NCBI C++ ToolKit
Macros | Functions | Variables
asci_blk.cpp File Reference
#include <ncbi_pch.hpp>
#include <set>
#include "ftacpp.hpp"
#include <objects/biblio/Id_pat.hpp>
#include <objects/biblio/Id_pat_.hpp>
#include <objects/seqloc/Textseq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seq/Seg_ext.hpp>
#include <objects/general/Int_fuzz.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/general/Date.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Numbering.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/biblio/Cit_gen.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/pub/Pub_set.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seq/seqport_util.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <serial/iterator.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqblock/EMBL_block.hpp>
#include <objects/seq/MolInfo.hpp>
#include "index.h"
#include "genbank.h"
#include "embl.h"
#include "sprot.h"
#include <objtools/flatfile/flatdefn.h>
#include "ftaerr.hpp"
#include "indx_blk.h"
#include "asci_blk.h"
#include "utilfun.h"
#include "fta_xml.h"
#include "add.h"
+ Include dependency graph for asci_blk.cpp:

Go to the source code of this file.

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Macros

#define THIS_FILE   "asci_blk.cpp"
 
#define Seq_descr_pub_same   50
 

Functions

 USING_SCOPE (objects)
 
void ShrinkSpaces (char *line)
 
void ShrinkSpaces (string &line)
 
static void InsertDatablkVal (DataBlkPtr *dbp, Int2 type, char *offset, size_t len)
 
void xGetGenBankBlocks (Entry &entry)
 
char * GetGenBankBlock (DataBlkPtr *chain, char *ptr, Int2 *retkw, char *eptr)
 
static void GetGenBankRefType (DataBlkPtr dbp, size_t bases)
 
static void BuildFeatureBlock (DataBlkPtr dbp)
 
static void fta_check_mult_ids (DataBlkPtr dbp, const char *mtag, const char *ptag)
 
void GetGenBankSubBlock (const DataBlk &entry, size_t bases)
 
void xGetGenBankSubBlocks (Entry &entry, size_t bases)
 
char * GetEmblBlock (DataBlkPtr *chain, char *ptr, short *retkw, Parser::EFormat format, char *eptr)
 
static bool TrimEmblFeatBlk (DataBlkPtr dbp)
 
static bool GetSubNodeType (const char *subkw, char **retbptr, char *eptr)
 
static void GetEmblRefType (size_t bases, Parser::ESource source, DataBlkPtr dbp)
 
void GetEmblSubBlock (size_t bases, Parser::ESource source, const DataBlk &entry)
 
void BuildSubBlock (DataBlkPtr dbp, Int2 subtype, const char *subkw)
 
void GetLenSubNode (DataBlkPtr dbp)
 
CRef< CPatent_seq_id > MakeUsptoPatSeqId (const char *acc)
 
static Uint1 ValidSeqType (const char *accession, Uint1 type)
 
CRef< CSeq_id > MakeAccSeqId (const char *acc, Uint1 seqtype, bool accver, Int2 vernum)
 
CRef< CSeq_id > MakeLocusSeqId (const char *locus, CSeq_id::E_Choice seqtype)
 
static CRef< CSeq_id > MakeSegSetSeqId (const char *accession, const string &locus, Uint1 seqtype, bool is_tpa)
 
char * SrchNodeSubType (const DataBlk &entry, Int2 type, Int2 subtype, size_t *len)
 
static void SetEmptyId (CBioseq &bioseq)
 
CRef< CBioseq > CreateEntryBioseq (ParserPtr pp)
 
char * GetDescrComment (char *offset, size_t len, Uint2 col_data, bool is_htg, bool is_pat)
 
static void fta_fix_secondaries (TokenBlkList &secs)
 
void GetExtraAccession (IndexblkPtr ibp, bool allow_uwsec, Parser::ESource source, TAccessionList &accessions)
 
static void fta_fix_tpa_keywords (TKeywordList &keywords)
 
void xFixEMBLKeywords (string &keywordData)
 
void GetSequenceOfKeywords (const DataBlk &entry, int type, Uint2 col_data, TKeywordList &keywords)
 
Int4 ScanSequence (bool warn, char **seqptr, std::vector< char > &bsp, unsigned char *conv, Char replacechar, int *numns)
 
bool GetSeqData (ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)
 
unique_ptr< unsigned char[]> GetDNAConv (void)
 
unique_ptr< unsigned char[]> GetProteinConv (void)
 
static CSeq_descr::Tdata::const_iterator GetDescrByChoice (const CSeq_descr &descr, Uint1 choice)
 
static void GetFirstSegDescrChoice (CBioseq &bioseq, Uint1 choice, CSeq_descr &descr_new)
 
static bool SameCitation_PubEquivMatch_Logic (const CPub_equiv &a, const CPub_equiv &b)
 
static bool CheckSegPub (const CPubdesc &pub, TEntryList &entries, std::set< CSeqdesc * > &same_pub_descr)
 
static void RemoveDescrByChoice (CSeq_descr &descr, Uint1 choice)
 
static void CleanUpSeqDescrChoice (TEntryList &entries, Uint1 choice)
 
static void CleanUpSeqDescrPub (TEntryList &entries, std::set< CSeqdesc * > &to_clean)
 
static void GetSegPub (TEntryList &entries, CSeq_descr &descr)
 
static bool CheckSegDescrChoice (const TEntryList &entries, Uint1 choice)
 
static optional< string > GetBioseqSetDescrTitle (const CSeq_descr &descr)
 
static void SrchSegDescr (TEntryList &entries, CSeq_descr &descr)
 
static void GetSegSetDblink (CSeq_descr &descr, TEntryList &entries, bool *drop)
 
static void GetBioseqSetDescr (TEntryList &entries, CSeq_descr &descr, bool *drop)
 
static const char * GetMoleculeClassString (Uint1 mol)
 
static CSeq_inst::EMol SrchSegSeqMol (const TEntryList &entries)
 
static Int4 SrchSegLength (const TEntryList &entries)
 
static CRef< CBioseq > GetBioseq (ParserPtr pp, const TEntryList &entries, const CSeq_loc &slp)
 
void GetSeqExt (ParserPtr pp, CSeq_loc &seq_loc)
 
void BuildBioSegHeader (ParserPtr pp, TEntryList &entries, const CSeq_loc &seqloc)
 
bool IsSegBioseq (const CSeq_id &id)
 
