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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/em__ascii_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/flatfile/em_ascii.cpp Source File

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(update.

()) {

(seq_entries.front().Empty()) {

(pp->

&& ! seq_entries.empty())

= seq_entries.front();

(

&

: ids) {

(id->IsStr() && id->GetStr() ==

) {

ids.push_back(obj_id);

valid_biosample;

xip = xil && ! xil->empty();

(eptr = bptr +

; bptr < eptr; bptr = ptr) {

name.assign(bptr, ptr);

name =

;

name =

;

(ptr && ptr < p) {

.assign(bptr, ptr);

(

.

()) {

(name ==

&& !

.

()) {

many_biosample = (!

.empty() && ! id1.empty());

valid_biosample =

;

(many_biosample || ! valid_biosample) {

q =

(

*

(drline),

);

(! valid_biosample)

(

&

: dr_biosample) {

dr_biosample.push_back(

);

(!

.

() && ! id1.empty()) {

q =

(

*

(drline),

);

(

&

: dr_ena) {

dr_ena.push_back(

);

new_xref->SetDbname().SetName(name);

new_xrefs.push_back(new_xref);

(! new_xrefs.empty())

embl.

().swap(new_xrefs);

(

.Which()) {

.SetGenbank();

.SetEmbl();

.SetSwissprot();

.SetOther();

.SetDdbj();

.SetGpipe();

.SetNamed_annot_track();

vector<string> taxLines;

(

& line : taxLines) {

(line.empty() || line.starts_with(

sv)) {

(! sTaxname.empty()) {

(sTaxname.empty()) {

openP = sTaxname.find(

);

(openP != string::npos) {

sCommonName = sTaxname.substr(0, openP);

commonTerm = sCommonName.find_last_not_of(

);

(commonTerm != string::npos) {

sCommonName = sCommonName.substr(0, commonTerm + 1);

allow_crossdb_featloc;

(! dbp || ! dbp->

.

)

(q = p; *q !=

; q++) {

(*q ==

) {

(q[1] ==

&& q[2] ==

&& q[3] ==

) {

(q = p,

= p; *q !=

; q++)

(q = p; *q !=

; q++)

((q[0] ==

&& q[1] ==

) || (q[0] ==

&& q[1] ==

) ||

(q[0] ==

&& q[1] ==

))

(

= 0, q = p; *q !=

; q++) {

pat_ref =

;

est_kwd =

;

sts_kwd =

;

gss_kwd =

;

htc_kwd =

;

fli_kwd =

;

wgs_kwd =

;

tpa_kwd =

;

tsa_kwd =

;

tls_kwd =

;

env_kwd =

;

mga_kwd =

;

(*bptr ==

|| *bptr ==

)

bptr = (

*)

;

(*bptr ==

|| *bptr ==

)

dataclass[3] =

;

bptr = (

*)

;

dataclass[0] =

;

embl->SetKeywords() = keywords;

(

&

: keywords) {

(

, &est_kwd, &sts_kwd, &gss_kwd, &htc_kwd, &fli_kwd, &wgs_kwd, &tpa_kwd, &env_kwd, &mga_kwd, &tsa_kwd, &tls_kwd);

* p = gbdiv.c_str();

(!

(embl->GetKeywords())) {

(ibp->

==

) {

}

(ibp->

) {

}

(ibp->

) {

(ibp->

==

) {

}

(ibp->

) {

(ibp->

==

) {

}

(ibp->

) {

(

== 2 && ibp->

> 0 && env_kwd)

(

,

,

);

((

== 2 && wgs_kwd && tpa_kwd) ||

(

== 2 && tsa_kwd && tpa_kwd)) {

}

(

!= 2 || env_kwd ==

||

(est_kwd ==

&& gss_kwd ==

&& wgs_kwd ==

)) {

(

,

,

);

wgs_kwd ==

&& tpa_kwd ==

&& env_kwd ==

) {

(! est_kwd && kw.find(

) != string::npos) {

(! sts_kwd && kw.find(

) != string::npos) {

(! gss_kwd && kw.find(

) != string::npos) {

(ibp->

, pat_ref, est_kwd, sts_kwd, gss_kwd, if_cds, gbdiv, &tech, ibp->

, pp->

, drop);

}

(gbdiv ==

) {

is_htc_div = (gbdiv ==

);

has_htc =

(embl->GetKeywords());

