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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__id__tree_8cpp_source.html below:

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

id_list.

(h2) != id_list.

();

( old_id.

() ) {

(old_id.

()) {

(

->IsLocked() ) {

= s.capacity();

(

+

(

*) >

(

) ) {

);

);

<<

<< endl;

pair<TIntMap::iterator, bool> ins =

= NStr::StringToNumeric<TPacked>(sid);

total_bytes = 0;

elem_size =

(

)+

(

*);

elem_size +=

(

)+3*

(

*);

elem_size +=

(

);

bytes =

*elem_size+extra_size;

total_bytes += bytes;

<<

<<

<<bytes<<

<< endl;

<<

<< it->second->GetSeqId()->AsFastaString() << endl;

.IsGibbsq();

.IsGibbmt();

TThis*

(

)->

= ret;

gi = NStr::StringToNumeric<TPacked>(sid);

<<

;

->Get();

->Get();

* start = &

[pos];

* ptr = start +

;

*--ptr = (char)(

+

% 10);

( ptr > start ) {

(

= pos;

< pos+

; ++

) {

(

= 0; variant &&

!=

; ++

) {

pair<CSeq_id_Handle::TVariant, CSeq_id_Handle::TVariant>

(

= 0; bit &&

!= ref.

(); ++

) {

cr =

(ref[

]);

make_pair(variant, bit);

pair<CSeq_id_Handle::TVariant, CSeq_id_Handle::TVariant>

= acc.size(), prefix_len =

, most_significant =

;

( prefix_len ) {

c = acc[--prefix_len];

( c >=

&& c <=

) {

most_significant = prefix_len;

( c !=

) {

( most_significant ==

) {

acc_digits =

- prefix_len, real_digits =

- most_significant;

( acc_digits < 2 || acc_digits > 12 ||

real_digits > 9 || acc_digits*2 < prefix_len ) {

( prefix_len <= 4 ) {

( prefix_len == 3 ) {

( (acc[0] !=

&& acc[0] !=

) ||

(acc[1] !=

&& acc[1] !=

) ||

( acc_digits > 6 && real_digits < acc_digits ) {

acc_digits =

(

(6), real_digits);

prefix_len =

- acc_digits;

( prefix_len >

.kMaxPrefixLen ) {

.m_PrefixLen =

(prefix_len);

memcpy(

.m_PrefixBuf, acc.data(), prefix_len);

(

= 0;

< 3 &&

< prefix_len; ++

) {

= (

<< 8) |

(acc_digits << 1);

.SetVersion(*ver);

( !

.IsSetAccession() ) {

& acc =

.SetAccession();

TThis*

(

)->

= ret;

this_acc, other_acc;

pother->RestoreAccession(other_acc, h_other.

(), 0);

(

vdiff =

() - pother->IsSetVersion()) {

(pother->IsSetVersion());

( !

.IsSetAccession() ) {

(

.Which());

&

,

(it->second, packed, it->first.ParseCaseVariant(acc));

variant = it->first.ParseCaseVariant(acc);

variant =

->ParseCaseVariant(tid);

&

,

( it->second ==

) {

str_map.

(it);

release ==

|| release ==

;

(

.IsSetVersion() ) {

( it->first.EqualAcc(

) ) {

( packed == 0 ) {

(

.IsSetVersion() ) {

.ResetVersion();

& name,

=

.Which();

(

.IsPacked() ) {

->Restore(tid,

.GetPacked(),

.GetVariant());

( !

->IsSetVersion() ) {

( it->first.EqualAcc(

) ) {

!

->IsSetVersion() &&

->RestoreAccession(acc,

.GetPacked(), 0);

( dot !=

) {

acc = sid.substr(0, dot);

(

.IsPacked() ) {

( !

->IsSetVersion() ) {

version1, version2;

(!

(version2, h2) || version1 > version2);

mine =

(

.Which());

(

.IsPacked() ) {

(

->IsSetVersion() ) {

.ResetVersion();

->RestoreAccession(acc,

.GetPacked(),

.GetVariant());

(id_list, acc,

->IsSetVersion()? &

->GetVersion(): 0);

(

|| !mine ) {

total_bytes = 0;

elem_size = 0, extra_size = 0;

elem_size =

(

)+

(

*);

elem_size +=

(

)+3*

(

*);

elem_size +=

(

);

(

.IsSetName() ) {

(

.IsSetRelease() ) {

bytes = extra_size +

*elem_size;

total_bytes += bytes;

<<

<<

<<

<<bytes<<

<<endl;

elem_size =

(

)+

(

*);

elem_size +=

(

)+3*

(

*);

bytes = extra_size +

*elem_size;

total_bytes += bytes;

<<

<<

<<

<<bytes<<

<<endl;

<<

<<

->AsFastaString() << endl;

<<

<< it->first.GetAccPrefix()<<

<<it->first.m_Version << endl;

(

.empty() ) {

first_char =

[0];

( first_char !=

&& (first_char < '0' || first_char >

) ) {

(

.size() != 1 ) {

(

> 0 ) {

( first_char ==

|| first_char ==

) {

( first_char !=

||

[1] ==

) {

( !oid.

