int main(int argc, char **argv)
{
AjPSeqall seq1;
AjPSeqset seq2;
AjPSeq a;
const AjPSeq b;
AjPStr m = 0;
AjPStr n = 0;
AjPFile errorf;
AjBool show = ajFalse;
ajint lena = 0;
ajint lenb = 0;
const char *p;
const char *q;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
ajint *compass = NULL;
float *path = NULL;
float gapopen;
float gapextend;
float score;
ajint begina;
ajint i;
ajuint k;
ajint beginb;
ajint start1 = 0;
ajint start2 = 0;
ajint end1 = 0;
ajint end2 = 0;
ajint width = 0;
AjPTable seq1MatchTable = 0;
ajint wordlen = 6;
ajint oldmax = 0;
AjPAlign align = NULL;
embInit("supermatcher", argc, argv);
matrix = ajAcdGetMatrixf("datafile");
seq1 = ajAcdGetSeqall("asequence");
seq2 = ajAcdGetSeqset("bsequence");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
wordlen = ajAcdGetInt("wordlen");
align = ajAcdGetAlign("outfile");
errorf = ajAcdGetOutfile("errorfile");
width = ajAcdGetInt("width"); /* not the same as awidth */
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
embWordLength(wordlen);
ajSeqsetTrim(seq2);
while(ajSeqallNext(seq1,&a))
{
ajSeqTrim(a);
begina = 1 + ajSeqGetOffset(a);
m = ajStrNewRes(1+ajSeqGetLen(a));
lena = ajSeqGetLen(a);
ajDebug("Read '%S'\n", ajSeqGetNameS(a));
if(!embWordGetTable(&seq1MatchTable, a)) /* get table of words */
ajErr("Could not generate table for %s\n",
ajSeqGetNameC(a));
for(k=0;k<ajSeqsetGetSize(seq2);k++)
{
b = ajSeqsetGetseqSeq(seq2, k);
lenb = ajSeqGetLen(b);
beginb = 1 + ajSeqGetOffset(b);
ajDebug("Processing '%S'\n", ajSeqGetNameS(b));
p = ajSeqGetSeqC(a);
q = ajSeqGetSeqC(b);
if(!supermatcher_findstartpoints(seq1MatchTable,b,a,
&start1, &start2,
&end1, &end2))
{
ajFmtPrintF(errorf,
"No wordmatch start points for "
"%s vs %s. No alignment\n",
ajSeqGetNameC(a),ajSeqGetNameC(b));
continue;
}
n=ajStrNewRes(1+ajSeqGetLen(b));
ajStrAssignC(&m,"");
ajStrAssignC(&n,"");
ajDebug("++ %S v %S start:%d %d end:%d %d\n",
ajSeqGetNameS(a), ajSeqGetNameS(b),
start1, start2, end1, end2);
if(end1-start1+1 > oldmax)
{
oldmax = ((end1-start1)+1);
AJRESIZE(path,oldmax*width*sizeof(float));
AJRESIZE(compass,oldmax*width*sizeof(ajint));
ajDebug("++ resize to oldmax: %d\n", oldmax);
}
for(i=0;i<((end1-start1)+1)*width;i++)
path[i] = 0.0;
ajDebug("Calling embAlignPathCalcFast "
"%d..%d [%d/%d] %d..%d [%d/%d]\n",
start1, end1, (end1 - start1 + 1), lena,
start2, end2, (end2 - start2 + 1), lenb);
score = embAlignPathCalcSWFast(&p[start1],&q[start2],
end1-start1+1,end2-start2+1,
0,width,
gapopen,gapextend,
path,sub,cvt,
compass,show);
embAlignWalkSWMatrixFast(path,compass,gapopen,gapextend,a,b,
&m,&n,end1-start1+1,end2-start2+1,
0,width,
&start1,&start2);
if(!ajAlignFormatShowsSequences(align))
{
ajAlignDefineCC(align, ajStrGetPtr(m),
ajStrGetPtr(n), ajSeqGetNameC(a),
ajSeqGetNameC(b));
ajAlignSetScoreR(align, score);
}
else
{
