NCBI C++ ToolKit
asci_blk.h File Reference
#include "ftablock.h"
#include "entry.h"
#include <objects/seqfeat/Org_ref.hpp>
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CRef< objects::CSeq_id > StrToSeqId (const char *pch, bool pid)
CRef< objects::CSeq_id > MakeAccSeqId (const char *acc, Uint1 seqtype, bool accver, Int2 vernum)
CRef< objects::CPatent_seq_id > MakeUsptoPatSeqId (const char *acc)
CRef< objects::CSeq_id > MakeLocusSeqId (const char *locus, objects::CSeq_id::E_Choice seqtype)
CRef< objects::CBioseq > CreateEntryBioseq (ParserPtr pp)
void StripSerialNumbers (TEntryList &seq_entries)
void PackEntries (TEntryList &seq_entries)
Int4 ScanSequence (bool warn, char **seqptr, std::vector< char > &bsp, unsigned char *conv, Char replacechar, int *numns)
char * GetGenBankBlock (DataBlkPtr *chain, char *ptr, short *retkw, char *eptr)
void xGetGenBankBlocks (Entry &entry)
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)
void GetEmblSubBlock (size_t bases, Parser::ESource source, const DataBlk &entry)
void BuildSubBlock (DataBlkPtr dbp, Int2 subtype, const char *subkw)
SectionPtr xBuildSubBlock (Section &, int subtype, const char *subKw)
void GetLenSubNode (DataBlkPtr dbp)
char * SrchNodeSubType (const DataBlk &entry, Int2 type, Int2 subtype, size_t *len)
char * GetDescrComment (char *offset, size_t len, Uint2 col_data, bool is_htg, bool is_pat)
void GetExtraAccession (IndexblkPtr ibp, bool allow_uwsec, Parser::ESource source, TAccessionList &accessions)
void GetSequenceOfKeywords (const DataBlk &entry, int type, Uint2 col_data, TKeywordList &keywords)
bool GetSeqData (ParserPtr pp, const DataBlk &entry, objects::CBioseq &cpp_bsp, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)
unique_ptr< unsigned char[]> GetDNAConv (void)
unique_ptr< unsigned char[]> GetProteinConv (void)
void GetSeqExt (ParserPtr pp, objects::CSeq_loc &seq_loc)
void BuildBioSegHeader (ParserPtr pp, TEntryList &entries, const objects::CSeq_loc &seqloc)
bool IsSegBioseq (const objects::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, int *tech, size_t bases, Parser::ESource source, bool &drop)
void EntryCheckDivCode (TEntryList &seq_entries, ParserPtr pp)
void AddNIDSeqId (objects::CBioseq &bioseq, const DataBlk &entry, Int2 type, Int2 coldata, Parser::ESource source)
void DefVsHTGKeywords (int tech, const DataBlk &entry, Int2 what, Int2 ori, bool cancelled)
void XMLDefVsHTGKeywords (int tech, const char *entry, XmlIndexPtr xip, bool cancelled)
void CheckHTGDivision (const char *div, int tech)
void fta_sort_biosource (objects::CBioSource &bio)
bool fta_EntryCheckGBBlock (TEntryList &seq_entries)
void ShrinkSpaces (char *line)
void ShrinkSpaces (string &line)
void fta_sort_descr (TEntryList &seq_entries)
void fta_sort_seqfeat_cit (TEntryList &seq_entries)
bool XMLCheckCDS (const char *entry, XmlIndexPtr xip)
void fta_set_strandedness (TEntryList &seq_entries)
bool GetEmblInstContig (const DataBlk &entry, objects::CBioseq &bioseq, ParserPtr pp)
bool fta_orgref_has_taxid (const objects::COrg_ref::TDb &dbtags)
void fta_fix_orgref_div (const objects::CBioseq::TAnnot &annots, objects::COrg_ref *org_ref, objects::CGB_block &gbb)
const char * GetEmblDiv (Uint1 num)
const objects::CSeq_descr & GetDescrPointer (const objects::CSeq_entry &entry)

