/* @source revseq application
**
** Reverse and complement a sequence
**
** @author Copyright (C) Gary Williams (gwilliam@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 revseq ***************************************************************
**
** Reverse and complement a sequence
**
******************************************************************************/

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

    AjPSeqall seqall;
    AjPSeq seq;
    AjPSeqout seqout;
    AjBool reverse;
    AjBool complement;

    embInit("revseq", argc, argv);

    seqall = ajAcdGetSeqall("sequence");
    seqout = ajAcdGetSeqoutall("outseq");

    reverse    = ajAcdGetBoolean("reverse");
    complement = ajAcdGetBoolean("complement");

    while(ajSeqallNext(seqall, &seq))
    {
	/* is this a nucleotide sequence */
	if(ajSeqIsProt(seq))
	    ajFatal("%s", "Input sequence must be nucleic");

	/* see if both reverse and complement */
	if(reverse && complement)
        {
	    ajSeqReverseForce(seq);	/* reverses and complements */
            ajSeqTagRev(seq);
        }
	else if(reverse)
	    ajSeqReverseOnly(seq);
	else if(complement)
	    ajSeqComplement(seq);
	else
	  ajDebug("No action was specified\n");

	ajSeqoutWriteSeq(seqout, seq);

    }

    ajSeqoutClose(seqout);

    ajSeqallDel(&seqall);
    ajSeqDel(&seq);
    ajSeqoutDel(&seqout);

    embExit();

    return 0;
}