embAlignReportLocal(align, a, b,
m,n,start1,start2,
gapopen, gapextend,
score,matrix, begina, beginb);
}
ajAlignWrite(align);
ajAlignReset(align);
ajStrDel(&n);
}
embWordFreeTable(&seq1MatchTable); /* free table of words */
seq1MatchTable=0;
ajStrDel(&m);
}
if(!ajAlignFormatShowsSequences(align))
{
ajMatrixfDel(&matrix);
}
AJFREE(path);
AJFREE(compass);
ajAlignClose(align);
ajAlignDel(&align);
ajSeqallDel(&seq1);
ajSeqDel(&a);
ajSeqsetDel(&seq2);
ajFileClose(&errorf);
embExit();
return 0;
}
static ajint supermatcher_findstartpoints(AjPTable seq1MatchTable,
const AjPSeq b,
const AjPSeq a, ajint *start1,
ajint *start2, ajint *end1,
ajint *end2)
{
ajint max = -10;
ajint offset = 0;
AjPList matchlist = NULL;
AjPList ordered = NULL;
ajint amax;
ajint bmax;
ajint bega;
ajint begb;
amax = ajSeqGetLen(a)-1;
bmax = ajSeqGetLen(b)-1;
bega = ajSeqGetOffset(a);
begb = ajSeqGetOffset(b);
ajDebug("supermatcher_findstartpoints len %d %d off %d %d\n",
amax, bmax, bega, begb);
matchlist = embWordBuildMatchTable(seq1MatchTable, b, ajTrue);
if(!matchlist)
return 0;
else if(!matchlist->Count)
{
embWordMatchListDelete(&matchlist);
return 0;
}
/* order and add if the gap is gapmax or less */
/* create list header bit*/
ordered = ajListNew();
supermatcher_orderandconcat(matchlist, ordered);
/* this sets global structure conmax to point to a matchlist element */
ajListMap(ordered,supermatcher_findmax, &max);
ajDebug("findstart conmax off:%d count:%d total:%d\n",
conmax->offset, conmax->count, conmax->total,
ajListGetLength(conmax->list));
offset = conmax->offset;
/* the offset is all we needed! we can delete everything */
ajListMap(ordered,supermatcher_removelists, NULL);
ajListFree(&ordered);
embWordMatchListDelete(&matchlist); /* free the match structures */
if(offset > 0)
{
*start1 = offset;
*start2 = 0;
}
else
{
*start2 = 0-offset;
*start1 = 0;
}
*end1 = *start1;
*end2 = *start2;
ajDebug("++ end1 %d -> %d end2 %d -> %d\n", *end1, amax, *end2, bmax);
while(*end1<amax && *end2<bmax)
{
(*end1)++;
(*end2)++;
}
ajDebug("++ end1 %d end2 %d\n", *end1, *end2);
ajDebug("supermatcher_findstartpoints has %d..%d [%d] %d..%d [%d]\n",
*start1, *end1, ajSeqGetLen(a), *start2, *end2, ajSeqGetLen(b));
return 1;
}
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;
}
int main(int argc, char **argv)
{
AjPSeq seq1;
AjPSeq seq2;
ajint wordlen;
AjPTable seq1MatchTable = 0;
AjPList matchlist = NULL;
AjPGraph graph = NULL;
AjPGraph xygraph = NULL;
AjBool boxit;
/*
** Different ticks as they need to be different for x and y due to
** length of string being important on x
*/
ajuint acceptableticksx[]=
{
1,10,50,100,500,1000,1500,10000,
500000,1000000,5000000
};
ajuint acceptableticks[]=
{
1,10,50,100,200,500,1000,2000,5000,10000,15000,
500000,1000000,5000000
};
ajint numbofticks = 10;
float xmargin;
float ymargin;
