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NCBI C++ ToolKit: src/objects/seq/seq_id_tree.hpp Source File

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User-defined methods of the data storage class.

User-defined methods of the data storage class.

CSeq_id_GB_Tree(CSeq_id_Mapper *mapper)

virtual bool x_Check(const CSeq_id::E_Choice &type) const

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

const string & GetDbtag(void) const

~CSeq_id_General_Id_Info(void)

static TPacked Pack(const TKey &key, const CDbtag &id)

CSeq_id_General_Id_Info(CSeq_id_Mapper *mapper, const TKey &key)

const TKey & GetKey(void) const

void Restore(CDbtag &id, TPacked param, TVariant variant) const

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

TVariant ParseCaseVariant(const CDbtag &dbtag) const

CSeq_id_General_PlainInfo(const CDbtag &dbid, CSeq_id_Mapper *mapper)

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

string x_GetStr(TPacked param) const

~CSeq_id_General_Str_Info(void)

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

static TKey Parse(const CDbtag &id)

CSeq_id_General_Str_Info(CSeq_id_Mapper *mapper, const TKey &key)

static TPacked Pack(const TKey &key, const CDbtag &id)

const string & GetStrPrefix(void) const

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

void Restore(CDbtag &id, TPacked param, TVariant variant) const

const TKey & GetKey(void) const

size_t GetStrDigits(void) const

const string & GetStrSuffix(void) const

const string & GetDbtag(void) const

CSeq_id_General_Tree(CSeq_id_Mapper *mapper)

map< string, STagMap, PNocase > TDbMap

virtual void x_Unindex(const CSeq_id_Info *info)

CSeq_id_General_Id_Info::TKey TPackedIdKey

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

CSeq_id_General_PlainInfo * x_FindInfo(const CDbtag &dbid) const

virtual bool Empty(void) const

TPackedIdMap m_PackedIdMap

CSeq_id_General_Str_Info::TKey TPackedStrKey

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

TPackedStrMap m_PackedStrMap

map< TPackedIdKey, CConstRef< CSeq_id_General_Id_Info >, CSeq_id_General_Id_Info::PKeyLess > TPackedIdMap

virtual void FindMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const

unordered_map< TPackedStrKey, CConstRef< CSeq_id_General_Str_Info >, CSeq_id_General_Str_Info::PHash > TPackedStrMap

virtual bool HaveMatch(const CSeq_id_Handle &id) const

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

~CSeq_id_General_Tree(void)

CSeq_id_Gi_Info(CSeq_id_Mapper *mapper)

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

CSeq_id_Gi_Tree(CSeq_id_Mapper *mapper)

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

virtual CSeq_id_Handle GetGiHandle(TGi gi)

virtual bool Empty(void) const

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

virtual void x_Unindex(const CSeq_id_Info *info)

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

CSeq_id_Info * m_ZeroInfo

TGi x_Get(const CSeq_id &id) const

CSeq_id_Info * m_SharedInfo

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

bool x_Check(const CSeq_id &id) const

virtual bool x_Check(const CSeq_id &id) const

CSeq_id_Gibbmt_Tree(CSeq_id_Mapper *mapper)

virtual TPacked x_Get(const CSeq_id &id) const

CSeq_id_Gibbsq_Tree(CSeq_id_Mapper *mapper)

virtual TPacked x_Get(const CSeq_id &id) const

virtual bool x_Check(const CSeq_id &id) const

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

virtual bool Empty(void) const

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

CSeq_id_Info * x_FindInfo(const CGiimport_id &gid) const

virtual void x_Unindex(const CSeq_id_Info *info)

CSeq_id_Giim_Tree(CSeq_id_Mapper *mapper)

map< TPacked, TGiimList > TIdMap

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

vector< CSeq_id_Info * > TGiimList

CSeq_id_Gpipe_Tree(CSeq_id_Mapper *mapper)

bool HasMatchingId() const

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

~CSeq_id_Local_Info(void)

