#include <ncbi_pch.hpp>
#include <corelib/ncbimisc.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include "ftacpp.hpp"
#include "ftaerr.hpp"
#include "xgbparint.h"

Include dependency graph for xgbparint.cpp:

Go to the SVN repository for this file.

Classes
struct	STokenInfo

class	CGBLocException

Macros
#define	THIS_FILE "xgbparint.cpp"

#define	TAKE_FIRST 1

#define	TAKE_SECOND 2

#define	ERR_FEATURE_LocationParsing_validatr 1, 5

Typedefs
using	TTokens = list< STokenInfo >

using	TTokenIt = TTokens::iterator

using	TTokenConstIt = TTokens::const_iterator

Enumerations
enum class	ETokenType { eToken_Undefined , eToken_App , eToken_Request , eUnknown , eJoin , eCompl , eLeft , eRight , eCaret , eDotDot , eAccession , eGt , eLt , eComma , eNumber , eOrder , eSingleDot , eGroup , eOneOf , eReplace , eSites , eString , eOneOfNum , eGap , eUnkGap }

Functions
	USING_SCOPE (objects)

static void	do_xgbparse_error (string_view msg, string_view details)

void	xinstall_gbparse_error_handler (X_gbparse_errfunc new_func)

void	xinstall_gbparse_range_func (void *data, X_gbparse_rangefunc new_func)

static string	xgbparse_point (TTokenConstIt head, TTokenConstIt current)

static void	xgbparse_error (string_view front, TTokenConstIt head, TTokenConstIt current)

static void	xgbparse_error (string_view front, const TTokens &tokens, TTokenConstIt current)

static void	xgbcheck_range (TSeqPos num, const CSeq_id &id, bool &keep_rawPt, int &numErrors, const TTokens &tokens, TTokenConstIt current)

static void	xfind_one_of_num (list< STokenInfo > &tokens)

static void	xlex_error_func (string_view msg, const string &line, unsigned int current_col)

static unsigned	advance_to (const char c, unsigned current_pos, const string &line)

static size_t	sParseAccessionPrefix (string_view accession)

static int	sGetAccession (string &accession, unsigned int &current_col, const string &line, bool accver)

static int	xgbparselex_ver (string_view linein, TTokens &tokens, bool accver)

static void	xgbparse_better_be_done (int &numErrors, TTokenIt current_token, const TTokens &tokens, bool &keep_rawPt, int paren_count)

static CRef< CSeq_loc >	XGapToSeqLocEx (Int4 range, bool unknown)

static void	xgbgap (TTokenIt &current_it, TTokenConstIt end_it, CRef< CSeq_loc > &loc, bool unknown)

static void	sConvertIntToPoint (CSeq_loc &loc)

static void	xgbload_number (TSeqPos &numPt, CInt_fuzz &fuzz, bool &keep_rawPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, int take_which)

static CRef< CSeq_loc >	xgbint_ver (bool &keep_rawPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, const TSeqIdList &seq_ids, bool accver)

static CRef< CSeq_loc >	xgbloc_ver (bool &keep_rawPt, int &parenPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, const TSeqIdList &seq_ids, bool accver)

static CRef< CSeq_loc >	xgbreplace_ver (bool &keep_rawPt, int &parenPt, TTokenIt &currentPt, const TTokens &tokens, int &numErrors, const TSeqIdList &seq_ids, bool accver)

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

Variables
const char *	seqlitdbtag = "SeqLit"

const char *	unkseqlitdbtag = "UnkSeqLit"

static X_gbparse_errfunc	Err_func = do_xgbparse_error

static X_gbparse_rangefunc	Range_func = nullptr

static void *	xgbparse_range_data = nullptr

Macro Definition Documentation

◆ ERR_FEATURE_LocationParsing_validatr

#define ERR_FEATURE_LocationParsing_validatr 1, 5

Definition at line 95 of file xgbparint.cpp.

◆ TAKE_FIRST

#define TAKE_FIRST 1

Definition at line 49 of file xgbparint.cpp.

◆ TAKE_SECOND

#define TAKE_SECOND 2

Definition at line 50 of file xgbparint.cpp.

◆ THIS_FILE

#define THIS_FILE "xgbparint.cpp"

Definition at line 47 of file xgbparint.cpp.

Typedef Documentation

◆ TTokenConstIt

using TTokenConstIt = TTokens::const_iterator

Definition at line 90 of file xgbparint.cpp.

◆ TTokenIt

using TTokenIt = TTokens::iterator

Definition at line 89 of file xgbparint.cpp.

◆ TTokens

using TTokens = list<STokenInfo>

Definition at line 88 of file xgbparint.cpp.

