ARB
prototypes.h
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1 /* This file is generated by aisc_mkpt.
2  * Any changes you make here will be overwritten later!
3  */
4 
5 #ifndef PROTOTYPES_H
6 #define PROTOTYPES_H
7 
8 /* define ARB attributes: */
9 #ifndef ATTRIBUTES_H
10 # include <attributes.h>
11 #endif
12 
13 
14 /* convert.cxx */
15 void convert(const FormattedFile& in, const FormattedFile& out);
16 
17 /* date.cxx */
18 const char *genbank_date(const char *other_date);
19 const char *today_date(void);
20 const char *gcg_date(const char *input);
21 
22 /* embl.cxx */
23 int comment_subkey(const char *line, char *key);
24 void embl_key_word(const char *line, int index, char *key);
25 void embl_out_header(const Embl& embl, const Seq& seq, Writer& write);
26 void embl_out(const Embl& embl, const Seq& seq, Writer& write);
27 int etog(const Embl& embl, GenBank& gbk, const Seq& seq) __ATTR__USERESULT;
28 int etom(const Embl& embl, Macke& macke, const Seq& seq) __ATTR__USERESULT;
29 int gtoe(const GenBank& gbk, Embl& embl, const Seq& seq) __ATTR__USERESULT;
30 int mtoe(const Macke& macke, Embl& embl, const Seq& seq) __ATTR__USERESULT;
31 
32 /* fconv.cxx */
38 void log_processed(int seqCount);
39 
40 /* gcg.cxx */
41 void to_gcg(const FormattedFile& in, const char *outf);
42 
43 /* genbank.cxx */
44 void genbank_key_word(const char *line, int index, char *key);
45 void genbank_out_header(const GenBank& gbk, const Seq& seq, Writer& write);
46 void genbank_out_base_count(const Seq& seq, Writer& write);
47 void genbank_out(const GenBank& gbk, const Seq& seq, Writer& write);
48 
49 /* macke.cxx */
50 void macke_origin(Seq& seq, char*& seqabbr, Reader& reader);
51 void macke_out_header(Writer& write);
52 void macke_seq_display_out(const Macke& macke, Writer& write, Format inType, bool first_sequence);
53 void macke_seq_info_out(const Macke& macke, Writer& write);
54 int macke_key_word(const char *line, int index, char *key);
55 void macke_seq_data_out(const Seq& seq, const Macke& macke, Writer& write);
56 
57 /* main.cxx */
58 int ARB_main(int argc, char *argv[]);
59 
60 /* mg.cxx */
61 int mtog(const Macke& macke, GenBank& gbk, const Seq& seq) __ATTR__USERESULT;
62 int gtom(const GenBank& gbk, Macke& macke) __ATTR__USERESULT;
63 
64 /* paup.cxx */
65 void to_paup(const FormattedFile& in, const char *outf);
66 
67 /* phylip.cxx */
68 void to_phylip(const FormattedFile& in, const char *outf, bool for_fastdnaml);
69 
70 /* printable.cxx */
71 void to_printable(const FormattedFile& in, const char *outf);
72 
73 /* rdp_info.cxx */
74 bool parse_RDP_comment(RDP_comments& comments, RDP_comment_parser one_comment_entry, const char *key, int index, Reader& reader);
75 
76 /* seq.cxx */
77 void read_alignment(Alignment& ali, const FormattedFile& in);
78 
79 /* util.cxx */
80 bool scan_token(char *to, const char *from) __ATTR__USERESULT;
81 void scan_token_or_die(char *to, const char *from);
82 void scan_token_or_die(char *to, Reader& reader, int offset);
83 void throw_error(int error_num, const char *error_message) __ATTR__NORETURN;
84 char *strf(const char *format, ...) __ATTR__FORMAT(1);
85 void throw_errorf(int error_num, const char *error_messagef, ...) __ATTR__FORMAT(2) __ATTR__NORETURN;
86 void warning(int warning_num, const char *warning_message);
87 void warningf(int warning_num, const char *warning_messagef, ...) __ATTR__FORMAT(2);
88 int Skip_white_space(const char *line, int index);
89 void Getstr(char *line, int linenum);
90 void terminate_with(char*& str, char ch);
