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)
 
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_idMakeUsptoPatSeqId (const char *acc)
 
static Uint1 ValidSeqType (const char *accession, Uint1 type)
 
CRef< CSeq_idMakeAccSeqId (const char *acc, Uint1 seqtype, bool accver, Int2 vernum)
 
CRef< CSeq_idMakeLocusSeqId (const char *locus, CSeq_id::E_Choice seqtype)
 
static CRef< CSeq_idMakeSegSetSeqId (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< CBioseqCreateEntryBioseq (ParserPtr pp)
 
char * GetDescrComment (char *offset, size_t len, Int2 col_data, bool is_htg, bool is_pat)
 
static void fta_fix_secondaries (TokenBlkPtr 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, int 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 char * 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< CBioseqGetBioseq (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_idStrToSeqId (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 CBioSourceGetTopBiosource (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_descrGetDescrPointer (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< stringgenbankKeywords
 
vector< stringemblKeywords
 
vector< stringswissProtKeywords
 

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 
)

◆ BuildBioSegHeader()

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

◆ BuildFeatureBlock()

static void BuildFeatureBlock ( DataBlkPtr  dbp)
static

◆ BuildSubBlock()

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

◆ 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 
)

◆ CheckDivCode()

static void CheckDivCode ( TEntryList seq_entries,
ParserPtr  pp 
)
static

◆ CheckGBBlock()

static void CheckGBBlock ( TSeqdescList descrs,
bool got 
)
static

◆ CheckHTGDivision()

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

◆ CheckSegDescrChoice()

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

◆ CheckSegPub()

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

◆ CleanUpSeqDescrChoice()

static void CleanUpSeqDescrChoice ( TEntryList entries,
Uint1  choice 
)
static

Definition at line 1965 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 1981 of file asci_blk.cpp.

References entries.

Referenced by GetSegPub().

◆ CleanVisString()

static void CleanVisString ( string str)
static

Definition at line 2938 of file asci_blk.cpp.

References str().

Referenced by CheckGBBlock(), and CleanVisStringList().

◆ CleanVisStringList()

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

Definition at line 2986 of file asci_blk.cpp.

References CleanVisString().

Referenced by CheckGBBlock().

◆ CreateEntryBioseq()

CRef<CBioseq> CreateEntryBioseq ( ParserPtr  pp)

◆ DefVsHTGKeywords()

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

◆ DeltaBioseqPack()

static void DeltaBioseqPack ( CBioseq bioseq)
static

◆ descr_cmp()

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

◆ EntryCheckDivCode()

void EntryCheckDivCode ( TEntryList seq_entries,
ParserPtr  pp 
)

Definition at line 2776 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

◆ fta_EntryCheckGBBlock()

bool fta_EntryCheckGBBlock ( TEntryList seq_entries)

Definition at line 3084 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 
)

◆ fta_fix_secondaries()

static void fta_fix_secondaries ( TokenBlkPtr  secs)
static

Definition at line 1218 of file asci_blk.cpp.

References fta_if_wgs_acc(), TokenBlk::next, TokenBlk::str, StringEqu(), and StringSave().

Referenced by GetExtraAccession().

◆ fta_fix_tpa_keywords()

static void fta_fix_tpa_keywords ( TKeywordList keywords)
static

◆ fta_if_pubs_sorted()

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

Definition at line 3120 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 3229 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)

◆ fta_sort_descr()

void fta_sort_descr ( TEntryList seq_entries)

Definition at line 3156 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 3213 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

◆ GetBioseqSetDescr()

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

Definition at line 2296 of file asci_blk.cpp.

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

Referenced by BuildBioSegHeader().

◆ GetBioseqSetDescrTitle()

static char* GetBioseqSetDescrTitle ( const CSeq_descr descr)
static

Definition at line 2095 of file asci_blk.cpp.

References CleanTailNoneAlphaChar(), CSeq_descr_Base::Get(), str(), StringSave(), and StringStr.

Referenced by GetBioseq(), and SrchSegDescr().

◆ GetDescrByChoice()

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

Definition at line 1793 of file asci_blk.cpp.

References CSeq_descr_Base::Get().

Referenced by CheckSegDescrChoice().

