RNAlib-2.4.3
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 
13 #include <stdio.h>
14 
19 #define VRNA_FILE_FORMAT_MSA_CLUSTAL 1U
20 
25 #define VRNA_FILE_FORMAT_MSA_STOCKHOLM 2U
26 
31 #define VRNA_FILE_FORMAT_MSA_FASTA 4U
32 
37 #define VRNA_FILE_FORMAT_MSA_MAF 8U
38 
47 #define VRNA_FILE_FORMAT_MSA_MIS 16U
48 
53 #define VRNA_FILE_FORMAT_MSA_DEFAULT ( \
54  VRNA_FILE_FORMAT_MSA_CLUSTAL \
55  | VRNA_FILE_FORMAT_MSA_STOCKHOLM \
56  | VRNA_FILE_FORMAT_MSA_FASTA \
57  | VRNA_FILE_FORMAT_MSA_MAF \
58  )
59 
64 #define VRNA_FILE_FORMAT_MSA_NOCHECK 4096U
65 
70 #define VRNA_FILE_FORMAT_MSA_UNKNOWN 8192U
71 
76 #define VRNA_FILE_FORMAT_MSA_APPEND 16384U
77 
82 #define VRNA_FILE_FORMAT_MSA_QUIET 32768U
83 
88 #define VRNA_FILE_FORMAT_MSA_SILENT 65536U
89 
142 int
143 vrna_file_msa_read(const char *filename,
144  char ***names,
145  char ***aln,
146  char **id,
147  char **structure,
148  unsigned int options);
149 
150 
207 int
209  char ***names,
210  char ***aln,
211  char **id,
212  char **structure,
213  unsigned int options);
214 
215 
241 unsigned int
242 vrna_file_msa_detect_format(const char *filename,
243  unsigned int options);
244 
245 
263 int
264 vrna_file_msa_write(const char *filename,
265  const char **names,
266  const char **aln,
267  const char *id,
268  const char *structure,
269  const char *source,
270  unsigned int options);
271 
272 
277 #endif
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.
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.
unsigned int vrna_file_msa_detect_format(const char *filename, unsigned int options)
Detect the format of a multiple sequence alignment file.