source: tags/ms_r16q3/CONVERTALN/prototypes.h

/* This file is generated by aisc_mkpt.
 * Any changes you make here will be overwritten later!
 */

#ifndef PROTOTYPES_H
#define PROTOTYPES_H

/* define ARB attributes: */
#ifndef ATTRIBUTES_H
# include <attributes.h>
#endif


/* convert.cxx */
void convert(const FormattedFile& in, const FormattedFile& out);

/* date.cxx */
const char *genbank_date(const char *other_date);
const char *today_date(void);
const char *gcg_date(const char *input);

/* embl.cxx */
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;

/* fconv.cxx */
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);

/* gcg.cxx */
void to_gcg(const FormattedFile& in, const char *outf);

/* genbank.cxx */
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);

/* macke.cxx */
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);

/* main.cxx */
int ARB_main(int argc, char *argv[]);

/* mg.cxx */
int mtog(const Macke& macke, GenBank& gbk, const Seq& seq) __ATTR__USERESULT;
int gtom(const GenBank& gbk, Macke& macke) __ATTR__USERESULT;

/* paup.cxx */
void to_paup(const FormattedFile& in, const char *outf);

/* phylip.cxx */
void to_phylip(const FormattedFile& in, const char *outf, bool for_fastdnaml);

/* printable.cxx */
void to_printable(const FormattedFile& in, const char *outf);

/* rdp_info.cxx */
bool parse_RDP_comment(RDP_comments& comments, RDP_comment_parser one_comment_entry, const char *key, int index, Reader& reader);

/* seq.cxx */
void read_alignment(Alignment& ali, const FormattedFile& in);

/* util.cxx */
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);

#else
#error prototypes.h included twice
#endif /* PROTOTYPES_H */