(is_htc_div && ! has_htc) {

(! is_htc_div && has_htc) {

(*p ==

|| *p ==

)

(

(p,

, 12))

(! gbdiv.empty()) {

(gbdiv ==

) {

}

(gbdiv ==

) {

}

(gbdiv ==

) {

}

(gbdiv ==

) {

}

((gbdiv ==

) && bio_src &&

(

& subtype : bio_src->

()) {

(! std_creation_date || ! std_update_date) {

embl->SetCreation_date().SetStd(*std_creation_date);

embl->SetUpdate_date().SetStd(*std_update_date);

ibp->

[0] =

;

found =

;

(

& acc : embl->SetExtra_acc()) {

(acc[0] ==

|| acc[0] ==

)) {

ibp->

[0] =

;

(! gbdiv.empty()) {

& subtype = bio_src->

();

find_if(begin(subtype), end(subtype), [](

pSubSource) {

}

(! bio_src ||

(! gbb->IsSetExtra_accessions() && ! gbb->IsSetKeywords() && ! gbb->IsSetDiv())

(

= 0, q = bptr; *q !=

; q++) {

(p =

+ 1; *p ==

|| *p ==

;)

(ibp->

) {

}

(ibp->

)

(mol_info->SetBiomol(), mol_info->GetTech(), bptr, pp, entry, org_ref);

mol_info->ResetBiomol();

(!

|| lst.empty())

(

& item : lst) {

field->

().SetStrs().push_back(item);

(dr_ena.empty() && dr_biosample.empty())

(

& descr : descrs) {

(! descr->IsUser() || ! descr->GetUser().IsSetType())

& obj_id = descr->GetUser().GetType();

(obj_id.

() && obj_id.

() ==

) {

user_obj_ptr = &descr->SetUser();

(! dr_biosample.empty())

(! dr_ena.empty()) {

(field_bs.

() && field_ena.

())

user_obj->

().SetStr(

);

user_obj_ptr->

().push_back(field_bs);

user_obj_ptr->

().push_back(field_ena);

descrs.push_back(descr);

dbuop->

(*user_obj_ptr);

(

& xref : embl_block.

()) {

(! xref->IsSetDbname() || ! xref->GetDbname().IsName() ||

! xref->GetDbname().GetName().starts_with(

sv))

(

&

: xref->GetId()) {

(id->IsStr() && ! id->GetStr().empty()) {

->SetDb(xref->GetDbname().GetName());

& id_str =

->SetTag().SetStr();

need_delimiter =

;

(

&

: xref->GetId()) {

(id->IsStr() && ! id->GetStr().empty()) {

need_delimiter =

;

id_str +=

->GetStr();

xrefs.push_back(

);

imp.

(

);

(annot.empty() || ! (*annot.begin())->IsFtable()) {

new_annot->

().SetFtable().push_back(feat);

annot.push_back(new_annot);

old_annot.

().SetFtable().push_front(feat);

line.starts_with(

sv) ||

line.starts_with(

sv) ||

line.starts_with(

sv) ||

line.starts_with(

sv) ||

line.starts_with(

sv) ||

line.starts_with(

sv);

is_htg =

;

(

pos = 0; pos <

.size();) {

pos =

.find(

, pos);

(pos == string::npos)

(

= pos;

<

.size() &&

[

] ==

; ++

)

(!

.empty()) {

c =

.back();

(c ==

|| c ==

)

.starts_with(

sv)) {

(ibp->

==

&&

.starts_with(

sv)) {

(ibp->

==

&&

.starts_with(

sv)) {

(

.starts_with(

sv)) {

str1 =

sv;

str1 =

sv;

str1 =

sv;

str1 =

sv;

.replace(0, 4, str1);

bioseq.

().Set().push_back(descr);

(title.empty() || ! title.starts_with(

sv))) {

(ibp->

&& (title.empty() || ! title.starts_with(

))) {

(

& ref_blk : chain) {

descr->

(*pubdesc);

bioseq.

().Set().push_back(descr);

(

& ref_blk : chain) {

descr->

(*pubdesc);

bioseq.

().Set().push_back(descr);

(

& descr : bioseq.