float ticklen;
float tickgap;
float onefifth = 0.0;
ajint i;
float k;
float max;
char ptr[10];
ajint begin1;
ajint begin2;
ajint end1;
ajint end2;
ajuint len1;
ajuint len2;
float fbegin1;
float fbegin2;
float fend1;
float fend2;
float flen1;
float flen2;
AjBool stretch;
embInit("dottup", argc, argv);
wordlen = ajAcdGetInt("wordsize");
seq1 = ajAcdGetSeq("asequence");
seq2 = ajAcdGetSeq("bsequence");
graph = ajAcdGetGraph("graph");
boxit = ajAcdGetBoolean("boxit");
stretch = ajAcdGetToggle("stretch");
xygraph = ajAcdGetGraphxy("xygraph");
begin1 = ajSeqGetBegin(seq1);
begin2 = ajSeqGetBegin(seq2);
end1 = ajSeqGetEnd(seq1);
end2 = ajSeqGetEnd(seq2);
len1 = end1 - begin1 + 1;
len2 = end2 - begin2 + 1;
flen1 = (float) len1;
flen2 = (float) len2;
fbegin1 = (float) begin1;
fbegin2 = (float) begin2;
fend1 = (float) end1;
fend2 = (float) end2;
offset1 = fbegin1;
offset2 = fbegin2;
ajSeqTrim(seq1);
ajSeqTrim(seq2);
embWordLength(wordlen);
if(embWordGetTable(&seq1MatchTable, seq1))
matchlist = embWordBuildMatchTable(seq1MatchTable, seq2, ajTrue);
if(stretch)
{
dottup_stretchplot(xygraph,matchlist,seq1,seq2,begin1,begin2,end1,
end2);
if(matchlist)
embWordMatchListDelete(&matchlist); /* free the match structures */
}
else
{
/* only here if stretch is false */
max= flen1;
if(flen2 > max)
max = flen2;
xmargin = ymargin = max * (float)0.15;
ajGraphOpenWin(graph, fbegin1-ymargin,fend1+ymargin,
fbegin2-xmargin,(float)fend2+xmargin);
ajGraphicsSetCharscale(0.5);
if(matchlist)
dottup_plotMatches(matchlist);
if(boxit)
{
ajGraphicsDrawposRect(fbegin1, fbegin2, fend1, fend2);
i = 0;
while(acceptableticksx[i]*numbofticks < len1)
i++;
if(i<=13)
tickgap = (float) acceptableticksx[i];
else
tickgap = (float) acceptableticksx[10];
ticklen = xmargin * (float) 0.1;
onefifth = xmargin * (float)0.2;
ajGraphicsDrawposTextAtmid(fbegin1+flen1*(float)0.5,
fbegin1-(onefifth*(float)3.0),
ajGraphGetYlabelC(graph));
if(len2/len1 > 10 )
{
/* a lot smaller then just label start and end */
ajGraphicsDrawposLine(fbegin1,fbegin2,fbegin1,
fbegin2-ticklen);
sprintf(ptr,"%u",ajSeqGetOffset(seq1));
ajGraphicsDrawposTextAtmid(fbegin1,fbegin2-(onefifth),ptr);
ajGraphicsDrawposLine(fend1,fbegin2,
fend1,fbegin2-ticklen);
sprintf(ptr,"%d",end1);
ajGraphicsDrawposTextAtmid(fend1,fbegin2-(onefifth),ptr);
}
else
for(k=fbegin1;k<fend1;k+=tickgap)
{
ajGraphicsDrawposLine(k,fbegin2,k,fbegin2-ticklen);
sprintf(ptr,"%d",(ajint)k);
ajGraphicsDrawposTextAtmid( k,fbegin2-(onefifth),ptr);
}
i = 0;
while(acceptableticks[i]*numbofticks < len2)
i++;
tickgap = (float) acceptableticks[i];
ticklen = ymargin*(float)0.1;
onefifth = ymargin*(float)0.2;
ajGraphicsDrawposTextAtlineJustify(fbegin1-(onefifth*(float)4.),
fbegin2+flen2*(float)0.5,
fbegin2-(onefifth*(float)4.),
fbegin2+flen2,
ajGraphGetXlabelC(graph),
0.5);
if(len1/len2 > 10 )
{