CObject_id::TId m_MatchingId

TVariant ParseCaseVariant(const string &str) const

CSeq_id_Local_Info(const CObject_id &oid, CSeq_id_Mapper *mapper)

CObject_id::TId GetMatchingId() const

virtual bool HaveMatch(const CSeq_id_Handle &id) const

map< CObject_id::TId, CSeq_id_Local_Info * > TById

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

CSeq_id_Local_Info * x_FindIdInfo(CObject_id::TId id) const

unordered_map< string, CSeq_id_Local_Info *, PHashNocase, PEqualNocase > TByStr

virtual void FindMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const

virtual void x_Unindex(const CSeq_id_Info *info)

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

virtual bool Empty(void) const

CSeq_id_Local_Tree(CSeq_id_Mapper *mapper)

CSeq_id_Local_Info * x_FindInfo(const CObject_id &oid) const

CSeq_id_Local_Info * x_FindStrInfo(const string &str) const

~CSeq_id_Local_Tree(void)

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

NCBI_EXCEPTION_DEFAULT(CSeq_id_MapperException, CException)

CSeq_id_Named_annot_track_Tree(CSeq_id_Mapper *mapper)

CSeq_id_Other_Tree(CSeq_id_Mapper *mapper)

static const int kYearBits

static const int kHourOffset

static pair< CConstRef< CSeq_id >, TVariant > Normalize(const CSeq_id &seq_id)

static const int kHourBits

static const int kDayBits

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

static const int kSecondBits

static const int kMinuteBits

static const int kMonthBits

CSeq_id_PDB_Info(const CConstRef< CSeq_id > &seq_id, CSeq_id_Mapper *mapper)

static const int kSecondOffset

static const int kNoChain_idOffset

static const int kNoChainOffset

static const int kYearOffset

static const int kMolLowerCaseBits

static const int kDayOffset

static const int kMonthOffset

static const int kMolLowerCaseOffset

static const int kMinuteOffset

static TVariant x_NormalizeDate(const CDate_std &date_std)

string x_IdToStrKey(const CPDB_seq_id &id) const

virtual bool HaveReverseMatch(const CSeq_id_Handle &id) const

virtual void FindReverseMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list)

virtual bool HaveMatch(const CSeq_id_Handle &id) const

virtual bool Empty(void) const

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

map< string, TSubMolList, PCase > TMolMap

virtual void x_Unindex(const CSeq_id_Info *info)

CSeq_id_PDB_Tree(CSeq_id_Mapper *mapper)

virtual void FindMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

vector< CSeq_id_Info * > TSubMolList

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

CSeq_id_Info * x_FindInfo(const CPatent_seq_id &pid) const

map< string, SPat_idMap, PNocase > TByCountry

~CSeq_id_Patent_Tree(void)

virtual bool Empty(void) const

CSeq_id_Patent_Tree(CSeq_id_Mapper *mapper)

virtual void x_Unindex(const CSeq_id_Info *info)

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

CSeq_id_Pir_Tree(CSeq_id_Mapper *mapper)

CSeq_id_Prf_Tree(CSeq_id_Mapper *mapper)

CSeq_id_Swissprot_Tree(CSeq_id_Mapper *mapper)

static TVariant ParseCaseVariant(const CSeq_id_Info *info, const string &acc)

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

int GetAccDigits(void) const

CTempString GetAccPrefix(void) const

bool GoodPrefix(const CTempString &acc) const

void Restore(CTextseq_id &id, TPacked param, TVariant variant) const

void RestoreAccession(string &acc, TPacked param, TVariant variant) const

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

static TPacked Pack(const TKey &key, const string &acc)

CSeq_id_Textseq_Info(CSeq_id::E_Choice type, CSeq_id_Mapper *mapper, const TKey &key)

