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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Seq__id_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seqloc/Seq_id.cpp Source File

CSeq_id_find_pred

* kSymbols;

operator()(

ch)

strchr(kSymbols, ch) != 0;

:

;

(verstr.

()) {

+

(acc_in)

+

);

(

() ) {

( src.

() ) {

(

.

() ) {

( tsip1->

(*tsip2) )

(

() ) {

( tsip1 && tsip2 ) {

tsip1->

(*tsip2);

(

() ) {

(it == sc_ChoiceMap.end()) {

(s.

() > 3 && s[2] ==

) {

}

(s.

() > 4 && s[3] ==

) {

(s.

() > 3 && s[2] ==

) {

}

(s.

() > 4 && s[3] ==

) {

pair<string, TAccInfo>

;

* key_used =

)

;

(

& filename);

* old_name,

& new_name);

(it == sc_AccInfoMap.end()) {

(fmt == prev_special_format) {

(acc_or_range == prev_special_key) {

prev_special_type = prev_type;

prev_special_type_name = prev_type_name;

}

(pfx == prev_special_base_key) {

prev_special_base_type;

prev_special_format = fmt;

prev_special_base_key = pfx;

prev_special_base_type = guide.

(fmt, pfx);

prev_special_base_type;

(prev_submap !=

&& prev_submap->first == fmt) {

prev_submap->second;

(it ==

.

() || it->first != fmt) {

prev_big_special = it->second.big_specials.end();

prev_small_special = it->second.small_specials.end();

vector<CTempStringEx> tokens;

.assign(rule, 0, rule.

(

));

(tokens.empty()) {

}

(tokens.size() == 2

<<

<< tokens[1]);

}

((pos = tokens[0].find(

)) !=

&& (tokens.size() == 3

|| (tokens.size() == 4 && tokens[3] ==

))) {

.assign(tokens[0], 0, pos);

unique_ptr<string> old_name;

old_name.reset(

);

( !key_used.empty() ) {

key_used =

+ key_used +

;

<<

<< tokens[1]

<<

<< *old_name << key_used

<<

<< tokens[2]);

*old_name = it->second;

<<

<< tokens[2]

<<

<< *old_name <<

<< tokens[1]);

*old_name =

;

<<

<<

<< tokens[2]

<<

<< tokens[1]);

(tokens.size() == 4) {

(tokens[1].find_first_of(

) ==

) {

(wit->first == tokens[1]) {

wit->second =

;

value_ptr = &wit->second;

(value_ptr ==

) {

value_ptr = &submap.

.back().second;

(old_name.get() !=

&& !old_name->empty());

[value_ptr] = make_pair(*old_name, tokens[2]);

pos = tokens[1].find_first_of(

);

pos2 = tokens[1].find(

, pos);

=

(pos, ((pos2 ==

) ? tokens[1].

() : pos2) - pos);

(fmt, tokens[1].substr(0, pos2), &key_used);

( !key_used.empty() ) {

<<

<<

);

unique_ptr<string> old_name;

(fmt, tokens[1].substr(0, pos2), &key_used);

old_name.reset(

);

( !key_used.empty() ) {

*old_name = it->second;

<<

<< tokens[2]

<<

<< *old_name <<

<< tokens[1]);

( !key_used.empty() ) {

key_used =

+ key_used +

;

<<

<< tokens[2]

<<

<< tokens[1]

<<

<< *old_name << key_used);

}

(old_name->empty()) {

*old_name =

;

<<

<< tokens[2]

<<

<< tokens[1]);

(pos2 ==

) {

= tmp2 = tokens[1];

.assign(tokens[1], 0, pos2);

}

(tokens.size() >= 3

<<

);

digits = NStr::StringToNumeric<unsigned short>(tmp2);

( !why.empty() ) {

<<

<<

);

(

= 2;

< tokens.size(); ++

) {

(

= 2;

< tokens.size(); ++

) {

why =

+ tokens[

] +

;

( !why.empty() ) {

why =

+ why +

;

<<

<< tokens[2]

<<

<< tokens[1]);

<<

<< tokens[2]

<<

<< tokens[1]

}

(tokens.size() >= 2 && tokens[0] ==

) {

<<

);

<<

<<

);

(

= 1;

< tokens.size(); ++

) {

(tmp2.

()) {

memcpy(p - tmp2.

(), tmp2.

(), tmp2.

());

(tokens[1]);

<<

<< tokens[2]

<<

<<

);

[&it2->second] = make_pair(old_name, tokens[2]);

<<

<<

<<

<< old_name <<

}

(tokens.size() == 3

<<

<<

<< rule);

* key_used)

& submap = it->second;

bad_match =

;

(pos !=

) {

( !