91 void skip_eolnl_and_append(char*& string1, const char *string2);
92 void skip_eolnl_and_append_spaced(char*& string1, const char *string2);
93 void Append(char*& string1, const char *string2);
94 void Append(char*& string1, char ch);
95 void upcase(char *str);
96 int fputs_len(const char *str, int len, Writer& write);
97 int find_pattern(const char *text, const char *pattern);
98 int skip_pattern(const char *text, const char *pattern);
99 int find_subspecies(const char *str, char expect_behind);
100 int skip_subspecies(const char *str, char expect_behind);
101 int find_strain(const char *str, char expect_behind);
102 int skip_strain(const char *str, char expect_behind);
103 const char *stristr(const char *str, const char *substring);
104 int ___lookup_keyword(const char *keyword, const char *const *lookup_table, int lookup_table_size);
105 int parse_key_word(const char *line, char *key, const char *separator);
106 
107 #else
108 #error prototypes.h included twice
109 #endif /* PROTOTYPES_H */
int macke_key_word(const char *line, int index, char *key)
Definition: macke.cxx:189
int comment_subkey(const char *line, char *key)
Definition: embl.cxx:83
static long linenum
Definition: mkptypes.cxx:79
Definition: reader.h:21
int gtom(const GenBank &gbk, Macke &macke) __ATTR__USERESULT
Definition: mg.cxx:454
Format
Definition: fun.h:10
const char * gcg_date(const char *input)
Definition: date.cxx:232
AliDataPtr format(AliDataPtr data, const size_t wanted_len, GB_ERROR &error)
Definition: insdel.cxx:615
void throw_errorf(int error_num, const char *error_messagef,...) __ATTR__FORMAT(2) __ATTR__NORETURN
Definition: util.cxx:41
Definition: ali.h:11
void convert(const FormattedFile &in, const FormattedFile &out)
Definition: convert.cxx:156
int etog(const Embl &embl, GenBank &gbk, const Seq &seq) __ATTR__USERESULT
Definition: embl.cxx:488
void warningf(int warning_num, const char *warning_messagef,...) __ATTR__FORMAT(2)
Definition: util.cxx:66
void throw_unsupported_input_format(Format inType) __ATTR__NORETURN
Definition: fconv.cxx:39
const char * stristr(const char *str, const char *substring)
Definition: util.cxx:250
void(* RDP_comment_parser)(char *&datastring, int start_index, Reader &reader)
Definition: fun.h:49
int find_pattern(const char *text, const char *pattern)
Definition: util.cxx:241
int fputs_len(const char *str, int len, Writer &write)
Definition: util.cxx:155
void skip_eolnl_and_append(char *&string1, const char *string2)
Definition: util.cxx:127
#define __ATTR__FORMAT(pos)
Definition: attributes.h:60
void warning(int warning_num, const char *warning_message)
Definition: util.cxx:61
char * strf(const char *format,...) __ATTR__FORMAT(1)
Definition: util.cxx:27
int skip_subspecies(const char *str, char expect_behind)
Definition: util.cxx:245
int find_strain(const char *str, char expect_behind)
Definition: util.cxx:247
void macke_out_header(Writer &write)
Definition: macke.cxx:78
Definition: reader.h:95
FILE * seq
Definition: rns.c:46
void embl_key_word(const char *line, int index, char *key)
Definition: embl.cxx:236
void throw_incomplete_entry(void) __ATTR__NORETURN
Definition: fconv.cxx:43
void genbank_out_header(const GenBank &gbk, const Seq &seq, Writer &write)
Definition: genbank.cxx:368
void genbank_out_base_count(const Seq &seq, Writer &write)
Definition: genbank.cxx:440
int find_subspecies(const char *str, char expect_behind)
Definition: util.cxx:244
Definition: seq.h:43
void throw_conversion_failure(Format inType, Format ouType) __ATTR__NORETURN
Definition: fconv.cxx:31
