RNAlib-2.3.1
file_formats_msa.h
Go to the documentation of this file.
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 
44 #define VRNA_FILE_FORMAT_MSA_DEFAULT ( \
45  VRNA_FILE_FORMAT_MSA_CLUSTAL \
46  | VRNA_FILE_FORMAT_MSA_STOCKHOLM \
47  | VRNA_FILE_FORMAT_MSA_FASTA \
48  | VRNA_FILE_FORMAT_MSA_MAF \
49  )
50 
55 #define VRNA_FILE_FORMAT_MSA_NOCHECK 4096U
56 
61 #define VRNA_FILE_FORMAT_MSA_UNKNOWN 8192U
62 
109 int
110 vrna_file_msa_read( const char *filename,
111  char ***names,
112  char ***aln,
113  char **id,
114  char **structure,
115  unsigned int options);
116 
167 int
169  char ***names,
170  char ***aln,
171  char **id,
172  char **structure,
173  unsigned int options);
174 
200 unsigned int
201 vrna_file_msa_detect_format(const char *filename,
202  unsigned int options);
203 
208 #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_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.