int main(int argc, char **argv)
{
AjPAlign align;
AjPSeq a;
AjPSeq b;
AjPSeqout seqout;
AjPStr m;
AjPStr n;
AjPStr merged = NULL;
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;
ajulong maxarr = 1000;
ajulong len; /* arbitrary. realloc'd if needed */
size_t stlen;
float score;
ajint begina;
ajint beginb;
embInit("merger", argc, argv);
a = ajAcdGetSeq("asequence");
b = ajAcdGetSeq("bsequence");
seqout = ajAcdGetSeqout("outseq");
matrix = ajAcdGetMatrixf("datafile");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
align = ajAcdGetAlign("outfile");
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
AJCNEW(path, maxarr);
AJCNEW(compass, maxarr);
/*
** make the two sequences lowercase so we can show which one we are
** using in the merge by uppercasing it
*/
ajSeqFmtLower(a);
ajSeqFmtLower(b);
m = ajStrNew();
n = ajStrNew();
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
begina = ajSeqGetBegin(a);
beginb = ajSeqGetBegin(b);
lena = ajSeqGetLen(a);
lenb = ajSeqGetLen(b);
if(lenb > (ULONG_MAX/(ajulong)(lena+1)))
ajFatal("Sequences too big. Try 'supermatcher'");
len = lena*lenb;
if(len>maxarr)
{
ajDebug("merger: resize path, len to %d (%d * $d)\n",
len, lena, lenb);
stlen = (size_t) len;
AJCRESIZE(path,stlen);
AJCRESIZE(compass,stlen);
maxarr=len;
}
p = ajSeqGetSeqC(a);
q = ajSeqGetSeqC(b);
ajStrAssignC(&m,"");
ajStrAssignC(&n,"");
score = embAlignPathCalc(p,q,lena,lenb,gapopen,gapextend,path,sub,cvt,
compass, ajFalse);
/*score = embAlignScoreNWMatrix(path,compass,gapopen,gapextend,
a,b,lena,lenb,sub,cvt,
&start1,&start2);*/
embAlignWalkNWMatrix(path,a,b,&m,&n,lena,lenb, &start1,&start2,gapopen,
gapextend,compass);
/*
** now construct the merged sequence, uppercase the bits of the two
** input sequences which are used in the merger
*/
merger_Merge(align, &merged,p,q,m,n,start1,start2,
ajSeqGetNameC(a),ajSeqGetNameC(b));
embAlignReportGlobal(align, a, b, m, n,
start1, start2, gapopen, gapextend,
score, matrix, begina, beginb);
ajAlignWrite(align);
ajAlignReset(align);
/* write the merged sequence */
ajSeqAssignSeqS(a, merged);
ajSeqoutWriteSeq(seqout, a);
ajSeqoutClose(seqout);
ajSeqoutDel(&seqout);
ajSeqDel(&a);
ajSeqDel(&b);
ajAlignClose(align);
ajAlignDel(&align);
ajStrDel(&merged);
AJFREE(compass);
AJFREE(path);
ajStrDel(&n);
ajStrDel(&m);
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;
}