Enumeration Type Documentation

◆ ETokenType

enum ETokenType

strong

Enumerator
eToken_Undefined
eToken_App
eToken_Request
eUnknown
eJoin
eCompl
eLeft
eRight
eCaret
eDotDot
eAccession
eGt
eLt
eComma
eNumber
eOrder
eSingleDot
eGroup
eOneOf
eReplace
eSites
eString
eOneOfNum
eGap
eUnkGap

Definition at line 58 of file xgbparint.cpp.

Function Documentation

◆ advance_to()

static unsigned advance_to	(	const char	c,
		unsigned	current_pos,
		const string &	line
	)

static

Definition at line 304 of file xgbparint.cpp.

Referenced by xgbparselex_ver().

◆ do_xgbparse_error()

static void do_xgbparse_error	(	string_view	msg,
		string_view	details
	)

static

Definition at line 97 of file xgbparint.cpp.

References ERR_FEATURE_LocationParsing_validatr, msg(), Nlm_ErrPostStr(), Nlm_ErrSetContext(), SEV_ERROR, and string.

◆ sConvertIntToPoint()

static void sConvertIntToPoint ( CSeq_loc & loc )

static

Definition at line 789 of file xgbparint.cpp.

References CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetId(), CSeq_point_Base::SetFuzz(), CSeq_point_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetPnt(), and CSeq_point_Base::SetPoint().

Referenced by xgbint_ver().

◆ sGetAccession()

static int sGetAccession	(	string &	accession,
		unsigned int &	current_col,
		const string &	line,
		bool	accver
	)

static

Definition at line 367 of file xgbparint.cpp.

References sParseAccessionPrefix(), string, and xlex_error_func().

Referenced by xgbparselex_ver().

◆ sParseAccessionPrefix()

static size_t sParseAccessionPrefix ( string_view accession )

static

Definition at line 317 of file xgbparint.cpp.

References isalpha(), and isdigit().

Referenced by sGetAccession().

◆ USING_SCOPE()

USING_SCOPE ( objects )

◆ xfind_one_of_num()

static void xfind_one_of_num ( list< STokenInfo > & tokens )

static

Definition at line 246 of file xgbparint.cpp.

References eComma, eDotDot, eLeft, eOneOf, eOneOfNum, eRight, and next().

Referenced by xgbparseint_ver().

◆ XGapToSeqLocEx()

static CRef<CSeq_loc> XGapToSeqLocEx	(	Int4	range,
		bool	unknown
	)

static

Definition at line 729 of file xgbparint.cpp.

References compile_time_bits::range(), CRef< C, Locker >::Reset(), seqlitdbtag, CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetNull(), CSeq_interval_Base::SetTo(), and unkseqlitdbtag.

Referenced by xgbgap().

◆ xgbcheck_range()

static void xgbcheck_range	(	TSeqPos	num,
		const CSeq_id &	id,
		bool &	keep_rawPt,
		int &	numErrors,
		const TTokens &	tokens,
		TTokenConstIt	current
	)

static

Definition at line 205 of file xgbparint.cpp.

References len, Range_func, xgbparse_error(), and xgbparse_range_data.

Referenced by xgbint_ver().

◆ xgbgap()

static void xgbgap	(	TTokenIt &	current_it,
		TTokenConstIt	end_it,
		CRef< CSeq_loc > &	loc,
		bool	unknown
	)

static

Definition at line 754 of file xgbparint.cpp.

References eLeft, eNumber, eRight, next(), CSeq_loc::SetNull(), and XGapToSeqLocEx().

Referenced by xgbloc_ver().

◆ xgbint_ver()

static CRef<CSeq_loc> xgbint_ver	(	bool &	keep_rawPt,
		TTokenIt &	currentPt,
		const TTokens &	tokens,
		int &	numErrors,
		const TSeqIdList &	seq_ids,
		bool	accver
	)

static

Definition at line 957 of file xgbparint.cpp.

References CSeq_id::Assign(), CInt_fuzz_Base::e_not_set, eAccession, eCaret, eComma, eCompl, eDotDot, eGroup, eGt, eJoin, eLeft, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, eLt, eNumber, eOneOfNum, eOrder, eRight, eSingleDot, CSeq_point_Base::GetPoint(), NCBI_FALLTHROUGH, CRef< C, Locker >::NotEmpty(), Ref(), CRef< C, Locker >::Reset(), sConvertIntToPoint(), CSeq_point_Base::SetFuzz(), CInt_fuzz_Base::SetLim(), CSeq_point_Base::SetPoint(), TAKE_FIRST, TAKE_SECOND, xgbcheck_range(), xgbload_number(), and xgbparse_error().