/* a lot smaller then just label start and end */
ajGraphicsDrawposLine(fbegin1,fbegin2,fbegin1-ticklen,
fbegin2);
sprintf(ptr,"%u",ajSeqGetOffset(seq2));
ajGraphicsDrawposTextAtend(fbegin1-(onefifth),fbegin2,ptr);
ajGraphicsDrawposLine(fbegin1,fend2,fbegin1-ticklen,
fend2);
sprintf(ptr,"%d",end2);
ajGraphicsDrawposTextAtend(fbegin2-(onefifth),fend2,ptr);
}
else
for(k=fbegin2;k<fend2;k+=tickgap)
{
ajGraphicsDrawposLine(fbegin1,k,fbegin1-ticklen,k);
sprintf(ptr,"%d",(ajint)k);
ajGraphicsDrawposTextAtend(fbegin1-(onefifth),k,ptr);
}
}
}
ajGraphicsClose();
ajSeqDel(&seq1);
ajSeqDel(&seq2);
ajGraphxyDel(&graph);
ajGraphxyDel(&xygraph);
embWordFreeTable(&seq1MatchTable);
if(matchlist)
embWordMatchListDelete(&matchlist); /* free the match structures */
embExit();
return 0;
}
void embPatternSeqSearch (AjPFeattable ftable, const AjPSeq seq,
const AjPPatternSeq pat, AjBool reverse)
{
const void *tidy;
ajuint hits;
ajuint i;
AjPPatComp pattern;
EmbPMatMatch m = NULL;
AjPFeature sf = NULL;
AjPSeq revseq = NULL;
AjPList list = ajListNew();
AjPStr seqstr = ajStrNew();
AjPStr seqname = ajStrNew();
AjPStr tmp = ajStrNew();
ajint adj;
ajint begin;
AjBool isreversed;
ajint seqlen;
seqlen = ajSeqGetLen(seq);
if(!seqlen)
return;
isreversed = ajSeqIsReversedTrue(seq);
if(isreversed)
seqlen += ajSeqGetOffset(seq);
begin = ajSeqGetBeginTrue(seq);
adj = ajSeqGetEndTrue(seq);
if(!ajStrGetLen(featMotifProt))
ajStrAssignC(&featMotifProt, "SO:0001067");
if(!ajStrGetLen(featMotifNuc))
ajStrAssignC(&featMotifNuc, "SO:0000714");
ajStrAssignS(&seqname,ajSeqGetNameS(seq));
pattern = ajPatternSeqGetCompiled(pat);
if (reverse)
{
revseq = ajSeqNewSeq(seq);
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq),
begin-1,adj-1);
ajSeqstrReverse(&seqstr);
}
else
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq),
begin-1,adj-1);
ajStrFmtUpper(&seqstr);
/*ajDebug("seqlen:%d len: %d offset: %d offend: %d begin: %d end: %d\n"
"'%S'\n",
seqlen , ajSeqGetLen(seq), ajSeqGetOffset(seq),
ajSeqGetOffend(seq), ajSeqGetBegin(seq), ajSeqGetEnd(seq),
seqstr);*/
ajDebug("embPatternSeqSearch '%S' protein: %B reverse: %B\n",
pattern->pattern, pat->Protein, reverse);
embPatFuzzSearchII(pattern,begin,seqname,seqstr,list,
ajPatternSeqGetMismatch(pat),&hits,&tidy);
ajDebug ("embPatternSeqSearch: found %d hits\n",hits);
if(!reverse)
ajListReverse(list);
for(i=0;i<hits;++i)
{
ajListPop(list,(void **)&m);
if (reverse)
sf = ajFeatNew(ftable, NULL, featMotifNuc,
adj - m->start - m->len + begin + 1,
adj - m->start + begin,
0.0, '-', 0);
else
{
if(ajSeqIsProt(seq) || ajFeattableIsProt(ftable))
sf = ajFeatNewProt(ftable, NULL, featMotifProt,
m->start,
m->start + m->len - 1,
0.0);
else
sf = ajFeatNew(ftable, NULL, featMotifNuc,
m->start,
m->start + m->len - 1,
0.0, '.', 0);
}
if(isreversed)
ajFeatReverse(sf, seqlen);
/*
