/*  File: translate.c
 *  Author: sre
 *  Copyright (c) J Thierry-Mieg and R Durbin, 1999
 * -------------------------------------------------------------------
 * Acedb 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.
 * 
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
 * -------------------------------------------------------------------
 * This file is part of the ACEDB genome database package, written by
 * 	Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk, and
 *	Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.crbm.cnrs-mop.fr
 *
 * Description: functions for translating nucleic acid sequence
 * Exported functions: (see below)
 * HISTORY:
 * Last edited: Aug 26 17:42 1999 (fw)
 * Created: Tue Jan 12 11:27:29 1993 (SRE)
 * CVS info:   $Id: translate.c,v 1.9 1999/09/01 11:00:49 fw Exp $
 *-------------------------------------------------------------------
 */

#define IUPACSYMNUM 17
#include "iupac.h"
#include "mystdlib.h"
#include "regular.h" /* for messalloc */

/*#include "squid.h"*/

/* Function: Translate(char *seq, char **code)
 * 
 * Given a ptr to the start of a nucleic acid sequence,
 * and a genetic code, translate the sequence into
 * amino acid sequence.
 * 
 * code is an array of 65 strings, representing
 * the translations of the 64 codons, arranged
 * in order AAA, AAC, AAG, AAU, ..., UUA, UUC, UUG, UUU.
 * '*' or '***' is used to represent termination
 * codons, usually. The final string, code[64],
 * is the code for an ambiguous amino acid.
 *
 * Because of the way space is allocated for the amino
 * acid sequence, the amino acid strings cannot be
 * longer than 3 letters each. (I don't foresee using
 * anything but the single- and triple- letter codes.)
 * 
 * Returns a ptr to the translation string on success,
 * or NULL on failure.
 */
char *
translate(seq, code)
     char  *seq;
     char **code;
{
  int   codon;			/* index for codon         */
  char *aaseq;                  /* RETURN: the translation */
  char *aaptr;                  /* ptr into aaseq */
  int   i;
  
  if (seq == NULL) return NULL;
  if ((aaseq = (char *) messalloc (strlen(seq) + 1)) == NULL)
      return NULL;

  aaptr = aaseq;
  for (; *seq != '\0' && *(seq+1) != '\0' && *(seq+2) != '\0'; seq += 3)
    {
				/* calculate the lookup value for
				   this codon */
      codon = 0;
      for (i = 0; i < 3; i++)
	{
	  codon *= 4;
	  switch (*(seq + i)) {
	  case 'A': case 'a':             break;
	  case 'C': case 'c': codon += 1; break;
	  case 'G': case 'g': codon += 2; break;
	  case 'T': case 't': codon += 3; break;
	  case 'U': case 'u': codon += 3; break;
	  default: codon = 64; break;
	  }
	  if (codon == 64) break;
	}

      strcpy(aaptr, code[codon]);
      aaptr += strlen(code[codon]);
    }
  
  return aaseq;
}


/* revcomp.c
 * 
 * Reverse complement of a IUPAC character string
 * 
 */

char *
revcomp(comp, seq)
     char *comp;
     char *seq;
{
  long  bases;
  char *bckp, *fwdp;
  int   idx;
  long  pos;
  int   c;

  if (comp == NULL) return NULL;
  if (seq == NULL)  return NULL;
  bases = strlen(seq);

  fwdp = comp;
  bckp = seq + bases -1;
  for (pos = 0; pos < bases; pos++)
    {
      c = *bckp;
      c = freeupper(c);
      for (idx = 0; c != iupac[idx].sym && idx < IUPACSYMNUM; idx++);
      if (idx > IUPACSYMNUM)
	{
	  *fwdp = '\0';
	  return NULL;
	}
      else
	*fwdp = iupac[idx].symcomp;
      if (islower(*bckp)) *fwdp = freelower(*fwdp);
      fwdp++;
      bckp--;
    }
  *fwdp = '\0';
  return comp;
}
  
/* compl.c
 * 
 * Just complement of a IUPAC character string
 * 
 * Note that it overwrites calling string!!!! (revcomp doesn't)
 */

void compl(char *seq)
{
  char *fwdp;
  int   idx;
  long  pos;
  int   c;

  if (seq == NULL)  return;

  fwdp = seq;
  for (pos = 0; pos < strlen(seq); pos++)
  {
      c = freeupper(*fwdp);
      for (idx = 0; c != iupac[idx].sym && idx < IUPACSYMNUM; idx++);
      if (idx > IUPACSYMNUM) {
	  *fwdp = '\0';
	  return;
      }
      else c = iupac[idx].symcomp;

      if (islower(*fwdp)) *fwdp = freelower(c);
      else *fwdp = c;
      fwdp++;
  }
  *fwdp = '\0';
}