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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__id__handle_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seq/seq_id_handle.cpp Source File

: m_Seq_id_Type(

),

: m_Seq_id_Type(seq_id->Which()),

);

.IsGi() &&

.GetGi() ==

(

);

.m_Info ? -1 : 0;

(!

.

)

1;

() >

.GetGi();

(*

==

)

0;

&&

->IsAllowedSNPScaleLimit(scale_limit);

( !

.IsGi() ) {

(

.IsGeneral() ) {

& dbtag =

.GetGeneral();

( obj_id.

() && dbtag.

() ==

) {

( !idh.

() ) {

(

.IsGeneral() ) {

& dbtag =

.GetGeneral();

( obj_id.

() && dbtag.

() ==

) {

ret =

.AsFastaString();

( idh.

() ) {

(

vector<CSeq_id_Handle>& ids)

( vector<CSeq_id_Handle>, it, ids ) {

score =

->TextScore();

( score < best_score ) {

<<

<< gi);

score =

.TextScore();

( score < best_score ) {

<<

<< gi);

( idh.

() ) {

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

virtual void DropInfo(const CSeq_id_Info *info)

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

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CStrictId< SStrictId_Gi, SStrictId_Gi::TId > TGi

#define INT_ID_TO(T, id)

Convert gi-compatible int to/from other types.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

string GetDirectLabel(const CSeq_id &id)

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

CSeq_id_Handle GetGiHandle(TGi gi)

Get seq-id handle.

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

bool x_IsBetter(const CSeq_id_Handle &h1, const CSeq_id_Handle &h2)

CSeq_id_Which_Tree & GetTree(void) const

bool x_Match(const CSeq_id_Handle &h1, const CSeq_id_Handle &h2)

CConstRef< CSeq_id > GetSeqId(void) const

bool HaveReverseMatch(void) const

bool HaveMatchingHandles(const CSeq_id_Handle &id)

Get the list of matching handles, do not create new handles.

bool HaveReverseMatch(const CSeq_id_Handle &id)

void GetReverseMatchingHandles(const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set)

CSeq_id_Mapper & GetMapper(void) const

int CompareOrdered(const CSeq_id &sid2) const

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

bool IsAllowedSNPScaleLimit(CSeq_id::ESNPScaleLimit scale_limit) const

bool MatchesTo(const CSeq_id_Handle &h) const

True if *this matches to h.

CConstRef< CSeq_id_Info, CSeq_id_InfoLocker > m_Info

virtual void WriteAsFasta(ostream &out) const

Implement serializable interface.

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

static CRef< CSeq_id_Mapper > GetInstance(void)

CSeq_id_Which_Tree & x_GetTree(CSeq_id::E_Choice type)

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

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

unsigned GetHash(void) const

void GetMatchingHandles(TMatches &matches) const

void x_RemoveLastLock(void) const

CSeq_id::E_Choice GetType(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

string GetLabel(const CSeq_id &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

CSeq_id_Mapper & GetMapper(void) const

CSeq_id_Handle GetHandle(const CSeq_id &id, bool do_not_create=false)

void GetMatchingHandles(const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set)

TPacked GetPacked(void) const

ESNPScaleLimit

SNP annotation scale limits.

bool HaveMatchingHandles(void) const

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetAccession(void) const

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

const TName & GetName(void) const

Get the Name member data.

TVersion GetVersion(void) const

Get the Version member data.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsSetVersion(void) const

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

bool IsSetName(void) const

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

const TAccession & GetAccession(void) const

Get the Accession member data.

Multi-threading – atomic pointer exchange function.

Multi-threading – mutexes; rw-locks; semaphore.

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

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