#include "embl.h"
#include "genbank.h"
#include "macke.h"
#include "wrap.h"

Include dependency graph for embl.cxx:

Functions
static void	embl_continue_line (const char pattern, char &Str, Reader &reader)

static void	embl_one_entry (Reader &reader, char &entry, const char key)

static void	embl_date (Embl &embl, Reader &reader)

static void	embl_correct_title (Emblref &ref)

int	comment_subkey (const char line, char key)

bool	is_embl_comment (const char *line)

static void	embl_one_comment_entry (char *&datastring, int start_index, Reader &reader)

static void	embl_comments (Embl &embl, Reader &reader)

static void	embl_skip_unidentified (const char *pattern, Reader &reader)

static void	embl_origin (Seq &seq, Reader &reader)

void	embl_key_word (const char line, int index, char key)

static void	embl_print_lines (Writer &write, const char key, const char content, const WrapMode &wrapMode)

static bool	embl_print_lines_if_content (Writer &write, const char key, const char content, const WrapMode &wrapMode, bool followed_by_spacer)

static void	embl_print_comment_if_content (Writer &write, const char key, const char content)

void	embl_print_completeness (Writer &write, char compX, char X)

static void	embl_out_comments (const Embl &embl, const Seq &seq, Writer &write)

static void	embl_out_origin (const Seq &seq, Writer &write)

void	embl_out_header (const Embl &embl, const Seq &seq, Writer &write)

void	embl_out (const Embl &embl, const Seq &seq, Writer &write)

static char *	etog_author (char *Str)

static char *	etog_journal (const char *eJournal)

static void	etog_convert_references (const Embl &embl, GenBank &gbk)

int	etog (const Embl &embl, GenBank &gbk, const Seq &seq)

int	etom (const Embl &embl, Macke &macke, const Seq &seq)

static char *	gtoe_author (char *author)

static char *	gtoe_journal (char *Str)

static void	gtoe_reference (const GenBank &gbk, Embl &embl)

int	gtoe (const GenBank &gbk, Embl &embl, const Seq &seq)

static int	partial_mtoe (const Macke &macke, Embl &embl)

int	mtoe (const Macke &macke, Embl &embl, const Seq &seq)

Function Documentation

static void embl_continue_line	(	const char *	pattern,
		char *&	Str,
		Reader &	reader
	)

static

Definition at line 6 of file embl.cxx.

References embl_key_word(), has_content(), Reader::line(), LINESIZE, p_nonkey_start, skip_eolnl_and_append_spaced(), Skip_white_space(), str_equal(), and TOKENSIZE.

Referenced by embl_one_entry().

static void embl_one_entry	(	Reader &	reader,
		char *&	entry,
		const char *	key
	)

static

Definition at line 26 of file embl.cxx.

References embl_continue_line(), Reader::line(), p_nonkey_start, and Skip_white_space().

static void embl_date	(	Embl &	embl,
		Reader &	reader
	)

static

Definition at line 33 of file embl.cxx.

References embl_key_word(), Reader::line(), p_nonkey_start, Skip_white_space(), str_equal(), TOKENSIZE, and warning().

static void embl_correct_title ( Emblref & ref )

static

Definition at line 59 of file embl.cxx.

References Append(), ARB_strdup(), NULp, str0len(), terminate_with(), and Emblref::title.

Referenced by gtoe_reference().

int comment_subkey	(	const char *	line,
		char *	key
	)

Definition at line 83 of file embl.cxx.

References parse_key_word().

Referenced by embl_comments(), and genbank_comments().

bool is_embl_comment ( const char * line )

inline

Definition at line 95 of file embl.cxx.

Referenced by embl_comments(), and embl_one_comment_entry().

static void embl_one_comment_entry	(	char *&	datastring,
		int	start_index,
		Reader &	reader
	)

static

Definition at line 97 of file embl.cxx.