().Set()) {

(descr->IsSource()) {

bio_src = &(descr->SetSource());

org_ref = &bio_src->

();

ibp->

&& ! mol_info->IsSetTech()) {

mol_info->ResetTech();

mol_info->SetTech(tech);

(mol_info->IsSetBiomol() || mol_info->IsSetTech()) {

bioseq.

().Set().push_back(descr);

(! dr_ena.empty() || ! dr_biosample.empty())

(embl_block.

()) {

(embl_block->GetExtra_acc().empty())

embl_block->ResetExtra_acc();

hasEmblBlock =

;

descr->

(*embl_block);

bioseq.

().Set().push_back(descr);

hasEmblBlock =

;

,

(ibp->

==

) ?

:

);

(hasEmblBlock && embl_block->IsSetDiv() && embl_block->GetDiv() < 15) {

(

& pAnnot : bioseq.

()) {

(pAnnot->IsFtable()) {

(

& pFeat : pAnnot->SetData().SetFtable()) {

(pFeat->IsSetData() && pFeat->SetData().IsBiosrc()) {

& biosrc = pFeat->SetData().SetBiosrc();

(biosrc.IsSetOrg() &&

(! biosrc.GetOrg().IsSetDb() ||

}

(gbb && gbb->IsSetDiv()) {

bioseq.

().Set().push_back(descr);

(

& user_obj : user_objs) {

bioseq.

().Set().push_back(descr);

(q =

, p = q; *p !=

;) {

(*p ==

&& (p[1] ==

|| p[1] ==

))

(*p ==

|| *p ==

) {

(p++; *p ==

|| *p ==

;)

(

[0] != 0) {

bioseq.

().Set().push_back(descr);

(std_creation_date.

()) {

bioseq.

().Set().push_back(descr);

(std_update_date.

()) {

bioseq.

().Set().push_back(descr);

crdate_str, update_str;

std_creation_date->

(&crdate_str,

);

std_update_date->

(&crdate_str,

);

(

& os_blk : chain) {

(org_ref.

())

bio_src->

(*org_ref);

& taxname_str = org_ref->

();

(taxname_str[off_pos] !=

&& off_pos < taxname_str.size())

(taxname_str[off_pos] ==

&& off_pos < taxname_str.size())

taxname_str = taxname_str.substr(off_pos);

(taxname_str ==

) {

taxname_str = taxname_str.substr(0, taxname_str.size() - 1);

(

& subdbp : os_blk.GetSubBlocks()) {

(subdbp.mType !=

|| ! subdbp.mBuf.ptr ||

(! lineage.empty()) {

it = lineage.find(

);

(it == string::npos)

lineage.erase(it, 5);

(! lineage.empty()) {

c = lineage.back();

(c !=

&& c !=

&& c !=

&& c !=

&& c !=

)

(! lineage.empty() && ! org_ref->

()) {

bioseq.

().Set().push_front(descr);

(*p ==

|| *p ==

)

(

= 0, p = entry.

.

; *p !=

&&

< 4; p++)

(*p ==

&& p[1] ==

)

(p++; *p ==

;)

seq_long =

;

(! ibp->

) {

ebp = pEntry->GetEntryData();

* ptr = pEntry->mBuf.ptr;

* eptr = ptr + pEntry->mBuf.len;

ebp->seq_entry->SetSeq(*bioseq);

(! ibp->

.empty())

(ibp->

== 4 || ibp->

== 1 || ibp->

== 2 ||

}

(! ibp->

.empty())

pEntry->mpQscore.clear();

->SetPatent(*ibp->

);

bioseq->

().push_back(

);

seq_entries.push_back(ebp->seq_entry);

ebp->seq_entry.

();

(ibp->

== 4 || ibp->

== 1 || ibp->

== 2) {

(! ibp->

) {

(! ibp->

) {

pat_ref =

;

est_kwd =

;

sts_kwd =

;

gss_kwd =

;

htc_kwd =

;

fli_kwd =

;

wgs_kwd =

;

tpa_kwd =

;

env_kwd =

;

mga_kwd =

;

tsa_kwd =

;

tls_kwd =

;

embl->SetKeywords().swap(ibp->

);

(

&

: embl->GetKeywords()) {

(

, &est_kwd, &sts_kwd, &gss_kwd, &htc_kwd, &fli_kwd, &wgs_kwd, &tpa_kwd, &env_kwd, &mga_kwd, &tsa_kwd, &tls_kwd);

dataclass[0] =

;

* p = gbdiv.c_str();

(!