(pfx[pos]) && pfx[pos] !=

) {

pos = wit->first.find(

, pos + 1);

(key_used && acc_or_pfx != wit->first) {

*key_used = wit->first;

(ssit->second.first[

]) {

ssit->second.second;

&& !(acc_or_pfx < bsit->second.first) ) {

bsit->second.second;

(key_used && key_used->empty()) {

*key_used = pfx.

(0, fmt >> 16);

file_is_old =

;

builtin_timestamp(

time_t

(kBuiltInGuide_Timestamp));

( !

.empty() &&

);

);

kNumBuiltInRules

=

(kBuiltInGuide) /

(*kBuiltInGuide);

(

= 0;

< kNumBuiltInRules; ++

) {

(kBuiltInGuide[

], hints);

(

&rit :

) {

(sit->second.first.any()) {

sit->second.first.optimize();

rit.second.small_specials.erase(sit);

*

kNucDBs[] = {

,

,

,

,

,

(

*

* p = kNucDBs; *p; ++p) {

}

( !

.AtEOF() );

* old_name,

* value_ptr =

;

(from_pfx != to_pfx) {

it->second.first.clear_range(left, right);

|| (--it)->first != from_pfx) {

(it->first != from_pfx) {

(it->first == from_pfx);

(value_ptr !=

) {

(old_name !=

&& !old_name->empty());

[value_ptr] = make_pair(*old_name, new_name);

(old_name ==

);

raw_digits = fmt & 0xffff, digits = raw_digits;

normal_size = (fmt >> 16) + digits;

(acc.

() == normal_size) {

pos = acc.

() - digits;

pos = (fmt >> 16) + 2;

(digits == raw_digits) {

+= (NStr::StringToNumeric<Uint1>(acc.

(pos, 2))

has_version =

;

(main_size ==

) {

has_version =

;

main_size = acc.

();

}

(main_size >= acc.

() - 1

kMainAccBufSize = 32;

(main_size <= kMainAccBufSize) {

* ucdata = (

*)acc.

();

main_acc_buf[kMainAccBufSize];

main_acc_buf[

] =

(ucdata[

]);

main_acc(acc, 0, main_size);

main_size = main_acc.

();

flag_char =

;

(digit_pos ==

) {

* ucdata = (

*)main_acc.

();

( !has_version && digit_pos == 0 && main_size >= 4

&& non_dig_pos < 5 &&

(ucdata[1])

(main_size > 4 && main_size <= 17

&& strchr(

, main_acc[4])

&& (main_size <= 6 ||

(ucdata[5]))) {

}

(main_size) {

(digit_pos == 1 && main_size == 6

&& (main_acc[0] ==

|| main_acc[0] ==

|| main_acc[0] ==

||

(ucdata[2]))

}

(digit_pos == 1 && main_size == 10

&& main_acc[0] !=

&& main_acc[0] !=

&& main_acc[0] !=

}

( !has_version && digit_pos == 0

&& (non_dig_pos == 6 || non_dig_pos == 7)

&& (main_size == non_dig_pos + 1

|| main_acc[non_dig_pos + 1] ==

|| (

(ucdata[non_dig_pos + 1])

&& (main_size == non_dig_pos + 2

|| main_acc[non_dig_pos + 2] ==

)))) {

}

(digit_pos >= 4 && non_dig_pos == digit_pos + 2

&& main_size - non_dig_pos >= 6 && main_acc[3] !=

&& (main_acc[non_dig_pos] ==

|| main_acc[non_dig_pos] ==

)

flag_char = main_acc[non_dig_pos];

(digit_pos == 0) {

&& main_acc[0] !=

flag_len = (flag_char ==

) ? 0 : 1;

digit_count = main_size - digit_pos - flag_len;

s_ReportedFallback;

s_ReportedFallback =

;

it = guide->fallbacks.find(&found_ai);

(it != guide->fallbacks.end()) {

<< it->second.first <<

<< main_acc <<

<< it->second.second <<

);

<<

<< main_acc

<<

);

(flag_char ==

) {

<<

(

, digit_pos

+ 2) ==

)) {

}

(type2 ==

) {

it == (*s_Guide)->general.end() ?

: it->second;

choice =

.Which();

*

+=

.GetGeneral().GetDb();

( !

.empty() ) {

(

.Which()) {

}

(oid.

()) {

& dbt =

.GetGeneral();

& idp =

.GetPatent().GetCit();

chain =

(pid.