References count_spaces(), is_embl_comment(), Reader::line(), LINESIZE, p_nonkey_start, RDP_CONTINUED_INDENT, RDP_SUBKEY_INDENT, skip_eolnl_and_append_spaced(), and Skip_white_space().

Referenced by embl_comments().

static void embl_comments	(	Embl &	embl,
		Reader &	reader
	)

static

Definition at line 118 of file embl.cxx.

References Append(), comment_subkey(), embl_one_comment_entry(), is_embl_comment(), Reader::line(), offset, RDP_comments::others, parse_RDP_comment(), Skip_white_space(), and TOKENSIZE.

static void embl_skip_unidentified	(	const char *	pattern,
		Reader &	reader
	)

static

Definition at line 138 of file embl.cxx.

References embl_key_word(), Reader::line(), str_equal(), and TOKENSIZE.

static void embl_origin	(	Seq &	seq,
		Reader &	reader
	)

static

Definition at line 156 of file embl.cxx.

References Seq::add(), ca_assert, Seq::is_empty(), is_sequence_terminator(), Reader::line(), and line.

void embl_key_word	(	const char *	line,
		int	index,
		char *	key
	)

Definition at line 236 of file embl.cxx.

References parse_key_word().

Referenced by embl_continue_line(), embl_date(), embl_skip_unidentified(), etog(), EmblSwissprotReader::get_key_word(), and EmblParser::parse_section().

static void embl_print_lines	(	Writer &	write,
		const char *	key,
		const char *	content,
		const WrapMode &	wrapMode
	)

static

Definition at line 240 of file embl.cxx.

References ca_assert, EMBLINDENT, EMBLMAXLINE, WrapMode::print(), and TOKENSIZE.

Referenced by embl_out_header(), and embl_print_lines_if_content().

static bool embl_print_lines_if_content	(	Writer &	write,
		const char *	key,
		const char *	content,
		const WrapMode &	wrapMode,
		bool	followed_by_spacer
	)

static

Definition at line 250 of file embl.cxx.

References embl_print_lines(), has_content(), and Writer::out().

Referenced by embl_out_comments(), and embl_out_header().

static void embl_print_comment_if_content	(	Writer &	write,
		const char *	key,
		const char *	content
	)

static

Definition at line 259 of file embl.cxx.

References EMBLINDENT, EMBLMAXLINE, has_content(), LINESIZE, WrapMode::print(), RDP_CONTINUED_INDENT, and RDP_SUBKEY_INDENT.

Referenced by embl_out_comments().

void embl_print_completeness	(	Writer &	write,
		char	compX,
		char	X
	)

inline

Definition at line 269 of file embl.cxx.

References ca_assert, and Writer::outf().

Referenced by embl_out_comments().

static void embl_out_comments	(	const Embl &	embl,
		const Seq &	seq,
		Writer &	write
	)

static

Definition at line 275 of file embl.cxx.

References OrgInfo::commname, SeqInfo::comp3, SeqInfo::comp5, OrgInfo::cultcoll, embl_print_comment_if_content(), embl_print_completeness(), embl_print_lines_if_content(), OrgInfo::exists(), SeqInfo::exists(), OrgInfo::formname, SeqInfo::gbkentry, Seq::get_len(), OrgInfo::hostorg, SeqInfo::methods, OrgInfo::nickname, Writer::out(), Writer::outf(), SeqInfo::RDPid, and OrgInfo::source.

Referenced by embl_out_header().

static void embl_out_origin	(	const Seq &	seq,
		Writer &	write
	)

static

Definition at line 305 of file embl.cxx.

References BaseCounts::a, BaseCounts::c, Seq::count(), EMBL, BaseCounts::g, Seq::get_len(), BaseCounts::other, Seq::out(), Writer::outf(), and BaseCounts::t.

Referenced by embl_out().

void embl_out_header	(	const Embl &	embl,
		const Seq &	seq,
		Writer &	write
	)

Definition at line 315 of file embl.cxx.

