RNAlib-2.2.9

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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
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
168 vrna_file_msa_read_record(FILE *fp,
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
vrna_file_msa_detect_format
unsigned int vrna_file_msa_detect_format(const char *filename, unsigned int options)
Detect the format of a multiple sequence alignment file.
vrna_file_msa_read
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.
vrna_file_msa_read_record
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.