file_formats_msa.h

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#ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_H
#define VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_H

#include <stdio.h>

#define VRNA_FILE_FORMAT_MSA_CLUSTAL      1U

#define VRNA_FILE_FORMAT_MSA_STOCKHOLM    2U

#define VRNA_FILE_FORMAT_MSA_FASTA        4U

#define VRNA_FILE_FORMAT_MSA_MAF          8U

#define VRNA_FILE_FORMAT_MSA_MIS          16U

#define VRNA_FILE_FORMAT_MSA_DEFAULT      ( \
    VRNA_FILE_FORMAT_MSA_CLUSTAL \
    | VRNA_FILE_FORMAT_MSA_STOCKHOLM \
    | VRNA_FILE_FORMAT_MSA_FASTA \
    | VRNA_FILE_FORMAT_MSA_MAF \
    )

#define VRNA_FILE_FORMAT_MSA_NOCHECK      4096U

#define VRNA_FILE_FORMAT_MSA_UNKNOWN      8192U

#define VRNA_FILE_FORMAT_MSA_APPEND       16384U

#define VRNA_FILE_FORMAT_MSA_QUIET        32768U

#define VRNA_FILE_FORMAT_MSA_SILENT       65536U

int
vrna_file_msa_read(const char   *filename,
                   char         ***names,
                   char         ***aln,
                   char         **id,
                   char         **structure,
                   unsigned int options);


int
vrna_file_msa_read_record(FILE          *fp,
                          char          ***names,
                          char          ***aln,
                          char          **id,
                          char          **structure,
                          unsigned int  options);


unsigned int
vrna_file_msa_detect_format(const char    *filename,
                            unsigned int  options);


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);


#endif