RNAlib-2.4.0
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 
14 #include <stdio.h>
15 
20 #define VRNA_FILE_FORMAT_MSA_CLUSTAL 1U
21 
26 #define VRNA_FILE_FORMAT_MSA_STOCKHOLM 2U
27 
32 #define VRNA_FILE_FORMAT_MSA_FASTA 4U
33 
38 #define VRNA_FILE_FORMAT_MSA_MAF 8U
39 
48 #define VRNA_FILE_FORMAT_MSA_MIS 16U
49 
54 #define VRNA_FILE_FORMAT_MSA_DEFAULT ( \
55  VRNA_FILE_FORMAT_MSA_CLUSTAL \
56  | VRNA_FILE_FORMAT_MSA_STOCKHOLM \
57  | VRNA_FILE_FORMAT_MSA_FASTA \
58  | VRNA_FILE_FORMAT_MSA_MAF \
59  )
60 
65 #define VRNA_FILE_FORMAT_MSA_NOCHECK 4096U
66 
71 #define VRNA_FILE_FORMAT_MSA_UNKNOWN 8192U
72 
73 #define VRNA_FILE_FORMAT_MSA_APPEND 16384U
74 
75 #define VRNA_FILE_FORMAT_MSA_QUIET 32768U
76 
77 #define VRNA_FILE_FORMAT_MSA_SILENT 65536U
78 
125 int
126 vrna_file_msa_read(const char *filename,
127  char ***names,
128  char ***aln,
129  char **id,
130  char **structure,
131  unsigned int options);
132 
133 
184 int
186  char ***names,
187  char ***aln,
188  char **id,
189  char **structure,
190  unsigned int options);
191 
192 
218 unsigned int
219 vrna_file_msa_detect_format(const char *filename,
220  unsigned int options);
221 
222 
237 int
238 vrna_file_msa_write(const char *filename,
239  const char **names,
240  const char **aln,
241  const char *id,
242  const char *structure,
243  const char *source,
244  unsigned int options);
245 
246 
251 #endif
unsigned int vrna_file_msa_detect_format(const char *filename, unsigned int options)
Detect the format of a multiple sequence alignment file.
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.