() ) {

TByStr::const_iterator it =

.find(

);

( oid.

() ) {

variant =

->ParseCaseVariant(oid);

( oid.

() ) {

( oid.

() ) {

( sinfo->

() ) {

( has_matching_id ) {

total_bytes = 0;

=

.size(), elem_size = 0, extra_size = 0;

elem_size =

(

)+

(

*);

elem_size +=

(

)+3*

(

*);

elem_size +=

(

);

bytes = extra_size +

*elem_size;

total_bytes += bytes;

<<

<<

<<

<<bytes<<

<< endl;

elem_size =

(

)+

(

*);

elem_size +=

(

)+3*

(

*);

elem_size +=

(

);

bytes =

*elem_size;

total_bytes += bytes;

<<

<<

<<

<<bytes<<

<< endl;

<<

<< it->second->GetSeqId()->AsFastaString() << endl;

<<

<< it->second->GetSeqId()->AsFastaString() << endl;

TThis*

(

)->

= ret;

id_this < id_other? -1: id_this > id_other;

t1.first | t2.first | t3.first;

=

.size(), prefix_len =

, str_digits = 0;

cur_digits = 0, total_digits = 0;

c = --

< 0? 0:

[

];

( c >=

&& c <=

) {

( !str_digits || cur_digits > str_digits+2 ) {

str_digits = cur_digits;

( str_digits > 9 ) {

prefix_len += str_digits - 9;

total_digits += str_digits - 9;

( str_digits*3 < total_digits*2 ) {

( prefix_len > 0 ) {

.m_StrPrefix =

.substr(0, prefix_len);

( prefix_len + str_digits <

.size() ) {

.m_StrSuffix =

.substr(prefix_len+str_digits);

(

= 0;

< 3 &&

< prefix_len; ++

) {

.m_StrPrefix.size(),

.GetStrDigits());

( !obj_id.

() ) {

TThis*

(

)->

= ret;

(param < 0) ++param;

t1.first | t2.first;

& dbtag =

->SetGeneral();

& tm = db->second;

( oid.

() ) {

STagMap::TByStr::const_iterator it = tm.

.find(oid.

());

(it != tm.

.end()) {

( oid.

() ) {

& dbid =

.GetGeneral();

(it->second, packed, it->first.ParseCaseVariant(dbid));

&

= dbid.

();

( packed == 0 ) {

& dbid =

.GetGeneral();

&

= dbid.

();

( oid.

() ) {

( oid.

() ) {

);

variant =

->ParseCaseVariant(dbid);

& dbid =

->GetGeneral();

( oid.

() ) {

( oid.

() ) {

( obj_id.

() ) {

= obj_id.

();

& s = obj_id.

();

= NStr::StringToNumeric<TPacked>(sid);

STagMap::TByStr::const_iterator str_it =

db_it->second.m_ByStr.find(sid);

(str_it != db_it->second.m_ByStr.end()) {

db_it->second.m_ById.find(

);

(int_it != db_it->second.m_ById.end()) {

total_bytes = 0;

= 0, bytes = 0;

bytes +=

(

)+3*

(

*);

bytes +=

(it2->first)+

(it2->second);

bytes +=

(

)+3*

(

*);

bytes +=

(it2->first)+

(it2->second);

bytes +=

(

)+3*

(

*);

total_bytes += bytes;

<<

<<

<<

<<bytes<<

<< endl;

elem_size +=

(

)+3*

(

*);

bytes = extra_size +

*elem_size;

total_bytes += bytes;

<<

<<

<<

<<bytes<<

<< endl;

elem_size +=

(

)+3*

(

*);

bytes = extra_size +

*elem_size;

total_bytes += bytes;

<<

<<

<<

<<bytes<<

<< endl;

<<

<<it2->second->GetSeqId()->AsFastaString() << endl;

<<

<<it2->second->GetSeqId()->AsFastaString() << endl;

<<

<<it->first << endl;

<<

<<it->first.m_Key<<

<<it->first.m_Db<<

<<it->first.m_StrPrefix<<

<<it->first.m_StrSuffix << endl;

( !gid.