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< CSeq_id > StrToSeqId (const char *pch, bool pid)
 
void AddNIDSeqId (CBioseq &bioseq, const DataBlk &entry, Int2 type, Int2 coldata, Parser::ESource source)
 
static void CheckDivCode (TEntryList &seq_entries, ParserPtr pp)
 
static const CBioSource * GetTopBiosource (const CSeq_entry &entry)
 
static bool SeqEntryCheckTaxonDiv (const CSeq_entry &entry)
 
void EntryCheckDivCode (TEntryList &seq_entries, ParserPtr pp)
 
void DefVsHTGKeywords (CMolInfo::TTech tech, const DataBlk &entry, Int2 what, Int2 ori, bool cancelled)
 
void XMLDefVsHTGKeywords (CMolInfo::TTech tech, const char *entry, XmlIndexPtr xip, bool cancelled)
 
void CheckHTGDivision (const char *div, CMolInfo::TTech tech)
 
const CSeq_descr & GetDescrPointer (const CSeq_entry &entry)
 
static void CleanVisString (string &str)
 
static void CleanVisStringList (list< string > &str_list)
 
static void CheckGBBlock (TSeqdescList &descrs, bool &got)
 
bool fta_EntryCheckGBBlock (TEntryList &seq_entries)
 
static int GetSerialNumFromPubEquiv (const CPub_equiv &pub_eq)
 
static bool fta_if_pubs_sorted (const CPub_equiv &pub1, const CPub_equiv &pub2)
 
static bool descr_cmp (const CRef< CSeqdesc > &desc1, const CRef< CSeqdesc > &desc2)
 
void fta_sort_descr (TEntryList &seq_entries)
 
static bool pub_cmp (const CRef< CPub > &pub1, const CRef< CPub > &pub2)
 
static void sort_feat_cit (CBioseq::TAnnot &annots)
 
void fta_sort_seqfeat_cit (TEntryList &seq_entries)
 
bool fta_orgref_has_taxid (const COrg_ref::TDb &dbtags)
 
void fta_fix_orgref_div (const CBioseq::TAnnot &annots, COrg_ref *org_ref, CGB_block &gbb)
 
bool XMLCheckCDS (const char *entry, XmlIndexPtr xip)
 
void fta_set_strandedness (TEntryList &seq_entries)
 
static bool SwissProtIDPresent (const TEntryList &seq_entries)
 
static bool IsCitEmpty (const CCit_gen &cit)
 
static void RemoveSerials (TPubList &pubs)
 
void StripSerialNumbers (TEntryList &seq_entries)
 
static void PackSeqData (CSeq_data::E_Choice code, CSeq_data &seq_data)
 
static void RawBioseqPack (CBioseq &bioseq)
 
static void DeltaBioseqPack (CBioseq &bioseq)
 
void PackEntries (TEntryList &seq_entries)
 

Variables

const char * magic_phrases []
 
vector< string > genbankKeywords
 
vector< string > emblKeywords
 
vector< string > swissProtKeywords
 

Macro Definition Documentation

◆ Seq_descr_pub_same

#define Seq_descr_pub_same   50

Definition at line 99 of file asci_blk.cpp.

◆ THIS_FILE

#define THIS_FILE   "asci_blk.cpp"

Definition at line 97 of file asci_blk.cpp.

Function Documentation

◆ AddNIDSeqId()

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

Definition at line 2726 of file asci_blk.cpp.

References Parser::DDBJ, Parser::EMBL, CRef< C, Locker >::Empty(), DataBlk::mOffset, offset, CBioseq_Base::SetId(), rapidjson::source, StrToSeqId(), and TrackNodeType().

Referenced by EmblAscii(), and GenBankAsciiOrig().

◆ BuildBioSegHeader()

void BuildBioSegHeader ( ParserPtr  pp,
TEntryList &  entries,
const CSeq_loc &  seqloc 
)

Definition at line 2498 of file asci_blk.cpp.

References Parser::curindx, Indexblk::drop, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, entries, Parser::entrylist, GetBioseq(), GetBioseqSetDescr(), CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by EmblAscii(), GenBankAsciiOrig(), and XMLAscii().

◆ BuildFeatureBlock()

static void BuildFeatureBlock ( DataBlkPtr  dbp)
static

Definition at line 377 of file asci_blk.cpp.

References InsertDatablkVal(), DataBlk::len, DataBlk::mOffset, DataBlk::mpData, ParFlat_COL_FEATKEY, ParFlat_FEATBLOCK, SrchTheChar(), and StringEquN().

Referenced by GetEmblSubBlock(), and GetGenBankSubBlock().

◆ BuildSubBlock()

void BuildSubBlock ( DataBlkPtr  dbp,
Int2  subtype,
const char *  subkw 
)

Definition at line 812 of file asci_blk.cpp.

References GetSubNodeType(), InsertDatablkVal(), DataBlk::len, DataBlk::mOffset, and DataBlk::mpData.

Referenced by GetEmblSubBlock(), GetGenBankSubBlock(), and GetSprotSubBlock().

◆ check_div()

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 
)

Definition at line 2569 of file asci_blk.cpp.

References Parser::EMBL, ERR_DIVISION_ESTHasCDSFeature, ERR_DIVISION_ESTHasSTSKeywords, ERR_DIVISION_GSSHasCDSFeature, ERR_DIVISION_LongESTSequence, ERR_DIVISION_LongGSSSequence, ERR_DIVISION_LongSTSSequence, ERR_DIVISION_MappedtoEST, ERR_DIVISION_MappedtoGSS, ERR_DIVISION_MappedtoPAT, ERR_DIVISION_MappedtoSTS, ERR_DIVISION_MissingESTKeywords, ERR_DIVISION_MissingGSSKeywords, ERR_DIVISION_MissingPatentRef, ERR_DIVISION_MissingSTSKeywords, ERR_DIVISION_NotMappedtoEST, ERR_DIVISION_NotMappedtoGSS, ERR_DIVISION_NotMappedtoSTS, ERR_DIVISION_PATHasCDSFeature, ERR_DIVISION_PATHasESTKeywords, ERR_DIVISION_PATHasGSSKeywords, ERR_DIVISION_PATHasSTSKeywords, ERR_DIVISION_ShouldBePAT, ERR_DIVISION_STSHasCDSFeature, ErrPostEx, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, SEV_INFO, SEV_REJECT, SEV_WARNING, rapidjson::source, and StringEqu().

Referenced by GetDescrEmblBlock(), GetGBBlock(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ CheckDivCode()

static void CheckDivCode ( TEntryList &  seq_entries,
ParserPtr  pp 
)
static

Definition at line 2745 of file asci_blk.cpp.