ajUser("isrev: %B reverse: %B begin: %d adj: %d "
"start: %d len: %d seqlen: %d %d..%d '%c'\n",
isreversed, reverse, begin, adj, m->start, m->len, seqlen,
sf->Start, sf->End, sf->Strand);
*/
ajFeatSetScore(sf, (float) (m->len - m->mm));
ajFmtPrintS(&tmp, "*pat %S: %S",
ajPatternSeqGetName(pat),
ajPatternSeqGetPattern(pat));
ajFeatTagAdd(sf,NULL,tmp);
if(m->mm)
{
ajFmtPrintS(&tmp, "*mismatch %d", m->mm);
ajFeatTagAdd(sf, NULL, tmp);
}
embMatMatchDel(&m);
}
ajStrDel(&seqname);
ajStrDel(&seqstr);
ajStrDel(&tmp);
ajListFree(&list);
if (reverse)
ajSeqDel(&revseq);
return;
}
void embPatternRegexSearch (AjPFeattable ftable, const AjPSeq seq,
const AjPPatternRegex pat, AjBool reverse)
{
ajint pos=0;
ajint off;
ajint len;
AjPFeature sf = NULL;
AjPStr substr = NULL;
AjPStr seqstr = NULL;
AjPStr tmpstr = NULL;
AjPStr tmp = ajStrNew();
AjPRegexp patexp = ajPatternRegexGetCompiled(pat);
ajint adj;
AjBool isreversed;
AjPSeq revseq;
ajint seqlen;
seqlen = ajSeqGetLen(seq);
if(!seqlen)
return;
isreversed = ajSeqIsReversedTrue(seq);
if(isreversed)
seqlen += ajSeqGetOffset(seq);
pos = ajSeqGetBeginTrue(seq);
adj = ajSeqGetEndTrue(seq);
if(!ajStrGetLen(featMotifProt))
ajStrAssignC(&featMotifProt, "SO:0001067");
if(!ajStrGetLen(featMotifNuc))
ajStrAssignC(&featMotifNuc, "SO:0000714");
/*ajDebug("embPatternRegexSearch pos: %d adj: %d reverse: %B\n",
pos, adj, reverse, isreversed);*/
/*ajDebug("seqlen:%d len: %d offset: %d offend: %d begin: %d end: %d\n",
seqlen , ajSeqGetLen(seq), ajSeqGetOffset(seq),
ajSeqGetOffend(seq), ajSeqGetBegin(seq), ajSeqGetEnd(seq));*/
if (reverse)
{
revseq = ajSeqNewSeq(seq);
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq), pos-1, adj-1);
ajSeqstrReverse(&seqstr);
}
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq), pos-1, adj-1);
ajStrFmtUpper(&seqstr);
while(ajStrGetLen(seqstr) && ajRegExec(patexp, seqstr))
{
off = ajRegOffset(patexp);
len = ajRegLenI(patexp, 0);
if(off || len)
{
ajRegSubI(patexp, 0, &substr);
ajRegPost(patexp, &tmp);
ajStrAssignS(&seqstr, substr);
ajStrAppendS(&seqstr, tmp);
pos += off;
/*ajDebug("match pos: %d adj: %d len: %d off:%d\n",
pos, adj, len, off);*/
if (reverse)
sf = ajFeatNew(ftable, NULL, featMotifNuc,
adj - pos - len + 2,
adj - pos + 1,
0.0, '-', 0);
else
{
if(ajSeqIsProt(seq) || ajFeattableIsProt(ftable))
sf = ajFeatNewProt(ftable, NULL, featMotifProt,
pos, pos + len - 1,
0.0);
else
sf = ajFeatNew(ftable, NULL, featMotifNuc,
pos, pos + len - 1,
0.0, '.', 0);
}
if(isreversed)
ajFeatReverse(sf, seqlen);
ajFmtPrintS (&tmpstr,"*pat %S: %S",
ajPatternRegexGetName(pat),
ajPatternRegexGetPattern(pat));
ajFeatTagAdd (sf,NULL,tmpstr);
pos += 1;
ajStrCutStart(&seqstr, 1);
}
else
{
pos++;
ajStrCutStart(&seqstr, 1);
}
}
ajStrDel(&tmpstr);
ajStrDel(&tmp);
ajStrDel(&substr);
ajStrDel(&seqstr);
if(reverse)
ajSeqDel(&revseq);
return;
}
