#include <objects/general/Date_std.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/object_manager.hpp>
#include "ftablock.h"
#include "entry.h"

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Namespaces
	objects

Macros
#define	Unknown 0

#define	ParFlat_UNKW 999

Functions
CRef< objects::CDate_std >	get_full_date (const Char *s, bool is_ref, Parser::ESource source)

unique_ptr< TokenStatBlk >	TokenString (const char *str, Char delimiter)

bool	ParseAccessionRange (TokenStatBlk *tsbp, unsigned skip)

bool	ParseAccessionRange (list< string > &tokens, unsigned skip)

void	UnwrapAccessionRange (const objects::CGB_block::TExtra_accessions &extra_accs, objects::CGB_block::TExtra_accessions &hist)

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

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

char *	StringIStr (const Char where, const Char what)

Int2	MatchArrayString (const Char *array, const Char text)

Int2	MatchArrayIString (const Char *array, const Char text)

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

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

string	GetBlkDataReplaceNewLine (string_view, Uint2 indent)

void	CleanTailNoneAlphaChar (char *str)

void	CleanTailNoneAlphaCharInString (std::string &str)

char *	PointToNextToken (char *ptr)

char *	GetTheCurrentToken (char **ptr)

char *	SrchTheChar (char bptr, char eptr, Char letter)

char *	SrchTheStr (char bptr, char eptr, const char *str)

void	CpSeqId (InfoBioseq *ibp, const objects::CSeq_id &id)

int	SrchKeyword (const CTempString &ptr, const vector< string > &keywordList)

bool	CheckLineType (char *ptr, Int4 line, const vector< string > &keywordList, bool after_origin)

char *	SrchNodeType (DataBlk entry, Int4 type, size_t len)

char *	xSrchNodeType (const DataBlk &entry, Int4 type, size_t *len)

string	xGetNodeData (const DataBlk &entry, int nodeType)

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

const Section *	xTrackNodeType (const Entry &, int type)

ValNode *	ConstructValNode (objects::CSeq_id::E_Choice choice, const char *data)

bool	fta_is_tpa_keyword (const char *str)

bool	fta_tpa_keywords_check (const TKeywordList &kwds)

bool	fta_is_tsa_keyword (const char *str)

bool	fta_is_tls_keyword (const char *str)

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

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

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

void	fta_StringCpy (char dst, const char src)

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

void	fta_remove_keywords (int tech, TKeywordList &kwds)

void	fta_remove_tpa_keywords (TKeywordList &kwds)

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

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

void	fta_remove_env_keywords (TKeywordList &kwds)

void	fta_remove_mag_keywords (TKeywordList &kwds)

bool	IsCancelled (const TKeywordList &keywords)

bool	HasHtg (const TKeywordList &keywords)

void	RemoveHtgPhase (TKeywordList &keywords)

bool	HasHtc (const TKeywordList &keywords)

bool	SetTextId (Uint1 seqtype, objects::CSeq_id &seqId, objects::CTextseq_id &textId)

void	check_est_sts_gss_tpa_kwds (ValNodePtr kwds, size_t len, IndexblkPtr entry, bool tpa_check, bool &specialist_db, bool &inferential, bool &experimental, bool &assembly)

void	xCheckEstStsGssTpaKeywords (const std::list< std::string > keywordList, bool tpa_check, IndexblkPtr entry)

objects::CScope &	GetScope ()

Macro Definition Documentation

◆ ParFlat_UNKW

#define ParFlat_UNKW 999

Definition at line 44 of file utilfun.h.

◆ Unknown

#define Unknown 0

Examples: /home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp.

Definition at line 40 of file utilfun.h.

Function Documentation

◆ check_est_sts_gss_tpa_kwds()

void check_est_sts_gss_tpa_kwds	(	ValNodePtr	kwds,
		size_t	len,
		IndexblkPtr	entry,
		bool	tpa_check,
		bool &	specialist_db,
		bool &	inferential,
		bool &	experimental,
		bool &	assembly
	)

Definition at line 1371 of file utilfun.cpp.

References ValNode::data, NStr::EqualNocase(), Indexblk::EST, fta_keywords_check(), Indexblk::GSS, Indexblk::HTC, Indexblk::is_tpa, len, MemFree(), ValNode::next, StringCat(), StringChr, StringNew(), and Indexblk::STS.

Referenced by GenBankIndex(), and XMLKeywordsCheck().

◆ CheckLineType()

bool CheckLineType	(	char *	ptr,
		Int4	line,
		const vector< string > &	keywordList,
		bool	after_origin
	)

Definition at line 910 of file utilfun.cpp.

References ERR_ENTRY_InvalidLineType, ErrPostEx, i, msg(), SEV_ERROR, StringChr, StringEquN(), and StringNCpy().

Referenced by EmblIndex(), and GenBankIndex().

◆ CleanTailNoneAlphaChar()

void CleanTailNoneAlphaChar ( char * str )

Definition at line 697 of file utilfun.cpp.

References last(), SeekLastAlphaChar(), and str().

Referenced by GetOneGeneRef(), and GetTheCurrentToken().

◆ CleanTailNoneAlphaCharInString()

void CleanTailNoneAlphaCharInString ( std::string & str )

◆ ConstructValNode()

ValNode* ConstructValNode	(	objects::CSeq_id::E_Choice	choice,
		const char *	data
	)

◆ CpSeqId()

void CpSeqId	(	InfoBioseq *	ibp,
		const objects::CSeq_id &	id
	)

◆ fta_check_mga_keywords()

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

◆ fta_is_tls_keyword()

bool fta_is_tls_keyword ( const char * str )

Definition at line 1187 of file utilfun.cpp.

References MatchArrayIString(), ParFlat_TLS_kw_array, and str().

◆ fta_is_tpa_keyword()

bool fta_is_tpa_keyword ( const char * str )

Definition at line 1170 of file utilfun.cpp.

References MatchArrayIString(), ParFlat_TPA_kw_array, and str().

Referenced by fta_fix_tpa_keywords().

◆ fta_is_tsa_keyword()

bool fta_is_tsa_keyword ( const char * str )

Definition at line 1179 of file utilfun.cpp.

References MatchArrayIString(), ParFlat_TSA_kw_array, and str().

◆ fta_keywords_check()

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