(gid2) ) {

(*dbr_it ==

) {

giims.erase(dbr_it);

( giims.empty() )

total_bytes = 0;

= 0, bytes = 0;

bytes +=

(it->first) +

(it->second);

bytes +=

(

)+3*

(

*);

size2 = it->second.size();

bytes += it->second.capacity()*

(

*);

bytes += size2*

(

);

&

= (*it2)->GetSeqId()->GetGiim();

(

.IsSetDb() ) {

(

.IsSetRelease() ) {

total_bytes += bytes;

<<

<<

<<bytes<<

<< endl;

<<

<<(*it2)->GetSeqId()->AsFastaString() << endl;

by_number = &cntry_it->second.m_ByNumber;

by_number = &cntry_it->second.m_ByApp_number;

(num_it == by_number->

())

num_it->second.find(pid.

());

(seqid_it != num_it->second.end()) {

seqid_it->second;

);

num_it->second.find(pid.

());

(seqid_it != num_it->second.end());

num_it->second.erase(seqid_it);

( num_it->second.empty() )

app_it->second.find(pid.

());

(seqid_it != app_it->second.end());

app_it->second.erase(seqid_it);

( app_it->second.empty() )

(country_it->second.m_ByNumber.empty() &&

country_it->second.m_ByApp_number.empty())

cit->second.m_ByNumber.find(sid);

(nit != cit->second.m_ByNumber.end()) {

cit->second.m_ByApp_number.find(sid);

(ait != cit->second.m_ByApp_number.end()) {

total_bytes = 0;

= 0, bytes = 0;

bytes +=

(it->first) +

(it->second);

bytes +=

(

)+3*

(

*);

bytes +=

(it2->first) +

(it2->second);

bytes +=

(

)+3*

(

*);

bytes +=

(it2->first) +

(it2->second);

bytes +=

(

)+3*

(

*);

total_bytes += bytes;

<<

<<

<<bytes<<

<< endl;

<<

<<it3->second->GetSeqId()->AsFastaString() << endl;

( variant & kMolLowerCaseMask ) {

& mol = pdb_id.

().Set();

variant &= ~kMolLowerCaseMask;

year = date_std.

();

pair<CConstRef<CSeq_id>,

> ret(

(&seq_id), 0);

( date.

() ) {

( !ret.second ) {

normal_has_chain =

normal_has_chain_id =

( need_upcase ) {

& mol = new_pdb_id.

().Set();

c = mol[

+1];

( normal_has_chain_id ) {

( normal_has_chain ) {

ret.first = new_seq_id;

skey =

.GetMol().Get();

(

.IsSetChain_id()) {

skey +=

.GetChain_id();

(

.IsSetChain()) {

skey += char(

.GetChain());

& pid = normalized_id.first->GetPdb();

( pid.

((*it)->GetSeqId()->GetPdb()) ) {

& pid = normalized_id.first->GetPdb();

( pid.

((*it)->GetSeqId()->GetPdb()) ) {

( normalized_id.first == &

) {

normalized_id.first = id_ref;

sub.push_back(

);

mol_it->second.erase(it);

( mol_it->second.empty() )

& pid2 = (*it)->GetSeqId()->GetPdb();

& pid2 = (*it)->GetSeqId()->GetPdb();

total_bytes = 0;

= 0, bytes = 0;

bytes +=

(it->first) +

(it->second);

bytes +=

(

)+3*

(

*);

size2 = it->second.size();

bytes += it->second.capacity()*

(

*);

bytes += size2*

(

);

&

= (*it2)->GetSeqId()->GetPdb();

(

.IsSetRel() ) {

bytes +=

(

);

total_bytes += bytes;

<<

<<

<<bytes<<

<< endl;

<<

<<(*it2)->GetSeqId()->AsFastaString() << endl;

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)

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

virtual CSeq_id_Handle FindOrCreate(const CSeq_id &id)

TPackedStrMap m_PackedStrMap

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)

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

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

const char * GetErrCodeString(void) const override

Get error code interpreted as text.

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

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

~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

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

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)

virtual bool Empty(void) const

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

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

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)

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)

virtual CSeq_id_Handle GetGiHandle(TGi gi)

virtual bool HaveReverseMatch(const CSeq_id_Handle &id) const

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 ~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

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

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

const_iterator find(const key_type &key) const

const_iterator lower_bound(const key_type &key) const

const_iterator end() const

iterator insert(const value_type &val)

container_type::iterator iterator

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

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

main entry point for tests

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

#define INT_ID_FROM(T, value)

#define GI_FROM(T, value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

const TPrim & Get(void) const

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

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

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

bool IsPacked(void) const

CSeq_id_Info::TVariant TVariant

CConstRef< CSeq_id > m_Seq_id

CSeq_id::E_Choice GetType(void) const

bool IsSetVariant(void) const

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

TPacked GetPacked(void) const

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

void AtomicResetFrom(const CConstRef &ref)

Reset reference object to new pointer.

bool ReferencedOnlyOnce(void) const THROWS_NONE

Check if object is referenced only once.

void AtomicReleaseTo(CConstRef &ref)

Release referenced object to another CConstRef<> object.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

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

Case-insensitive compare of a substring with another string.