References Begin(), NStr::CompareNocase(), Parser::curindx, Indexblk::division, Parser::entrylist, ERR_DIVISION_GBBlockDivision, ErrPostEx, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::GetTech(), CGB_block_Base::IsSetDiv(), CGB_block_Base::SetDiv(), and SEV_WARNING.

Referenced by EntryCheckDivCode().

◆ CheckGBBlock()

static void CheckGBBlock ( TSeqdescList &  descrs,
bool &  got 
)
static

Definition at line 3028 of file asci_blk.cpp.

References buf, CleanVisString(), CleanVisStringList(), NStr::CompareNocase(), CGB_block_Base::GetDiv(), GetEmblDiv(), CGB_block_Base::GetExtra_accessions(), CGB_block_Base::GetKeywords(), CGB_block_Base::IsSetDate(), CGB_block_Base::IsSetDiv(), CGB_block_Base::IsSetEntry_date(), CGB_block_Base::IsSetExtra_accessions(), CGB_block_Base::IsSetKeywords(), CGB_block_Base::IsSetOrigin(), CGB_block_Base::IsSetSource(), CGB_block_Base::ResetDate(), CGB_block_Base::ResetDiv(), CGB_block_Base::ResetExtra_accessions(), CGB_block_Base::ResetKeywords(), CGB_block_Base::ResetOrigin(), CGB_block_Base::ResetSource(), CGB_block_Base::SetDate(), CGB_block_Base::SetDiv(), CGB_block_Base::SetExtra_accessions(), CGB_block_Base::SetKeywords(), CGB_block_Base::SetOrigin(), and CGB_block_Base::SetSource().

Referenced by fta_EntryCheckGBBlock().

◆ CheckHTGDivision()

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

Definition at line 2946 of file asci_blk.cpp.

References ERR_DIVISION_ShouldBeHTG, ERR_DIVISION_ShouldNotBeHTG, ErrPostEx, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, SEV_ERROR, SEV_WARNING, and StringEqu().

Referenced by GetDescrEmblBlock(), GetGBBlock(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ CheckSegDescrChoice()

static bool CheckSegDescrChoice ( const TEntryList &  entries,
Uint1  choice 
)
static

Definition at line 2083 of file asci_blk.cpp.

References CSerialObject::Assign(), CDate::Compare(), CSeqdesc_Base::e_Modif, CDate_Base::e_not_set, CSeqdesc_Base::e_Org, CDate::eCompare_same, entries, CSeq_descr_Base::Get(), GetDescrByChoice(), val, and CDate_Base::Which().

Referenced by SrchSegDescr().

◆ CheckSegPub()

static bool CheckSegPub ( const CPubdesc &  pub,
TEntryList &  entries,
std::set< CSeqdesc * > &  same_pub_descr 
)
static

Definition at line 1938 of file asci_blk.cpp.

References entries, ERR_SEGMENT_PubMatch, ErrPostStr, CPub_equiv_Base::Get(), CPub_Base::GetGen(), CPubdesc_Base::GetPub(), CCit_gen_Base::GetSerial_number(), CPub_Base::IsGen(), CPub_equiv_Base::IsSet(), CPubdesc_Base::IsSetPub(), CCit_gen_Base::IsSetSerial_number(), not_found, SameCitation_PubEquivMatch_Logic(), CSeq_descr_Base::Set(), and SEV_WARNING.

Referenced by GetSegPub().

◆ CleanUpSeqDescrChoice()

static void CleanUpSeqDescrChoice ( TEntryList &  entries,
Uint1  choice 
)
static

Definition at line 2011 of file asci_blk.cpp.

References entries, and RemoveDescrByChoice().

Referenced by SrchSegDescr().

◆ CleanUpSeqDescrPub()

static void CleanUpSeqDescrPub ( TEntryList &  entries,
std::set< CSeqdesc * > &  to_clean 
)
static

Definition at line 2027 of file asci_blk.cpp.

References entries.

Referenced by GetSegPub().

◆ CleanVisString()

static void CleanVisString ( string &  str)
static

Definition at line 2967 of file asci_blk.cpp.

References str().

Referenced by CheckGBBlock(), and CleanVisStringList().

◆ CleanVisStringList()

static void CleanVisStringList ( list< string > &  str_list)
static

Definition at line 3015 of file asci_blk.cpp.

References CleanVisString().

Referenced by CheckGBBlock().

◆ CreateEntryBioseq()

CRef<CBioseq> CreateEntryBioseq ( ParserPtr  pp)

Definition at line 1074 of file asci_blk.cpp.

References Parser::accver, Indexblk::acnum, Parser::curindx, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Tpe, Parser::EMBL, Indexblk::embl_new_ID, Parser::entrylist, Indexblk::is_tpa, NStr::IsBlank(), Indexblk::locusname, MakeUsptoPatSeqId(), Parser::mode, Ref(), Parser::Relaxed, Parser::seqtype, SetEmptyId(), CBioseq_Base::SetId(), SetTextId(), Parser::source, StringEqu(), Parser::USPTO, ValidSeqType(), and Indexblk::vernum.

Referenced by EmblAscii(), GenBankAscii(), GenBankAsciiOrig(), SpPrepareEntry(), and XMLAscii().

◆ DefVsHTGKeywords()

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

Definition at line 2821 of file asci_blk.cpp.

References b, ERR_DEFINITION_HTGNotInProgress, ERR_DEFINITION_HTGShouldBeComplete, ERR_SEQUENCE_UnknownBaseHTG3, ErrPostEx, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, fta_StringCpy(), DataBlk::len, magic_phrases, MemFree(), DataBlk::mOffset, r(), SEV_ERROR, SEV_WARNING, StringEquN(), StringNCpy(), StringSave, StringStr, tmp, and TrackNodeType().

Referenced by GetDescrEmblBlock(), and GetGBBlock().

◆ DeltaBioseqPack()

static void DeltaBioseqPack ( CBioseq &  bioseq)
static

Definition at line 3494 of file asci_blk.cpp.

References delta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CSeq_ext_Base::IsDelta(), CSeq_inst_Base::IsSetExt(), CSeqportUtil::Pack(), and CBioseq_Base::SetInst().

Referenced by PackEntries().

◆ descr_cmp()

static bool descr_cmp ( const CRef< CSeqdesc > &  desc1,
const CRef< CSeqdesc > &  desc2 
)
static

Definition at line 3158 of file asci_blk.cpp.