int main(int argc, char **argv)
{
AjPSeqall queryseqs;
AjPSeqset targetseqs;
AjPSeq queryseq;
const AjPSeq targetseq;
AjPStr queryaln = 0;
AjPStr targetaln = 0;
AjPFile errorf;
AjBool show = ajFalse;
const char *queryseqc;
const char *targetseqc;
AjPMatrixf matrix;
AjPSeqCvt cvt = 0;
float **sub;
ajint *compass = NULL;
float *path = NULL;
float gapopen;
float gapextend;
float score;
float minscore;
ajuint j, k;
ajint querystart = 0;
ajint targetstart = 0;
ajint queryend = 0;
ajint targetend = 0;
ajint width = 0;
AjPTable kmers = 0;
ajint wordlen = 6;
ajint oldmax = 0;
ajint newmax = 0;
ajuint ntargetseqs;
ajuint nkmers;
AjPAlign align = NULL;
EmbPWordMatch maxmatch; /* match with maximum score */
/* Cursors for the current sequence being scanned,
** i.e., until which location it was scanned.
** Separate cursor/location entries for each sequence in the seqset.
*/
ajuint* lastlocation;
EmbPWordRK* wordsw = NULL;
AjPList* matchlist = NULL;
embInit("supermatcher", argc, argv);
matrix = ajAcdGetMatrixf("datafile");
queryseqs = ajAcdGetSeqall("asequence");
targetseqs= ajAcdGetSeqset("bsequence");
gapopen = ajAcdGetFloat("gapopen");
gapextend = ajAcdGetFloat("gapextend");
wordlen = ajAcdGetInt("wordlen");
align = ajAcdGetAlign("outfile");
errorf = ajAcdGetOutfile("errorfile");
width = ajAcdGetInt("width"); /* width for banded Smith-Waterman */
minscore = ajAcdGetFloat("minscore");
gapopen = ajRoundFloat(gapopen, 8);
gapextend = ajRoundFloat(gapextend, 8);
sub = ajMatrixfGetMatrix(matrix);
cvt = ajMatrixfGetCvt(matrix);
embWordLength(wordlen);
/* seqset sequence is the reference sequence for SAM format */
ajAlignSetRefSeqIndx(align, 1);
ajSeqsetTrim(targetseqs);
ntargetseqs = ajSeqsetGetSize(targetseqs);
AJCNEW0(matchlist, ntargetseqs);
/* get tables of words */
for(k=0;k<ntargetseqs;k++)
{
targetseq = ajSeqsetGetseqSeq(targetseqs, k);
embWordGetTable(&kmers, targetseq);
ajDebug("Number of distinct kmers found so far: %d\n",
ajTableGetLength(kmers));
}
AJCNEW0(lastlocation, ntargetseqs);
if(ajTableGetLength(kmers)<1)
ajErr("no kmers found");
nkmers = embWordRabinKarpInit(kmers, &wordsw, wordlen, targetseqs);
while(ajSeqallNext(queryseqs,&queryseq))
{
ajSeqTrim(queryseq);
queryaln = ajStrNewRes(1+ajSeqGetLen(queryseq));
ajDebug("Read '%S'\n", ajSeqGetNameS(queryseq));
for(k=0;k<ntargetseqs;k++)
{
lastlocation[k]=0;
matchlist[k] = ajListstrNew();
}
embWordRabinKarpSearch(ajSeqGetSeqS(queryseq), targetseqs,
(const EmbPWordRK*)wordsw, wordlen, nkmers,
matchlist, lastlocation, ajFalse);
for(k=0;k<ajSeqsetGetSize(targetseqs);k++)
{
targetseq = ajSeqsetGetseqSeq(targetseqs, k);
ajDebug("Processing '%S'\n", ajSeqGetNameS(targetseq));
if(ajListGetLength(matchlist[k])==0)
{
ajFmtPrintF(errorf,
"No wordmatch start points for "
"%s vs %s. No alignment\n",
ajSeqGetNameC(queryseq),ajSeqGetNameC(targetseq));
