prototypes.h File Reference

#include <attributes.h>

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Functions
void	convert (const FormattedFile &in, const FormattedFile &out)
const char *	genbank_date (const char *other_date)
const char *	today_date (void)
const char *	gcg_date (const char *input)
int	comment_subkey (const char *line, char *key)
void	embl_key_word (const char *line, int index, char *key)
void	embl_out_header (const Embl &embl, const Seq &seq, Writer &write)
void	embl_out (const Embl &embl, const Seq &seq, Writer &write)
int	etog (const Embl &embl, GenBank &gbk, const Seq &seq) __ATTR__USERESULT
int	etom (const Embl &embl, Macke &macke, const Seq &seq) __ATTR__USERESULT
int	gtoe (const GenBank &gbk, Embl &embl, const Seq &seq) __ATTR__USERESULT
int	mtoe (const Macke &macke, Embl &embl, const Seq &seq) __ATTR__USERESULT
void	throw_conversion_not_supported (Format inType, Format ouType) __ATTR__NORETURN
void	throw_conversion_failure (Format inType, Format ouType) __ATTR__NORETURN
void	throw_conversion_not_implemented (Format inType, Format ouType) __ATTR__NORETURN
void	throw_unsupported_input_format (Format inType) __ATTR__NORETURN
void	throw_incomplete_entry (void) __ATTR__NORETURN
void	log_processed (int seqCount)
void	to_gcg (const FormattedFile &in, const char *outf)
void	genbank_key_word (const char *line, int index, char *key)
void	genbank_out_header (const GenBank &gbk, const Seq &seq, Writer &write)
void	genbank_out_base_count (const Seq &seq, Writer &write)
void	genbank_out (const GenBank &gbk, const Seq &seq, Writer &write)
void	macke_origin (Seq &seq, char *&seqabbr, Reader &reader)
void	macke_out_header (Writer &write)
void	macke_seq_display_out (const Macke &macke, Writer &write, Format inType, bool first_sequence)
void	macke_seq_info_out (const Macke &macke, Writer &write)
int	macke_key_word (const char *line, int index, char *key)
void	macke_seq_data_out (const Seq &seq, const Macke &macke, Writer &write)
int	ARB_main (int argc, char *argv[])
int	mtog (const Macke &macke, GenBank &gbk, const Seq &seq) __ATTR__USERESULT
int	gtom (const GenBank &gbk, Macke &macke) __ATTR__USERESULT
void	to_paup (const FormattedFile &in, const char *outf)
void	to_phylip (const FormattedFile &in, const char *outf, bool for_fastdnaml)
void	to_printable (const FormattedFile &in, const char *outf)
bool	parse_RDP_comment (RDP_comments &comments, RDP_comment_parser one_comment_entry, const char *key, int index, Reader &reader)
void	read_alignment (Alignment &ali, const FormattedFile &in)
bool	scan_token (char *to, const char *from) __ATTR__USERESULT
void	scan_token_or_die (char *to, const char *from)
void	scan_token_or_die (char *to, Reader &reader, int offset)
void	throw_error (int error_num, const char *error_message) __ATTR__NORETURN
char *	strf (const char *format,...) __ATTR__FORMAT(1)
void	throw_errorf (int error_num, const char *error_messagef,...) __ATTR__FORMAT(2) __ATTR__NORETURN
void	warning (int warning_num, const char *warning_message)
void	warningf (int warning_num, const char *warning_messagef,...) __ATTR__FORMAT(2)
int	Skip_white_space (const char *line, int index)
void	Getstr (char *line, int linenum)
void	terminate_with (char *&str, char ch)
void	skip_eolnl_and_append (char *&string1, const char *string2)
void	skip_eolnl_and_append_spaced (char *&string1, const char *string2)
void	Append (char *&string1, const char *string2)
void	Append (char *&string1, char ch)
void	upcase (char *str)
int	fputs_len (const char *str, int len, Writer &write)
int	find_pattern (const char *text, const char *pattern)
int	skip_pattern (const char *text, const char *pattern)
int	find_subspecies (const char *str, char expect_behind)
int	skip_subspecies (const char *str, char expect_behind)
int	find_strain (const char *str, char expect_behind)
int	skip_strain (const char *str, char expect_behind)
const char *	stristr (const char *str, const char *substring)
int	___lookup_keyword (const char *keyword, const char *const *lookup_table, int lookup_table_size)
int	parse_key_word (const char *line, char *key, const char *separator)

Function Documentation

void convert	(	const FormattedFile &	in,
		const FormattedFile &	out
	)

Definition at line 154 of file convert.cxx.