void macke_seq_display_out(const Macke &macke, Writer &write, Format inType, bool first_sequence)
Definition: macke.cxx:85
void log_processed(int seqCount)
Definition: fconv.cxx:50
void skip_eolnl_and_append_spaced(char *&string1, const char *string2)
Definition: util.cxx:135
int mtoe(const Macke &macke, Embl &embl, const Seq &seq) __ATTR__USERESULT
Definition: embl.cxx:772
const char * today_date(void)
Definition: date.cxx:214
int etom(const Embl &embl, Macke &macke, const Seq &seq) __ATTR__USERESULT
Definition: embl.cxx:543
void macke_seq_info_out(const Macke &macke, Writer &write)
Definition: macke.cxx:162
void scan_token_or_die(char *to, const char *from)
Definition: util.cxx:14
int Skip_white_space(const char *line, int index)
Definition: util.cxx:84
void Getstr(char *line, int linenum)
Definition: util.cxx:92
void macke_origin(Seq &seq, char *&seqabbr, Reader &reader)
Definition: macke.cxx:72
void throw_error(int error_num, const char *error_message) __ATTR__NORETURN
Definition: util.cxx:23
void Append(char *&string1, const char *string2)
Definition: util.cxx:141
int ARB_main(int argc, char *argv[])
Definition: mkptypes.cxx:1545
static cstr error_message
Definition: readcfg.c:10
void embl_out(const Embl &embl, const Seq &seq, Writer &write)
Definition: embl.cxx:360
void throw_conversion_not_implemented(Format inType, Format ouType) __ATTR__NORETURN
Definition: fconv.cxx:35
#define __ATTR__USERESULT
Definition: attributes.h:58
int skip_strain(const char *str, char expect_behind)
Definition: util.cxx:248
void upcase(char *str)
Definition: util.cxx:149
bool scan_token(char *to, const char *from) __ATTR__USERESULT
Definition: util.cxx:10
void to_paup(const FormattedFile &in, const char *outf)
Definition: paup.cxx:88
bool parse_RDP_comment(RDP_comments &comments, RDP_comment_parser one_comment_entry, const char *key, int index, Reader &reader)
Definition: rdp_info.cxx:12
int ___lookup_keyword(const char *keyword, const char *const *lookup_table, int lookup_table_size)
Definition: util.cxx:255
static int pattern[maxsites+1]
void throw_conversion_not_supported(Format inType, Format ouType) __ATTR__NORETURN
Definition: fconv.cxx:27
static int line
Definition: arb_a2ps.c:296
void genbank_out(const GenBank &gbk, const Seq &seq, Writer &write)
Definition: genbank.cxx:450
void genbank_key_word(const char *line, int index, char *key)
Definition: genbank.cxx:9
int parse_key_word(const char *line, char *key, const char *separator)
Definition: util.cxx:265
void read_alignment(Alignment &ali, const FormattedFile &in)
Definition: seq.cxx:46
#define __ATTR__NORETURN
Definition: attributes.h:56
#define offset(field)
Definition: GLwDrawA.c:73
void embl_out_header(const Embl &embl, const Seq &seq, Writer &write)
Definition: embl.cxx:315
int mtog(const Macke &macke, GenBank &gbk, const Seq &seq) __ATTR__USERESULT
Definition: mg.cxx:414
int skip_pattern(const char *text, const char *pattern)
Definition: util.cxx:242
void to_phylip(const FormattedFile &in, const char *outf, bool for_fastdnaml)
Definition: phylip.cxx:64
void terminate_with(char *&str, char ch)
Definition: util.cxx:110
void to_printable(const FormattedFile &in, const char *outf)
Definition: printable.cxx:37
const char * genbank_date(const char *other_date)
Definition: date.cxx:164
int gtoe(const GenBank &gbk, Embl &embl, const Seq &seq) __ATTR__USERESULT
Definition: embl.cxx:677
void macke_seq_data_out(const Seq &seq, const Macke &macke, Writer &write)
Definition: macke.cxx:196
void to_gcg(const FormattedFile &in, const char *outf)
Definition: gcg.cxx:199