());

*

+=

(chain);

list<string> secondary_id_list;

(!primary_id.empty())

*

+= primary_id;

(secondary_id_list.size() > 0)

*

+= *secondary_id_list.begin();

((*

)[

->size() - 1] ==

) {

the_type =

();

pgp[] =

;

.write(pgp,

(pgp) - 1);

tr[] =

;

.write(tr,

(tr) - 1);

the_type =

();

<<

;

( (*iter)->IsGi() ) {

(*iter)->WriteAsFasta(out_str);

found_gi =

;

((*id)->IsGi()) {

(*id)->WriteAsFasta(ostr);

(dbtag, set_as_general);

(set_as_general) {

+ dbtag.

());

(the_id.

()) {

);

(colon_pos !=

) {

db = the_id.

(0, colon_pos);

& whitelist = kSupportedRawDbtags;

(whitelist.find(db) != whitelist.end()) {

the_id.

(colon_pos + 1));

+

(the_id));

mol(the_id, 0, 4), chain;

(the_id.

() > 5) {

chain = the_id.

(5);

}

(the_id.

() == 5 && the_id[4] !=

) {

(

, mol, chain);

list<CTempString> fasta_pieces;

fasta_pieces.pop_front();

( !fasta_pieces.empty() ) {

(list<CTempString>, it, fasta_pieces) {

( !it->empty() ) {

+

(the_id)

+

);

(

, the_type, the_content);

list<CTempString> fasta_pieces;

( !fasta_pieces.empty()

fasta_pieces.pop_front();

(fasta_pieces, the_type, tv);

* kIllegal =

;

CSeq_id_find_pred pred; pred.kSymbols = kIllegal;

(find_if(s.

(), s.

(), pred) != s.

()) {

allow_partial_failure)

(allow_partial_failure) {

ids.push_back(

);

list<CTempString> fasta_pieces;

(fasta_pieces.size() > 0);

(fasta_pieces.size() == 1)

ids.push_back(

);

(fasta_pieces.size() == 2) {

fasta_pieces.pop_front();

( !fasta_pieces.empty() ) {

=

->x_Init(fasta_pieces,

, tv);

fasta_pieces.pop_front();

+ typestr);

( !fasta_pieces.empty() );

fasta_pieces.pop_front();

ids.push_back(

);

}

(std::exception& e) {

(fasta_pieces.empty()) {

= fasta_pieces.front().size();

(

!= 2 &&

!= 3) {

fasta_pieces.pop_front();

}

( !fasta_pieces.empty() );

(!fasta_pieces.empty());

vector<CTempString> fields(3);

min_fields = max_fields = 1;

min_fields = max_fields = 3;

min_fields = max_fields = 2;

(fasta_pieces.empty()) {

(

>= min_fields) {

(

>= min_fields && fasta_pieces.size() > 1

&& (fasta_pieces.front().size() == 2

|| fasta_pieces.front().size() == 3)

list<CTempString>::iterator it = fasta_pieces.begin();

(it != fasta_pieces.end());

((it->size() == 2 || it->size() == 3)

next_type = next_type_2;

}

(it->find_first_not_of(

) ==

&& ++it == fasta_pieces.end()) {

fields[

] = fasta_pieces.front();

fasta_pieces.pop_front();

&& !fasta_pieces.empty() ) {

fields[1] = snp_name;

fasta_pieces.clear();

( !fasta_pieces.empty() && fasta_pieces.front().empty() ) {

fasta_pieces.pop_front();

fields[2] =

;

fields[2] =

;

+

(fields[2]) +

+

(fields[0]) +

+

(fields[1]));

(fields[0].

() < 4

|| (fields[0].

() > 5

&& ( !fields[1].

()

|| strchr(

, fields[0][4]) ==

))) {

+

(fields[0]));

(fields[0].

() > 4 && fields[1].

()) {

(fields[0].

() > 5) {

fields[1] = fields[0].substr(5);

(fields[0][4] !=

);

fields[1] = fields[0].substr(4);

fields[0] = fields[0].substr(0, 4);

(

, fields[0]

, fields[1]

, ver,

(the_type, the_id);

((the_id < 0) || (the_type ==

&& the_id == 0)) {

(the_type, acc_in, name_in,

, release_in);

allow_dot =

;

( the_type ==

) {

gi = NStr::StringToNumeric<TGi>(acc);

(the_type, the_id);

+

+

(acc));

: tsid = &

(); allow_dot =

;

;

: tsid = &

(); allow_dot =

;

;

dbt.

