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

}

(condiv && ibp->

==

&& ibp->

==

) {

allow_crossdb_featloc;

(q = p,

= p; *q !=

; q++)

(*q !=

&& *q !=

&& *q !=

)

(q = p; *q !=

; q++)

((q[0] ==

&& q[1] ==

) || (q[0] ==

&& q[1] ==

) ||

(q[0] ==

&& q[1] ==

))

(loc->

()) {

unique_ptr<string> topstr;

unique_ptr<string> strandstr;

(

& xip : ibp->

) {

pat_ref =

;

est_kwd =

;

sts_kwd =

;

gss_kwd =

;

htc_kwd =

;

fli_kwd =

;

wgs_kwd =

;

tpa_kwd =

;

tsa_kwd =

;

tls_kwd =

;

env_kwd =

;

mga_kwd =

;

(p && p >

&& p[1] ==

&& *(p - 1) ==

)

gbb->SetSource(

);

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

);

(

&

: gbb->GetKeywords()) {

(

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

div_str(bptr, bptr + 3);

gbb->SetDiv(div_str);

gbb->SetDiv(

);

* p_div = gbb->GetDiv().c_str();

(!

(gbb->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) {

p_div = gbb->GetDiv();

(ibp->

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

, pp->

, drop);

}

(gbb->GetDiv() ==

) {

gbb->GetDiv() !=

) {

is_htc_div = gbb->GetDiv() ==

,

has_htc =

(gbb->GetKeywords());

(is_htc_div && ! has_htc) {

(! is_htc_div && has_htc) {

(*

==

|| *

==

)

(! gbb->GetDiv().empty()) {

(gbb->GetDiv() ==

) {

}

(gbb->GetDiv() ==

) {

}

(gbb->GetDiv() ==

) {

}

(gbb->GetDiv() ==

) {

}

(gbb->GetDiv() ==

&& bio_src && bio_src->

() &&

(

& subtype : bio_src->

()) {

(gbb->IsSetDiv() &&

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

mol_info->ResetBiomol();

unique_ptr<string> organism;

unique_ptr<string> taxonomy;

(

& xip : xil) {

p = organism->c_str();

(*p !=

&& *p !=

)

(q--; *q ==

|| *q ==

; q--)

(*q !=

&& *q !=

)

bioseq.

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

(p =

; *p ==

|| *p ==

;)

(p++; *p ==

;)

(p += 2, q = p; *q ==

;)

(p =

; *p ==

;)

(p =

; *p !=

;)

(*p ==

|| *p ==

|| *p ==

|| *p ==

||

*p ==

|| *p ==

) {

(

& descr : bioseq.

().Set()) {

(descr->IsSource()) {

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

org_ref = &bio_src->

();

(p =

; *p ==

;)

(! p || p[1] !=

) {

bioseq.

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

title.starts_with(

sv)) {

(! ibp->

&& title.starts_with(

sv)) {

(! ibp->

&& title.starts_with(

sv)) {

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

sv))) {

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

))) {

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

sv))) {

(

& dbp : dbl) {

descr->

(*pubdesc);

bioseq.

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

(

& dbp : dbl) {

descr->

(*pubdesc);

bioseq.

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

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

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

bioseq.

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

(embl.

()) {

}

(gbb.

()) {

(embl->GetExtra_acc().empty())

embl->ResetExtra_acc();

(! gbdiv.empty()) {

bioseq.

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

,

(ibp->

==

) ?

:

);

(pp->

== 1 && 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 ==

;)

bioseq.

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

bioseq.

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

bioseq.

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

(! ibp || ! entry)

(

(ibp->division,

)) {

(ibp->tsa_allowed ==

)

ibp->is_tsa =

;

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

unique_ptr<DataBlk> dbp(

());

dbp->SetEntryData(ebp);

dbp->mBuf.ptr = entry;

(! ibp->gaps.empty())

(ibp->htg == 4 || ibp->htg == 1 || ibp->htg == 2 ||

}

(! ibp->gaps.empty())

(!

(dbp->mpQscore, *bioseq, ibp->acnum, ibp->vernum,

,

)) {

dbp->mpQscore.clear();

}

(ibp->is_wgs) {

gene_refs.