References FormatReader::create(), EMBL, FASTDNAML, GCG, GENBANK, MACKE, FormattedFile::name(), NEXUS, PHYLIP, PRINTABLE, seq, str_equal(), SWISSPROT, throw_conversion_not_supported(), throw_error(), to_gcg(), to_macke(), to_paup(), to_phylip(), to_printable(), FormattedFile::type(), write_to_embl(), and write_to_genbank().

Referenced by do_conversion().

const char* genbank_date

(

const char *

other_date

)

Definition at line 164 of file date.cxx.

References ca_assert, days_in_month, find_date(), find_date_long_form(), genbank_date(), is_genbank_date(), length, result, SIZE, str0len(), and warningf().

Referenced by etog(), genbank_date(), FINAL_TYPE< SEQTYPE >::get_date(), and mtog().

const char* today_date

(

void

)

Definition at line 214 of file date.cxx.

References line, and SIZE.

Referenced by etog(), gcg_seq_out(), FINAL_TYPE< SEQTYPE >::get_date(), macke_out_header(), mtog(), and paup_print_headerstart().

const char* gcg_date

(

const char *

input

)

Definition at line 232 of file date.cxx.

References ca_assert, IF_ASSERTION_USED, ismonth(), and SIZE.

Referenced by gcg_seq_out().

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().

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().

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().

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().

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().

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().

void throw_conversion_not_supported	(	Format	inType,
		Format	ouType
	)

Definition at line 27 of file fconv.cxx.

References format2name(), and throw_errorf().

Referenced by convert(), to_gcg(), to_paup(), to_phylip(), and to_printable().

void throw_conversion_failure	(	Format	inType,
		Format	ouType
	)

Definition at line 31 of file fconv.cxx.

References format2name(), and throw_errorf().

Referenced by ConvertibleData::to_embl(), ConvertibleData::to_genbank(), and ConvertibleData::to_macke().

void throw_conversion_not_implemented	(	Format	inType,
		Format	ouType
	)

Definition at line 35 of file fconv.cxx.

References format2name(), and throw_errorf().

Referenced by ConvertibleData::to_embl(), ConvertibleData::to_genbank(), and ConvertibleData::to_macke().

void throw_unsupported_input_format

(

Format

inType

)

Definition at line 39 of file fconv.cxx.

References format2name(), and throw_errorf().

Referenced by FormatReader::create().

void throw_incomplete_entry

(

void

)

Definition at line 43 of file fconv.cxx.

References throw_error().

Referenced by Parser::parse_entry().

void log_processed

(

int

seqCount

)

Definition at line 50 of file fconv.cxx.

Referenced by FileWriter::~FileWriter().

void to_gcg	(	const FormattedFile &	in,
		const char *	outf
	)

Definition at line 199 of file gcg.cxx.

References EMBL, embl_to_gcg(), GCG, GENBANK, genbank_to_gcg(), MACKE, macke_to_gcg(), FormattedFile::name(), SWISSPROT, throw_conversion_not_supported(), and FormattedFile::type().

Referenced by convert().

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

Definition at line 9 of file genbank.cxx.

References ca_assert, GBINDENT, and parse_key_word().

Referenced by genbank_reference(), genbank_source(), GenbankReader::get_key_word(), gtom(), and GenbankParser::parse_section().

void genbank_out_header	(	const GenBank &	gbk,
		const Seq &	seq,
		Writer &	write
	)

Definition at line 368 of file genbank.cxx.

References OrgInfo::commname, SeqInfo::comp3, SeqInfo::comp5, OrgInfo::cultcoll, OrgInfo::exists(), SeqInfo::exists(), RDP_comments::exists(), OrgInfo::formname, GBINDENT, SeqInfo::gbkentry, genbank_out_one_entry(), genbank_out_one_reference(), genbank_print_comment_if_content(), genbank_print_completeness(), Seq::get_len(), OrgInfo::hostorg, length, SeqInfo::methods, OrgInfo::nickname, NOPERIOD, RDP_comments::orginf, RDP_comments::others, Writer::out(), Writer::outf(), PERIOD, SeqInfo::RDPid, Writer::repeated(), RDP_comments::seqinf, OrgInfo::source, and str0len().