().SetStrOrId(name);

(name_in.

()) {

}

(name.

()) {

}

(name.

() == 1) {

pdb.

(

(name[0]));

<<

<<

(name)

<<

<< acc <<

);

(name.

()) {

tsid->

(acc, name_in,

, release_in, allow_dot);

(

()) {

:

10;

:

20;

:

90;

(

()) {

:

60;

(

()) {

(db.compare(

) == 0 ||

db.compare(

) == 0 ||

db.compare(

) == 0 )

:

80;

:

20;

(

()) {

(db.compare(

) == 0 ||

db.compare(

) == 0 ||

db.compare(

) == 0)

:

70;

:

50;

:

30;

:

60;

(

()) {

:

30;

:

40;

:

80;

:

90;

:

100;

:

140;

(db.compare(

) == 0 ||

db.compare(

) == 0 ||

db.compare(

) == 0)

:

251;

:

255;

score = base_score * 10;

( db ==

) {

( !text_id->IsSetVersion() ) {

( !text_id->IsSetAccession() ) {

( !text_id->IsSetName() ) {

&

.SetGenbank();

&

.SetEmbl();

&

.SetPir();

&

.SetSwissprot();

&

.SetOther();

&

.SetDdbj();

&

.SetPrf();

&

.SetTpg();

&

.SetTpe();

&

.SetTpd();

&

.SetGpipe();

&

.SetNamed_annot_track();

( !

)

;

=

->IsSetAccession();

v =

->IsSetVersion();

=

->IsSetName();

=

->IsSetRelease();

(

&& (v ||

||

)) {

(v && (

||

)) {

(

&& (v ||

)) {

(

() ) {

(

().IsSetRel() ) {

.Assign(*

);

.SetPdb().ResetRel();

SEQ_ID_PREFER_ACCESSION_OVER_GI);

TPreferAccessionOverGi::GetDefault() ||

();

TAvoidGi::GetDefault();

secondary_id;

mixed_case =

;

(seqid_type) {

secondary_id = primary_id;

secondary_id = primary_id;

secondary_id = primary_id;

primary_id = tsid->

();

(secondary_id_list) {

(secondary_id_list) {

(!suffix.empty())

(secondary_id_list) {

((parse_flags &

) != 0 && secondary_id_list) {

}

(oid.

()) {

secondary_id = oid.

();

( secondary_id_list ) {

&& !primary_id.empty()) {

secondary_id = primary_id +

+ to_string(tsid->

());

secondary_id = primary_id +

;

secondary_id = tsid->

();

(secondary_id_list && !secondary_id.empty()) {

secondary_id_list->emplace_back(secondary_id);

:

;

(!text_id || !text_id->IsSetAccession() || !text_id->IsSetVersion())

;

(scale_limit < min_limit)

;

: start(0), stop(0), digits(0), acc_info(

::eAcc_unknown)

pos = 0,

= s.

();

&& (

((

) s[pos])

(pos <

&&

((

) s[pos])) {

}

(s[pos++] !=

) {

+

(s));

&& (

((

) s[pos])

( !pfx2.empty() && pfx2 !=

) {

+

(s));

+

(s));

(pos <

&&

((

) s[pos])) {

=

* 10 + s[pos++] -

;

:

:

:

:

:

:

oss << m_Range->prefix << setw(m_Range->digits) << setfill(

) << m_Number;

User-defined methods of the data storage class.

NCBI_PARAM_DECL(bool, SeqId, PreferAccessionOverGi)

static const TChoiceMapEntry sc_ChoiceArray[]

bool CanCmpAcc(CSeq_id::E_Choice choice)

static void x_GetLabel_Content(const CSeq_id &id, string *label, CSeq_id::TLabelFlags flags, int *version)

static const char *const s_TextId[CSeq_id::e_MaxChoice+1]

static const char * sc_SupportedRawDbtags[]

DEFINE_STATIC_ARRAY_MAP_WITH_COPY(CStaticArraySet< string >, kSupportedRawDbtags, sc_SupportedRawDbtags)

typedef NCBI_PARAM_TYPE(SeqId, PreferAccessionOverGi) TPreferAccessionOverGi

static CSeq_id::E_Choice s_CheckForFastaTag(const CTempString &s)

CStaticPairArrayMap< CTempString, CSeq_id::E_Choice, PNocase_Generic< CTempString > > TChoiceMap

static const unsigned int kMaxSmallSpecialDigits

void x_Assign(CObject_id &dst, const CObject_id &src)

static const TAccInfoMapEntry sc_AccInfoArray[]

