#include "genbank.h"
#include "macke.h"

Include dependency graph for mg.cxx:

Functions
static int	paren_string (char line, char pstring, int index)

static void	get_atcc_string (const char line, char temp, int index)

static char *	get_atcc (const Macke &macke, char *source)

static char *	genbank_get_atcc (const GenBank &gbk, const Macke &macke)

static void	correct_subspecies (char *subspecies)

static void	check_consistency (const char what, char const &var, const char *New)

static void	get_string (char temp, const char line, int index)

static void	copy_subspecies_and_check_consistency (char const &subspecies, const char from, int indj)

static void	copy_strain_and_check_consistency (char const &strain, const char from, int indj)

static void	check_strain_from (char const &strain, const char from)

static char *	genbank_get_strain (const GenBank &gbk)

static char *	genbank_get_subspecies (const GenBank &gbk)

static void	mtog_decode_ref_and_remarks (const Macke &macke, GenBank &gbk)

static void	mtog_genbank_def_and_source (const Macke &macke, GenBank &gbk)

int	mtog (const Macke &macke, GenBank &gbk, const Seq &seq)

int	gtom (const GenBank &gbk, Macke &macke)

Function Documentation

static int paren_string	(	char *	line,
		char *	pstring,
		int	index
	)

static

Definition at line 6 of file mg.cxx.

References str0len().

Referenced by get_atcc().

static void get_atcc_string	(	const char *	line,
		char *	temp,
		int	index
	)

static

Definition at line 25 of file mg.cxx.

References str0len().

Referenced by get_atcc().

static char* get_atcc	(	const Macke &	macke,
		char *	source
	)

static

Definition at line 47 of file mg.cxx.

References buffer, find_pattern(), get_atcc_string(), length, LONGTEXT, paren_string(), Skip_white_space(), and str0len().

Referenced by genbank_get_atcc().

static char* genbank_get_atcc	(	const GenBank &	gbk,
		const Macke &	macke
	)

static

Definition at line 90 of file mg.cxx.

References get_atcc(), has_content(), LONGTEXT, and NULp.

Referenced by gtom().

static void correct_subspecies ( char * subspecies )

static

Definition at line 175 of file mg.cxx.

References ca_assert, find_pattern(), and find_strain().

Referenced by copy_subspecies_and_check_consistency().

static void check_consistency	(	const char *	what,
		char *const &	var,
		const char *	New
	)

static

Definition at line 186 of file mg.cxx.

References has_content(), str_equal(), and warningf().

Referenced by copy_strain_and_check_consistency(), and copy_subspecies_and_check_consistency().

static void get_string	(	char *	temp,
		const char *	line,
		int	index
	)

static

Definition at line 199 of file mg.cxx.

References is_end_mark(), Skip_white_space(), and str0len().

Referenced by copy_strain_and_check_consistency(), and copy_subspecies_and_check_consistency().

static void copy_subspecies_and_check_consistency	(	char *const &	subspecies,
		const char *	from,
		int	indj
	)

static

Definition at line 228 of file mg.cxx.

References check_consistency(), correct_subspecies(), get_string(), and LONGTEXT.

Referenced by genbank_get_subspecies().

static void copy_strain_and_check_consistency	(	char *const &	strain,
		const char *	from,
		int	indj
	)

static

Definition at line 234 of file mg.cxx.

References check_consistency(), get_string(), and LONGTEXT.

Referenced by check_strain_from(), and genbank_get_strain().

static void check_strain_from	(	char *const &	strain,
		const char *	from
	)

static

Definition at line 240 of file mg.cxx.

References copy_strain_and_check_consistency(), has_content(), and skip_strain().

Referenced by genbank_get_strain().

static char* genbank_get_strain ( const GenBank & gbk )

static

Definition at line 247 of file mg.cxx.

References check_strain_from(), copy_strain_and_check_consistency(), find_pattern(), has_content(), LONGTEXT, and skip_pattern().

Referenced by gtom().

static char* genbank_get_subspecies ( const GenBank & gbk )

static

Definition at line 267 of file mg.cxx.

References copy_subspecies_and_check_consistency(), find_pattern(), has_content(), LONGTEXT, skip_pattern(), and skip_subspecies().

Referenced by gtom().

static void mtog_decode_ref_and_remarks	(	const Macke &	macke,
		GenBank &	gbk
	)

static

Definition at line 297 of file mg.cxx.

References Append(), ca_assert, OrgInfo::commname, SeqInfo::comp3, SeqInfo::comp5, OrgInfo::formname, has_content(), OrgInfo::hostorg, macke_key_word(), SeqInfo::methods, OrgInfo::nickname, offset, RDP_comments::orginf, RDP_comments::others, SeqInfo::RDPid, GenbankRef::ref, scan_token_or_die(), RDP_comments::seqinf, OrgInfo::source, str_equal(), terminate_with(), and TOKENSIZE.

Referenced by mtog().

static void mtog_genbank_def_and_source	(	const Macke &	macke,
		GenBank &	gbk
	)

static

Definition at line 374 of file mg.cxx.

References Append(), copy_content(), has_content(), skip_eolnl_and_append(), terminate_with(), and warning().

Referenced by mtog().

int mtog	(	const Macke &	macke,
		GenBank &	gbk,
		const Seq &	seq
	)

Definition at line 414 of file mg.cxx.

References copy_content(), OrgInfo::cultcoll, SeqInfo::gbkentry, genbank_date(), Seq::get_len(), has_content(), LONGTEXT, SeqInfo::methods, mtog_decode_ref_and_remarks(), mtog_genbank_def_and_source(), RDP_comments::orginf, RDP_comments::seqinf, str0len(), terminate_with(), and today_date().

Referenced by mtoe(), and ConvertibleData::to_genbank().

int gtom	(	const GenBank &	gbk,
		Macke &	macke
	)

Definition at line 454 of file mg.cxx.

References Append(), ASSERT_RESULT, buffer, copy_content(), OrgInfo::cultcoll, SeqInfo::gbkentry, genbank_get_atcc(), genbank_get_strain(), genbank_get_subspecies(), genbank_key_word(), has_content(), LONGTEXT, SeqInfo::methods, scan_token_or_die(), str0len(), str_equal(), strf(), and TOKENSIZE.

Referenced by etom(), and ConvertibleData::to_macke().

Functions

Function Documentation