/*
Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

   * Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
   * Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following disclaimer
in the documentation and/or other materials provided with the
distribution.
   * Neither the names of the copyright holders nor contributors may
be used to endorse or promote products derived from this software
without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

#include "dpal.h"
#include <string.h>
#include <stdio.h>
#include <stdlib.h>

int
main(argc, argv)
    int argc;
    const char**argv;
{
    dpal_args a;
    dpal_results r;
    const char *s1, *s2;
    int tmp_ret;
    int i;
    int print_align_end = 0; /* 
                              * Print align_end_1 and align_end_2 from
                              * dpal_results.
			      */
    int use_ambiguity_codes = 0;
    int use_h_matrix = 0;
    char mode;
    char *endptr;
    const char *msg = 
      "\nUsage: %s [-g <gval>] [-l <lval>] [-m <mval>]\n"
      "                 [-f2] [-p] [-s] [-e] <seq1> <seq2> <mode>"
      "\n\nwhere\n\n"
      "<gval> and <lval> are (positive) floats (.01 precision)\n"
      "    specifying penalties for creating or lengthening a gap\n"
      "    respectively (the penalties are subtracted from the\n"
      "    output score).\n\n"
      "-a causes the scoring matrix to be modified by dpal_set_ambiguity_codes.\n\n"
      "-e causes the end postion of the alignment in both sequences to\n"
      "   be printed.  Do not confuse with the 'e' <mode>.\n\n"
      "-f1, -f2, f3\n"
      "    force specific implementations.\n"
      "    -f2 forces use an implementation that might provide more\n"
      "    informative error messages, possibly at the expense\n"
      "    of some speed.\n\n"
      "-h use a different scoring matrix: G and C matches = 3, A and T = 2,\n"
      "   and mismatches = -0.5.\n"
      "   (The default scoring matrix assigns 1 to a match,\n"
      "   and -1 to a mismatch.)\n\n"
      "-p causes the alignment to be displayed on stderr.\n\n"
      "-s causes _only_ the score to printed.\n\n"
      "<mval> is the maximum allowed gap (default is 3).\n\n"
      "<seq1> and <seq2> are the sequences to be aligned.\n\n"
      "<mode> is one of g, G, l, or L specifying a global,\n"
      "       global end-anchored, local, or local end-achored\n"
      "       alignment respectively.  For backward compatibility\n"
      "       e is equivalent to G.\n\n";

    if (argc < 4) {
	tmp_ret = fprintf(stderr, msg, argv[0]);
	exit(-1);
    }
    dpal_set_default_nt_args(&a);
    for (i=1; i < argc; ++i) {
	if (!strncmp("-p", argv[i], 2)) {
	    a.debug = 1;
	} else if (!strncmp("-l", argv[i], 2)) {
	    a.gapl = strtod(argv[i+1],(char **)NULL) * -100;
	    i++;
        } else if (!strncmp("-e", argv[i], 2)) {
	    print_align_end = 1;
	} else if (!strncmp("-a", argv[i], 2)) {
	    use_ambiguity_codes = 1;
	} else if (!strncmp("-h", argv[i], 2)) {
	    use_h_matrix = 1;
	} else if (!strncmp("-g", argv[i], 2)) {
	    a.gap = strtod(argv[i+1],(char **)NULL) * -100;
	    i++;
	} else if (!strncmp("-m", argv[i], 2)) {
	    a.max_gap = strtol(argv[i+1], &endptr, 10);
	    if ('\0' != *endptr) {
		fprintf(stderr, msg, argv[0]);
		exit(-1);
	    }
	    i++;
	} else if (!strncmp("-s", argv[i], 2)) {
	    a.score_only = 1;
	} else if (!strncmp("-e", argv[i], 2)) {
	    print_align_end = 1;
	} else if (!strncmp("-f1", argv[i], 3)) {
	    a.force_generic = 1;
	} else if (!strncmp("-f2", argv[i], 3)) {
	    a.force_long_generic = 1;
	} else if (!strncmp("-f3", argv[i], 3)) {
	    a.force_long_maxgap1 = 1;
	} else if (!strncmp("-", argv[i], 1)) {
	    /* Unknown option. */
	    fprintf(stderr, msg, argv[0]);
	    exit(-1);
	} else
	    break;		/* all args processed. go on to sequences. */
    }
    if (use_h_matrix) dpal_set_h_nt_matrix(&a);
    if (use_ambiguity_codes) dpal_set_ambiguity_code_matrix(&a);
    if (a.score_only && a.debug) {
	fprintf(stderr, msg, argv[0]);
	exit(-1);
    }
    a.flag = -1;
    
    if ((argc - i) != 3){
      /* Not enough remaining arguments. */
      fprintf(stderr, msg, argv[0]);
      exit(-1);
    }
    s1 = argv[i];
    s2 = argv[i+1];
    mode = *argv[i+2];
    if ('l' == mode)
	a.flag = DPAL_LOCAL;
    else if ('e' == mode || 'G' == mode)
	a.flag = DPAL_GLOBAL_END;
    else if ('g' == mode)
	a.flag = DPAL_GLOBAL;
    else if ('L' == mode)
	a.flag = DPAL_LOCAL_END;
    else {
	fprintf(stderr, msg, argv[0]);
	exit(-1);
    }
    if(print_align_end == 1) a.force_long_generic = 1;
    dpal(s1, s2, &a, &r);
    if (r.score == DPAL_ERROR_SCORE) {
      tmp_ret = fprintf(stderr, "Error: %s\n", r.msg);
      exit(-1);
    }
    if (a.score_only) {
      printf("%.2f\n", 0.01 * r.score);
      if (print_align_end) {
	if(r.align_end_1 >= 0) printf("align_end_1=%d ",r.align_end_1);
	if(r.align_end_2 >= 0) printf("align_end_2=%d\n ",r.align_end_2);
      }
    } else {
      printf("|%s|  |%s| %c ", s1, s2, mode); 
      printf("score=%.2f len=%d ", (0.01 * r.score), r.path_length);
      if (print_align_end) {
	if(r.align_end_1 >= 0) printf("align_end_1=%d ",r.align_end_1);
	if(r.align_end_2 >= 0) printf("align_end_2=%d ",r.align_end_2);
      }
      for (i=0; i<r.path_length; i++)
	printf("|%d,%d", r.path[i][0],r.path[i][1]);
      printf("|\n");
    }
    return 0;
}