(embl->GetKeywords())) {

(ibp->

==

) {

}

(ibp->

) {

}

(ibp->

) {

(ibp->

==

) {

}

(ibp->

) {

(ibp->

==

) {

}

(ibp->

) {

(

== 2 && ibp->

> 0 && env_kwd)

(

,

,

);

(

!= 2 || env_kwd ==

||

(est_kwd ==

&& gss_kwd ==

&& wgs_kwd ==

)) {

(

,

,

);

wgs_kwd ==

&& tpa_kwd ==

&& env_kwd ==

) {

(! est_kwd && kw->find(

) != string::npos) {

(! sts_kwd && kw->find(

) != string::npos) {

(! gss_kwd && kw->find(

) != string::npos) {

(ibp->

, pat_ref, est_kwd, sts_kwd, gss_kwd, if_cds, gbdiv, &tech, ibp->

, pp->

, drop);

}

(gbdiv ==

) {

is_htc_div = (gbdiv ==

);

has_htc =

(embl->GetKeywords());

(is_htc_div && ! has_htc) {

(! is_htc_div && has_htc) {

(*

==

|| *

==

)

(! gbdiv.empty()) {

(gbdiv ==

) {

}

(gbdiv ==

) {

}

(gbdiv ==

) {

}

(gbdiv ==

) {

}

((gbdiv ==

) && bio_src &&

ibp->

[0] =

;

embl->SetCreation_date().SetStd(*std_creation_date);

embl->SetUpdate_date().SetStd(*std_update_date);

(std_update_date.

() && std_creation_date.

())

embl->SetUpdate_date().SetStd(*std_creation_date);

found =

;

(

& acc : embl->SetExtra_acc()) {

(acc[0] ==

|| acc[0] ==

)) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void AssemblyGapsToDelta(CBioseq &bioseq, TGapFeatsList &gf, bool *drop)

bool no_reference(const CBioseq &bioseq)

void SeqToDelta(CBioseq &bioseq, Int2 tech)

CMolInfo::TTech fta_check_con_for_wgs(CBioseq &bioseq)

bool fta_check_htg_kwds(TKeywordList &kwds, IndexblkPtr ibp, CMolInfo &mol_info)

void fta_set_molinfo_completeness(CBioseq &bioseq, const Indexblk *ibp)

void fta_add_hist(ParserPtr pp, CBioseq &bioseq, CGB_block::TExtra_accessions &extra_accs, Parser::ESource source, CSeq_id::E_Choice acctype, bool pricon, const char *acc)

bool fta_parse_tpa_tsa_block(CBioseq &bioseq, char *offset, char *acnum, Int2 vernum, size_t len, Int2 col_data, bool tpa)

Int4 fta_fix_seq_loc_id(TSeqLocList &locs, ParserPtr pp, string_view location, string_view name, bool iscon)

string GetQSFromFile(FILE *fd, const Indexblk *ibp)

CRef< CSeq_loc > fta_get_seqloc_int_whole(const CSeq_id &seq_id, size_t len)

bool check_cds(const DataBlk &entry, Parser::EFormat format)

bool fta_if_valid_sra(string_view id, bool dblink)

void fta_create_far_fetch_policy_user_object(CBioseq &bsp, Int4 num)

void fta_tsa_tls_comment_dblink_check(const CBioseq &bioseq, bool is_tsa)

void fta_remove_cleanup_user_object(CSeq_entry &seq_entry)

bool fta_dblink_has_sra(const CRef< CUser_object > &uop)

void GapsToDelta(CBioseq &bioseq, TGapFeatsList &gf, bool *drop)

void fta_get_project_user_object(TSeqdescList &descrs, const char *offset, Parser::EFormat format, bool *drop, Parser::ESource source)

void err_install(const Indexblk *ibp, bool accver)

bool fta_if_valid_biosample(string_view id, bool dblink)

void fta_parse_structured_comment(char *str, bool &bad, TUserObjVector &objs)

void StripSerialNumbers(TEntryList &seq_entries)

void AddNIDSeqId(CBioseq &bioseq, const DataBlk &entry, Int2 type, Int2 coldata, Parser::ESource source)

void fta_fix_orgref_div(const CBioseq::TAnnot &annots, COrg_ref *org_ref, CGB_block &gbb)

