/* @source dreg application
**
** DNA regular expressions (perl style)
**
** @author Copyright (C) Peter Rice
** @@
**
** 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 dreg *****************************************************************
**
** regular expression search of a nucleotide sequence
**
******************************************************************************/

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

    AjPSeqall seqall;
    AjPRegexp patexp = NULL;
    AjPPatlistRegex plist = NULL;
    AjPReport report=NULL;
    AjPFeattable feat=NULL;
    AjPSeq seq = NULL;
    AjPStr str = NULL;
    AjPStr tmpstr = NULL;
    AjPStr substr = NULL;
    ajint adj;

    embInit("dreg", argc, argv);

    report = ajAcdGetReport ("outfile");
    seqall = ajAcdGetSeqall("sequence");
    plist  = ajAcdGetRegexp("pattern");

    ajFmtPrintAppS (&tmpstr, "Pattern: %S\n", ajAcdGetValue("pattern"));
    ajReportSetHeaderS(report, tmpstr);

    while(ajSeqallNext(seqall, &seq))
    {
	if(ajSeqIsReversed(seq))
	    adj = ajSeqGetLen(seq) - ajSeqGetOffend(seq);
	else
	    adj = ajSeqGetOffset(seq);
	ajDebug("begin:%d end:%d len:%d offset:%d offend:%d "
		"rev:%B nuc:%B adj:%d\n",
	       ajSeqGetBegin(seq), ajSeqGetEnd(seq), ajSeqGetLen(seq),
	       ajSeqGetOffset(seq), ajSeqGetOffend(seq),
	       ajSeqIsReversed(seq), ajSeqIsNuc(seq), adj);

	ajStrAssignS(&str, ajSeqGetSeqS(seq));
	ajStrFmtUpper(&str);
	ajDebug("Testing '%s' len: %d %d regex %x\n",
		ajSeqGetNameC(seq), ajSeqGetLen(seq), ajStrGetLen(str),
		patexp);
	feat = ajFeattableNewSeq(seq);
	embPatlistRegexSearch(feat, seq, plist, ajFalse);
	(void) ajReportWrite (report,feat,seq);

        ajFeattableDel(&feat);
    }
    ajReportSetSeqstats(report, seqall);
    
    ajReportClose(report);
    ajReportDel(&report);

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

    ajStrDel(&tmpstr);
    ajStrDel(&substr);
    ajStrDel(&str);
    ajPatlistRegexDel(&plist);

    embExit();

    return 0;
}