Referenced by genbank_out(), and genbank_to_gcg().

void genbank_out_base_count	(	const Seq &	seq,
		Writer &	write
	)

Definition at line 440 of file genbank.cxx.

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

Referenced by genbank_out(), and genbank_to_gcg().

void genbank_out	(	const GenBank &	gbk,
		const Seq &	seq,
		Writer &	write
	)

Definition at line 450 of file genbank.cxx.

References genbank_out_base_count(), genbank_out_header(), genbank_out_origin(), and Writer::out().

Referenced by write_to_genbank().

void macke_origin	(	Seq &	seq,
		char *&	seqabbr,
		Reader &	reader
	)

Definition at line 72 of file macke.cxx.

References ca_assert, and macke_read_seq().

void macke_out_header

(

Writer &

write

)

Definition at line 78 of file macke.cxx.

References Writer::out(), Writer::outf(), and today_date().

Referenced by to_macke().

void macke_seq_display_out	(	const Macke &	macke,
		Writer &	write,
		Format	inType,
		bool	first_sequence
	)

Definition at line 85 of file macke.cxx.

References Writer::out(), Writer::outf(), and SWISSPROT.

Referenced by write_to_macke().

void macke_seq_info_out	(	const Macke &	macke,
		Writer &	write
	)

Definition at line 162 of file macke.cxx.

References macke_is_genbank_entry_comment(), macke_print_keyword_rem(), macke_print_prefixed_line(), macke_print_prefixed_line_if_content(), and Writer::name().

Referenced by macke_to_gcg(), and write_to_macke().

int macke_key_word	(	const char *	line,
		int	index,
		char *	key
	)

Definition at line 189 of file macke.cxx.

References parse_key_word().

Referenced by macke_is_genbank_entry_comment(), and mtog_decode_ref_and_remarks().

void macke_seq_data_out	(	const Seq &	seq,
		const Macke &	macke,
		Writer &	write
	)

Definition at line 196 of file macke.cxx.

References Seq::get_len(), Seq::get_seq(), MACKELIMIT, Writer::out(), Writer::outf(), and warningf().

Referenced by write_to_macke().

int ARB_main	(	int	argc,
		char *	argv[]
	)

Definition at line 1545 of file mkptypes.cxx.

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().

void to_paup	(	const FormattedFile &	in,
		const char *	outf
	)

Definition at line 88 of file paup.cxx.

References ARB_strdup(), ca_assert, FileWriter::expect_written(), Alignment::get(), Alignment::get_count(), FileWriter::get_FILE(), Alignment::get_len(), Alignment::get_max_len(), Alignment::getSeqPtr(), is_input_format(), NEXUS, FileWriter::out(), paup_print_header(), paup_print_header_counters(), paup_print_headerstart(), paup_print_line(), paup_verify_name(), read_alignment(), seq, FileWriter::seq_done(), SEQLINE, throw_conversion_not_supported(), and FormattedFile::type().

Referenced by convert().

void to_phylip	(	const FormattedFile &	in,
		const char *	outf,
		bool	for_fastdnaml
	)

Definition at line 64 of file phylip.cxx.

References ca_assert, FileWriter::expect_written(), Alignment::get(), Alignment::get_count(), FileWriter::get_FILE(), Alignment::get_max_len(), inject_STDIN(), is_input_format(), FileWriter::out(), FileWriter::outf(), PHYLIP, phylip_print_line(), read_alignment(), FileWriter::seq_done(), SEQLINE, throw_conversion_not_supported(), throw_error(), throw_errorf(), and FormattedFile::type().

Referenced by convert().

void to_printable	(	const FormattedFile &	in,
		const char *	outf
	)

Definition at line 37 of file printable.cxx.

References ca_assert, FileWriter::expect_written(), Alignment::get(), Alignment::get_count(), Seq::get_id(), Seq::get_len(), Alignment::get_max_len(), Seq::get_seq(), implicated, is_gapchar(), is_input_format(), length, FileWriter::out(), PRINTABLE, printable_print_line(), PRTLENGTH, read_alignment(), seq, FileWriter::seq_done(), start, throw_conversion_not_supported(), and FormattedFile::type().

