static void digest_report_hits(AjPFeattable TabRpt, AjPList l, ajint be,
const char* s)
{
AjPFeature gf = NULL;
EmbPPropFrag fr;
AjPStr t;
ajint len;
AjPStr tmpStr = NULL;
size_t stlen;
t = ajStrNew();
stlen = strlen(s);
len = (ajint) stlen;
while(ajListPop(l,(void **)&fr))
{
ajStrAssignSubC(&t,s,fr->start,fr->end);
gf = ajFeatNewII(TabRpt,fr->start+be,fr->end+be);
ajFmtPrintS(&tmpStr, "*molwt %.3f", fr->molwt);
ajFeatTagAdd(gf, NULL, tmpStr);
if(fr->start>0)
{
ajFmtPrintS(&tmpStr, "*cterm %c", *(s+(fr->start)-1));
ajFeatTagAdd(gf, NULL, tmpStr);
}
if(fr->end<len-1)
{
ajFmtPrintS(&tmpStr, "*nterm %c", *(s+(fr->end+1)));
ajFeatTagAdd(gf, NULL, tmpStr);
}
AJFREE(fr);
}
ajStrDel(&t);
ajStrDel(&tmpStr);
return;
}
static void silent_fmt_hits(AjPList hits, AjPFeattable feat,
AjBool silent, AjBool rev)
{
PSilent res;
AjPFeature sf = NULL;
AjPStr tmpFeatStr = NULL;
ajListSort(hits,silent_basecompare);
while(ajListPop(hits,(void **)&res))
{
if (rev)
sf = ajFeatNewIIRev(feat,
res->match, res->match+ajStrGetLen(res->site)-1);
else
sf = ajFeatNewII(feat,
res->match, res->match+ajStrGetLen(res->site)-1);
if (silent)
{
ajFmtPrintS(&tmpFeatStr, "*silent Yes");
ajFeatTagAdd (sf, NULL, tmpFeatStr);
}
ajFmtPrintS(&tmpFeatStr, "*enzyme %S", res->code);
ajFeatTagAdd (sf, NULL, tmpFeatStr);
ajFmtPrintS(&tmpFeatStr, "*rspattern %S", res->site);
ajFeatTagAdd (sf, NULL, tmpFeatStr);
ajFmtPrintS(&tmpFeatStr, "*baseposn %d", res->base);
ajFeatTagAdd (sf, NULL, tmpFeatStr);
ajFmtPrintS(&tmpFeatStr, "*aa %S.%S", res->seqaa, res->reaa);
ajFeatTagAdd (sf, NULL, tmpFeatStr);
ajFmtPrintS(&tmpFeatStr, "*mutation %c->%c", res->obase,res->nbase);
ajFeatTagAdd (sf, NULL, tmpFeatStr);
ajStrDel(&res->code);
ajStrDel(&res->site);
ajStrDel(&res->seqaa);
ajStrDel(&res->reaa);
AJFREE(res);
}
ajStrDel(&tmpFeatStr);
return;
}
static void jaspscan_ReportHits(AjPFeattable TabRpt, const AjPTable mattab,
AjPList hits)
{
PJsphits hit = NULL;
PJspmat info = NULL;
AjPFeature feat = NULL;
AjPStr str = NULL;
float fnum = 0.;
str = ajStrNew();
while(ajListPop(hits,(void **)&hit))
{
if(hit->start <= hit->end)
feat = ajFeatNewII(TabRpt,hit->start,hit->end);
else
feat = ajFeatNewIIRev(TabRpt,hit->start,hit->end);
ajFmtPrintS(&str,"*pc %.3f",hit->scorepc);
ajFeatTagAdd(feat, NULL, str);
ajFmtPrintS(&str,"*id %S",hit->matname);
ajFeatTagAdd(feat, NULL, str);
info = ajTableFetch(mattab,hit->matname);
if(!info)
ajWarn("No info for matrix %S",hit->matname);
if(ajStrGetLen(info->name))
{
ajFmtPrintS(&str,"*name %S",info->name);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->species))
{
ajFmtPrintS(&str,"*species %S",info->species);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->klass))
{
ajFmtPrintS(&str,"*class %S",info->klass);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->sgroup))
{
ajFmtPrintS(&str,"*supergroup %S",info->sgroup);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->protseq))
{
ajFmtPrintS(&str,"*pseq %S",info->protseq);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->exp))
{
ajFmtPrintS(&str,"*exp %S",info->exp);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->pmid))
{
ajFmtPrintS(&str,"*pmid %S",info->pmid);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->num))
{
ajStrToFloat(info->num,&fnum);
ajFmtPrintS(&str,"*info %.3f",fnum);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->jaspar))
{
ajFmtPrintS(&str,"*jaspar %S",info->jaspar);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->transfac))
{
ajFmtPrintS(&str,"*transfac %S",info->transfac);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->mcs))
{
ajStrToFloat(info->mcs,&fnum);
ajFmtPrintS(&str,"*mcs %.3f",fnum);
ajFeatTagAdd(feat, NULL, str);
}
if(ajStrGetLen(info->models))
{
ajFmtPrintS(&str,"*built %S",info->models);
ajFeatTagAdd(feat, NULL, str);
}
jaspscan_hitsdel(&hit);
}
ajStrDel(&str);
return;
}
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;
}
