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NCBI C++ ToolKit: include/objects/seq/seq_id_handle.hpp Source File

p1 < p2 || (p1 == p2 &&

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);

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())

;

(!seq_id)

;

text_id = seq_id->GetTextseq_Id();

text_id->IsSetAccession() &&

text_id->IsSetVersion();

(NCBI_NS_NCBI::objects::CSeq_id_Handle& idh1,

NCBI_NS_NCBI::objects::CSeq_id_Handle& idh2)

std::ofstream out("events_result.xml")

main entry point for tests

CStrictId< SStrictId_Gi, SStrictId_Gi::TId > TGi

#define INT_ID_TO(T, id)

Convert gi-compatible int to/from other types.

string GetDirectLabel(const CSeq_id &id)

Return best label for a sequence from single Seq-id, or set of Seq-ids.

bool operator()(const CSeq_id_Handle &id1, const CSeq_id_Handle &id2) const

void RemoveLock(void) const

CSeq_id_Handle(const CSeq_id_Info *info, TPacked packed=0, TVariant variant=0)

virtual int CompareOrdered(const CSeq_id_Info &other, const CSeq_id_Handle &h_this, const CSeq_id_Handle &h_other) const

atomic< Uint8 > m_LockCounter

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

void Lock(const CSeq_id_Info *info) const

bool operator!=(const CSeq_id_Handle &handle) const

bool IsPacked(void) const

CSeq_id_Info::TVariant TVariant

CSeq_id_Which_Tree & GetTree(void) const

CConstRef< CSeq_id > GetSeqId(void) const

bool HaveReverseMatch(void) const

BEGIN_STD_SCOPE void swap(NCBI_NS_NCBI::objects::CSeq_id_Handle &idh1, NCBI_NS_NCBI::objects::CSeq_id_Handle &idh2)

CRef< CSeq_id_Mapper > m_Mapper

void Reset(void)

Reset the handle (remove seq-id reference)

void Unlock(const CSeq_id_Info *info) const

EAccessionInfo

For IdentifyAccession (below)

CSeq_id_Mapper & GetMapper(void) const

CConstRef< CSeq_id > GetSeqIdOrNull(void) const

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

CConstRef< CSeq_id > m_Seq_id

virtual CConstRef< CSeq_id > GetPackedSeqId(TPacked packed, TVariant variant) const

CSeq_id_Info(const CSeq_id_Info &)

CSeq_id_Info::TPacked TPacked

bool IsAllowedSNPScaleLimit(CSeq_id::ESNPScaleLimit scale_limit) const

bool MatchesTo(const CSeq_id_Handle &h) const

True if *this matches to h.

CSeq_id::EAccessionInfo IdentifyAccession(void) const

bool operator<(const CSeq_id_Handle &handle) const

CConstRef< CSeq_id_Info, CSeq_id_InfoLocker > m_Info

CConstRef< CSeq_id > Get_ConstRef_Seq_id(const CSeq_id_Handle &idh)

Get CConstRef<CSeq_id> from a seq-id handle (for container searching template functions)

TVariant GetVariant(void) const

bool IsAccVer(void) const

const CSeq_id_Info & operator=(const CSeq_id_Info &)

void GetReverseMatchingHandles(TMatches &matches) const

bool operator==(const CSeq_id_Handle &handle) const

int CompareOrdered(const CSeq_id_Handle &id) const

Compare ids in a defined order (see CSeq_id::CompareOrdered())

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

DECLARE_OPERATOR_BOOL_REF(m_Info)

Check if the handle is a valid or an empty one.

CNcbiOstream & operator<<(CNcbiOstream &out, const CSeq_id_Handle &idh)

CSeq_id_Info(CSeq_id::E_Choice type, CSeq_id_Mapper *mapper)

atomic< CSeq_id::E_Choice > m_Seq_id_Type

const CSeq_id_Info * x_GetInfo(void) const

unsigned GetHash(void) const

void GetMatchingHandles(TMatches &matches) const

void Swap(CSeq_id_Handle &idh)

void x_RemoveLastLock(void) const

CSeq_id::E_Choice GetType(void) const

bool IsSetVariant(void) const

bool IsBetter(const CSeq_id_Handle &h) const

True if "this" is a better bioseq than "h".

CSeq_id::E_Choice Which(void) const

void Relock(const CSeq_id_Info *info) const

set< CSeq_id_Handle > TMatches

string GetLabel(const CSeq_id &id)

CConstRef< CSeq_id > GetSeqId(void) const

CSeq_id_Mapper & GetMapper(void) const

bool IsLocked(void) const

TPacked GetPacked(void) const

ESNPScaleLimit

SNP annotation scale limits.

bool HaveMatchingHandles(void) const

void Reset(void)

Reset reference object.

void Swap(TThisType &ref)

Swaps the pointer with another reference.

void Unlock(const CObject *object) const

void Lock(const CObject *object) const

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_STD_SCOPE

Place it for adding new funtionality to STD scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define END_STD_SCOPE

End previously defined STD scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

E_Choice

Choice variants.

@ e_Gi

GenInfo Integrated Database.

Predicate for sorting CSeq_id_Handles in a defined order.

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