RNAlib-2.5.1
file_formats_msa.h
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1#ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_H
2#define VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_H
3
10#include <stdio.h>
11
22#define VRNA_FILE_FORMAT_MSA_CLUSTAL 1U
23
28#define VRNA_FILE_FORMAT_MSA_STOCKHOLM 2U
29
34#define VRNA_FILE_FORMAT_MSA_FASTA 4U
35
40#define VRNA_FILE_FORMAT_MSA_MAF 8U
41
50#define VRNA_FILE_FORMAT_MSA_MIS 16U
51
56#define VRNA_FILE_FORMAT_MSA_DEFAULT ( \
57 VRNA_FILE_FORMAT_MSA_CLUSTAL \
58 | VRNA_FILE_FORMAT_MSA_STOCKHOLM \
59 | VRNA_FILE_FORMAT_MSA_FASTA \
60 | VRNA_FILE_FORMAT_MSA_MAF \
61 )
62
67#define VRNA_FILE_FORMAT_MSA_NOCHECK 4096U
68
73#define VRNA_FILE_FORMAT_MSA_UNKNOWN 8192U
74
79#define VRNA_FILE_FORMAT_MSA_APPEND 16384U
80
85#define VRNA_FILE_FORMAT_MSA_QUIET 32768U
86
91#define VRNA_FILE_FORMAT_MSA_SILENT 65536U
92
145int
146vrna_file_msa_read(const char *filename,
147 char ***names,
148 char ***aln,
149 char **id,
150 char **structure,
151 unsigned int options);
152
153
210int
212 char ***names,
213 char ***aln,
214 char **id,
215 char **structure,
216 unsigned int options);
217
218
244unsigned int
245vrna_file_msa_detect_format(const char *filename,
246 unsigned int options);
247
248
266int
267vrna_file_msa_write(const char *filename,
268 const char **names,
269 const char **aln,
270 const char *id,
271 const char *structure,
272 const char *source,
273 unsigned int options);
274
275
280#endif
int vrna_file_msa_write(const char *filename, const char **names, const char **aln, const char *id, const char *structure, const char *source, unsigned int options)
Write multiple sequence alignment file.
int vrna_file_msa_read(const char *filename, char ***names, char ***aln, char **id, char **structure, unsigned int options)
Read a multiple sequence alignment from file.
int vrna_file_msa_read_record(FILE *fp, char ***names, char ***aln, char **id, char **structure, unsigned int options)
Read a multiple sequence alignment from file handle.
unsigned int vrna_file_msa_detect_format(const char *filename, unsigned int options)
Detect the format of a multiple sequence alignment file.