Referenced by convert().

bool parse_RDP_comment	(	RDP_comments &	comments,
		RDP_comment_parser	one_comment_entry,
		const char *	key,
		int	index,
		Reader &	reader
	)

Definition at line 12 of file rdp_info.cxx.

References OrgInfo::commname, SeqInfo::comp3, SeqInfo::comp5, OrgInfo::cultcoll, OrgInfo::formname, SeqInfo::gbkentry, OrgInfo::hostorg, SeqInfo::methods, OrgInfo::nickname, RDP_comments::orginf, SeqInfo::RDPid, scan_token_or_die(), RDP_comments::seqinf, OrgInfo::source, str_equal(), and TOKENSIZE.

Referenced by embl_comments(), and genbank_comments().

void read_alignment	(	Alignment &	ali,
		const FormattedFile &	in
	)

Definition at line 46 of file seq.cxx.

References Alignment::add(), FormatReader::create(), and seq.

Referenced by to_paup(), to_phylip(), and to_printable().

bool scan_token	(	char *	to,
		const char *	from
	)

Definition at line 10 of file util.cxx.

Referenced by gtoe_journal(), and scan_token_or_die().

void scan_token_or_die	(	char *	to,
		const char *	from
	)

Definition at line 14 of file util.cxx.

References scan_token(), and throw_error().

Referenced by etog_journal(), gtoe(), gtom(), mtog_decode_ref_and_remarks(), parse_RDP_comment(), and scan_token_or_die().

void scan_token_or_die	(	char *	to,
		Reader &	reader,
		int	offset
	)

Definition at line 19 of file util.cxx.

References Reader::line(), offset, and scan_token_or_die().

void throw_error	(	int	error_num,
		const char *	error_message
	)

Definition at line 23 of file util.cxx.

Referenced by ask_for_conversion_params(), convert(), scan_token_or_die(), throw_errorf(), throw_incomplete_entry(), and to_phylip().

char* strf	(	const char *	format,
			...
	)

Definition at line 27 of file util.cxx.

References buffer, BUFSIZE, ca_assert, strndup(), va_end(), and va_start().

Referenced by add_link_attributes(), check_specific_duplicates(), genbank_verify_accession(), gtoe(), gtoe_reference(), gtom(), and Helpfile::readHelp().

void throw_errorf	(	int	error_num,
		const char *	error_messagef,
			...
	)

Definition at line 41 of file util.cxx.

References buffer, BUFSIZE, throw_error(), va_end(), and va_start().

Referenced by ask_for_conversion_params(), command_line_conversion(), FileWriter::expect_written(), FileWriter::FileWriter(), genbank_verify_accession(), macke_read_seq(), parse_intype(), parse_outtype(), Reader::Reader(), throw_conversion_failure(), throw_conversion_not_implemented(), throw_conversion_not_supported(), throw_unsupported_input_format(), Writer::throw_write_error(), to_phylip(), valid_name_or_die(), and warningf().

void warning	(	int	warning_num,
		const char *	warning_message
	)

Definition at line 61 of file util.cxx.

References Warnings::shown().

Referenced by MG_remap::add_reference(), alignToNextRelative(), ARB_main(), awt_create_input_mask(), AWTC_pars_names(), compress_sequence_tree(), embl_date(), GB_login(), GEN_root::GEN_root(), genbank_verify_keywords(), main(), MERGE_sequences_simple(), MG_create_remap(), mtog_genbank_def_and_source(), pars_start_cb(), readCfg(), reorder_keys(), reorder_up_down(), StorableSelectionList::save(), KeySorter::save_changes(), GB_MAIN_TYPE::save_quick_as(), scan_existing_input_masks(), and warningf().

void warningf	(	int	warning_num,
		const char *	warning_messagef,
			...
	)

Definition at line 66 of file util.cxx.

References buffer, BUFSIZE, Warnings::shown(), throw_errorf(), va_end(), va_start(), and warning().

Referenced by cfgReadWarning(), check_consistency(), do_conversion(), etog_journal(), genbank_date(), genbank_reference(), macke_seq_data_out(), readCfg(), and GcgWriter::set_species_name().

int Skip_white_space	(	const char *	line,
		int	index
	)

Definition at line 84 of file util.cxx.