void DefVsHTGKeywords(CMolInfo::TTech tech, const DataBlk &entry, Int2 what, Int2 ori, bool cancelled)

unsigned char *const GetDNAConvTable()

void fta_sort_seqfeat_cit(TEntryList &seq_entries)

void PackEntries(TEntryList &seq_entries)

void fta_set_strandedness(TEntryList &seq_entries)

void CheckHTGDivision(const char *div, CMolInfo::TTech tech)

bool fta_orgref_has_taxid(const COrg_ref::TDb &dbtags)

bool XMLCheckCDS(const char *entry, const TXmlIndexList &xil)

char * GetDescrComment(char *offset, size_t len, Uint2 col_data, bool is_htg, bool is_pat)

char * GetEmblBlock(TDataBlkList &chain, char *ptr, short *retkw, Parser::EFormat format, char *eptr)

void EntryCheckDivCode(TEntryList &seq_entries, ParserPtr pp)

void GetEmblSubBlock(size_t bases, Parser::ESource source, const DataBlk &entry)

void XMLDefVsHTGKeywords(CMolInfo::TTech tech, const char *entry, const TXmlIndexList &xil, bool cancelled)

bool GetSeqData(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)

bool fta_EntryCheckGBBlock(TEntryList &seq_entries)

void fta_sort_descr(TEntryList &seq_entries)

void GetExtraAccession(IndexblkPtr ibp, bool allow_uwsec, Parser::ESource source, TAccessionList &accessions)

bool check_div(bool pat_acc, bool pat_ref, bool est_kwd, bool sts_kwd, bool gss_kwd, bool if_cds, string &div, CMolInfo::TTech *tech, size_t bases, Parser::ESource source, bool &drop)

CRef< CBioseq > CreateEntryBioseq(ParserPtr pp)

list< string > TStringList

void ProcessCitations(TEntryList &seq_entries)

CDate::ECompare Compare(const CDate_std &date) const

Indicate how *this relates to another date.

void GetDate(string *label, const string &format) const

Append a custom string representation of the date to the label.

@ eCompare_after

*this comes second.

void PostTotals() override

CRef< objects::CSeq_entry > xGetEntry() override

@Imp_feat.hpp User-defined methods of the data storage class.

const list< string > KeywordList() const

namespace ncbi::objects::

static bool IsNa(EMol mol)

EntryBlk * GetEntryData() const

struct DataBlk::@1166 mBuf

void fta_build_ena_user_object(list< CRef< CSeqdesc >> &descrs, TStringList &dr_ena, TStringList &dr_biosample, CRef< CUser_object > &dbuop)

static bool CheckEmblContigEverywhere(const IndexblkPtr ibp, Parser::ESource source)

static const char * ParFlat_DRname_array[]

static CRef< CSeq_entry > OutputEmblAsn(bool seq_long, ParserPtr pp, TEntryList &seq_entries)

static const char * ParFlat_Embl_DIV_array[]

static void GetEmblDescr(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq)

const char * GetEmblDiv(Uint1 num)

static CRef< CUser_field > fta_create_user_field(const char *tag, TStringList &lst)

static void fta_create_imgt_misc_feat(CBioseq &bioseq, CEMBL_block &embl_block, IndexblkPtr ibp)

static bool s_DuplicatesBiosource(const CBioSource &biosource, const string &gbdiv)

static CTextseq_id & SetTextIdRef(CSeq_id &id)

static void EmblGetDivisionNewID(IndexblkPtr ibp, const DataBlk &entry)

static const char * ParFlat_DBname_array[]

static bool s_GetEmblInst(ParserPtr pp, const DataBlk &entry, unsigned char *const dnaconv)

bool GetEmblInstContig(const DataBlk &entry, CBioseq &bioseq, ParserPtr pp)

static void EmblGetDivision(IndexblkPtr ibp, const DataBlk &entry)

static CRef< CMolInfo > GetEmblMolInfo(ParserPtr pp, const DataBlk &entry, const COrg_ref *org_ref)

static void GetEmblBlockXref(const DataBlk &entry, const TXmlIndexList *xil, const char *chentry, TStringList &dr_ena, TStringList &dr_biosample, bool *drop, CEMBL_block &embl)