CStaticPairArrayMap< CTempString, CSeq_id::EAccessionInfo, PNocase_Generic< CTempString > > TAccInfoMap

static CSafeStatic< CRef< SAccGuide > > s_Guide(s_CreateGuide, NULL)

static const bm::bvector ::size_type kBVSizes[kMaxSmallSpecialDigits+1]

static void x_GetLabel_Type(const CSeq_id &id, string *label, CSeq_id::TLabelFlags flags)

SStaticPair< const char *, CSeq_id::EAccessionInfo > TAccInfoMapEntry

static bool s_HasFastaTag(const CTempString &s)

static CRef< SAccGuide > * s_CreateGuide(void)

CTextseq_id * s_GetTextseq_id(const CSeq_id::E_Choice &choice, CSeq_id &match)

NCBI_PARAM_DEF_EX(bool, SeqId, PreferAccessionOverGi, false, eParam_NoThread, SEQ_ID_PREFER_ACCESSION_OVER_GI)

static void s_SplitVersion(const CTempString &acc_in, CTempString &acc, int &ver)

static const SAccGuide::TAccInfo kUnrecognized

SStaticPair< const char *, CSeq_id::E_Choice > TChoiceMapEntry

static const char kDigits[]

EDbtagType GetType(void) const

int Compare(const CDbtag &dbt2) const

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void SetStrOrId(CTempString str)

ostream & AsString(ostream &s) const

int Compare(const CObject_id &oid2) const

bool Match(const CObject_id &oid2) const

int Compare(const CPDB_seq_id &psip2) const

bool Match(const CPDB_seq_id &psip2) const

ostream & AsFastaString(ostream &s) const

ostream & AsFastaString(ostream &s) const

int Compare(const CPatent_seq_id &psip2) const

bool Match(const CPatent_seq_id &psip2) const

Base class for all serializable objects.

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

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

ostream & AsFastaString(ostream &s, bool allow_version=true) const

Format the contents FASTA string style.

CTextseq_id & Set(const CTempString &acc_in, const CTempString &name_in=kEmptyStr, int version=0, const CTempString &release_in=kEmptyStr, bool allow_dot_version=true)

Set all fields with a single call.

int Compare(const CTextseq_id &tsip2) const

bool Match(const CTextseq_id &tsip2) const

Comparison functions.

Abstract base class for lightweight line-by-line reading.

bvector_size_type size_type

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 lower_bound(const key_type &key) const

const_iterator end() const

const_iterator begin() const

container_type::iterator iterator

iterator_bool insert(const value_type &val)

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

main entry point for tests

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

#define GI_FROM(T, value)

constexpr size_t ArraySize(const Element(&)[Size])

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define INT_ID_TO(T, id)

Convert gi-compatible int to/from other types.

#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 STD_CATCH_ALL_X(err_subcode, message)

Standard handling of "exception"-derived exceptions; catches non-standard exceptions and generates "u...

#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.

void Info(CExceptionArgs_Base &args)

ESerialRecursionMode

How to assign and compare child sub-objects of serial objects.

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

Set object to copy of another one.

const TPrim & Get(void) const

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

void x_WriteContentAsFasta(ostream &out) const

CSeq_id(void)

See also CSeq_id related functions in "util/sequence.hpp":

string ComposeOSLT(list< string > *secondary_ids=nullptr, TComposeOSLTFlags parse_flags=0) const

JIRA ID-5188 : Compose OSLT string for the primary id, as well as OSLT strings for the secondary ids,...

const string AsFastaString(void) const

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...

static bool IsValid(const CBioseq::TId &ids, TParseFlags flags=fParse_Default)

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

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

int BaseBlastScore(void) const

int BaseFastaAAScore(void) const

static const size_t kMaxLocalIDLength

ID length restrictions.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

E_Choice x_Init(list< CTempString > &fasta_pieces, E_Choice type, ETypeVariant tv)

EAccessionInfo

For IdentifyAccession (below)

static ESNPScaleLimit GetSNPScaleLimit_Value(const string &name)

int CompareOrdered(const CSeq_id &sid2) const

const SSeqIdRange * m_Range

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

static E_Choice GetAccType(EAccessionInfo info)

E_SIC

Compare return values.

