/*
Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.

    This file is part of the oligotm library.

    The oligotm library is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    The oligotm library is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with the oligtm library (file gpl.txt in the source
    distribution); if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA

*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "oligotm.h"

/* Print the melting temperature of an oligo on stdout. */
/* This program provides a command line interface to
   the function oligotm() in oligtm.c
*/
int
main(int argc, char **argv)
{
  double tm;

  char *msg = "USAGE: %s OPTIONS oligo\n"
    "\n"
    "where oligo is a DNA sequence of between 2 and 36 bases\n"
    "\n"
    "and\n"
     "\n"
     "OPTIONS can include any of the the following:\n"
     "\n"
     "-mv monovalent_conc - concentration of monovalent cations in mM, by default 50mM\n"
     "\n"
     "-dv divalent_conc   - concentration of divalent cations in mM, by default 0mM\n"
     "\n"
     "-n  dNTP_conc       - concentration of deoxynycleotide triphosphate in mM, by default 0mM\n"
     "\n"
     "-d  dna_conc        - concentration of DNA strands in nM, by default 50nM\n"
     "\n"

    "-tp [0|1]     - Specifies the table of thermodynamic parameters and\n"
    "                the method of melting temperature calculation:\n"
    "                 0  Breslauer et al., 1986 and Rychlik et al., 1990\n"
    "                    (used by primer3 up to and including release 1.1.0).\n"
    "                    This is the default, but _not_ the recommended value.\n"
    "                 1  Use nearest neighbor parameters from SantaLucia 1998\n"
    "                    *THIS IS THE RECOMMENDED VALUE*\n"
    "\n"
    "-sc [0..2]    - Specifies salt correction formula for the melting \n"
    "                 temperature calculation\n"
    "                  0  Schildkraut and Lifson 1965, used by primer3 up to \n"
    "                     and including release 1.1.0.\n"
    "                     This is the default but _not_ the recommended value.\n"
    "                  1  SantaLucia 1998\n"
    "                     *THIS IS THE RECOMMENDED VAULE*\n"
    "                  2  Owczarzy et al., 2004\n\n"
    "-i             - prints references to publications which were used for thermodynamic calculations\n"
    "\n\n"
    "Prints oligo's melting temperature on stdout.\n";
   
  char *info = "1. Breslauer KJ, Frank R, Blöcker H and Marky LA. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci., 83, 4746-50.\n\n"
    "2. Rychlik W, Spencer WJ and Rhoads RE. (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res., 118, 6409-12.\n\n"
    "3. SantaLucia JR. (1998). A unified view of polymer, dumbbell and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci., 95, 1460-65.\n\n"
    "4. Schildkraut, C, and Lifson, S. (1965) Dependence of the melting temperature of DNA on salt concentration. Biopolymers, 3, 195-208.\n\n"
    "5. Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, Behlke MA and Walder JA. (2004) Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures. Biochemistry, 43, 3537-54.\n";
   
   char *copyright = 
"Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006\n"
"Whitehead Institute for Biomedical Research, Steve Rozen\n"
"(http://jura.wi.mit.edu/rozen), and Helen Skaletsky\n"
"All rights reserved.\n"
"\n"
"    This file is part of the oligotm library.\n"
"\n"
"    The oligotm library is free software; you can redistribute it and/or modify\n"
"    it under the terms of the GNU General Public License as published by\n"
"    the Free Software Foundation; either version 2 of the License, or\n"
"    (at your option) any later version.\n"
"\n"
"    The oligotm library is distributed in the hope that it will be useful,\n"
"    but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
"    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n"
"    GNU General Public License for more details.\n"
"\n"
"    You should have received a copy of the GNU General Public License\n"
"    along with the oligtm library (file gpl.txt in the source\n"
"    distribution or see http://www.gnu.org/licenses/gpl.txt);\n"
"    if not, write to the Free Software Foundation, Inc.,\n"
"    51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA\n";

   char *endptr, *seq;
   long mv = 50, d = 50;
   double dv = 0, n = 0;
   int tm_santalucia=0, salt_corrections=0;
   int i, j, len;
   if (argc < 2 || argc > 14) {
     fprintf(stderr, msg, argv[0]);       
     fprintf(stderr, copyright);
     return -1;
   }

   for (i=1; i < argc; ++i) {
     if (!strncmp("-mv", argv[i], 3)) { /* conc of monovalent cations */
       mv = strtol(argv[i+1], &endptr, 10);
       if ('\0' != *endptr) {
	 fprintf(stderr, msg, argv[0]);
	 exit(-1);
       }
       i++;
     } else if (!strncmp("-dv", argv[i], 3)) { /* conc of divalent cations; added by T.Koressaar */
       dv = strtod(argv[i+1], &endptr);
       if('\0' != *endptr) {
	 fprintf(stderr, msg, argv[0]);
	 exit(-1);
       }
       i++;
     } else if (!strncmp("-n", argv[i], 2)) { /* conc of dNTP; added by T.Koressaar */
       n = strtod(argv[i+1], &endptr);
       if('\0' != *endptr) {
	 fprintf(stderr, msg, argv[0]);
	 exit(-1);
       }
       i++;
     } else if (!strncmp("-d", argv[i], 2)) {
       d = strtol(argv[i+1], &endptr, 10);
       if ('\0' != *endptr) {
	 fprintf(stderr, msg, argv[0]);
	 exit(-1);
       }
       i++;
     } else if (!strncmp("-tp", argv[i], 3)) { /* added by T.Koressaar */
       tm_santalucia = (int)strtol(argv[i+1], &endptr, 10);
       if ('\0' != *endptr || tm_santalucia<0 || tm_santalucia>1) {	  
	 fprintf(stderr, msg, argv[0]);
	 exit(-1);
       }
       i++;
     } else if (!strncmp("-sc", argv[i], 3)) { /* added by T.Koressaar */
       salt_corrections = (int)strtol(argv[i+1], &endptr, 10);
       if ('\0' != *endptr || salt_corrections<0 || salt_corrections>2) {
	 fprintf(stderr, msg, argv[0]);
	 exit(-1);
       }
       i++;
     } else if (!strncmp("-i", argv[i], 2)) {
       fprintf(stderr, info, argv[0]);
       exit(-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(!argv[i]) { /* if no oligonucleotide sequence is specified */
    fprintf(stderr, msg, argv[0]);
    exit(-1);
  }
  /* input sequence to uppercase */
  seq = argv[i];
  len=strlen(seq);
  for(j=0;j<len;j++) seq[j]=toupper(seq[j]);
   
  tm = oligotm(seq, d, mv, dv, n, tm_santalucia, salt_corrections);
  if (OLIGOTM_ERROR == tm) {
    fprintf(stderr,
	    "%s ERROR: length of sequence %s is less than 2 or\n"
	    "             the sequence contains an illegal character or\n" 
	    "             you have specified incorrect value for concentration of divalent cations or\n"
	    "             you have specified incorrect value for concentration of dNTPs\n",
	    argv[0], argv[i]);
    return -1;
  }
  fprintf(stdout, "%f\n", tm);
  return 0;
}