static CRef< CGB_block > GetEmblGBBlock(ParserPtr pp, const DataBlk &entry, const string &gbdiv, CBioSource *bio_src)

static const char * ParFlat_Embl_dataclass_array[]

static bool s_HasTPAPrefix(string_view line)

static CRef< CEMBL_block > GetDescrEmblBlock(ParserPtr pp, const DataBlk &entry, CMolInfo &mol_info, string &gbdiv, const CBioSource *bio_src, TStringList &dr_ena, TStringList &dr_biosample)

static void FakeEmblBioSources(const DataBlk &entry, CBioseq &bioseq)

static CRef< COrg_ref > GetEmblOrgRef(const DataBlk &dbp)

static void SetXrefObjId(CEMBL_xref &xref, const string &str)

static const char * ParFlat_GBDIV_array[]

static void GetReleaseInfo(const DataBlk &entry)

CRef< CEMBL_block > XMLGetEMBLBlock(ParserPtr pp, const char *entry, CMolInfo &mol_info, string &gbdiv, CBioSource *bio_src, TStringList &dr_ena, TStringList &dr_biosample)

static void GetEmblDate(Parser::ESource source, const DataBlk &entry, CRef< CDate_std > &crdate, CRef< CDate_std > &update)

#define ParFlat_COL_DATA_EMBL

DataBlk * LoadEntry(ParserPtr pp, size_t offset, size_t len)

void FinalCleanup(TEntryList &seq_entries)

#define ERR_DRXREF_DuplicatedSRA

#define ERR_SEQUENCE_BadData

#define ERR_TPA_TpaSpansMissing

#define ERR_ENTRY_LongSequence

#define ERR_FORMAT_MissingContigFeature

#define ERR_KEYWORD_ShouldNotBeTPA

#define ERR_DIVISION_BadTSADivcode

#define ERR_FORMAT_MissingSequenceData

#define ERR_DIVISION_InvalidHTCKeyword

#define ERR_DRXREF_InvalidSRA

#define ERR_KEYWORD_IllegalForCON

#define ERR_DIVISION_MissingHTGKeywords

#define ERR_QSCORE_FailedToParse

#define ERR_ENTRY_LongHTGSSequence

#define ERR_KEYWORD_MissingTSA

#define ERR_DIVISION_BadTPADivcode

#define ERR_DRXREF_InvalidBioSample

#define ERR_LOCUS_WrongTopology

#define ERR_TPA_TpaCommentMissing

#define ERR_REFERENCE_No_references

#define ERR_KEYWORD_ShouldNotBeTLS

#define ERR_ENTRY_GBBlock_not_Empty

#define ERR_KEYWORD_HTGPlusENV

#define ERR_DEFINITION_MissingTPA

#define ERR_ENTRY_Skipped

#define ERR_DEFINITION_MissingTLS

#define ERR_KEYWORD_ESTSubstring

#define ERR_KEYWORD_ConflictingKeywords

#define ERR_DIVISION_ConDivLacksContig

#define ERR_LOCATION_ContigHasNull

#define ERR_KEYWORD_ENV_NoMatchingQualifier

#define ERR_KEYWORD_ShouldNotBeTSA

#define ERR_KEYWORD_STSSubstring

#define ERR_DIVISION_UnknownDivCode

#define ERR_KEYWORD_MissingTLS

#define ERR_DEFINITION_ShouldNotBeTSA

#define ERR_DIVISION_MissingHTCKeyword

#define ERR_DIVISION_MappedtoCON

#define ERR_FORMAT_ContigWithSequenceData

#define ERR_DRXREF_UnknownDBname

#define ERR_DRXREF_DuplicatedBioSamples

#define ERR_KEYWORD_NoGeneExpressionKeywords

#define ERR_DEFINITION_MissingTSA

#define ERR_KEYWORD_GSSSubstring

#define ERR_DEFINITION_ShouldNotBeTPA

#define ERR_FORMAT_MissingEnd

#define ERR_KEYWORD_MissingTPA

#define ERR_ENTRY_ParsingComplete

#define ERR_ORGANISM_NoOrganism

#define ERR_DATE_IllegalDate

#define ERR_DIVISION_HTCWrongMolType

#define ERR_KEYWORD_ShouldNotBeCAGE

#define ERR_DEFINITION_ShouldNotBeTLS

#define ERR_TSA_UnexpectedPrimaryAccession

list< CRef< objects::CSeq_entry > > TEntryList

bool QscoreToSeqAnnot(const string &qscore, CBioseq &bioseq, char *acc, Int2 ver, bool check_minmax, bool allow_na)

unique_ptr< string > XMLFindTagValue(const char *entry, const TXmlIndexList &xil, Int4 tag)

unique_ptr< string > XMLConcatSubTags(const char *entry, const TXmlIndexList &xil, Int4 tag, Char sep)

