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

= objects::edit::CHugeFile;

= objects::ILineErrorListener;

(std::unique_ptr<TFile>

);

(std::string_view memory);

= std::unordered_multimap<std::string, const CMemBlockInfo*>;

= std::pair<TContainer::const_iterator, TContainer::const_iterator>;

= list<CRef<objects::CSeq_annot>>;

(std::unique_ptr<TFile>

);

void Open(const std::string &filename)

CAtomicBitSet m_used_annots

size_t index_size() const

std::list< CMemBlockInfo > m_blocks

std::unique_ptr< TFile > m_hugefile

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::string m_seqid_prefix

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

std::unordered_multimap< std::string, const CMemBlockInfo * > TContainer

~CFast5colReader() override

void x_IndexFile(std::string_view memory)

size_t unused_annots() const

std::string_view m_memory

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

list< CRef< objects::CSeq_annot > > TAnnots

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

void AddAnnots(TAnnots &annots)

std::string m_genome_center_id

set< string > m_MatchedAnnots

std::string m_seqid_prefix

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

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

CWholeFileAnnotation()=default

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)

std::shared_mutex m_Mutex

virtual ~IIndexedFeatureReader()

virtual std::list< CRef< objects::CSeq_annot > > GetAndUseAnnot(CRef< objects::CSeq_id > seqid)=0

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

objects::edit::CHugeFile TFile

objects::ILineErrorListener TLogger

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

The NCBI C++/STL use hints.

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