/* @source union application
**
** Read a list of sequences, combine them into one sequence and write it
**
** @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 origunion ************************************************************
**
** Reads sequence fragments and builds one sequence
**
******************************************************************************/

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

    AjPSeqall seqall;
    AjPSeqout seqout;
    AjPSeq seq    = NULL;
    AjPSeq uniseq = NULL;
    AjPStr unistr = NULL;
    AjBool first  = ajTrue;

    embInit("origunion", argc, argv);

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

    while(ajSeqallNext(seqall, &seq))
    {
	if(first)
	{
	    uniseq = ajSeqNewSeq(seq);
	    first  = ajFalse;
	}
	ajSeqTrim(seq);

	ajStrAppendS(&unistr, ajSeqGetSeqS(seq));
    }

    ajSeqAssignSeqS(uniseq, unistr);
    ajSeqoutWriteSeq(seqout, uniseq);
    ajSeqoutClose(seqout);

    embExit();

    return 0;
}