◆ GetDescrComment()

char* GetDescrComment ( char *  offset,
size_t  len,
Int2  col_data,
bool  is_htg,
bool  is_pat 
)

◆ GetDescrPointer()

const CSeq_descr& GetDescrPointer ( const CSeq_entry entry)

◆ GetDNAConv()

unique_ptr<unsigned char[]> GetDNAConv ( void  )

◆ GetEmblBlock()

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

◆ GetEmblRefType()

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

◆ GetEmblSubBlock()

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

◆ GetExtraAccession()

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

◆ GetFirstSegDescrChoice()

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

Definition at line 1816 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 
)

◆ GetGenBankRefType()

static void GetGenBankRefType ( DataBlkPtr  dbp,
size_t  bases 
)
static

◆ GetGenBankSubBlock()

void GetGenBankSubBlock ( const DataBlk entry,
size_t  bases 
)

◆ GetLenSubNode()

void GetLenSubNode ( DataBlkPtr  dbp)

◆ GetMoleculeClassString()

static const char* GetMoleculeClassString ( Uint1  mol)
static

Definition at line 2309 of file asci_blk.cpp.

Referenced by SrchSegSeqMol().

◆ GetProteinConv()

unique_ptr<unsigned char[]> GetProteinConv ( void  )

◆ GetSegPub()

static void GetSegPub ( TEntryList entries,
CSeq_descr descr 
)
static

◆ GetSegSetDblink()

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

◆ GetSeqData()

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

◆ GetSeqExt()

void GetSeqExt ( ParserPtr  pp,
CSeq_loc seq_loc 
)

◆ GetSequenceOfKeywords()

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

◆ GetSerialNumFromPubEquiv()

static int GetSerialNumFromPubEquiv ( const CPub_equiv pub_eq)
static

Definition at line 3104 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 594 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 2751 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 177 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

◆ IsSegBioseq()

bool IsSegBioseq ( const CSeq_id id)

◆ MakeAccSeqId()

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

◆ MakeLocusSeqId()

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

Definition at line 936 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 954 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 830 of file asci_blk.cpp.

References StringChr.

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

◆ PackEntries()

void PackEntries ( TEntryList seq_entries)

◆ PackSeqData()

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

◆ pub_cmp()

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

◆ RawBioseqPack()

static void RawBioseqPack ( CBioseq bioseq)
static

◆ RemoveDescrByChoice()

static void RemoveDescrByChoice ( CSeq_descr descr,
Uint1  choice 
)
static

Definition at line 1946 of file asci_blk.cpp.

References CSeq_descr_Base::Set().

Referenced by CleanUpSeqDescrChoice().

◆ RemoveSerials()

static void RemoveSerials ( TPubList pubs)
static

Definition at line 3360 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

◆ ScanSequence()

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

Definition at line 1576 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

◆ SetEmptyId()

static void SetEmptyId ( CBioseq bioseq)
static

Definition at line 1008 of file asci_blk.cpp.

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

Referenced by CreateEntryBioseq().

◆ ShrinkSpaces()

void ShrinkSpaces ( char *  line)

◆ sort_feat_cit()

static void sort_feat_cit ( CBioseq::TAnnot annots)
static

Definition at line 3190 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 
)

◆ SrchSegDescr()

static void SrchSegDescr ( TEntryList entries,
CSeq_descr descr 
)
static

◆ SrchSegLength()

static Int4 SrchSegLength ( const TEntryList entries)
static

Definition at line 2356 of file asci_blk.cpp.

References entries, and CBioseq::GetLength().

Referenced by GetBioseq().

◆ SrchSegSeqMol()

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

◆ StripSerialNumbers()

void StripSerialNumbers ( TEntryList seq_entries)

◆ StrToSeqId()

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

Definition at line 2660 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 3331 of file asci_blk.cpp.

References Begin().

Referenced by StripSerialNumbers().

◆ TrimEmblFeatBlk()

static bool TrimEmblFeatBlk ( DataBlkPtr  dbp)
static

Definition at line 550 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

◆ xFixEMBLKeywords()

void xFixEMBLKeywords ( string keywordData)

Definition at line 1466 of file asci_blk.cpp.

References NStr::FindNoCase(), and i.

Referenced by GetSequenceOfKeywords().

◆ xGetGenBankBlocks()

void xGetGenBankBlocks ( Entry entry)

◆ xGetGenBankSubBlocks()

void xGetGenBankSubBlocks ( Entry entry,
size_t  bases 
)

◆ XMLCheckCDS()

bool XMLCheckCDS ( const char *  entry,
XmlIndexPtr  xip 
)

◆ XMLDefVsHTGKeywords()

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

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().

Modified on Thu Feb 29 12:16:33 2024 by modify_doxy.py rev. 669887