embWordMatchListDelete(&matchlist[k]);
continue;
}
/* only the maximum match is used as seed
* (if there is more than one location with the maximum match
* only the first one is used)
* TODO: we should add a new option to make above limit optional
*/
maxmatch = embWordMatchFirstMax(matchlist[k]);
supermatcher_findendpoints(maxmatch,targetseq, queryseq,
&targetstart, &querystart,
&targetend, &queryend);
targetaln=ajStrNewRes(1+ajSeqGetLen(targetseq));
queryseqc = ajSeqGetSeqC(queryseq);
targetseqc = ajSeqGetSeqC(targetseq);
ajStrAssignC(&queryaln,"");
ajStrAssignC(&targetaln,"");
ajDebug("++ %S v %S start:%d %d end:%d %d\n",
ajSeqGetNameS(targetseq), ajSeqGetNameS(queryseq),
targetstart, querystart, targetend, queryend);
newmax = (targetend-targetstart+2)*width;
if(newmax > oldmax)
{
AJCRESIZE0(path,oldmax,newmax);
AJCRESIZE0(compass,oldmax,newmax);
oldmax=newmax;
ajDebug("++ memory re/allocation for path/compass arrays"
" to size: %d\n", newmax);
}
else
{
AJCSET0(path,newmax);
AJCSET0(compass,newmax);
}
ajDebug("Calling embAlignPathCalcSWFast "
"%d..%d [%d/%d] %d..%d [%d/%d] width:%d\n",
querystart, queryend, (queryend - querystart + 1),
ajSeqGetLen(queryseq),
targetstart, targetend, (targetend - targetstart + 1),
ajSeqGetLen(targetseq),
width);
score = embAlignPathCalcSWFast(&targetseqc[targetstart],
&queryseqc[querystart],
targetend-targetstart+1,
queryend-querystart+1,
0,width,
gapopen,gapextend,
path,sub,cvt,
compass,show);
if(score>minscore)
{
embAlignWalkSWMatrixFast(path,compass,gapopen,gapextend,
targetseq,queryseq,
&targetaln,&queryaln,
targetend-targetstart+1,
queryend-querystart+1,
0,width,
&targetstart,&querystart);
if(!ajAlignFormatShowsSequences(align))
{
ajAlignDefineCC(align, ajStrGetPtr(targetaln),
ajStrGetPtr(queryaln),
ajSeqGetNameC(targetseq),
ajSeqGetNameC(queryseq));
ajAlignSetScoreR(align, score);
}
else
{
ajDebug(" queryaln:%S \ntargetaln:%S\n",
queryaln,targetaln);
embAlignReportLocal(align,
queryseq, targetseq,
queryaln, targetaln,
querystart, targetstart,
gapopen, gapextend,
score, matrix,
1 + ajSeqGetOffset(queryseq),
1 + ajSeqGetOffset(targetseq)
);
}
ajAlignWrite(align);
ajAlignReset(align);
}
ajStrDel(&targetaln);
embWordMatchListDelete(&matchlist[k]);
}
ajStrDel(&queryaln);
}
for(k=0;k<nkmers;k++)
{
AJFREE(wordsw[k]->seqindxs);
AJFREE(wordsw[k]->nSeqMatches);
for(j=0;j<wordsw[k]->nseqs;j++)
AJFREE(wordsw[k]->locs[j]);
AJFREE(wordsw[k]->nnseqlocs);
AJFREE(wordsw[k]->locs);
AJFREE(wordsw[k]);
}
embWordFreeTable(&kmers);
if(!ajAlignFormatShowsSequences(align))
ajMatrixfDel(&matrix);
AJFREE(path);
AJFREE(compass);
AJFREE(kmers);
AJFREE(wordsw);
AJFREE(matchlist);
AJFREE(lastlocation);
ajAlignClose(align);
ajAlignDel(&align);
ajSeqallDel(&queryseqs);
ajSeqDel(&queryseq);
ajSeqsetDel(&targetseqs);
ajFileClose(&errorf);
embExit();
return 0;
}
