#define PROG_NAME "dm_match_bank"
#define PROG_DESC "multiscale matching of a DNA/RNA seq against a seq bank"
#define PROG_VERS "1.0"

/* Copyright © 2006 by the State University of Campinas (UNICAMP).
** See the copyright, authorship, and warranty notice at end of file.
** Last edited on 2007-12-27 03:15:52 by stolfi
*/

#define PROG_HELP \
  PROG_NAME " \\\n" \
  "  SEQ_DIR QUERY_SEQ BANK_NAME \\\n" \
  "  MAX_LEVEL MAX_MATCHES MIN_BASES MAX_DIFF \\\n" \
  "  OUT_NAME"

#include <dm_basic.h>
#include <dm_seq.h>
#include <dm_seq_bank.h>

#include <msm_pairing.h>
#include <msm_multi.h>

#include <math.h>
#include <assert.h>
#include <affirm.h>
#include <stdlib.h>

typedef struct dm_options_t 
  { char *seqDir;     /* Directory where to find the sequences. */
    char *dbName;     /* Name of sequence bank file (minus ".gdb" ext). */
    char *queryName;  /* Name of query sequence (minus dir and ".bas" ext). */
    int maxLevel;     /* Maximum filtering level. */
    int maxMatches;   /* Max number o matches to report. */
    int minBases;     /* Max difference metric. */
    double maxDiff;   /* Max difference metric. */
    char *outName;    /* Output file name prefix (minus extensions). */
  } dm_options_t;

int main(int argc, char**argv);

dm_options_t *dm_get_options(int argc, char**argv);

dm_seq_t dm_read_input_sequence(char *seqName);
  /* Reads a DNA sequence from file "{seqName}.bas". */

void dm_output_matches(dm_pairing_vec_t cand, char *outName);
  /* Writes the list of pairings {cand} to the file named {outName}. */

int main(int argc, char**argv)
  { dm_options_t *o = dm_get_options(argc, argv);
    dm_seq_bank_t db = dm_seq_bank_read(o->dbName, o->seqDir);
    dm_seq_t q = dm_seq_read(o->queryName, o->seqDir);
    dm_pairing_vec_t cand = dm_pairing_vec_new(100);
    int ncand = 0;
    int ib;
    double sigma0 = 2.0; /* TO FIX!!! */
    double sigma1 = 1.5; /* TO FIX!!! */
    double_vec_t wtb0 = dm_make_weight_table(sigma0);
    double_vec_t wtb1 = dm_make_weight_table(sigma1);
    dm_seq_t qr[o->maxLevel + 1];
    dm_seq_t br[o->maxLevel + 1];
    dm_multi_seq_filter(q, o->maxLevel, &wtb0, &wtb1, qr);
    for (ib = 0; ib < db.seq.nel; ib++)
      { dm_multi_seq_filter(db.seq.el[ib], o->maxLevel, &wtb0, &wtb1, br);
        dm_pairing_vec_t part = dm_multi_find_matches
          ( qr, br, o->maxMatches, o->maxLevel, o->minBases, o->maxDiff );
        int ic;
	for (ic = 0; ic < part.nel; ic++)
	  { dm_pairing_vec_expand(&cand, ncand);
            cand.el[ncand] = part.el[ic];
            ncand++;
	  }
        free(part.el);
	dm_multi_seq_free(br, o->maxLevel);
      }
    dm_pairing_vec_trim(&cand, ncand);
    dm_output_matches(cand, o->outName);
    dm_multi_seq_free(qr, o->maxLevel);
    return 0;
  }
  
dm_seq_t dm_read_input_sequence(char *seqName, char*seqDir)
  { char *fileName = NULL;
    char *fileName = jsprintf("%s/%s.bas", seqName, seqDir);
    FILE *fsq = open_read(fileName, TRUE);
    dm_seq_t seq = dm_seq_read(fsq);
    fclose(fsq);
    free(fileName);
    return seq;
  }

dm_options_t* dm_get_options(int argc, char**argv)
  { 
    dm_options_t *o = (dm_options_t *)notnull(malloc(sizeof(dm_options_t)), "no mem");
    char *endptr;
    demand(argc == 8, "wrong num of args");
    o->seqDir = argv[1];
    o->dbName = argv[2];
    o->queryName = argv[3];
    o->maxLevel = strtod(argv[4], &endptr); demand((*endptr) == '\000', "bad maxLevel");
    o->maxMatches = strtod(argv[5], &endptr); demand((*endptr) == '\000', "bad maxMatches");
    o->minBases = strtod(argv[6], &endptr); demand((*endptr) == '\000', "bad minBases");
    o->maxDiff = strtod(argv[7], &endptr); demand((*endptr) == '\000', "bad maxDiff");
    o->outName = argv[8];
    return o;
  }

/* COPYRIGHT, AUTHORSHIP, AND WARRANTY NOTICE:
**
**   Copyright © 2006 by the State University of Campinas (UNICAMP).
**
** Created feb/2006 by Jorge Stolfi, IC-UNICAMP.
**
** Permission to use, copy, modify, and redistribute this software and
** its documentation for any purpose and without fee is hereby
** granted, provided that: (1) the copyright notice at the top of this
** file and this copyright, authorship, and warranty notice is retained
** in all derived source files and documentation; (2) no executable
** code derived from this file is published or distributed without the
** corresponding source code; and (3) these same rights are granted to
** any recipient of such code, under the same conditions.
** This software is provided "as is", WITHOUT ANY EXPLICIT OR IMPLICIT
** WARRANTIES, not even the implied warranties of merchantibility and
** fitness for a particular purpose. END OF NOTICE.
*/