References Emblref::author, embl_out_comments(), embl_print_lines(), embl_print_lines_if_content(), has_content(), Emblref::journal, Writer::out(), Writer::outf(), Emblref::processing, and Emblref::title.

Referenced by embl_out(), and embl_to_gcg().

void embl_out	(	const Embl &	embl,
		const Seq &	seq,
		Writer &	write
	)

Definition at line 360 of file embl.cxx.

References embl_out_header(), and embl_out_origin().

Referenced by write_to_embl().

static char* etog_author ( char * Str )

static

Definition at line 366 of file embl.cxx.

References Append(), ARB_strdup(), has_content(), str0len(), and TOKENSIZE.

Referenced by etog_convert_references().

static char* etog_journal ( const char * eJournal )

static

Definition at line 393 of file embl.cxx.

References Append(), ARB_realloc(), ca_assert, no_content(), NULp, scan_token_or_die(), str0len(), str_equal(), strndup(), TOKENSIZE, and warningf().

Referenced by etog_convert_references().

static void etog_convert_references	(	const Embl &	embl,
		GenBank &	gbk
	)

static

Definition at line 440 of file embl.cxx.

References Emblref::author, GenbankRef::author, etog_author(), etog_journal(), has_content(), Emblref::journal, GenbankRef::journal, LONGTEXT, no_content(), Emblref::processing, GenbankRef::ref, GenbankRef::standard, start, str0len(), Emblref::title, and GenbankRef::title.

Referenced by etog().

int etog	(	const Embl &	embl,
		GenBank &	gbk,
		const Seq &	seq
	)

Definition at line 488 of file embl.cxx.

References ASSERT_RESULT, copy_content(), embl_key_word(), etog_convert_references(), genbank_date(), Seq::get_len(), has_content(), LONGTEXT, str0len(), str_equal(), terminate_with(), today_date(), and TOKENSIZE.

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

int etom	(	const Embl &	embl,
		Macke &	macke,
		const Seq &	seq
	)

Definition at line 543 of file embl.cxx.

References etog(), and gtom().

Referenced by ConvertibleData::to_macke().

static char* gtoe_author ( char * author )

static

Definition at line 579 of file embl.cxx.

References Append(), find_pattern(), and str0len().

Referenced by gtoe_reference().

static char* gtoe_journal ( char * Str )

static

Definition at line 611 of file embl.cxx.

References scan_token(), str0len(), str_equal(), terminate_with(), and TOKENSIZE.

Referenced by gtoe_reference().

static void gtoe_reference	(	const GenBank &	gbk,
		Embl &	embl
	)

static

Definition at line 642 of file embl.cxx.

References Emblref::author, GenbankRef::author, embl_correct_title(), gtoe_author(), gtoe_journal(), Emblref::journal, GenbankRef::journal, no_content(), Emblref::processing, GenbankRef::ref, start, strf(), terminate_with(), Emblref::title, GenbankRef::title, and TOKENSIZE.

Referenced by gtoe().

int gtoe	(	const GenBank &	gbk,
		Embl &	embl,
		const Seq &	seq
	)

Definition at line 677 of file embl.cxx.

References copy_content(), Seq::get_len(), gtoe_reference(), has_content(), LONGTEXT, min, scan_token_or_die(), str0len(), strf(), terminate_with(), TOKENSIZE, and upcase().

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

static int partial_mtoe	(	const Macke &	macke,
		Embl &	embl
	)

static

Definition at line 741 of file embl.cxx.

References Append(), find_subspecies(), has_content(), is_end_mark(), skip_eolnl_and_append(), skip_pattern(), str0len(), and stristr().

Referenced by mtoe().

int mtoe	(	const Macke &	macke,
		Embl &	embl,
		const Seq &	seq
	)

Definition at line 772 of file embl.cxx.

References gtoe(), mtog(), and partial_mtoe().

Referenced by ConvertibleData::to_embl().

Functions

Function Documentation