~CSeq_id_Textseq_Info(void)

static TKey ParseAcc(const string &acc, const TVersion *ver)

const TKey & GetKey(void) const

static TKey ParseAcc(const string &acc, const CTextseq_id &tid)

bool IsSetVersion(void) const

const TVersion & GetVersion(void) const

CTextseq_id::TVersion TVersion

CSeq_id_Textseq_PlainInfo(const CConstRef< CSeq_id > &seq_id, CSeq_id_Mapper *mapper)

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

TVariant ParseCaseVariant(const string &acc) const

static void x_Erase(TStringMap &str_map, const string &key, const CSeq_id_Info *info)

virtual bool x_Check(const CSeq_id::E_Choice &type) const

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

void x_FindRevMatchByAccNonPacked(TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const

CSeq_id_Textseq_Info::TKey TPackedKey

CTextseq_id::TVersion TVersion

virtual void x_Unindex(const CSeq_id_Info *info)

const CTextseq_id & x_Get(const CSeq_id &id) const

virtual bool HaveMatch(const CSeq_id_Handle &id) const

TPackedMap::const_iterator TPackedMap_CI

TPackedMap::value_type TPackedMapValue

bool x_GetVersion(TVersion &version, const CSeq_id_Handle &id) const

virtual bool Match(const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const

~CSeq_id_Textseq_Tree(void)

void x_FindRevMatchByAcc(TSeq_id_MatchList &id_list, const string &acc, const CTextseq_id *tid) const

virtual bool Empty(void) const

pair< TStringMapCI, TStringMapCI > TVersions

void x_FindMatchByName(TSeq_id_MatchList &id_list, const string &name, const CTextseq_id *tid=nullptr, EAllowFields allow_fields=eAnyFields) const

static bool x_Equals(const CTextseq_id &id1, const CTextseq_id &id2)

virtual bool HaveReverseMatch(const CSeq_id_Handle &id) const

CSeq_id_Textseq_PlainInfo * x_FindStrInfo(CSeq_id::E_Choice type, const CTextseq_id &tid) const

void x_FindMatchByAcc(TSeq_id_MatchList &id_list, const string &acc, const CTextseq_id *tid) const

virtual void FindReverseMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list)

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

virtual bool IsBetterVersion(const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const

multimap< string, CSeq_id_Textseq_PlainInfo *, PNocase > TStringMap

TStringMap::const_iterator TStringMapCI

void x_FindRevMatchByAcc(TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

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

map< TPackedKey, CConstRef< CSeq_id_Textseq_Info > > TPackedMap

void x_FindRevMatchByAccPacked(TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

TStringMap::value_type TStringMapValue

TPackedMap::iterator TPackedMap_I

virtual void FindMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const

void x_FindRevMatchByName(TSeq_id_MatchList &id_list, const string &name, const CTextseq_id *tid=0) const

void x_FindMatchByAcc(TSeq_id_MatchList &id_list, const string &acc, const TVersion *ver=0) const

CSeq_id_Tpd_Tree(CSeq_id_Mapper *mapper)

CSeq_id_Tpe_Tree(CSeq_id_Mapper *mapper)

CSeq_id_Tpg_Tree(CSeq_id_Mapper *mapper)

TTreeLock::TReadLockGuard TReadLockGuard

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const =0

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const =0

virtual CSeq_id_Handle GetGiHandle(TGi gi)

virtual bool HaveReverseMatch(const CSeq_id_Handle &id) const

TTreeLock::TWriteLockGuard TWriteLockGuard

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const =0

const CSeq_id_Which_Tree & operator=(const CSeq_id_Which_Tree &tree)

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)=0

CSeq_id_Which_Tree(const CSeq_id_Which_Tree &tree)

static const CSeq_id * GetSeqId(const CSeq_id_Info *info)

CSeq_id_Info * CreateInfo(CSeq_id::E_Choice type)

CSeq_id_Info::TPacked TPacked

virtual void DropInfo(const CSeq_id_Info *info)

