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/* @source seqmatchall application
**
** All against all comparison of a set of sequences
**
** @author Copyright (C) Ian Longden (guess by ajb)
** @@
**
** 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"
static void seqmatchall_matchListPrint(void *x,void *cl);
static void seqmatchall_listPrint(AjPAlign align, const AjPList list);
static AjPSeq *seqs = NULL;
static ajuint iseq1 = 0;
static ajuint iseq2 = 0;
ajuint statwordlen;
/* @prog seqmatchall **********************************************************
**
** Does an all-against-all comparison of a set of sequences
**
******************************************************************************/
int main(int argc, char **argv)
{
AjPTable seq1MatchTable = 0;
AjPList matchlist;
AjPSeqset seqset;
AjPAlign align = NULL;
ajuint i;
ajuint j;
ajuint nseqs;
embInit("seqmatchall", argc, argv);
seqset = ajAcdGetSeqset("sequence1");
statwordlen = ajAcdGetInt("wordsize");
align = ajAcdGetAlign("outfile");
ajAlignSetExternal(align, ajTrue);
embWordLength(statwordlen);
seqs = ajSeqsetGetSeqarray(seqset);
nseqs = ajSeqsetGetSize(seqset);
for(i=0;i<nseqs;i++)
{
iseq1 = i;
seq1MatchTable = 0;
if(ajSeqGetLen(seqs[iseq1]) > statwordlen)
{
if(embWordGetTable(&seq1MatchTable, seqs[i])) /* get word table */
{
for(j=i+1;j<ajSeqsetGetSize(seqset);j++)
{
iseq2 = j;
if(ajSeqGetLen(seqs[j]) >= statwordlen)
{
matchlist = embWordBuildMatchTable(seq1MatchTable,
seqs[j], ajTrue);
if (ajListGetLength(matchlist))
{
seqmatchall_listPrint(align, matchlist);
ajAlignWrite(align);
ajAlignReset(align);
}
/* free the match structures */
embWordMatchListDelete(&matchlist);
}
}
}
embWordFreeTable(&seq1MatchTable); /* free table of words */
}
}
ajAlignClose(align);
ajAlignDel(&align);
ajSeqsetDel(&seqset);
ajSeqDelarray(&seqs);
embExit();
return 0;
}
/* @funcstatic seqmatchall_matchListPrint *************************************
**
** Undocumented.
**
** @param [r] x [void*] Undocumented
** @param [r] cl [void*] Undocumented
** @return [void]
** @@
******************************************************************************/
static void seqmatchall_matchListPrint(void *x,void *cl)
{
EmbPWordMatch p;
AjPAlign align;
p = (EmbPWordMatch)x;
align = (AjPAlign) cl;
/*
ajFmtPrintF(outfile, "%d %d %d %s %d %d %s\n",
(*p).length,
(*p).seq1start+1,(*p).seq1start+(*p).length,seq1->Name->Ptr,
(*p).seq2start+1,(*p).seq2start+(*p).length,seq2->Name->Ptr);
*/
ajAlignDefineSS(align, seqs[iseq1], seqs[iseq2]);
ajAlignSetScoreI(align, p->length);
/* ungapped so same length for both sequences */
ajAlignSetSubRange(align,
p->seq1start, 1, p->length,
ajSeqIsReversed(seqs[iseq1]), ajSeqGetLen(seqs[iseq1]),
p->seq2start, 1, p->length,
ajSeqIsReversed(seqs[iseq2]), ajSeqGetLen(seqs[iseq2]));
return;
}
/* @funcstatic seqmatchall_listPrint ******************************************
**
** Undocumented.
**
** @param [u] align [AjPAlign] Alignment object
** @param [r] list [const AjPList] Undocumented
** @@
******************************************************************************/
static void seqmatchall_listPrint(AjPAlign align, const AjPList list)
{
ajListMapread(list, &seqmatchall_matchListPrint, align);
return;
}
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