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/* @source degapseq application
**
** Remove gaps from sequences
**
** @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 degapseq *************************************************************
**
** Remove gaps from a sequence
**
******************************************************************************/
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeqout seqout;
AjPSeq seq = NULL;
AjPStr str = NULL;
embInit("degapseq", argc, argv);
seqout = ajAcdGetSeqoutall ("outseq");
seqall = ajAcdGetSeqall ("sequence");
while(ajSeqallNext(seqall, &seq))
{
/* get a copy of the sequence string */
str = ajStrNew();
ajStrAssignS(&str, ajSeqGetSeqS(seq));
ajStrRemoveGap(&str);
ajSeqAssignSeqS(seq, str);
ajStrDel(&str);
ajSeqoutWriteSeq(seqout, seq);
}
ajSeqoutClose(seqout);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajSeqoutDel(&seqout);
embExit();
return 0;
}
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