Referenced by embl_comments(), embl_continue_line(), embl_date(), embl_one_comment_entry(), embl_one_entry(), genbank_comments(), genbank_continue_line(), genbank_one_comment_entry(), genbank_one_entry_in(), genbank_source(), get_atcc(), get_string(), and macke_abbrev().

void Getstr	(	char *	line,
		int	linenum
	)

Definition at line 92 of file util.cxx.

Referenced by ask_for_conversion_params().

void terminate_with	(	char *&	str,
		char	ch
	)

Definition at line 110 of file util.cxx.

References append_known_len(), ca_assert, and str0len().

Referenced by embl_correct_title(), etog(), genbank_reference(), genbank_verify_keywords(), gtoe(), gtoe_journal(), gtoe_reference(), mtog(), mtog_decode_ref_and_remarks(), and mtog_genbank_def_and_source().

void skip_eolnl_and_append	(	char *&	string1,
		const char *	string2
	)

Definition at line 127 of file util.cxx.

References append_known_len(), and str0len().

Referenced by genbank_verify_accession(), mtog_genbank_def_and_source(), and partial_mtoe().

void skip_eolnl_and_append_spaced	(	char *&	string1,
		const char *	string2
	)

Definition at line 135 of file util.cxx.

References append_known_len(), and str0len().

Referenced by FINAL_TYPE< SEQTYPE >::copy_multi_rem(), embl_continue_line(), embl_one_comment_entry(), genbank_continue_line(), macke_continue_line(), and macke_one_entry_in().

void Append	(	char *&	string1,
		const char *	string2
	)

Definition at line 141 of file util.cxx.

References append_known_len(), and str0len().

Referenced by FINAL_TYPE< SEQTYPE >::add_remark(), embl_comments(), embl_correct_title(), etog_author(), etog_journal(), genbank_comments(), genbank_verify_accession(), gtoe_author(), gtom(), mtog_decode_ref_and_remarks(), mtog_genbank_def_and_source(), and partial_mtoe().

void Append	(	char *&	string1,
		char	ch
	)

Definition at line 145 of file util.cxx.

References append_known_len(), and str0len().

void upcase

(

char *

str

)

Definition at line 149 of file util.cxx.

Referenced by gtoe().

int fputs_len	(	const char *	str,
		int	len,
		Writer &	write
	)

Definition at line 155 of file util.cxx.

References Writer::out().

int find_pattern	(	const char *	text,
		const char *	pattern
	)

Definition at line 241 of file util.cxx.

References FIND_START, and findPattern().

Referenced by correct_subspecies(), genbank_get_strain(), genbank_get_subspecies(), get_atcc(), gtoe_author(), and stristr().

int skip_pattern	(	const char *	text,
		const char *	pattern
	)

Definition at line 242 of file util.cxx.

References FIND_SKIP_OVER, and findPattern().

Referenced by genbank_get_strain(), genbank_get_subspecies(), and partial_mtoe().

int find_subspecies	(	const char *	str,
		char	expect_behind
	)

Definition at line 244 of file util.cxx.

References FIND_START, and findSubspecies().

Referenced by partial_mtoe().

int skip_subspecies	(	const char *	str,
		char	expect_behind
	)

Definition at line 245 of file util.cxx.

References FIND_SKIP_OVER, and findSubspecies().

Referenced by genbank_get_subspecies().

int find_strain	(	const char *	str,
		char	expect_behind
	)

Definition at line 247 of file util.cxx.

References FIND_START, and findStrain().

Referenced by correct_subspecies().

int skip_strain	(	const char *	str,
		char	expect_behind
	)

Definition at line 248 of file util.cxx.

References FIND_SKIP_OVER, and findStrain().

Referenced by check_strain_from().

const char* stristr	(	const char *	str,
		const char *	substring
	)

Definition at line 250 of file util.cxx.

References find_pattern(), NULp, and offset.

Referenced by partial_mtoe().

int ___lookup_keyword	(	const char *	keyword,
		const char *const *	lookup_table,
		int	lookup_table_size
	)

Definition at line 255 of file util.cxx.

References str_equal().

int parse_key_word	(	const char *	line,
		char *	key,
		const char *	separator
	)

Definition at line 265 of file util.cxx.

References occurs_in(), and TOKENSIZE.

Referenced by comment_subkey(), embl_key_word(), genbank_key_word(), macke_abbrev(), and macke_key_word().