RNAlib-2.6.3
 
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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
23#define VRNA_FILE_FORMAT_MSA_CLUSTAL 1U
24
30#define VRNA_FILE_FORMAT_MSA_STOCKHOLM 2U
31
37#define VRNA_FILE_FORMAT_MSA_FASTA 4U
38
44#define VRNA_FILE_FORMAT_MSA_MAF 8U
45
54#define VRNA_FILE_FORMAT_MSA_MIS 16U
55
61#define VRNA_FILE_FORMAT_MSA_DEFAULT ( \
62 VRNA_FILE_FORMAT_MSA_CLUSTAL \
63 | VRNA_FILE_FORMAT_MSA_STOCKHOLM \
64 | VRNA_FILE_FORMAT_MSA_FASTA \
65 | VRNA_FILE_FORMAT_MSA_MAF \
66 )
67
73#define VRNA_FILE_FORMAT_MSA_NOCHECK 4096U
74
80#define VRNA_FILE_FORMAT_MSA_UNKNOWN 8192U
81
87#define VRNA_FILE_FORMAT_MSA_APPEND 16384U
88
94#define VRNA_FILE_FORMAT_MSA_QUIET 32768U
95
101#define VRNA_FILE_FORMAT_MSA_SILENT 65536U
102
154int
155vrna_file_msa_read(const char *filename,
156 char ***names,
157 char ***aln,
158 char **id,
159 char **structure,
160 unsigned int options);
161
162
218int
220 char ***names,
221 char ***aln,
222 char **id,
223 char **structure,
224 unsigned int options);
225
226
252unsigned int
253vrna_file_msa_detect_format(const char *filename,
254 unsigned int options);
255
256
274int
275vrna_file_msa_write(const char *filename,
276 const char **names,
277 const char **aln,
278 const char *id,
279 const char *structure,
280 const char *source,
281 unsigned int options);
282
283
288#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.