Function Documentation

◆ AddNIDSeqId()

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

◆ BuildBioSegHeader()

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

◆ 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,
int tech,
size_t  bases,
Parser::ESource  source,
bool drop 

◆ CheckHTGDivision()

void CheckHTGDivision ( const char *  div,
int  tech 

◆ CreateEntryBioseq()

CRef<objects::CBioseq> CreateEntryBioseq ( ParserPtr  pp)

◆ DefVsHTGKeywords()

void DefVsHTGKeywords ( int  tech,
const DataBlk entry,
Int2  what,
Int2  ori,
bool  cancelled 

◆ 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_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 objects::CBioseq::TAnnot &  annots,
objects::COrg_ref *  org_ref,
objects::CGB_block &  gbb 

◆ fta_orgref_has_taxid()

bool fta_orgref_has_taxid ( const objects::COrg_ref::TDb &  dbtags)

◆ fta_set_strandedness()

void fta_set_strandedness ( TEntryList seq_entries)

◆ fta_sort_biosource()

void fta_sort_biosource ( objects::CBioSource &  bio)

◆ 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().

◆ GetDescrComment()

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

◆ GetDescrPointer()

const objects::CSeq_descr& GetDescrPointer ( const objects::CSeq_entry &  entry)

◆ GetDNAConv()

unique_ptr<unsigned char[]> GetDNAConv ( void  )

◆ GetEmblBlock()

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

◆ GetEmblDiv()

const char* GetEmblDiv ( Uint1  num)

Definition at line 2401 of file em_ascii.cpp.

References ParFlat_Embl_DIV_array.

Referenced by CheckGBBlock().

◆ GetEmblInstContig()

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

Referenced by get_bioseq().

◆ 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 

◆ GetGenBankBlock()

char* GetGenBankBlock ( DataBlkPtr chain,
char *  ptr,
short *  retkw,
char *  eptr 

◆ GetGenBankSubBlock()

void GetGenBankSubBlock ( const DataBlk entry,
size_t  bases 

◆ GetLenSubNode()

void GetLenSubNode ( DataBlkPtr  dbp)

◆ GetProteinConv()

unique_ptr<unsigned char[]> GetProteinConv ( void  )

◆ GetSeqData()

bool GetSeqData ( ParserPtr  pp,
const DataBlk entry,
objects::CBioseq &  cpp_bsp,
Int4  nodetype,
unsigned char *  seqconv,
Uint1  seq_data_type 

◆ GetSeqExt()

void GetSeqExt ( ParserPtr  pp,
objects::CSeq_loc &  seq_loc 

◆ GetSequenceOfKeywords()

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

◆ IsSegBioseq()

bool IsSegBioseq ( const objects::CSeq_id &  id)

◆ MakeAccSeqId()

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

◆ MakeLocusSeqId()

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

◆ MakeUsptoPatSeqId()

CRef<objects::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)

◆ 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().

◆ ShrinkSpaces() [1/2]

void ShrinkSpaces ( char *  line)

◆ ShrinkSpaces() [2/2]

void ShrinkSpaces ( string line)

Definition at line 166 of file asci_blk.cpp.

References i.

◆ SrchNodeSubType()

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

◆ StripSerialNumbers()

void StripSerialNumbers ( TEntryList seq_entries)

◆ StrToSeqId()

CRef<objects::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().

◆ xBuildSubBlock()

SectionPtr xBuildSubBlock ( Section ,
int  subtype,
const char *  subKw 

◆ xGetGenBankBlocks()

void xGetGenBankBlocks ( Entry entry)

◆ xGetGenBankSubBlocks()

void xGetGenBankSubBlocks ( Entry entry,
size_t  bases 

◆ XMLCheckCDS()

bool XMLCheckCDS ( const char *  entry,
XmlIndexPtr  xip 

◆ XMLDefVsHTGKeywords()

void XMLDefVsHTGKeywords ( int  tech,
const char *  entry,
XmlIndexPtr  xip,
bool  cancelled 
Modified on Thu May 30 12:20:30 2024 by rev. 669887