References fta_if_pubs_sorted(), CPubdesc_Base::GetPub(), CSeqdesc_Base::GetPub(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CSeqdesc_Base::IsPub(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CSeqdesc_Base::IsUser(), util::strcmp(), and CSeqdesc_Base::Which().

Referenced by fta_sort_descr().

◆ EntryCheckDivCode()

void EntryCheckDivCode ( TEntryList &  seq_entries,
ParserPtr  pp 
)

Definition at line 2810 of file asci_blk.cpp.

References CheckDivCode(), and SeqEntryCheckTaxonDiv().

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().

◆ fta_check_mult_ids()

static void fta_check_mult_ids ( DataBlkPtr  dbp,
const char *  mtag,
const char *  ptag 
)
static

Definition at line 410 of file asci_blk.cpp.

References ERR_REFERENCE_MultipleIdentifiers, ErrPostEx, DataBlk::len, DataBlk::mOffset, SEV_ERROR, StringChr, StringEquN(), and StringLen().

Referenced by GetEmblSubBlock(), and GetGenBankSubBlock().

◆ fta_EntryCheckGBBlock()

bool fta_EntryCheckGBBlock ( TEntryList &  seq_entries)

Definition at line 3113 of file asci_blk.cpp.

References Begin(), and CheckGBBlock().

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().

◆ fta_fix_orgref_div()

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

Definition at line 3270 of file asci_blk.cpp.

References fta_orgref_has_taxid(), COrg_ref_Base::GetDb(), CGB_block_Base::GetDiv(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CGB_block_Base::IsSetDiv(), COrgName_Base::IsSetDiv(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CGB_block_Base::ResetDiv(), and COrg_ref_Base::SetOrgname().

Referenced by GetEmblDescr(), GetGenBankDescr(), and XMLGetDescr().

◆ fta_fix_secondaries()

static void fta_fix_secondaries ( TokenBlkList &  secs)
static

Definition at line 1272 of file asci_blk.cpp.

References fta_if_wgs_acc(), and next().

Referenced by GetExtraAccession().

◆ fta_fix_tpa_keywords()

static void fta_fix_tpa_keywords ( TKeywordList &  keywords)
static

Definition at line 1482 of file asci_blk.cpp.

References buf, NStr::CompareNocase(), fta_is_tpa_keyword(), ncbi::grid::netcache::search::fields::key, StringEquNI(), and swap().

Referenced by GetSequenceOfKeywords().

◆ fta_if_pubs_sorted()

static bool fta_if_pubs_sorted ( const CPub_equiv &  pub1,
const CPub_equiv &  pub2 
)
static

Definition at line 3149 of file asci_blk.cpp.

References GetSerialNumFromPubEquiv().

Referenced by descr_cmp().

◆ fta_orgref_has_taxid()

bool fta_orgref_has_taxid ( const COrg_ref::TDb &  dbtags)

Definition at line 3258 of file asci_blk.cpp.

References tag.

Referenced by fta_fix_orgref_div(), and GetEmblDescr().

◆ fta_set_strandedness()

void fta_set_strandedness ( TEntryList &  seq_entries)

Definition at line 3341 of file asci_blk.cpp.

References Begin(), CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, CSeq_inst_Base::eStrand_ds, and CSeq_inst_Base::eStrand_ss.

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().

◆ fta_sort_descr()

void fta_sort_descr ( TEntryList &  seq_entries)

Definition at line 3185 of file asci_blk.cpp.

References Begin(), and descr_cmp().

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().

◆ fta_sort_seqfeat_cit()

void fta_sort_seqfeat_cit ( TEntryList &  seq_entries)

Definition at line 3242 of file asci_blk.cpp.

References Begin(), and sort_feat_cit().

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().

◆ GetBioseq()

static CRef<CBioseq> GetBioseq ( ParserPtr  pp,
const TEntryList &  entries,
const CSeq_loc &  slp 
)
static

Definition at line 2413 of file asci_blk.cpp.

References Indexblk::acnum, CSeq_loc::Assign(), CSeq_loc::begin(), Indexblk::blocusname, Parser::curindx, CInt_fuzz_Base::eLim_gt, CSeq_loc::end(), entries, Parser::entrylist, CSeq_inst_Base::eRepr_seg, GetBioseqSetDescrTitle(), CBioseq_Base::GetDescr(), CSeq_entry_Base::GetSeq(), Indexblk::is_tpa, MakeSegSetSeqId(), Parser::seg_acc, Parser::seqtype, CBioseq_Base::SetDescr(), CSeq_inst_Base::SetExt(), CSeq_inst_Base::SetFuzz(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetMol(), CSeq_loc::SetNull(), CSeq_inst_Base::SetRepr(), CSeqdesc_Base::SetTitle(), SrchSegLength(), and SrchSegSeqMol().

Referenced by BuildBioSegHeader().

◆ GetBioseqSetDescr()

static void GetBioseqSetDescr ( TEntryList &  entries,
CSeq_descr &  descr,
bool *  drop 
)
static

Definition at line 2334 of file asci_blk.cpp.

References entries, GetSegSetDblink(), and SrchSegDescr().

Referenced by BuildBioSegHeader().

◆ GetBioseqSetDescrTitle()

static optional<string> GetBioseqSetDescrTitle ( const CSeq_descr &  descr)
static

Definition at line 2141 of file asci_blk.cpp.

References CleanTailNoneAlphaCharInString(), and CSeq_descr_Base::Get().

Referenced by GetBioseq(), and SrchSegDescr().

◆ GetDescrByChoice()

static CSeq_descr::Tdata::const_iterator GetDescrByChoice ( const CSeq_descr &  descr,
Uint1  choice 
)
static

Definition at line 1839 of file asci_blk.cpp.

References CSeq_descr_Base::Get().

Referenced by CheckSegDescrChoice().

◆ GetDescrComment()

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

Definition at line 1159 of file asci_blk.cpp.

References fta_StringCpy(), len, MemCpy(), MemFree(), offset, r(), ncbi::grid::netcache::search::fields::size, SrchTheChar(), str(), StringChr, StringEquN(), StringNew(), and StringStr.

Referenced by GetEmblDescr(), and GetGenBankDescr().

◆ GetDescrPointer()

const CSeq_descr& GetDescrPointer ( const CSeq_entry &  entry)

Definition at line 2958 of file asci_blk.cpp.

References CBioseq_Base::GetDescr(), CBioseq_set_Base::GetDescr(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), and CSeq_entry_Base::IsSeq().

Referenced by GetGcode(), and GetTopBiosource().

◆ GetDNAConv()

unique_ptr<unsigned char[]> GetDNAConv ( void  )

Definition at line 1790 of file asci_blk.cpp.