Referenced by xgbloc_ver(), and xgbparseint_ver().

◆ xgbload_number()

static void xgbload_number	(	TSeqPos &	numPt,
		CInt_fuzz &	fuzz,
		bool &	keep_rawPt,
		TTokenIt &	currentPt,
		const TTokens &	tokens,
		int &	numErrors,
		int	take_which
	)

static

Definition at line 805 of file xgbparint.cpp.

References eCaret, eComma, eGt, eLeft, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eLt, eNumber, eOneOf, eOneOfNum, eRight, eSingleDot, CInt_fuzz_Base::C_Range::GetMax(), CInt_fuzz_Base::C_Range::GetMin(), CInt_fuzz_Base::GetRange(), CInt_fuzz_Base::SetLim(), CInt_fuzz_Base::C_Range::SetMax(), CInt_fuzz_Base::C_Range::SetMin(), CInt_fuzz_Base::SetRange(), TAKE_FIRST, TAKE_SECOND, and xgbparse_error().

Referenced by xgbint_ver().

◆ xgbloc_ver()

static CRef<CSeq_loc> xgbloc_ver	(	bool &	keep_rawPt,
		int &	parenPt,
		TTokenIt &	currentPt,
		const TTokens &	tokens,
		int &	numErrors,
		const TSeqIdList &	seq_ids,
		bool	accver
	)

static

Definition at line 1186 of file xgbparint.cpp.

References eAccession, eCaret, eComma, eCompl, eDotDot, eGap, eGroup, eGt, eJoin, eLeft, eLt, eNumber, eOneOf, eOneOfNum, eOrder, eReplace, eRight, eSingleDot, eSites, eString, eUnkGap, eUnknown, CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPnt(), CRef< C, Locker >::NotEmpty(), Ref(), CSeq_loc_Base::Reset(), SeqLocRevCmpl(), CSeq_loc::SetEquiv(), CSeq_loc::SetMix(), CSeq_loc::SetNull(), CSeq_loc::SetWhole(), xgbgap(), xgbint_ver(), and xgbparse_error().

Referenced by xgbparseint_ver(), and xgbreplace_ver().

◆ xgbparse_better_be_done()

static void xgbparse_better_be_done	(	int &	numErrors,
		TTokenIt	current_token,
		const TTokens &	tokens,
		bool &	keep_rawPt,
		int	paren_count
	)

static

Definition at line 685 of file xgbparint.cpp.

References eRight, and xgbparse_error().

Referenced by xgbparseint_ver().

◆ xgbparse_error() [1/2]

static void xgbparse_error	(	string_view	front,
		const TTokens &	tokens,
		TTokenConstIt	current
	)

static

Definition at line 198 of file xgbparint.cpp.

References ctll::front(), and xgbparse_error().

◆ xgbparse_error() [2/2]

static void xgbparse_error	(	string_view	front,
		TTokenConstIt	head,
		TTokenConstIt	current
	)

static

Definition at line 191 of file xgbparint.cpp.

References Err_func, ctll::front(), head, and xgbparse_point().

Referenced by xgbcheck_range(), xgbint_ver(), xgbload_number(), xgbloc_ver(), xgbparse_better_be_done(), xgbparse_error(), xgbparseint_ver(), and xgbreplace_ver().

◆ xgbparse_point()

static string xgbparse_point	(	TTokenConstIt	head,
		TTokenConstIt	current
	)

static

Definition at line 124 of file xgbparint.cpp.

References eAccession, eCaret, eComma, eCompl, eDotDot, eGroup, eGt, eJoin, eLeft, eLt, eNumber, eOneOf, eOneOfNum, eOrder, eReplace, eRight, eSingleDot, eString, eUnknown, head, and next().

Referenced by xgbparse_error().

◆ xgbparseint_ver()

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

Definition at line 1465 of file xgbparint.cpp.

References eAccession, eCaret, eComma, eCompl, eDotDot, eGroup, eGt, eJoin, eLeft, eLt, eNumber, eOneOf, eOneOfNum, eOrder, eReplace, eRight, eSingleDot, eSites, eString, eUnknown, NCBI_FALLTHROUGH, xfind_one_of_num(), xgbint_ver(), xgbloc_ver(), xgbparse_better_be_done(), xgbparse_error(), xgbparselex_ver(), and xgbreplace_ver().

Referenced by BOOST_AUTO_TEST_CASE(), GetCdRegionCB(), GetEmblInstContig(), GetGenBankInstContig(), GetSeqLocation(), GetTrnaAnticodon(), and XMLGetInstContig().

