/* @source backtranseq application
**
** Backward translation to the most likely DNA sequence
**
** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
** @@
**
** This program 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.
******************************************************************************/

#include "emboss.h"




/* @prog backtranambig *******************************************************
**
** Back translate a protein sequence to ambiguous codons
**
******************************************************************************/

int main(int argc, char **argv)
{
    AjPSeqall  seqall;
    AjPSeq     a;
    AjPSeqout  outf;
    AjPStr     substr;
    AjPStr     back;
    AjPStr     gctable;
    AjPCod     codon = NULL;
 
    ajint      gctablenum;

    ajint beg;
    ajint end;

    embInit("backtranambig", argc, argv);

    seqall    = ajAcdGetSeqall("sequence");
    outf      = ajAcdGetSeqoutall("outfile");
    gctable   = ajAcdGetListSingle("table");
    ajStrToInt(gctable, &gctablenum);

    codon = ajCodNewCodenum(gctablenum);
    while(ajSeqallNext(seqall, &a))
    {
        substr = ajStrNew();
        beg    = ajSeqGetBegin(a);
        end    = ajSeqGetEnd(a);
        ajStrAssignSubC(&substr,ajSeqGetSeqC(a),beg-1,end-1);

        back = ajStrNew();
        ajCodBacktranslateAmbig(&back,substr,codon);

        ajSeqAssignSeqS (a, back);
        ajSeqSetNuc(a);

        ajSeqoutWriteSeq(outf,a);
    }

    ajSeqoutClose(outf);

    ajStrDel(&back);
    ajStrDel(&substr);
    ajSeqoutDel(&outf);
    ajCodDel(&codon);
    ajStrDel(&gctable);
    ajSeqallDel(&seqall);
    ajSeqDel(&a);

    embExit();

    return 0;
}