References eSeq_code_type_iupacna, CSeqportUtil::GetCode(), CSeqportUtil::GetCodeIndexFromTo(), i, int, MemSet(), compile_time_bits::range(), and tolower().

Referenced by EmblAscii(), GenBankAscii(), GenBankAsciiOrig(), get_bioseq(), and XMLAscii().

◆ GetEmblBlock()

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

Definition at line 545 of file asci_blk.cpp.

References emblKeywords, format, InsertDatablkVal(), len, offset, ParFlat_END, ParFlat_UNKW, Parser::SPROT, SrchKeyword(), StringEquN(), and swissProtKeywords.

Referenced by CheckOutsideEntry(), EmblAscii(), get_bioseq(), and SpPrepareEntry().

◆ GetEmblRefType()

static void GetEmblRefType ( size_t  bases,
Parser::ESource  source,
DataBlkPtr  dbp 
)
static

Definition at line 684 of file asci_blk.cpp.

References Parser::EMBL, GetSubNodeType(), DataBlk::len, DataBlk::mOffset, DataBlk::mType, Parser::NCBI, ParFlat_REF_BTW, ParFlat_REF_END, ParFlat_REF_NO_TARGET, ParFlat_REF_SITES, rapidjson::source, SrchTheStr(), and str().

Referenced by GetEmblSubBlock().

◆ GetEmblSubBlock()

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

Definition at line 740 of file asci_blk.cpp.

References BuildFeatureBlock(), BuildSubBlock(), EntryBlk::chain, ERR_FEATURE_NoFeatData, ErrPostStr, fta_check_mult_ids(), GetEmblRefType(), GetLenSubNode(), DataBlk::mpData, DataBlk::mpNext, DataBlk::mType, ParFlat_FH, ParFlat_OC, ParFlat_OG, ParFlat_OS, ParFlat_RA, ParFlat_RC, ParFlat_RG, ParFlat_RL, ParFlat_RN, ParFlat_RP, ParFlat_RT, ParFlat_RX, SEV_WARNING, rapidjson::source, TrackNodeType(), and TrimEmblFeatBlk().

Referenced by EmblAscii().

◆ GetExtraAccession()

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

Definition at line 1321 of file asci_blk.cpp.

References a, Indexblk::acnum, NStr::CommonSuffixSize(), Parser::DDBJ, DelNonDigitTail(), Indexblk::drop, CSeq_id_Base::e_Embl, Parser::EMBL, ERR_ACCESSION_ScfldHasWGSContigSec, ERR_ACCESSION_UnusualWGS_Secondary, ERR_ACCESSION_WGSMasterAsSecondary, ERR_ACCESSION_WGSWithNonWGS_Sec, ErrPostEx, fta_fix_secondaries(), fta_if_wgs_acc(), GetNucAccOwner(), i, Indexblk::is_contig, MemFree(), Parser::NCBI, Parser::Refseq, Indexblk::secaccs, SEV_REJECT, SEV_WARNING, rapidjson::source, StringEquN(), StringLen(), StringSave, text(), and Indexblk::wgssec.

Referenced by GetDescrEmblBlock(), GetDescrSPBlock(), GetEmblGBBlock(), GetGBBlock(), XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ GetFirstSegDescrChoice()

static void GetFirstSegDescrChoice ( CBioseq &  bioseq,
Uint1  choice,
CSeq_descr &  descr_new 
)
static

Definition at line 1862 of file asci_blk.cpp.

References CSeq_descr_Base::Set(), and CBioseq_Base::SetDescr().

Referenced by SrchSegDescr().

◆ GetGenBankBlock()

char* GetGenBankBlock ( DataBlkPtr *  chain,
char *  ptr,
Int2 *  retkw,
char *  eptr 
)

Definition at line 284 of file asci_blk.cpp.

References genbankKeywords, InsertDatablkVal(), len, offset, ParFlat_UNKW, SrchKeyword(), and StringEquN().

Referenced by GenBankAsciiOrig(), and get_bioseq().

◆ GetGenBankRefType()

static void GetGenBankRefType ( DataBlkPtr  dbp,
size_t  bases 
)
static

Definition at line 337 of file asci_blk.cpp.

References NStr::Find(), DataBlk::len, DataBlk::mOffset, DataBlk::mType, NPOS, ParFlat_REF_BTW, ParFlat_REF_END, ParFlat_REF_NO_TARGET, ParFlat_REF_SITES, and str().

Referenced by GetGenBankSubBlock().

◆ GetGenBankSubBlock()

void GetGenBankSubBlock ( const DataBlk &  entry,
size_t  bases 
)

Definition at line 454 of file asci_blk.cpp.

References BuildFeatureBlock(), BuildSubBlock(), fta_check_mult_ids(), GetGenBankRefType(), GetLenSubNode(), DataBlk::mpNext, DataBlk::mType, ParFlat_AUTHORS, ParFlat_CONSRTM, ParFlat_FEATURES, ParFlat_JOURNAL, ParFlat_MEDLINE, ParFlat_ORGANISM, ParFlat_PUBMED, ParFlat_REFERENCE, ParFlat_REMARK, ParFlat_SOURCE, ParFlat_STANDARD, ParFlat_TITLE, and TrackNodeType().

Referenced by GenBankAsciiOrig().

◆ GetLenSubNode()

void GetLenSubNode ( DataBlkPtr  dbp)

Definition at line 835 of file asci_blk.cpp.

References done, ERR_FORMAT_LineTypeOrder, ErrPostEx, isdigit(), len, DataBlk::len, DataBlk::mOffset, DataBlk::mpData, DataBlk::mpNext, n, offset, and SEV_WARNING.

Referenced by GetEmblSubBlock(), GetGenBankSubBlock(), and GetSprotSubBlock().

◆ GetMoleculeClassString()

static const char* GetMoleculeClassString ( Uint1  mol)
static

Definition at line 2347 of file asci_blk.cpp.

Referenced by SrchSegSeqMol().

◆ GetProteinConv()

unique_ptr<unsigned char[]> GetProteinConv ( void  )

Definition at line 1818 of file asci_blk.cpp.

References eSeq_code_type_iupacaa, CSeqportUtil::GetCode(), CSeqportUtil::GetCodeIndexFromTo(), i, int, MemSet(), and compile_time_bits::range().

Referenced by GenBankAscii(), GenBankAsciiOrig(), get_bioseq(), SprotAscii(), and XMLAscii().