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

Convert int to string.

PNocase_Generic< string > PNocase

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 bool IsUpper(const CTempString str)

Checks if all letters in the given string have a upper case.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

size_type size(void) const

Return the length of the represented array.

@ fConvErr_NoThrow

Do not throw an exception on error.

#define DEFINE_STATIC_FAST_MUTEX(id)

Define static fast mutex and initialize it.

bool IsApp_number(void) const

Check if variant App_number is selected.

bool IsNumber(void) const

Check if variant Number is selected.

const TId & GetId(void) const

Get the Id member data.

const TNumber & GetNumber(void) const

Get the variant data.

const TApp_number & GetApp_number(void) const

Get the variant data.

const TCountry & GetCountry(void) const

Get the Country member data.

bool IsStr(void) const

Check if variant Str is selected.

TMinute GetMinute(void) const

Get the Minute member data.

bool IsSetDb(void) const

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

void SetYear(TYear value)

Assign a value to Year data member.

void SetMinute(TMinute value)

Assign a value to Minute data member.

bool IsStd(void) const

Check if variant Std is selected.

const TTag & GetTag(void) const

Get the Tag member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

bool IsId(void) const

Check if variant Id is selected.

void SetHour(THour value)

Assign a value to Hour data member.

TSecond GetSecond(void) const

Get the Second member data.

void SetMonth(TMonth value)

Assign a value to Month data member.

THour GetHour(void) const

Get the Hour member data.

void SetDay(TDay value)

Assign a value to Day data member.

const TDb & GetDb(void) const

Get the Db member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetDay(void) const

day of month (1-31) Check if a value has been assigned to Day data member.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

void SetSecond(TSecond value)

Assign a value to Second data member.

bool IsSetMinute(void) const

minute of hour (0-59) Check if a value has been assigned to Minute data member.

bool IsSetHour(void) const

hour of day (0-23) Check if a value has been assigned to Hour data member.

bool IsSetSeason(void) const

for "spring", "may-june", etc Check if a value has been assigned to Season data member.

bool IsSetMonth(void) const

month (1-12) Check if a value has been assigned to Month data member.

TYear GetYear(void) const

Get the Year member data.

TMonth GetMonth(void) const

Get the Month member data.

void SetDb(const TDb &value)

Assign a value to Db data member.

TDay GetDay(void) const

Get the Day member data.

const TStd & GetStd(void) const

Get the variant data.

TId & SetId(void)

Select the variant.

bool IsSetSecond(void) const

second of minute (0-59) Check if a value has been assigned to Second data member.

TId GetId(void) const

Get the variant data.

bool IsPatent(void) const

Check if variant Patent is selected.

void SetRel(TRel &value)

Assign a value to Rel data member.

TGeneral & SetGeneral(void)

Select the variant.

TChain GetChain(void) const

Get the Chain member data.

TNamed_annot_track & SetNamed_annot_track(void)

Select the variant.

const TEmbl & GetEmbl(void) const

Get the variant data.

const TPdb & GetPdb(void) const

Get the variant data.

void SetMol(const TMol &value)

Assign a value to Mol data member.

TId GetId(void) const

Get the Id member data.

bool IsSetChain_id(void) const

chain identifier; length-independent generalization of 'chain' Check if a value has been assigned to ...

bool IsSetChain(void) const

Deprecated: 'chain' can't support multiple character PDB chain identifiers (introduced in 2015).

bool IsSetAccession(void) const

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

TEmbl & SetEmbl(void)

Select the variant.

void SetName(const TName &value)

Assign a value to Name data member.

TOther & SetOther(void)

Select the variant.

const TGenbank & GetGenbank(void) const

Get the variant data.

const TName & GetName(void) const

Get the Name member data.

void SetAccession(const TAccession &value)

Assign a value to Accession data member.

bool IsGeneral(void) const

Check if variant General is selected.

E_Choice Which(void) const

Which variant is currently selected.

bool IsPdb(void) const

Check if variant Pdb is selected.

void ResetChain_id(void)

Reset Chain_id data member.

TGi GetGi(void) const

Get the variant data.

