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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/annot__match_8cpp_source.html below:

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

std::istream istr(&istrbuf);

& idString,

it = m_AnnotMap.lower_bound(idString);

matchMap.emplace(it->first, it);

!matchMap.

();

& idString,

x_HasExactMatch(idString, annots);

hasMatch =

;

shared_lock<shared_mutex> sLock{m_Mutex};

(!s_HasPrefixMatch(idString, matchMap)) {

unique_lock<shared_mutex> uLock{m_Mutex};

(

: matchMap) {

& annotId =

.first;

it =

.second;

(m_MatchedAnnots.insert(annotId).second) {

annots.splice(annots.end(), it->second);

m_AnnotMap.erase(it);

& idString,

shared_lock<shared_mutex> sLock{m_Mutex};

it = m_AnnotMap.find(idString);

(it == m_AnnotMap.end()) {

annotId = it->first;

unique_lock<shared_mutex> uLock{m_Mutex};

(m_MatchedAnnots.insert(annotId).second) {

annots = std::move(it->second);

m_AnnotMap.erase(it);

m_reader_flags = reader_flags;

m_genome_center_id = genome_center_id;

(genome_center_id.empty())

m_seqid_prefix.clear();

m_seqid_prefix =

+ genome_center_id +

;

(

annot: annots) {

list<CRef<CSeq_annot>> annots;

hasMatch =

;

matchVersions = (pSeqId->

() ==

);

hasMatch = x_HasMatch(matchVersions, idString, annots);

matchVersions =

;

hasMatch = x_HasMatch(matchVersions, idString, annots);

pAnnotId = GetAnnotId(*pAnnot);

idString = pAnnotId->GetSeqIdString();

it = m_AnnotMap.find(idString);

(it == m_AnnotMap.end()) {

it->second.push_back(pAnnot);

User-defined methods of the data storage class.

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

bool IsFtable(void) const

list< CRef< objects::CSeq_annot > > TAnnots

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

void AddAnnots(TAnnots &annots)

bool x_HasExactMatch(const string &idString, list< CRef< objects::CSeq_annot >> &annots)

void AddAnnot(CRef< objects::CSeq_annot > annot)

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

bool s_HasPrefixMatch(const string &idString, map< string, TAnnotMap::iterator > &matchMap)

bool x_HasMatch(bool matchVersions, const string &idString, list< CRef< objects::CSeq_annot >> &annots)

void Open(std::unique_ptr< TFile > file)

static CRef< objects::CSeq_id > GetAnnotId(const objects::CSeq_annot &annot)

objects::ILineErrorListener TLogger

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

Set object to copy of another one.

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TGeneral & SetGeneral(void)

Select the variant.

bool IsGeneral(void) const

Check if variant General is selected.

TLocal & SetLocal(void)

Select the variant.

const TGeneral & GetGeneral(void) const

Get the variant data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsGeneral(void) const

Check if variant General is selected.

bool IsSetId(void) const

Check if a value has been assigned to Id data member.

const TId & GetId(void) const

Get the Id member data.

const TFtable & GetFtable(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsLocal(void) const

Check if variant Local is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

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)

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

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