static ajint prima_primalign(const AjPStr a, const AjPStr b)
{
ajint plen;
ajint qlen;
ajint limit;
ajint i;
ajint n = 0;
ajint mm = 0;
ajint j;
const char *p;
const char *q;
ajint alen;
ajint blen;
alen = ajStrGetLen(a);
blen = ajStrGetLen(b);
if(alen > blen)
{
plen = alen;
qlen = blen;
p = ajStrGetPtr(a);
q = ajStrGetPtr(b);
}
else
{
plen = blen;
qlen = alen;
p = ajStrGetPtr(b);
q = ajStrGetPtr(a);
}
limit = plen-qlen+1;
for(i=0; i<limit; ++i)
{
for(j=0; j<qlen; ++j)
if(p[j]==q[j])
++n;
mm = AJMAX(mm, n);
++p;
}
return (ajint)(((float)mm/(float)qlen)*100.0);
}
static PSilent silent_checktrans(const AjPStr seq,const EmbPMatMatch match,
const PRinfo rlp, ajint begin, ajint radj,
AjBool rev, ajint end)
{
PSilent ret;
const char *p = NULL;
const char *q = NULL;
const char *s = NULL;
char *t;
const char *u;
ajint matchpos;
ajint framep;
ajint count;
AjPTrn table = NULL;
AjPStr s1 = NULL;
AjPStr s2 = NULL;
char c;
char rc;
ajint min = INT_MAX; /* Reverse sense intentional! */
ajint max = -INT_MAX;
ajint fpos;
ajint rpos;
ajint x;
AjPStr tstr = NULL;
matchpos = match->start;
fpos = matchpos;
rpos=radj-fpos-match->len;
tstr = ajStrNewS(seq);
t = ajStrGetuniquePtr(&tstr);
p = t+fpos-(begin+1);
u = q = ajStrGetPtr(rlp->site);
/* Test here for whether cut site is within sequence substring */
if(rlp->ncuts==4)
{
min = AJMIN(rlp->cut1,rlp->cut2);
max = AJMAX(rlp->cut3,rlp->cut4);
}
else if(rlp->ncuts==2)
{
min = AJMIN(rlp->cut1,rlp->cut2);
max = AJMAX(rlp->cut1,rlp->cut2);
}
else
{
ajWarn("Possibly corrupt RE file");
ajStrDel(&tstr);
return NULL;
}
if(!rev) /* forward strand */
{
if(matchpos+min<0||matchpos+max>end+1)
{
/*Cut site not in sequence range*/
ajStrDel(&tstr);
return NULL;
}
}
else /* reverse strand */
{
if(radj-matchpos-1-min>end+1||radj-matchpos-1-max<begin)
{
/*Cut site not in sequence range*/
ajStrDel(&tstr);
return NULL;
}
}
count=0;
while(ajBaseAlphaToBin(*q++) & ajBaseAlphaToBin(*p++))
++count;
/* Changed base postion */
x = fpos+count-(begin+1);
/* Where the frame starts on the reverse strand */
framep = (end-begin+1)%3;
c = t[x];
rc = u[count];
if(!rev) /* forward strand */
s = t+x-x%3;
else /* reverse strand */
s = t+x-(x-framep)%3;
table = ajTrnNewI(0);
/* translates codon pointed to by s (original seq) */
s1 = ajStrNewK(ajTrnCodonC(table,s));
t[x] = rc;
/* translates codon pointed to by s (mutated base from RS pattern */
s2 = ajStrNewK(ajTrnCodonC(table,s));
t[x] = c; /* changes mutated base in seq back to original base */
AJNEW(ret);
ret->obase = c;
ret->nbase = rc;
ret->code = ajStrNewC(ajStrGetPtr(rlp->code));
ret->site = ajStrNewC(ajStrGetPtr(rlp->site));
ret->seqaa = ajStrNewC(ajStrGetPtr(s1));
ret->reaa = ajStrNewC(ajStrGetPtr(s2));
if(ajStrMatchS(s1,s2))
ret->issilent = ajTrue;
else
ret->issilent = ajFalse;
if(!rev)
{
ret->match = matchpos;
ret->base = matchpos+count;
}
else
{
ret->match = rpos;
ret->base = rpos+match->len-1-count;
}
ajStrDel(&tstr);
ajStrDel(&s1);
ajStrDel(&s2);
ajTrnDel(&table);
return ret;
}
static void pscan_print_hits(AjPFile outf, AjPList l, ajuint nmotifs,
ajuint begin)
{
EmbPMatMatch mm;
ajuint i;
ajuint j;
AjBool found;
ajuint nleft;
ajuint maxelem = 0;
ajuint maxhpm;
ajuint hpm = 0;
nleft = nmotifs;
ajFmtPrintF(outf,"\n\nCLASS 1\n");
ajFmtPrintF(outf,"Fingerprints with all elements in order\n\n");
found = ajTrue;
while(found && nleft)
{
found = ajFalse;
maxelem = 0;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
if(mm->all && mm->ordered)
{
maxelem = AJMAX(maxelem,mm->n);
found = ajTrue;
}
hpm = mm->hpm;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(found)
{
found = ajFalse;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