◆ xgbparselex_ver()

static int xgbparselex_ver	(	string_view	linein,
		TTokens &	tokens,
		bool	accver
	)

static

Definition at line 407 of file xgbparint.cpp.

References advance_to(), STokenInfo::choice, STokenInfo::data, eAccession, eCaret, eComma, eCompl, eDotDot, eGap, eGroup, eGt, eJoin, eLeft, eLt, NStr::eNocase, eNumber, eOneOf, eOrder, eReplace, eRight, eSingleDot, eSites, eString, eUnkGap, CTempString::find_first_not_of(), isdigit(), isspace(), len, sGetAccession(), NStr::StartsWith(), string, NStr::TruncateSpacesInPlace(), and xlex_error_func().

Referenced by xgbparseint_ver().

◆ xgbreplace_ver()

static CRef<CSeq_loc> xgbreplace_ver	(	bool &	keep_rawPt,
		int &	parenPt,
		TTokenIt &	currentPt,
		const TTokens &	tokens,
		int &	numErrors,
		const TSeqIdList &	seq_ids,
		bool	accver
	)

static

Definition at line 1428 of file xgbparint.cpp.

References eComma, eLeft, xgbloc_ver(), and xgbparse_error().

Referenced by xgbparseint_ver().

◆ xinstall_gbparse_error_handler()

void xinstall_gbparse_error_handler ( X_gbparse_errfunc new_func )

Definition at line 110 of file xgbparint.cpp.

References Err_func.

Referenced by GetTrnaAnticodon().

◆ xinstall_gbparse_range_func()

void xinstall_gbparse_range_func	(	void *	data,
		X_gbparse_rangefunc	new_func
	)

Definition at line 117 of file xgbparint.cpp.

References data, Range_func, and xgbparse_range_data.

Referenced by LoadFeat().

◆ xlex_error_func()

static void xlex_error_func	(	string_view	msg,
		const string &	line,
		unsigned int	current_col
	)

static

Definition at line 294 of file xgbparint.cpp.

References Err_func, and msg().

Referenced by sGetAccession(), and xgbparselex_ver().

Variable Documentation

◆ Err_func

X_gbparse_errfunc Err_func = do_xgbparse_error

static

Definition at line 104 of file xgbparint.cpp.

Referenced by xgbparse_error(), xinstall_gbparse_error_handler(), and xlex_error_func().

◆ Range_func

X_gbparse_rangefunc Range_func = nullptr

static

Definition at line 105 of file xgbparint.cpp.

Referenced by xgbcheck_range(), and xinstall_gbparse_range_func().

◆ seqlitdbtag

const char* seqlitdbtag = "SeqLit"

Definition at line 55 of file xgbparint.cpp.

Referenced by XGapToSeqLocEx(), and XISAGappedSeqLoc().

◆ unkseqlitdbtag

const char* unkseqlitdbtag = "UnkSeqLit"

Definition at line 56 of file xgbparint.cpp.

Referenced by XGappedSeqLocsToDeltaSeqs(), XGapToSeqLocEx(), and XISAGappedSeqLoc().

◆ xgbparse_range_data

void* xgbparse_range_data = nullptr

static

Definition at line 106 of file xgbparint.cpp.

Referenced by xgbcheck_range(), and xinstall_gbparse_range_func().

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Macro Definition Documentation

◆ ERR_FEATURE_LocationParsing_validatr

◆ TAKE_FIRST

◆ TAKE_SECOND

◆ THIS_FILE

Typedef Documentation

◆ TTokenConstIt

◆ TTokenIt

◆ TTokens

Enumeration Type Documentation

◆ ETokenType

Function Documentation

◆ advance_to()

◆ do_xgbparse_error()

◆ sConvertIntToPoint()

◆ sGetAccession()

◆ sParseAccessionPrefix()

◆ USING_SCOPE()

◆ xfind_one_of_num()

◆ XGapToSeqLocEx()

◆ xgbcheck_range()

◆ xgbgap()

◆ xgbint_ver()

◆ xgbload_number()

◆ xgbloc_ver()

◆ xgbparse_better_be_done()

◆ xgbparse_error() [1/2]

◆ xgbparse_error() [2/2]

◆ xgbparse_point()

◆ xgbparseint_ver()

◆ xgbparselex_ver()

◆ xgbreplace_ver()

◆ xinstall_gbparse_error_handler()

◆ xinstall_gbparse_range_func()

◆ xlex_error_func()

Variable Documentation

◆ Err_func

◆ Range_func

◆ seqlitdbtag

◆ unkseqlitdbtag

◆ xgbparse_range_data