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/* @source water application
**
** True Smith-Waterman best local alignment
** @author Copyright (C) Alan Bleasby (ableasby@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 water ****************************************************************
**
** Smith-Waterman local alignment
**
******************************************************************************/
int main(int argc, char **argv)
{
AjPAlign align;
AjPSeqall seqall;
AjPSeq a;
AjPSeq b;
AjPStr m;
AjPStr n;
AjPStr ss;
AjBool show = ajFalse;
ajuint lena;
ajuint lenb;
const char *p;
const char *q;
ajint start1 = 0;
ajint start2 = 0;
float *path;
ajint *compass;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
float gapopen;
float gapextend;
size_t maxarr = 1000;
size_t len;
float score;
ajint begina;
ajint beginb;
AjBool dobrief = ajTrue;
AjPStr tmpstr = NULL;
float id = 0.;
float sim = 0.;
float idx = 0.;
float simx = 0.;
embInit("water", argc, argv);
matrix = ajAcdGetMatrixf("datafile");
a = ajAcdGetSeq("asequence");
ajSeqTrim(a);
seqall = ajAcdGetSeqall("bsequence");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
dobrief = ajAcdGetBoolean("brief");
align = ajAcdGetAlign("outfile");
/* obsolete. Can be uncommented in acd file and here to reuse */
/* show = ajAcdGetBoolean("showinternals"); */
m = ajStrNew();
n = ajStrNew();
ss = ajStrNew();
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
begina=ajSeqGetBegin(a)+ajSeqGetOffset(a);
while(ajSeqallNext(seqall,&b))
{
lena = ajSeqGetLen(a);
ajSeqTrim(b);
lenb = ajSeqGetLen(b);
if(lenb > (LONG_MAX/(size_t)(lena+1)))
ajDie("Sequences too big. Try 'matcher' or 'supermatcher'");
len = (size_t)lena*(size_t)lenb;
if(len>maxarr)
{
AJCRESIZETRY0(path,maxarr,len);
if(!path)
ajDie("Sequences too big. Try 'matcher' or 'supermatcher'");
AJCRESIZETRY0(compass,maxarr,len);
if(!compass)
ajDie("Sequences too big. Try 'matcher' or 'supermatcher'");
maxarr=len;
}
beginb=ajSeqGetBegin(b)+ajSeqGetOffset(b);
p = ajSeqGetSeqC(a);
q = ajSeqGetSeqC(b);
ajStrAssignC(&m,"");
ajStrAssignC(&n,"");
score = embAlignPathCalcSW(p,q,lena,lenb,gapopen,gapextend,path,sub,cvt,
compass,show);
/*score=embAlignScoreSWMatrix(path,compass,gapopen,gapextend,a,b,lena,
lenb,sub,cvt,&start1,&start2);*/
embAlignWalkSWMatrix(path,compass,gapopen,gapextend,a,b,&m,&n,
lena,lenb,&start1,&start2);
ajDebug("ReportLocal call start1:%d begina:%d start2:%d beginb:%d\n",
start1, begina, start2, beginb);
embAlignReportLocal(align, a, b, m, n,
start1, start2,
gapopen, gapextend,
score, matrix, begina, beginb);
if(!dobrief)
{
embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx,
&simx);
ajFmtPrintS(&tmpstr,"Longest_Identity = %5.2f%%\n",
id);
ajFmtPrintAppS(&tmpstr,"Longest_Similarity = %5.2f%%\n",
sim);
ajFmtPrintAppS(&tmpstr,"Shortest_Identity = %5.2f%%\n",
idx);
ajFmtPrintAppS(&tmpstr,"Shortest_Similarity = %5.2f%%",
simx);
ajAlignSetSubHeaderApp(align, tmpstr);
}
ajAlignWrite(align);
ajAlignReset(align);
}
ajAlignClose(align);
ajAlignDel(&align);
AJFREE(compass);
AJFREE(path);
AJFREE(compass);
AJFREE(path);
ajStrDel(&n);
ajStrDel(&m);
ajStrDel(&ss);
ajStrDel(&tmpstr);
ajSeqallDel(&seqall);
ajSeqDel(&a);
ajSeqDel(&b);
embExit();
return 0;
}
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