hpm = mm->hpm;
if(mm->all && mm->ordered && maxelem==mm->n)
break;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(mm->all && mm->ordered && maxelem==mm->n)
{
ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",
ajStrGetPtr(mm->cod),mm->n);
ajFmtPrintF(outf," Accession number %s\n",
ajStrGetPtr(mm->acc));
ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit));
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
for(i=1;i<hpm;++i)
{
ajListPop(l,(void **)&mm);
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
--nleft;
}
}
ajFmtPrintF(outf,"\n\nCLASS 2\n");
ajFmtPrintF(outf,"All elements match but not all in the "
"correct order\n\n");
found = ajTrue;
while(found && nleft)
{
found = ajFalse;
maxelem = 0;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
if(mm->all)
{
maxelem = AJMAX(maxelem,mm->n);
found = ajTrue;
}
hpm = mm->hpm;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(found)
{
found=ajFalse;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
hpm = mm->hpm;
if(mm->all && maxelem==mm->n)
break;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(mm->all && maxelem==mm->n)
{
ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",
ajStrGetPtr(mm->cod),mm->n);
ajFmtPrintF(outf," Accession number %s\n",
ajStrGetPtr(mm->acc));
ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit));
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
for(i=1;i<hpm;++i)
{
ajListPop(l,(void **)&mm);
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
--nleft;
}
}
ajFmtPrintF(outf,"\n\nCLASS 3\n");
ajFmtPrintF(outf,
"Not all elements match but those that do are in order\n\n");
found = ajTrue;
while(found && nleft)
{
found = ajFalse;
maxhpm = 0;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
if(mm->ordered)
{
maxhpm = AJMAX(maxelem,mm->hpm);
found = ajTrue;
}
hpm = mm->hpm;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(found)
{
found = ajFalse;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
hpm = mm->hpm;
if(mm->ordered && maxhpm==mm->hpm)
break;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(mm->ordered && maxhpm==mm->hpm)
{
ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",
ajStrGetPtr(mm->cod),mm->n);
ajFmtPrintF(outf," Accession number %s\n",
ajStrGetPtr(mm->acc));
ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit));
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
for(i=1;i<hpm;++i)
{
ajListPop(l,(void **)&mm);
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
--nleft;
}
}
ajFmtPrintF(outf,"\n\nCLASS 4\n");
ajFmtPrintF(outf,
"Remaining partial matches\n\n");
found = ajTrue;
while(found && nleft)
{
found = ajFalse;
maxhpm = 0;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
maxhpm = AJMAX(maxelem,mm->hpm);
found = ajTrue;
hpm = mm->hpm;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(found)
{
found = ajFalse;
for(i=0;i<nleft;++i)
{
ajListPop(l,(void **)&mm);
hpm = mm->hpm;
if(maxhpm==mm->hpm)
break;
ajListPushAppend(l,(void *)mm);
for(j=1;j<hpm;++j)
{
ajListPop(l,(void **)&mm);
ajListPushAppend(l,(void *)mm);
}
}
if(maxhpm==mm->hpm)
{
ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",
ajStrGetPtr(mm->cod),mm->n);
ajFmtPrintF(outf," Accession number %s\n",
ajStrGetPtr(mm->acc));
ajFmtPrintF(outf," %s\n",ajStrGetPtr(mm->tit));
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
for(i=1;i<hpm;++i)
{
ajListPop(l,(void **)&mm);
ajFmtPrintF(outf," Element %d Threshold %d%% Score %d%%\n",
mm->element+1, mm->thresh, mm->score);
ajFmtPrintF(outf," Start position %d Length %d\n",
mm->start+begin,mm->len);
embMatMatchDel(&mm);
}
--nleft;
}
}
while(ajListPop(l,(void **)&mm))
if(mm)
embMatMatchDel(&mm);
return;
}