EFastaAsTypeAndContent

Tag for method variants that would otherwise be ambiguous.

static ETypeVariant x_IdentifyTypeVariant(E_Choice type, const CTempString &str)

virtual void WriteAsFasta(ostream &out) const

Implement serializable interface.

int BaseBestRankScore(void) const

int TFlags

binary OR of EFlags

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

SSeqIdRange(const CTempString &s, TFlags flags=0)

static E_Choice WhichInverseSeqId(const CTempString &SeqIdCode)

Converts a string to a choice, no need to require a member.

static const char * GetSNPScaleLimit_Name(ESNPScaleLimit value)

static bool IsValidLocalID(const CTempString &s)

Perform rudimentary validation on potential local IDs, whose contents should be pure ASCII and limite...

static string GetStringDescr(const CBioseq &bioseq, EStringFormat fmt)

static void LoadAccessionGuide(const string &filename)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

int AdjustScore(int base_score, TAdjustScoreFlags flags=TAdjustScoreFlags()) const

EStringFormat

Get a string representation of the sequence IDs of a given bioseq.

CSeq_id::EAccessionInfo acc_info

virtual const char * GetErrCodeString(void) const override

Translate from the error code value to its string representation.

bool IsAllowedSNPScaleLimit(ESNPScaleLimit scale_limit) const

static EAccessionInfo x_IdentifyAccession(const CTempString &main_acc, TParseFlags flags, bool has_version)

CRef< CSeq_id > GetID(void) const

void GetMatchingTextseqIds(TSeqIdHandles &matches) const

Collect partially matching textseq-ids.

ELabelType

return the label for a given string

const string & x_SetAccession(void) const

void GetMatchingIds(TSeqIdHandles &matches) const

Collect partially matching seq-ids: no-version, no-name etc.

static int FastaNARank(const CRef< CSeq_id > &id)

int BaseTextScore(void) const

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

static bool PreferAccessionOverGi(void)

Check if the option to prefer accession.version over GI is enabled (SeqId/PreferAccessionOverGi or SE...

static bool AvoidGi(void)

Check if the option to avoid GI ids is enabled (SeqId/AvoidGi or SEQ_ID_AVOID_GI).

virtual ~CSeq_id(void)

Destructor.

static TErrorFlags CheckLocalID(const CTempString &s)

Perform rudimentary validation on potential local IDs, whose contents should not exceed fifty charact...

int BaseFastaNAScore(void) const

static const char * WhichFastaTag(E_Choice choice)

Converts a choice to a FASTA tag, with no trailing vertical bar.

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

ESNPScaleLimit

SNP annotation scale limits.

static int FastaAARank(const CRef< CSeq_id > &id)

@ fLabel_Trimmed

Trim trailing FASTA delimeters.

@ fLabel_UpperCase

Upper case label, with special encoding for PDB chain-ids.

@ fLabel_Version

Show the version.

@ fLabel_GeneralDbIsContent

For type general, use the database name as the tag and the (text or numeric) key as the content.

@ eUnknownType

Unrecognized Seq-id type.

@ eFormat

Contents not parsable as expected.

@ eAcc_refseq_wgsv_intermed

@ eAcc_refseq_unique_prot

@ eAcc_ddbj_tpa_wgsvm_prot

@ eAcc_ddbj_tpa_targeted_nuc

@ eAcc_ddbj_tpa_targetedvm_nuc

@ eAcc_embl_tpa_wgsvm_nuc

@ eAcc_refseq_contig_ncbo

@ eAcc_ddbj_tpa_tsam_prot

@ eAcc_ddbj_tpa_tsav_prot

@ eAcc_refseq_mrna_predicted

@ eAcc_embl_tpa_wgsvm_prot

@ eAcc_ddbj_tpa_wgsm_prot

@ eAcc_ddbj_tpa_tsavm_nuc

@ eAcc_embl_tpa_wgsm_prot

@ eAcc_ddbj_tpa_targetedm_nuc

@ eAcc_ddbj_tpa_targetedv_nuc

@ eAcc_ddbj_tpa_tsavm_prot

@ eAcc_ddbj_targetedvm_nuc

@ eAcc_refseq_prot_predicted

@ eAcc_embl_tpa_tsam_prot

@ eAcc_embl_tpa_tsav_prot

@ eAcc_ddbj_targetedv_nuc

@ eAcc_embl_tpa_tsavm_prot

@ eAcc_refseq_wgsm_intermed

@ eAcc_ddbj_tpa_chromosome

@ eAcc_ddbj_tpa_wgsvm_nuc

@ eAcc_embl_tpa_wgsv_prot

@ eAcc_refseq_chromosome_ncbo

@ eAcc_refseq_ncrna_predicted

@ eAcc_refseq_wgsvm_intermed

@ eAcc_embl_tpa_tsavm_nuc

@ eAcc_refseq_wgs_intermed

@ eAcc_ddbj_targetedm_nuc

@ eAcc_ddbj_tpa_wgsv_prot

@ e_NO

different SeqId types-can't compare

@ e_YES

SeqIds compared, but are different.