◆ GetSegPub()

static void GetSegPub ( TEntryList &  entries,
CSeq_descr &  descr 
)
static

Definition at line 2054 of file asci_blk.cpp.

References CheckSegPub(), CleanUpSeqDescrPub(), entries, CSeq_descr_Base::Set(), CBioseq_Base::SetDescr(), and CPubdesc_Base::SetPub().

Referenced by SrchSegDescr().

◆ GetSegSetDblink()

static void GetSegSetDblink ( CSeq_descr &  descr,
TEntryList &  entries,
bool *  drop 
)
static

Definition at line 2214 of file asci_blk.cpp.

References CUser_object_Base::CanGetType(), CRef< C, Locker >::Empty(), entries, CSerialObject::Equals(), ERR_SEGMENT_DBLinkMissingOrNonUnique, ERR_SEGMENT_GPIDMissingOrNonUnique, ErrPostEx, CSeq_descr_Base::Get(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CSeq_descr_Base::Set(), and SEV_REJECT.

Referenced by GetBioseqSetDescr().

◆ GetSeqData()

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

Definition at line 1678 of file asci_blk.cpp.

References Indexblk::bases, buf, Parser::curindx, Parser::DDBJ, Indexblk::drop, CSeq_data_Base::e_Iupacaa, Parser::EMBL, Parser::entrylist, ERR_SEQUENCE_AllNs, ERR_SEQUENCE_SeqLenNotEq, ERR_SEQUENCE_TooShort, ERR_SEQUENCE_TooShortIsPatent, ErrPostEx, Parser::format, Parser::GenBank, CBioseq::GetLength(), INSDSEQ_SEQUENCE, Indexblk::is_contig, Indexblk::is_mga, Indexblk::is_pat, Indexblk::is_prot, isalpha(), len, MemFree(), DataBlk::mOffset, ScanSequence(), CBioseq_Base::SetInst(), SEV_INFO, SEV_REJECT, SEV_WARNING, Parser::source, str(), StringLen(), StringSave, Parser::USPTO, Indexblk::xip, Parser::XML, XMLFindTagValue(), and xSrchNodeType().

Referenced by get_bioseq(), GetEmblInst(), GetGenBankInst(), GetSPInst(), s_DoNWalign(), s_GetCdsSequence(), COligoSpecificityCheck::x_NW_alignment(), and XMLGetInst().

◆ GetSeqExt()

void GetSeqExt ( ParserPtr  pp,
CSeq_loc &  seq_loc 
)

Definition at line 2473 of file asci_blk.cpp.

References Parser::accver, Indexblk::acnum, CSeq_loc::Add(), Parser::curindx, Parser::entrylist, MakeAccSeqId(), Parser::seqtype, CSeq_loc::SetWhole(), and Indexblk::vernum.

Referenced by EmblAscii(), GenBankAsciiOrig(), and XMLAscii().

◆ GetSequenceOfKeywords()

void GetSequenceOfKeywords ( const DataBlk &  entry,
int  type,
Uint2  col_data,
TKeywordList &  keywords 
)

Definition at line 1551 of file asci_blk.cpp.

References fta_fix_tpa_keywords(), GetBlkDataReplaceNewLine(), last(), ParFlatSP_KW, NStr::Split(), StripECO(), NStr::TrimSuffixInPlace(), NStr::TruncateSpacesInPlace(), xFixEMBLKeywords(), and xGetNodeData().

Referenced by CollectGapFeats(), GetDescrSPBlock(), and GetGBBlock().

◆ GetSerialNumFromPubEquiv()

static int GetSerialNumFromPubEquiv ( const CPub_equiv &  pub_eq)
static

Definition at line 3133 of file asci_blk.cpp.

References CPub_equiv_Base::Get().

Referenced by fta_if_pubs_sorted().

◆ GetSubNodeType()

static bool GetSubNodeType ( const char *  subkw,
char **  retbptr,
char *  eptr 
)
static

Definition at line 648 of file asci_blk.cpp.

References SrchTheChar(), StringEquN(), and StringLen().

Referenced by BuildSubBlock(), and GetEmblRefType().

◆ GetTopBiosource()

static const CBioSource* GetTopBiosource ( const CSeq_entry &  entry)
static

Definition at line 2785 of file asci_blk.cpp.

References GetDescrPointer().

Referenced by SeqEntryCheckTaxonDiv().

◆ InsertDatablkVal()

static void InsertDatablkVal ( DataBlkPtr *  dbp,
Int2  type,
char *  offset,
size_t  len 
)
static

Definition at line 231 of file asci_blk.cpp.

References len, and offset.

Referenced by BuildFeatureBlock(), BuildSubBlock(), GetEmblBlock(), and GetGenBankBlock().

◆ IsCitEmpty()

static bool IsCitEmpty ( const CCit_gen &  cit)
static

Definition at line 3377 of file asci_blk.cpp.

References CCit_gen_Base::IsSetAuthors(), CCit_gen_Base::IsSetCit(), CCit_gen_Base::IsSetDate(), CCit_gen_Base::IsSetIssue(), CCit_gen_Base::IsSetJournal(), CCit_gen_Base::IsSetMuid(), CCit_gen_Base::IsSetPages(), CCit_gen_Base::IsSetPmid(), CCit_gen_Base::IsSetSerial_number(), CCit_gen_Base::IsSetTitle(), and CCit_gen_Base::IsSetVolume().

Referenced by RemoveSerials().

◆ IsSegBioseq()

bool IsSegBioseq ( const CSeq_id &  id)

Definition at line 2540 of file asci_blk.cpp.

References CSeq_id_Base::e_Patent, CTextseq_id_Base::GetName(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), and StringEquN().

Referenced by FindCd(), FindFeatSeqLoc(), and FindGene().

◆ MakeAccSeqId()

CRef<CSeq_id> MakeAccSeqId ( const char *  acc,
Uint1  seqtype,
bool  accver,
Int2  vernum 
)

Definition at line 960 of file asci_blk.cpp.

References CSeq_id_Base::e_not_set, SetTextId(), and ValidSeqType().

Referenced by GetDRlineDataSP(), GetSeqExt(), GetSeqLocIntSP(), GetSPSeqLoc(), and LoadFeat().

◆ MakeLocusSeqId()

CRef<CSeq_id> MakeLocusSeqId ( const char *  locus,
CSeq_id::E_Choice  seqtype 
)

Definition at line 990 of file asci_blk.cpp.

References CRef< C, Locker >::Reset(), and SetTextId().

Referenced by GetDRlineDataSP().

