nover != label_with_ver)

m_blocks_map.emplace(std::make_pair(label_nover, &rec));

(!m_seqid_prefix.empty()) {

(rec.seqid.find(

) == std::string_view::npos || id->IsLocal())

m_blocks_map.emplace(std::make_pair(m_seqid_prefix + label_only, &rec));

(rec.seqid.find(

) == std::string_view::npos && !id->IsLocal())

m_blocks_map.emplace(std::make_pair(

+ label_only, &rec));

m_used_annots.Init(m_blocks.size());

void Open(const std::string &filename)

std::list< CRef< objects::CSeq_id > > FindAnnots(CRef< objects::CSeq_id > seqid) const

void Init(const std::string &genome_center_id, long reader_flags, TLogger *logger=nullptr)

TRange x_FindAnnots(CRef< objects::CSeq_id > id) const

std::list< CRef< objects::CSeq_annot > > GetAndUseAnnot(CRef< objects::CSeq_id > seqid) override

~CFast5colReader() override

void x_IndexFile(std::string_view memory)

std::pair< TContainer::const_iterator, TContainer::const_iterator > TRange

static bool ParseInitialFeatureLine(const CTempString &line_arg, CTempStringEx &out_seqid, CTempStringEx &out_annotname)

If line_arg is a feature line (e.g.

CRef< CSeq_annot > ReadSequinFeatureTable(const TFlags flags=0, ITableFilter *filter=nullptr, const string &seqid_prefix=kEmptyStr)

Simple implementation of ILineReader for regions of memory (such as memory-mapped files).

objects::ILineErrorListener TLogger

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

@ fLabel_Version

Show the version.

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_ValidLocal

Treat otherwise unidentified strings as raw accessions, provided that they pass rudimentary validatio...

@ eContent

Untagged human-readable accession or the like.

@ eBoth

Type and content, delimited by a vertical bar.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string & ToLower(string &str)

Convert string to lower case – string& version.

void Stop(void)

Suspend the timer.

void Start(void)

Start the timer.

list< CRef< CSeq_id > > TId

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