#define INSDSEQ_DATABASE_REFERENCE

#define INSDSEQ_CREATE_DATE

void XMLGetKeywords(const char *entry, const TXmlIndexList &xil, TKeywordList &keywords)

#define INSDSEQ_UPDATE_DATE

std::list< std::string > TKeywordList

forward_list< XmlIndex > TXmlIndexList

std::vector< CRef< objects::CUser_object > > TUserObjVector

bool fta_StartsWith(const char *s1, string_view s2)

bool StringEquN(const char *s1, const char *s2, size_t n)

bool StringEqu(const char *s1, const char *s2)

void StringCpy(char *d, const char *s)

void StringNCpy(char *d, const char *s, size_t n)

size_t StringLen(const char *s)

void FtaDeletePrefix(int prefix)

#define FtaErrPost(sev, level,...)

void fta_find_pub_explore(ParserPtr pp, TEntryList &seq_entries)

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

void DealWithGenes(CRef< CSeq_entry > &pEntry, ParserPtr pp)

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

void ResetDataAndHistory(void)

Clear all information in the scope except added data loaders.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

char Char

Alias for char.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert string to int.

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 void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

@ fAllowTrailingSymbols

Ignore trailing non-numerics characters.

@ eNocase

Case insensitive compare.

list< CRef< CObject_id > > TId

const TXref & GetXref(void) const

Get the Xref member data.

TXref & SetXref(void)

Assign a value to Xref data member.

TId & SetId(void)

Assign a value to Id data member.

bool IsSetXref(void) const

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

list< CRef< CEMBL_xref > > TXref

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

TGenome GetGenome(void) const

Get the Genome member data.

TOrigin GetOrigin(void) const

Get the Origin member data.

bool IsSetOrg(void) const

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

bool IsSetSubtype(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsSetOrigin(void) const

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

void SetOrg(TOrg &value)

Assign a value to Org data member.

@ eSubtype_environmental_sample

@ eOrigin_synthetic

purely synthetic

bool IsStr(void) const

Check if variant Str is selected.

void SetYear(TYear value)

Assign a value to Year data member.

void SetMonth(TMonth value)

Assign a value to Month data member.

TStd & SetStd(void)

Select the variant.

void SetDay(TDay value)

Assign a value to Day data member.

TData & SetData(void)

Assign a value to Data data member.

void SetNum(TNum value)

Assign a value to Num data member.

const TStr & GetStr(void) const

Get the variant data.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

TYear GetYear(void) const

Get the Year member data.

TMonth GetMonth(void) const

Get the Month member data.

TDay GetDay(void) const

Get the Day member data.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

const TDiv & GetDiv(void) const

Get the Div member data.

void SetCommon(const TCommon &value)

Assign a value to Common data member.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetDiv(void) const

GenBank division code Check if a value has been assigned to Div data member.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

bool IsSetOrgname(void) const

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

void SetOrgname(TOrgname &value)

Assign a value to Orgname data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSeq_code_type_iupacna

IUPAC 1 letter nuc acid code.

vector< CRef< CDbtag > > TDbxref

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetKey(const TKey &value)

Assign a value to Key data member.

bool IsMix(void) const

Check if variant Mix is selected.

const TMix & GetMix(void) const

Get the variant data.

@ 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_Named_annot_track

Internal named annotation tracking ID.

@ e_Tpg

Third Party Annot/Seq Genbank.

virtual void Reset(void)

Reset the whole object.

TRepr GetRepr(void) const

Get the Repr member data.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

TTitle & SetTitle(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

TTopology GetTopology(void) const

Get the Topology member data.

bool IsSetAnnot(void) const

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

TGenbank & SetGenbank(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

TTech GetTech(void) const

Get the Tech member data.

