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/* Memory-efficient multiple sequence alignment i/o from Pfam format
* Legacy interface, now that ESL_MSAFILE is rewritten. Still need
* to support --small option in various tools, so the necessary parts
* of the old interface were moved here.
* To-do:
* :: add memory-efficient interface in ESL_MSAFILE
* :: add memory-efficient ESL_MSA w/ API
* :: add space-efficient MSA file format
#include "esl_config.h"
#include "easel.h"
#include "esl_alphabet.h" /* digital alphabet */
#include "esl_keyhash.h" /* string hashes, for mapping unique seq names */
#include "esl_msa.h" /* ESL_MSA structure */
#include "esl_msafile.h" /* preferred msafile interface, inc. fmt codes shared w/ ESL_MSAFILE2 */
#include "esl_ssi.h" /* indexing large flatfiles on disk */
/* Object: ESL_MSAFILE2
* Defines an alignment file that we open for reading,
* in our legacy version. See ESL_MSAFILE (esl_msafile.c) for the
* preferred version.
typedef struct {
FILE *f; /* open file pointer */
char *fname; /* name of file. used for diagnostic output */
int linenumber; /* what line are we on in the file */
char errbuf[eslERRBUFSIZE]; /* buffer for holding parse error info */
char *buf; /* buffer for line input w/ sre_fgets() */
int buflen; /* current allocated length for buf */
int do_gzip; /* TRUE if f is "gzip -dc |" (will pclose(f))*/
int do_stdin; /* TRUE if f is stdin (won't close f) */
int format; /* format of alignment file we're reading */
int do_digital; /* TRUE to digitize seqs directly into ax */
const ESL_ALPHABET *abc; /* digitized input */
ESL_SSI *ssi; /* open SSI index file; or NULL, if none. */
ESL_MSA *msa_cache; /* occasional lookahead at next MSA; GuessAlphabet() */
/* 1. The ESL_MSAFILE2 object */
extern int esl_msafile2_Open(const char *filename, const char *env, ESL_MSAFILE2 **ret_afp);
extern int esl_msafile2_OpenDigital(const ESL_ALPHABET *abc, const char *filename, const char *env, ESL_MSAFILE2 **ret_afp);
extern void esl_msafile2_Close(ESL_MSAFILE2 *afp);
/* 2. Memory efficient reading/writing in Pfam format */
extern int esl_msafile2_ReadInfoPfam(ESL_MSAFILE2 *afp, FILE *listfp, ESL_ALPHABET *abc, int64_t known_alen, char *known_rf, char *known_ss_cons, ESL_MSA **ret_msa,
int *opt_nseq, int64_t *opt_alen, int *opt_ngs, int *opt_maxname, int *opt_maxgf, int *opt_maxgc, int *opt_maxgr,
double ***opt_abc_ct, double ***opt_pp_ct, double ****opt_bp_ct, int **opt_spos_ct, int **opt_epos_ct);
extern int esl_msafile2_RegurgitatePfam(ESL_MSAFILE2 *afp, FILE *ofp, int maxname, int maxgf, int maxgc, int maxgr,
int do_header, int do_trailer, int do_blanks, int do_comments, int do_gf,
int do_gs, int do_gc, int do_gr, int do_aseq, ESL_KEYHASH *seqs2regurg, ESL_KEYHASH *seqs2skip,
int *useme, int *add2me, int exp_alen, char gapchar2add, int *opt_nseq_read, int *opt_nseq_written);
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