=

;

(ebp->seq_entry.Empty()) {

seq_entries.push_back(ebp->seq_entry);

ebp->seq_entry.Reset();

seq_long{

};

(ibp->htg == 1 || ibp->htg == 2 || ibp->htg == 4) {

= seq_entries.front();

,

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)

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)

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 err_install(const Indexblk *ibp, bool accver)

bool no_date(Parser::EFormat format, const TSeqdescList &descrs)

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

void StripSerialNumbers(TEntryList &seq_entries)

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

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

void EntryCheckDivCode(TEntryList &seq_entries, ParserPtr pp)

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)

unsigned char *const GetProtConvTable()

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 SetToTime(const CTime &time, CDate::EPrecision prec=CDate::ePrecision_second)

@ eCompare_after

*this comes second.

static bool IsNa(EMol mol)

CRef< objects::CSeq_entry > xGetEntry() override

void PostTotals() override

struct DataBlk::@1166 mBuf

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

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

void FinalCleanup(TEntryList &seq_entries)

#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_KEYWORD_IllegalForCON

#define ERR_DIVISION_MissingHTGKeywords

#define ERR_QSCORE_FailedToParse

#define ERR_ENTRY_LongHTGSSequence

#define ERR_KEYWORD_MissingTSA

#define ERR_DIVISION_BadTPADivcode

#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_DIVISION_MappedtoEST

#define ERR_FORMAT_ContigWithSequenceData

#define ERR_KEYWORD_NoGeneExpressionKeywords

#define ERR_DEFINITION_MissingTSA

#define ERR_DEFINITION_ShouldNotBeTPA

#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)

#define INSDSEQ_DEFINITION

#define INSDSEQ_STRANDEDNESS

TDataBlkList XMLBuildRefDataBlk(char *entry, const TXmlIndexList &xil, int type)

unique_ptr< string > XMLGetTagValue(const char *entry, const XmlIndex &xip)

char * XMLLoadEntry(ParserPtr pp, bool err)

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

#define INSDSEQ_CREATE_DATE

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

#define INSDSEQ_UPDATE_DATE

DataBlk::TList TDataBlkList

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)

size_t StringLen(const char *s)

void MemCpy(void *p, const void *q, size_t sz)

char * StringRChr(char *s, const char c)

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.

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.

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.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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

Case-insensitive equality of a substring with another string.

@ eNocase

Case insensitive compare.

@ eCurrent

Use current time. See also CCurrentTime.

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

TStd & SetStd(void)

Select the variant.

const TDiv & GetDiv(void) const

Get the Div member data.

void SetCommon(const TCommon &value)

Assign a value to Common data member.

const TTaxname & GetTaxname(void) const

Get the Taxname 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_iupacaa

IUPAC 1 letter amino acid code.

@ eSeq_code_type_iupacna

IUPAC 1 letter nuc acid code.

bool IsMix(void) const

Check if variant Mix is selected.

const TMix & GetMix(void) const

Get the variant data.

TRepr GetRepr(void) const

Get the Repr member data.

const TInst & GetInst(void) const

Get the Inst member data.

TTitle & SetTitle(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

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 TId & GetId(void) const

Get the Id member data.

TTech GetTech(void) const

Get the Tech member data.

const Tdata & Get(void) const

Get the 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.

ETopology

topology of molecule

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

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetTech(TTech value)

Assign a value to Tech data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

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.

Int4 IsNewAccessFormat(const Char *acnum)

Int2 XMLCheckTPG(string_view str)

Int2 CheckDIV(const char *str)

Int2 XMLCheckSTRAND(string_view 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)

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)

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

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

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)

bool HasHtc(const TKeywordList &keywords)

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

void RemoveHtgPhase(TKeywordList &keywords)

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

void fta_remove_tpa_keywords(TKeywordList &kwds)

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

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

void fta_StringCpy(char *dst, const char *src)

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)

bool fta_check_mga_keywords(CMolInfo &mol_info, const TKeywordList &kwds)

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

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

bool XMLGetInst(ParserPtr pp, const DataBlk &dbp, unsigned char *dnaconv, CBioseq &bioseq)

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

static CRef< CGB_block > XMLGetGBBlock(ParserPtr pp, const char *entry, CMolInfo &mol_info, CBioSource *bio_src)

static void XMLCheckContigEverywhere(IndexblkPtr ibp, Parser::ESource source)

static void XMLFakeBioSources(const TXmlIndexList &xil, const char *entry, CBioseq &bioseq, Parser::ESource source)

static void XMLGetDivision(const char *entry, IndexblkPtr ibp)

static bool XMLGetInstContig(const TXmlIndexList &xil, const DataBlk &dbp, CBioseq &bioseq, ParserPtr pp)

static void XMLGetDescrComment(char *offset)

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

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