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/* @source aligncopy application
**
** Reads and writes (returns) alignments
** @author Copyright (C) Jon Ison (jison@ebi.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 aligncopypair *********************************************************
**
** Reads and writes (returns) alignments
**
******************************************************************************/
int main(int argc, char **argv)
{
/* Variable Declarations */
AjPSeqset seqset = NULL;
AjPAlign align = NULL;
AjPStr name = NULL;
AjPStr comment = NULL;
AjBool append = ajFalse;
AjPSeq *seqs = NULL;
AjPStr header = NULL;
ajuint i;
ajuint j;
ajuint nseqs;
ajuint imax;
/* ACD File Processing */
embInit("aligncopypair", argc, argv);
seqset = ajAcdGetSeqset("sequences");
align = ajAcdGetAlign("outfile");
name = ajAcdGetString("name");
comment = ajAcdGetString("comment");
append = ajAcdGetBoolean("append");
/* Application logic */
nseqs = ajSeqsetGetSize(seqset);
seqs = ajSeqsetGetSeqarray(seqset);
if(ajStrGetLen(name))
ajFmtPrintS(&header, "Alignment: %S\n\n", name);
ajStrAppendS(&header, comment);
if(append)
ajAlignSetHeaderApp(align, header);
else
ajAlignSetHeader(align, header);
imax = nseqs-1;
for(i=0;i<imax;i++)
{
for(j=i+1;j<nseqs;j++)
ajAlignDefineSS(align, seqs[i], seqs[j]);
}
ajAlignWrite(align);
ajAlignClose(align);
/* Memory management and exit */
ajSeqsetDel(&seqset);
ajAlignDel(&align);
ajStrDel(&name);
ajStrDel(&comment);
ajStrDel(&header);
ajSeqDelarray(&seqs);
embExit();
return 0;
}
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