@ fGpipeAddSecondary

Add "ACC.VER(=1)" for a 2ndary id.

@ fParse_NoFASTA

Don't bother checking for a tag.

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_RawGI

Treat raw numbers as GIs, not local IDs.

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

@ fParse_FallbackOK

For IdentifyAccession, don't warn about falling back to a different specific type because broad ident...

@ fParse_ValidLocal

Treat otherwise unidentified strings as raw accessions, provided that they pass rudimentary validatio...

@ eFormat_BestWithoutVersion

@ eFormat_BestWithVersion

@ eFastaContent

Like eFasta, but without any tag.

@ eContent

Untagged human-readable accession or the like.

@ eDefault

default is to show type + content

@ eBoth

Type and content, delimited by a vertical bar.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

@ eType

FASTA-style type, or database in GeneralDbIsContent mode.

@ fAllowUnderscores

Allow prefixes to contain underscores.

@ eSNPScaleLimit_Supercontig

@ eSNPScaleLimit_Chromosome

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

@ eParam_NoThread

Do not use per-thread values.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

const_iterator end() const

Return an iterator to the string's ending position (one past the end of the represented sequence)

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

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 list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool MatchesMask(CTempString str, CTempString mask, ECase use_case=eCase)

Match "str" against the "mask".

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

CTempString & assign(const char *src_str, size_type len)

Assign new values to the content of the a string.

static TNumeric StringToNumeric(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to a numeric value.

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

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

const char * data(void) const

Return a pointer to the array represented.

void erase(size_type pos=0)

Truncate the string at some specified position Note: basic_string<> supports additional erase() optio...

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

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

Convert UInt to string.

void clear(void)

Clears the string.

size_type find_last_not_of(const CTempString match, size_type pos=npos) const

Find the last occurrence of any character not in the matching string within the current string,...

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

size_type length(void) const

Return the length of the represented array.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

size_type find_first_not_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character not in the matching string within the current string,...

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

size_type find_first_of(const CTempString match, size_type pos=0) const

Find the first occurrence of any character in the matching string within the current string,...

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 find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

static string & ToUpper(string &str)

Convert string to upper case – string& version.

const char *const kEmptyCStr

Empty "C" string (points to a '\0').

size_type size(void) const

Return the length of the represented array.

const_iterator begin() const

Return an iterator to the string's starting position.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ eTrunc_Both

Truncate whitespace at both begin and end of string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

void SetCountry(const TCountry &value)

Assign a value to Country data member.

bool IsNumber(void) const

Check if variant Number is selected.

TApp_number & SetApp_number(void)

Select the variant.

void SetId(TId &value)

Assign a value to Id data member.

TNumber & SetNumber(void)

Select the variant.

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.

void ResetDoc_type(void)

Reset Doc_type data member.

const TCountry & GetCountry(void) const

Get the Country member data.

bool IsStr(void) const

Check if variant Str 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.

const TDb & GetDb(void) const

Get the Db member data.

E_Choice Which(void) const

Which variant is currently selected.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

virtual void Reset(void)

Reset the whole object.

void SetDb(const TDb &value)

Assign a value to Db data member.

TId & SetId(void)

Select the variant.

TId GetId(void) const

Get the variant data.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

@ e_not_set

No variant selected.

const TRelease & GetRelease(void) const

Get the Release member data.

void SetSeqid(TSeqid value)

Assign a value to Seqid data member.

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.

TGibbsq GetGibbsq(void) const

Get the variant data.

TPatent & SetPatent(void)

Select the variant.

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.

const TTpe & GetTpe(void) const

Get the variant data.

bool IsSetRelease(void) const

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

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 SetId(TId value)

Assign a value to Id data member.

void ResetVersion(void)

Reset Version data member.

const TTpd & GetTpd(void) const

Get the variant data.

void SetAccession(const TAccession &value)

Assign a value to Accession data member.

bool IsGeneral(void) const

Check if variant General is selected.

TTpe & SetTpe(void)

Select the variant.

void SetRelease(const TRelease &value)

Assign a value to Release data member.

bool CanGetName(void) const

Check if it is safe to call GetName method.

const TTpg & GetTpg(void) const

Get the variant data.

TTpg & SetTpg(void)

Select the variant.

void ResetAccession(void)

Reset Accession data member.

E_Choice Which(void) const

Which variant is currently selected.

void ResetRelease(void)

Reset Release data member.

virtual void Reset(void)

Reset the whole object.