TComment & SetComment(void)

Select the variant.

void SetInst(TInst &value)

Assign a value to Inst data member.

void ResetTech(void)

Reset Tech data member.

TSource & SetSource(void)

Select the variant.

void SetTopology(TTopology value)

Assign a value to Topology data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

bool IsSetTech(void) const

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

TUser & SetUser(void)

Select the variant.

TEmbl & SetEmbl(void)

Select the variant.

void SetRepr(TRepr value)

Assign a value to Repr data member.

EStrand

strandedness in living organism

list< CRef< CSeq_annot > > TAnnot

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetTech(TTech value)

Assign a value to Tech data member.

TMolinfo & SetMolinfo(void)

Select the variant.

TCreate_date & SetCreate_date(void)

Select the variant.

TUpdate_date & SetUpdate_date(void)

Select the variant.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_htc

high throughput cDNA

@ eTech_targeted

targeted locus sets/studies

@ eTech_sts

Sequence Tagged Site.

@ eTech_htgs_3

finished High Throughput sequence

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_survey

one-pass genomic sequence

@ eTech_htgs_0

single genomic reads for coordination

@ eTech_fli_cdna

full length insert cDNA

@ eTech_est

Expressed Sequence Tag.

int fta_if_wgs_acc(string_view accession)

int CheckSTRAND(const string &str)

CRef< CDate_std > GetUpdateDate(string_view str, Parser::ESource source)

void GetFlatBiomol(CMolInfo::TBiomol &biomol, CMolInfo::TTech tech, char *molstr, ParserPtr pp, const DataBlk &entry, const COrg_ref *org_ref)

void LoadFeat(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq)

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

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

const CharType(& source)[N]

std::list< SeqLoc > TSeqLocList

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

CRef< CPubdesc > DescrRefs(ParserPtr pp, DataBlk &dbp, Uint2 col_data)

CRef< objects::CSeq_entry > seq_entry

CRef< objects::CPatent_seq_id > psip

char *(* ff_get_qscore_pp)(const char *accession, Int2 v, Parser *pp)

vector< IndexblkPtr > entrylist

bool allow_crossdb_featloc

CKeywordParser & KeywordParser()

char *(* ff_get_qscore)(const char *accession, Int2 v)

bool GetGenomeInfo(CBioSource &bsp, string_view bptr)

void MaybeCutGbblockSource(TEntryList &seq_entries)

bool HasHtg(const TKeywordList &keywords)

char * SrchTheChar(string_view sv, Char letter)

bool HasHtc(const TKeywordList &keywords)

bool fta_tls_keywords_check(const TKeywordList &kwds, Parser::ESource source)

void PointToNextToken(char *&ptr)

void RemoveHtgPhase(TKeywordList &keywords)

string GetBlkDataReplaceNewLine(string_view instr, Uint2 indent)

void fta_remove_tsa_keywords(TKeywordList &kwds, Parser::ESource source)

void fta_remove_tpa_keywords(TKeywordList &kwds)

bool SrchNodeType(const DataBlk &entry, Int4 type, size_t *plen, char **pptr)

TDataBlkList & TrackNodes(const DataBlk &entry)

void fta_remove_keywords(CMolInfo::TTech tech, TKeywordList &kwds)

void fta_remove_tls_keywords(TKeywordList &kwds, Parser::ESource source)

char * SrchTheStr(string_view sv, string_view leadstr)

Int2 fta_StringMatch(const Char **array, string_view text)

DataBlk * TrackNodeType(const DataBlk &entry, Int2 type)

void fta_keywords_check(string_view str, bool *estk, bool *stsk, bool *gssk, bool *htck, bool *flik, bool *wgsk, bool *tpak, bool *envk, bool *mgak, bool *tsak, bool *tlsk)

bool IsCancelled(const TKeywordList &keywords)

bool fta_tsa_keywords_check(const TKeywordList &kwds, Parser::ESource source)

void fta_remove_env_keywords(TKeywordList &kwds)

bool fta_tpa_keywords_check(const TKeywordList &kwds)

void CleanTailNonAlphaChar(string &str)

CRef< CSeq_loc > xgbparseint_ver(string_view raw_intervals, bool &keep_rawPt, int &numErrors, const TSeqIdList &seq_ids, bool accver)

void XGappedSeqLocsToDeltaSeqs(const TSeqLocList &locs, TDeltaList &deltas)

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