◆ MakeSegSetSeqId()

static CRef<CSeq_id> MakeSegSetSeqId ( const char *  accession,
const string &  locus,
Uint1  seqtype,
bool  is_tpa 
)
static

Definition at line 1008 of file asci_blk.cpp.

References CSeq_id_Base::e_not_set, CRef< C, Locker >::Reset(), SetTextId(), and ValidSeqType().

Referenced by GetBioseq().

◆ MakeUsptoPatSeqId()

CRef<CPatent_seq_id> MakeUsptoPatSeqId ( const char *  acc)

Definition at line 884 of file asci_blk.cpp.

References StringChr.

Referenced by CreateEntryBioseq(), fta_fix_seq_id(), GetProtRefSeqId(), and LoadFeat().

◆ PackEntries()

void PackEntries ( TEntryList &  seq_entries)

Definition at line 3506 of file asci_blk.cpp.

References Begin(), DeltaBioseqPack(), CSeq_inst_Base::eRepr_const, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, and RawBioseqPack().

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().

◆ PackSeqData()

static void PackSeqData ( CSeq_data::E_Choice  code,
CSeq_data &  seq_data 
)
static

Definition at line 3439 of file asci_blk.cpp.

References CSeqConvert::Convert(), CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Ncbi8aa, CSeqUtil::e_Ncbi8aa, CSeqUtil::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqUtil::e_Ncbistdaa, CSeqUtil::e_not_set, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacaa(), CSeq_data_Base::GetNcbi8aa(), CSeq_data_Base::GetNcbistdaa(), CAliasBase< TPrim >::Set(), and CSeq_data_Base::SetNcbieaa().

Referenced by RawBioseqPack().

◆ pub_cmp()

static bool pub_cmp ( const CRef< CPub > &  pub1,
const CRef< CPub > &  pub2 
)
static

Definition at line 3201 of file asci_blk.cpp.

References CCit_gen_Base::GetCit(), CPub_Base::GetGen(), CPub_Base::GetMuid(), CPub_Base::IsGen(), CPub_Base::IsMuid(), CCit_gen_Base::IsSetCit(), and CPub_Base::Which().

Referenced by sort_feat_cit().

◆ RawBioseqPack()

static void RawBioseqPack ( CBioseq &  bioseq)
static

Definition at line 3482 of file asci_blk.cpp.

References CBioseq_Base::GetInst(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsGap(), CSeq_inst::IsNa(), CSeq_inst_Base::IsSetMol(), CSeq_inst_Base::IsSetSeq_data(), CSeqportUtil::Pack(), PackSeqData(), CBioseq_Base::SetInst(), and CSeq_data_Base::Which().

Referenced by PackEntries().

◆ RemoveDescrByChoice()

static void RemoveDescrByChoice ( CSeq_descr &  descr,
Uint1  choice 
)
static

Definition at line 1992 of file asci_blk.cpp.

References CSeq_descr_Base::Set().

Referenced by CleanUpSeqDescrChoice().

◆ RemoveSerials()

static void RemoveSerials ( TPubList &  pubs)
static

Definition at line 3389 of file asci_blk.cpp.

References IsCitEmpty().

Referenced by StripSerialNumbers().

◆ SameCitation_PubEquivMatch_Logic()

static bool SameCitation_PubEquivMatch_Logic ( const CPub_equiv &  a,
const CPub_equiv &  b 
)
static

Definition at line 1883 of file asci_blk.cpp.

References a, b, CPub_Base::e_Gen, CCit_gen_Base::GetSerial_number(), CCit_gen_Base::IsSetAuthors(), CCit_gen_Base::IsSetCit(), CCit_gen_Base::IsSetDate(), CCit_gen_Base::IsSetIssue(), CCit_gen_Base::IsSetJournal(), CCit_gen_Base::IsSetMuid(), CCit_gen_Base::IsSetPages(), CCit_gen_Base::IsSetSerial_number(), CCit_gen_Base::IsSetTitle(), and CCit_gen_Base::IsSetVolume().

Referenced by CheckSegPub().

◆ ScanSequence()

Int4 ScanSequence ( bool  warn,
char **  seqptr,
std::vector< char > &  bsp,
unsigned char *  conv,
Char  replacechar,
int *  numns 
)

Definition at line 1622 of file asci_blk.cpp.

References buf, conv, copy(), ERR_SEQUENCE_BadResidue, ErrPostEx, int, isalpha(), and SEV_ERROR.

Referenced by GetSeqData().

◆ SeqEntryCheckTaxonDiv()

static bool SeqEntryCheckTaxonDiv ( const CSeq_entry &  entry)
static

Definition at line 2797 of file asci_blk.cpp.

References CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), GetTopBiosource(), COrgName_Base::IsSetDiv(), CBioSource_Base::IsSetOrg(), and COrg_ref_Base::IsSetOrgname().

Referenced by EntryCheckDivCode().

◆ SetEmptyId()

static void SetEmptyId ( CBioseq &  bioseq)
static

Definition at line 1062 of file asci_blk.cpp.

References CBioseq_Base::SetId(), CObject_id::SetId8(), and CSeq_id_Base::SetLocal().

Referenced by CreateEntryBioseq().

◆ ShrinkSpaces() [1/2]

void ShrinkSpaces ( char *  line)

Definition at line 118 of file asci_blk.cpp.

References fta_StringCpy().

Referenced by DescrRefs(), fta_fix_affil(), fta_get_trna_from_comment(), fta_get_trna_from_product(), fta_remark_is_er(), fta_strip_pub_comment(), fta_vnp_structured_comment(), GetSPDescrTitle(), GetViralHostsFrom_OH(), ParseFeatureBlock(), RemoveSourceFeatSpaces(), SPFeatProtRef(), StripCDSComment(), and XMLParseFeatureBlock().

◆ ShrinkSpaces() [2/2]

void ShrinkSpaces ( string &  line)

Definition at line 166 of file asci_blk.cpp.

References i.

◆ sort_feat_cit()

static void sort_feat_cit ( CBioseq::TAnnot &  annots)
static

Definition at line 3219 of file asci_blk.cpp.

References pub_cmp(), and swap().

Referenced by fta_sort_seqfeat_cit().

◆ SrchNodeSubType()

char* SrchNodeSubType ( const DataBlk &  entry,
Int2  type,
Int2  subtype,
size_t *  len 
)

Definition at line 1039 of file asci_blk.cpp.

References len, DataBlk::len, DataBlk::mOffset, DataBlk::mpData, DataBlk::mpNext, DataBlk::mType, and TrackNodeType().