CSeq_id_Which_Tree(CSeq_id_Mapper *mapper)

virtual bool HaveMatch(const CSeq_id_Handle &id) const

virtual void FindReverseMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list)

CSeq_id_Mapper * m_Mapper

static const CSeq_id_Info * GetInfo(const CSeq_id_Handle &id)

virtual void x_Unindex(const CSeq_id_Info *info)=0

virtual bool Match(const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const

virtual void FindMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const

static void Initialize(CSeq_id_Mapper *mapper, vector< CRef< CSeq_id_Which_Tree > > &v)

virtual bool Empty(void) const =0

set< CSeq_id_Handle > TSeq_id_MatchList

virtual ~CSeq_id_Which_Tree(void)

virtual bool IsBetterVersion(const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const

virtual void x_Unindex(const CSeq_id_Info *info)

virtual TPacked x_Get(const CSeq_id &id) const =0

virtual bool Empty(void) const

virtual bool x_Check(const CSeq_id &id) const =0

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

CSeq_id_int_Tree(CSeq_id_Mapper *mapper)

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

map< TPacked, CSeq_id_Info * > TIntMap

virtual size_t Dump(CNcbiOstream &out, CSeq_id::E_Choice type, int details) const

virtual void FindMatchStr(const string &sid, TSeq_id_MatchList &id_list) const

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

virtual void FindReverseMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list)

virtual bool Empty(void) const

virtual void DropInfo(const CSeq_id_Info *info)

virtual void x_Unindex(const CSeq_id_Info *info)

~CSeq_id_not_set_Tree(void)

bool x_Check(const CSeq_id &id) const

virtual CSeq_id_Handle FindInfo(const CSeq_id &id) const

CSeq_id_not_set_Tree(CSeq_id_Mapper *mapper)

virtual void FindMatch(const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

container_type::const_iterator const_iterator

container_type::iterator iterator

container_type::value_type value_type

container_type::const_iterator const_iterator

container_type::value_type value_type

The NCBI C++ standard methods for dealing with std::string.

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

main entry point for tests

static const char * str(char *buf, int n)

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

uint8_t Uint1

1-byte (8-bit) unsigned integer

#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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

PEqualNocase_Generic< string > PEqualNocase

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.

@ eNocase

Case insensitive compare.

TVersion GetVersion(void) const

Get the Version member data.

E_Choice

Choice variants.

bool IsSetVersion(void) const

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

const string version

version string

const struct ncbi::grid::netcache::search::fields::KEY key

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

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

TPacked operator()(const TKey &a) const

bool operator()(const TKey &a, const TKey &b) const

TVariant ParseCaseVariant(const CDbtag &dbtag) const

bool operator!=(const TKey &b) const

size_t GetStrDigits(void) const

bool operator==(const TKey &b) const

unordered_map< string, CSeq_id_General_PlainInfo *, PHashNocase, PEqualNocase > TByStr

map< TPacked, CSeq_id_General_PlainInfo * > TById

map< string, TBySeqid, PNocase > TByNumber

map< TPacked, CSeq_id_Info * > TBySeqid

size_t GetPrefixLen() const

CTempString GetAccPrefix(void) const

bool operator<(const TKey &b) const

char m_PrefixBuf[kMaxPrefixLen]

int GetAccDigits(void) const

DECLARE_OPERATOR_BOOL(m_Hash !=0)

bool operator!=(const TKey &b) const

bool operator==(const TKey &b) const

bool SameHash(const TKey &b) const

bool IsSetVersion(void) const

bool EqualAcc(const TKey &b) const

bool SameHashNoVer(const TKey &b) const

TVariant ParseCaseVariant(const string &acc) const

const TVersion & GetVersion(void) const

void SetVersion(TVersion version)

bool operator()(const string &s1, const string &s2) const

size_t operator()(const string &s) const

static char get_hash(char c)

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