1 /* @source aligncopy application
2 **
3 ** Reads and writes (returns) alignments
4 ** @author Copyright (C) Jon Ison (jison@ebi.ac.uk)
5 ** @@
6 **
7 ** This program is free software; you can redistribute it and/or
8 ** modify it under the terms of the GNU General Public License
9 ** as published by the Free Software Foundation; either version 2
10 ** of the License, or (at your option) any later version.
11 **
12 ** This program is distributed in the hope that it will be useful,
13 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
14 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 ** GNU General Public License for more details.
16 **
17 ** You should have received a copy of the GNU General Public License
18 ** along with this program; if not, write to the Free Software
19 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
20 ******************************************************************************/
21
22 #include "emboss.h"
23
24
25
26
27 /* @prog aligncopypair *********************************************************
28 **
29 ** Reads and writes (returns) alignments
30 **
31 ******************************************************************************/
32
main(int argc,char ** argv)33 int main(int argc, char **argv)
34 {
35 /* Variable Declarations */
36 AjPSeqset seqset = NULL;
37 AjPAlign align = NULL;
38 AjPStr name = NULL;
39 AjPStr comment = NULL;
40 AjBool append = ajFalse;
41
42 AjPSeq *seqs = NULL;
43 AjPStr header = NULL;
44 ajuint i;
45 ajuint j;
46 ajuint nseqs;
47
48 ajuint imax;
49
50 /* ACD File Processing */
51 embInit("aligncopypair", argc, argv);
52 seqset = ajAcdGetSeqset("sequences");
53 align = ajAcdGetAlign("outfile");
54 name = ajAcdGetString("name");
55 comment = ajAcdGetString("comment");
56 append = ajAcdGetBoolean("append");
57
58
59 /* Application logic */
60 nseqs = ajSeqsetGetSize(seqset);
61 seqs = ajSeqsetGetSeqarray(seqset);
62 if(ajStrGetLen(name))
63 ajFmtPrintS(&header, "Alignment: %S\n\n", name);
64 ajStrAppendS(&header, comment);
65 if(append)
66 ajAlignSetHeaderApp(align, header);
67 else
68 ajAlignSetHeader(align, header);
69
70 imax = nseqs-1;
71 for(i=0;i<imax;i++)
72 {
73 for(j=i+1;j<nseqs;j++)
74 ajAlignDefineSS(align, seqs[i], seqs[j]);
75 }
76
77 ajAlignWrite(align);
78 ajAlignClose(align);
79
80
81 /* Memory management and exit */
82 ajSeqsetDel(&seqset);
83 ajAlignDel(&align);
84
85 ajStrDel(&name);
86 ajStrDel(&comment);
87 ajStrDel(&header);
88 ajSeqDelarray(&seqs);
89
90 embExit();
91
92 return 0;
93 }
94
95