Referenced by FakeGenBankBioSources().

◆ SrchSegDescr()

static void SrchSegDescr ( TEntryList &  entries,
CSeq_descr &  descr 
)
static

Definition at line 2185 of file asci_blk.cpp.

References CheckSegDescrChoice(), CleanUpSeqDescrChoice(), CSeqdesc_Base::e_Modif, CSeqdesc_Base::e_Org, CSeqdesc_Base::e_Update_date, entries, GetBioseqSetDescrTitle(), CBioseq_Base::GetDescr(), GetFirstSegDescrChoice(), GetSegPub(), CSeq_descr_Base::Set(), CSeq_entry_Base::SetSeq(), and CSeqdesc_Base::SetTitle().

Referenced by GetBioseqSetDescr().

◆ SrchSegLength()

static Int4 SrchSegLength ( const TEntryList &  entries)
static

Definition at line 2394 of file asci_blk.cpp.

References entries, and CBioseq::GetLength().

Referenced by GetBioseq().

◆ SrchSegSeqMol()

static CSeq_inst::EMol SrchSegSeqMol ( const TEntryList &  entries)
static

Definition at line 2369 of file asci_blk.cpp.

References CSeq_inst_Base::eMol_na, entries, ERR_SEGMENT_DiffMolType, ErrPostEx, CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), GetMoleculeClassString(), and SEV_WARNING.

Referenced by GetBioseq().

◆ StripSerialNumbers()

void StripSerialNumbers ( TEntryList &  seq_entries)

Definition at line 3406 of file asci_blk.cpp.

References Begin(), CImp_feat_Base::GetKey(), CImp_feat_Base::IsSetKey(), RemoveSerials(), and SwissProtIDPresent().

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), SpPrepareEntry(), and XMLAscii().

◆ StrToSeqId()

CRef<CSeq_id> StrToSeqId ( const char *  pch,
bool  pid 
)

Definition at line 2694 of file asci_blk.cpp.

References CDbtag_Base::SetDb(), CDbtag_Base::SetTag(), and tag.

Referenced by AddNIDSeqId(), and QualsToSeqID().

◆ SwissProtIDPresent()

static bool SwissProtIDPresent ( const TEntryList &  seq_entries)
static

Definition at line 3360 of file asci_blk.cpp.

References Begin().

Referenced by StripSerialNumbers().

◆ TrimEmblFeatBlk()

static bool TrimEmblFeatBlk ( DataBlkPtr  dbp)
static

Definition at line 604 of file asci_blk.cpp.

References DataBlk::len, DataBlk::mOffset, and SrchTheChar().

Referenced by GetEmblSubBlock().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ ValidSeqType()

static Uint1 ValidSeqType ( const char *  accession,
Uint1  type 
)
static

Definition at line 918 of file asci_blk.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::GetAccType(), CSeq_id::IdentifyAccession(), and type.

Referenced by CreateEntryBioseq(), MakeAccSeqId(), and MakeSegSetSeqId().

◆ xFixEMBLKeywords()

void xFixEMBLKeywords ( string &  keywordData)

Definition at line 1512 of file asci_blk.cpp.

References NStr::FindNoCase(), and i.

Referenced by GetSequenceOfKeywords().

◆ xGetGenBankBlocks()

void xGetGenBankBlocks ( Entry &  entry)

Definition at line 256 of file asci_blk.cpp.

References genbankKeywords, Entry::mBaseData, Entry::mSections, ParFlat_LOCUS, ParFlat_UNKW, NStr::Split(), SrchKeyword(), and NStr::StartsWith().

Referenced by GenBankAscii().

◆ xGetGenBankSubBlocks()

void xGetGenBankSubBlocks ( Entry &  entry,
size_t  bases 
)

Definition at line 493 of file asci_blk.cpp.

References Entry::mSections, ParFlat_AUTHORS, ParFlat_CONSRTM, ParFlat_FEATURES, ParFlat_JOURNAL, ParFlat_MEDLINE, ParFlat_ORGANISM, ParFlat_PUBMED, ParFlat_REFERENCE, ParFlat_REMARK, ParFlat_SOURCE, ParFlat_STANDARD, and ParFlat_TITLE.

Referenced by GenBankAscii().

◆ XMLCheckCDS()

bool XMLCheckCDS ( const char *  entry,
XmlIndexPtr  xip 
)

Definition at line 3310 of file asci_blk.cpp.

References XmlIndex::end, INSDFEATURE_KEY, INSDSEQ_FEATURE_TABLE, XmlIndex::next, XmlIndex::start, StringEquN(), XmlIndex::subtags, and XmlIndex::tag.

Referenced by XMLGetEMBLBlock(), and XMLGetGBBlock().

◆ XMLDefVsHTGKeywords()

void XMLDefVsHTGKeywords ( CMolInfo::TTech  tech,
const char *  entry,
XmlIndexPtr  xip,
bool  cancelled 
)

Definition at line 2889 of file asci_blk.cpp.

References b, ERR_DEFINITION_HTGNotInProgress, ERR_DEFINITION_HTGShouldBeComplete, ERR_SEQUENCE_UnknownBaseHTG3, ErrPostEx, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, INSDSEQ_DEFINITION, INSDSEQ_SEQUENCE, magic_phrases, MemFree(), r(), SEV_ERROR, SEV_WARNING, StringSave, StringStr, tmp, and XMLFindTagValue().

Referenced by XMLGetEMBLBlock(), and XMLGetGBBlock().

Variable Documentation

◆ emblKeywords

vector<string> emblKeywords
extern

Definition at line 56 of file em_index.cpp.

Referenced by EmblIndex(), and GetEmblBlock().

◆ genbankKeywords

vector<string> genbankKeywords
extern

Definition at line 56 of file gb_index.cpp.

Referenced by GenBankIndex(), GetGenBankBlock(), and xGetGenBankBlocks().

◆ magic_phrases

const char* magic_phrases[]
Initial value:
= {
"*** SEQUENCING IN PROGRESS ***",
"***SEQUENCING IN PROGRESS***",
"WORKING DRAFT SEQUENCE",
"LOW-PASS SEQUENCE SAMPLING",
"*** IN PROGRESS ***",
nullptr
}

Definition at line 104 of file asci_blk.cpp.

Referenced by DefVsHTGKeywords(), and XMLDefVsHTGKeywords().

◆ swissProtKeywords

vector<string> swissProtKeywords
extern

Definition at line 54 of file sp_index.cpp.

Referenced by GetEmblBlock(), and SprotIndex().

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