TPir & SetPir(void)

Select the variant.

bool IsSwissprot(void) const

Check if variant Swissprot 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.

TTpd & SetTpd(void)

Select the variant.

TVersion GetVersion(void) const

Get the Version member data.

TGibbmt & SetGibbmt(void)

Select the variant.

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.

void ResetRel(void)

Reset Rel data member.

const TOther & GetOther(void) const

Get the variant data.

const TGiim & GetGiim(void) const

Get the variant data.

const TSwissprot & GetSwissprot(void) const

Get the variant data.

void SetRelease(const TRelease &value)

Assign a value to Release data member.

void ResetDb(void)

Reset Db data member.

TLocal & SetLocal(void)

Select the variant.

TGiim & SetGiim(void)

Select the variant.

const TDdbj & GetDdbj(void) const

Get the variant data.

const TLocal & GetLocal(void) const

Get the variant data.

void ResetName(void)

Reset Name data member.

void ResetRelease(void)

Reset Release data member.

const TPir & GetPir(void) const

Get the variant data.

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

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.

void SetDb(const TDb &value)

Assign a value to Db data member.

TPrf & SetPrf(void)

Select the variant.

virtual void Reset(void)

Reset the whole object.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

TGibbsq & SetGibbsq(void)

Select the variant.

TGenbank & SetGenbank(void)

Select the variant.

const TPatent & GetPatent(void) const

Get the variant data.

TGibbmt GetGibbmt(void) const

Get the variant data.

const TPrf & GetPrf(void) const

Get the variant data.

TSwissprot & SetSwissprot(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).

void SetCit(TCit &value)

Assign a value to Cit data member.

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.

bool IsSetDb(void) const

dbase used in Check if a value has been assigned to Db 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.

const TDb & GetDb(void) const

Get the Db member data.

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

const TInst & GetInst(void) const

Get the Inst member data.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

TMol GetMol(void) const

Get the Mol member data.

Definition of all error codes used in objects libraries.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

Lightweight interface for getting lines of data with minimal memory copying.

bm::id_t bvector_size_type

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

const string version

version string

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

Compressed bitset (entry point to bm.h)

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Useful/utility classes and methods.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

Define Case-insensitive string comparison methods.

TSmallSpecialMap::iterator prev_small_special

CTempString prev_special_type_name

SSubMap * special2_submap

TBigSpecialMap::iterator prev_big_special

TAccInfo FindAccInfo(CTempString name)

SSubMap & FindSubMap(TMainMap &rules, TFormatCode fmt)

unique_ptr< string > special2_old_name

TAccInfo prev_special_type

map< string, CTempString > default_fallbacks

TAccInfo prev_special_base_type

string prev_special_base_key

TMainMap::value_type * prev_submap

CTempString prev_type_name

TFormatCode prev_special_format

TAccInfo FindSpecial(const SAccGuide &guide, TFormatCode fmt, CTempString acc_or_range)

TBigSpecialMap big_specials

TSmallSpecialMap small_specials

void x_Load(const string &filename)

SAccGuide(const string &filename)

map< string, TPair > TBigSpecialMap

pair< bm::bvector<>, TAccInfo > TSmallSpecialOption

static TFormatCode s_Key(unsigned short letters, unsigned short digits)

pair< string, TAccInfo > TPair

pair< string, string > TFallback

CSeq_id::EAccessionInfo TAccInfo

multimap< string, TSmallSpecialOption > TSmallSpecialMap

static bm::bvector_size_type x_SplitSpecial(CTempString &acc, TFormatCode fmt)

const TAccInfo & Find(TFormatCode fmt, const CTempString &acc_or_pfx, string *key_used=NULL) const

SAccGuide(ILineReader &lr)

map< string, TAccInfo > TPrefixes

map< const TAccInfo *, TFallback > TFallbackMap

void x_AddSpecial(SSubMap &submap, SHints &hints, TFormatCode fmt, CTempString from, CTempString to, TAccInfo value, const string *old_name, const CTempString &new_name)

map< TFormatCode, SSubMap > TMainMap

void AddRule(const CTempString &rule, SHints &hints)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

static const char * kUnknown

string g_FindDataFile(const CTempString &name, CDirEntry::EType type=CDirEntry::eFile)

Look for an NCBI application data file or directory of the given name and type; in general,...

bool g_IsDataFileOld(const CTempString &path, const CTempString &id_line)

Check whether the given file (a full path, as returned by g_FindDataFile) is older than a built-in ve...

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