int main(int argc, char **argv)
{
AjPAlign align;
AjPSeqall seqall;
AjPSeq a;
AjPSeq b;
AjPStr alga;
AjPStr algb;
AjPStr ss;
ajuint lena;
ajuint lenb;
const char *p;
const char *q;
ajint start1 = 0;
ajint start2 = 0;
float *path;
ajint *compass;
float* ix;
float* iy;
float* m;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
float gapopen;
float gapextend;
float endgapopen;
float endgapextend;
ajulong maxarr = 1000; /* arbitrary. realloc'd if needed */
ajulong len;
float score;
AjBool dobrief = ajTrue;
AjBool endweight = ajFalse; /* whether end gap penalties should be applied */
float id = 0.;
float sim = 0.;
float idx = 0.;
float simx = 0.;
AjPStr tmpstr = NULL;
size_t stlen;
embInit("needle", argc, argv);
matrix = ajAcdGetMatrixf("datafile");
a = ajAcdGetSeq("asequence");
ajSeqTrim(a);
seqall = ajAcdGetSeqall("bsequence");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
endgapopen = ajAcdGetFloat("endopen");
endgapextend = ajAcdGetFloat("endextend");
dobrief = ajAcdGetBoolean("brief");
endweight = ajAcdGetBoolean("endweight");
align = ajAcdGetAlign("outfile");
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
AJCNEW(m, maxarr);
AJCNEW(ix, maxarr);
AJCNEW(iy, maxarr);
alga = ajStrNew();
algb = ajStrNew();
ss = ajStrNew();
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
lena = ajSeqGetLen(a);
while(ajSeqallNext(seqall,&b))
{
ajSeqTrim(b);
lenb = ajSeqGetLen(b);
if(lenb > (ULONG_MAX/(ajulong)(lena+1)))
ajFatal("Sequences too big. Try 'stretcher' or 'supermatcher'");
len = lena*lenb;
if(len>maxarr)
{
stlen = (size_t) len;
AJCRESIZETRY(path,stlen);
if(!path)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(compass,stlen);
if(!compass)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(m,stlen);
if(!m)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(ix,stlen);
if(!ix)
ajDie("Sequences too big. Try 'stretcher'");
AJCRESIZETRY(iy,stlen);
if(!iy)
ajDie("Sequences too big. Try 'stretcher'");
maxarr=len;
}
p = ajSeqGetSeqC(a);
q = ajSeqGetSeqC(b);
ajStrAssignC(&alga,"");
ajStrAssignC(&algb,"");
score = embAlignPathCalcWithEndGapPenalties(p, q, lena, lenb,
gapopen, gapextend, endgapopen, endgapextend,
&start1, &start2, path, sub, cvt,
m, ix, iy, compass, ajTrue, endweight);
embAlignWalkNWMatrixUsingCompass(p, q, &alga, &algb,
lena, lenb, &start1, &start2,
compass);
embAlignReportGlobal(align, a, b, alga, algb,
start1, start2,
gapopen, gapextend,
score, matrix,
ajSeqGetOffset(a), ajSeqGetOffset(b));
if(!dobrief)
{
embAlignCalcSimilarity(alga,algb,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);
ajSeqallDel(&seqall);
ajSeqDel(&a);
ajSeqDel(&b);
AJFREE(compass);
AJFREE(path);
AJFREE(ix);
AJFREE(iy);
AJFREE(m);
ajStrDel(&alga);
ajStrDel(&algb);
ajStrDel(&ss);
ajStrDel(&tmpstr);
embExit();
return 0;
}
static AjBool ssematch_NWScore(AjPScop temp_scop,
AjPSeq pseq,
ajint mode,
AjPMatrixf matrix,
float gapopen,
float gapextend)
{
ajint start1 =0; /* Start of seq 1, passed as arg but not used.*/
ajint start2 =0; /* Start of seq 2, passed as arg but not used.*/
ajint maxarr =300; /* Initial size for matrix. */
ajint len;
ajint *compass;
const char *p; /* Query sequence. */
const char *q; /* Subject sequence from scop object. */
float **sub;
float id =0.; /* Passed as arg but not used here. */
float sim =0.;
float idx =0.; /* Passed as arg but not used here. */
float simx =0.; /* Passed as arg but not used here. */
float *path;
AjPStr pstr = NULL; /* m walk alignment for first sequence
Passed as arg but not used here. */
AjPStr qstr = NULL; /* n walk alignment for second sequence
Passed as arg but not used here. */
AjPSeq qseq = NULL; /* Subject sequence. */
ajint lenp; /* Length of query sequence. */
ajint lenq; /* Length of subject sequence. */
AjPSeqCvt cvt = 0;
AjBool show = ajFalse; /*Passed as arg but not used here. */
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
pstr = ajStrNew();
qstr = ajStrNew();
gapopen = ajRoundFloat(gapopen,8);
gapextend = ajRoundFloat(gapextend,8);
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
/* Extract subject sequence from scop object, convert to 3 letter code. */
if (mode == 0)
qseq = ssematch_convertbases(temp_scop->Sse);
else if (mode == 1)
qseq = ssematch_convertbases(temp_scop->Sss);
lenp = ajSeqGetLen(pseq); /* Length of query sequence. */
lenq = ajSeqGetLen(qseq); /* Length of subject sequence. */
/* Start of main application loop */
/* Intitialise variables for use by alignment functions*/
len = (lenp * lenq);
if(len>maxarr)
{
AJCRESIZE(path,len);
AJCRESIZE(compass,len);
maxarr=len;
}
p = ajSeqGetSeqC(pseq);
q = ajSeqGetSeqC(qseq);
ajStrAssignC(&pstr,"");
ajStrAssignC(&qstr,"");
/* Check that no sequence length is 0. */
if((lenp == 0)||(lenq == 0))
{
AJFREE(compass);
AJFREE(path);
ajStrDel(&pstr);
ajStrDel(&qstr);
}
/* Call alignment functions. */
embAlignPathCalc(p,q,lenp,lenq, gapopen,
gapextend,path,sub,cvt,compass,show);
/*embAlignScoreNWMatrix(path,compass,gapopen,gapextend,
pseq, qseq,
lenp,lenq,sub,cvt,
&start1,&start2);*/
embAlignWalkNWMatrix(path,pseq,qseq,&pstr,&qstr,
lenp,lenq,&start1,&start2,
gapopen,gapextend,compass);
embAlignCalcSimilarity(pstr,qstr,sub,cvt,lenp,
lenq,&id,&sim,&idx, &simx);
/* Assign score. */
temp_scop->Score = sim;
/* Tidy up */
AJFREE(compass);
AJFREE(path);
ajStrDel(&pstr);
ajStrDel(&qstr);
ajSeqDel(&qseq);
/* Bye Bye */
return ajTrue;
}