TGi & SetGi(void)

Select the variant.

TVersion GetVersion(void) const

Get the Version member data.

bool IsSetRelease(void) const

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

const TRelease & GetRelease(void) const

Get the Release member data.

TGpipe & SetGpipe(void)

Select the variant.

bool IsSetRel(void) const

release date, month and year Check if a value has been assigned to Rel data member.

const TMol & GetMol(void) const

Get the Mol member data.

TSeqid GetSeqid(void) const

Get the Seqid member data.

E_Choice

Choice variants.

TDdbj & SetDdbj(void)

Select the variant.

const TOther & GetOther(void) const

Get the variant data.

void SetRelease(const TRelease &value)

Assign a value to Release data member.

TLocal & SetLocal(void)

Select the variant.

const TDdbj & GetDdbj(void) const

Get the variant data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsGiim(void) const

Check if variant Giim is selected.

bool IsLocal(void) const

Check if variant Local is selected.

const TGpipe & GetGpipe(void) const

Get the variant data.

const TChain_id & GetChain_id(void) const

Get the Chain_id member data.

void ResetChain(void)

Reset Chain data member.

const TGeneral & GetGeneral(void) const

Get the variant data.

TGenbank & SetGenbank(void)

Select the variant.

bool IsSetVersion(void) const

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

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

const TRel & GetRel(void) const

Get the Rel member data.

void SetChain_id(const TChain_id &value)

Assign a value to Chain_id data member.

const TCit & GetCit(void) const

Get the Cit member data.

bool IsSetName(void) const

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

void SetVersion(TVersion value)

Assign a value to Version data member.

const TNamed_annot_track & GetNamed_annot_track(void) const

Get the variant data.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

const TAccession & GetAccession(void) const

Get the Accession member data.

void SetChain(TChain value)

Assign a value to Chain data member.

TPdb & SetPdb(void)

Select the variant.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gpipe

Internal NCBI genome pipeline processing ID.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Named_annot_track

Internal named annotation tracking ID.

@ e_not_set

No variant selected.

@ e_Tpg

Third Party Annot/Seq Genbank.

@ e_MaxChoice

== e_Named_annot_track+1

unsigned int

A callback function used to compare two keys in a database.

Definition of all error codes used in objects libraries.

constexpr bool empty(list< Ts... >) noexcept

const string version

version string

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

const GenericPointer< typename T::ValueType > T2 value

Common macro to detect used sanitizers and suppress memory leaks if run under LeakSanitizer.

#define NCBI_LSAN_DISABLE_GUARD

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

static bool x_InRange0(int value, int bits)

static void s_RestoreNumber(string &str, size_t pos, size_t len, TIntId number)

static TIntId s_ParseNumber(const string &str, size_t pos, size_t len)

static void s_AssignTextseq_id(CTextseq_id &new_tid, const CTextseq_id &old_tid)

static bool sx_ParseLocalStrId(const string &str, CObject_id::TId &id)

static const size_t kMallocOverhead

static const size_t kMinGeneralStrDigits

static pair< CSeq_id_Handle::TVariant, CSeq_id_Handle::TVariant > s_ParseCaseVariant(CTempString ref, const char *str, CSeq_id_Handle::TVariant bit)

static bool x_IsDefaultSwissprotRelease(const string &release)

static bool sx_AllDigits(const string &s)

static bool x_GetUnset1(int)

static bool s_PackTextidEnabled(void)

NCBI_PARAM_DECL(bool, OBJECTS, PACK_TEXTID)

static void s_AssignSeq_id(CSeq_id &new_id, const CSeq_id &old_id)

static bool x_InRange1(int value, int bits)

static void s_AssignObject_id(CObject_id &new_id, const CObject_id &old_id)

static CSeq_id_Handle::TVariant s_RestoreCaseVariant(string &str, size_t len, CSeq_id_Handle::TVariant variant)

static int x_GetUnset0(int bits)

static size_t sx_StringMemory(const string &s)

static void s_RestoreNumberAndCaseVariant(string &str, size_t pos, size_t len, TIntId number, CSeq_id_Handle::TVariant variant)

static void s_AssignDbtag(CDbtag &new_id, const CDbtag &old_id)

NCBI_PARAM_DEF_EX(bool, OBJECTS, PACK_TEXTID, true, eParam_NoThread, OBJECTS_PACK_TEXTID)

static bool s_PackGeneralEnabled(void)

TVariant ParseCaseVariant(const CDbtag &dbtag) const

size_t GetStrDigits(void) const

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

CTempString GetAccPrefix(void) const

TVariant ParseCaseVariant(const string &acc) const

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