static Palindrome palindrome_New(ajint fstart, ajint fend, ajint rstart,
ajint rend)
{
Palindrome pal;
AJNEW(pal);
pal->forwardStart = fstart;
pal->forwardEnd = fend;
pal->revStart = rstart;
pal->revEnd = rend;
pal->next = NULL;
return pal;
}
static void supermatcher_matchListOrder(void **x,void *cl)
{
EmbPWordMatch p;
AjPList ordered;
ajint offset;
AjIList listIter;
concat *con;
concat *c=NULL;
p = (EmbPWordMatch)*x;
ordered = (AjPList) cl;
offset = (*p).seq1start-(*p).seq2start;
/* iterate through ordered list to find if it exists already*/
listIter = ajListIterNewread(ordered);
while(!ajListIterDone( listIter))
{
con = ajListIterGet(listIter);
if(con->offset == offset)
{
/* found so add count and set offset to the new value */
con->offset = offset;
con->total+= (*p).length;
con->count++;
ajListPushAppend(con->list,p);
ajListIterDel(&listIter);
return;
}
}
ajListIterDel(&listIter);
/* not found so add it */
AJNEW(c);
c->offset = offset;
c->total = (*p).length;
c->count = 1;
c->list = ajListNew();
ajListPushAppend(c->list,p);
ajListPushAppend(ordered, c);
return;
}
static AjPTable dastestGetTitleCount(const AjPDasServer server)
{
AjIList iter = NULL;
AjPTable titlecount = NULL;
AjPDasSource source = NULL;
AjPStr title = NULL;
ajuint* count = NULL;
titlecount = ajTablestrNewCaseConst(ajListGetLength(server->sources)+20);
iter = ajListIterNew(server->sources);
while(!ajListIterDone(iter))
{
source = ajListIterGet(iter);
title = source->title;
count = ajTableFetchmodS(titlecount,title);
if (count != NULL)
{
(*count)++;
}
else
{
AJNEW(count);
*count = 1;
ajTablePut(titlecount, title, (void*)count);
}
}
ajListIterDel(&iter);
return titlecount;
}
static void primersearch_initialise_pguts(PGuts* primer)
{
AJNEW(*primer);
(*primer)->patstr = NULL;
(*primer)->origpat = ajStrNew();
(*primer)->type = 0;
(*primer)->len = 0;
(*primer)->real_len = 0;
(*primer)->re = NULL;
(*primer)->amino = 0;
(*primer)->carboxyl = 0;
(*primer)->tidy = NULL;
(*primer)->mm = 0;
(*primer)->buf = NULL;
(*primer)->sotable = NULL;
(*primer)->solimit = 0;
(*primer)->re = NULL;
(*primer)->skipm = NULL;
return;
}
static void primersearch_store_hits(const Primer primdata,
AjPList fhits, AjPList rhits,
const AjPSeq seq, AjBool reverse)
{
ajint amplen = 0;
AjIList fi;
AjIList ri;
PHit primerhit = NULL;
fi = ajListIterNewread(fhits);
while(!ajListIterDone(fi))
{
EmbPMatMatch fm = NULL;
EmbPMatMatch rm = NULL;
amplen = 0;
fm = ajListIterGet(fi);
ri = ajListIterNewread(rhits);
while(!ajListIterDone(ri))
{
ajint seqlen = ajSeqGetLen(seq);
ajint s = (fm->start);
ajint e;
rm = ajListIterGet(ri);
e = (rm->start-1);
amplen = seqlen-(s-1)-e;
if (amplen > 0) /* no point making a hit if -ve length! */
{
primerhit = NULL;
AJNEW(primerhit);
primerhit->desc=NULL; /* must be NULL for ajStrAss */
primerhit->seqname=NULL; /* must be NULL for ajStrAss */
primerhit->acc=NULL;
primerhit->forward=NULL;
primerhit->reverse=NULL;
ajStrAssignC(&primerhit->seqname,ajSeqGetNameC(seq));
ajStrAssignS(&primerhit->desc, ajSeqGetDescS(seq));
ajStrAssignS(&primerhit->acc, ajSeqGetAccS(seq));
primerhit->forward_pos = fm->start;
primerhit->reverse_pos = rm->start;
primerhit->forward_mismatch = fm->mm;
primerhit->reverse_mismatch = rm->mm;
primerhit->amplen = amplen;
if(!reverse)
{
ajStrAssignS(&primerhit->forward,
primdata->forward->patstr);
ajStrAssignS(&primerhit->reverse,
primdata->reverse->patstr);
}
else
{
ajStrAssignS(&primerhit->forward,
primdata->reverse->patstr);
ajStrAssignS(&primerhit->reverse,
primdata->forward->patstr);
}
ajListPushAppend(primdata->hitlist, primerhit);
}
}
/*
** clean up rListIter here as it will be new'ed again next
** time through
*/
ajListIterDel(&ri);
}
ajListIterDel(&fi);
return;
}
static void primersearch_read_primers(AjPList *primerList, AjPFile primerFile,
ajint mmp)
{
AjPStr rdline = NULL;
AjPStrTok handle = NULL;
ajint nprimers = 0;
Primer primdata = NULL;
while (ajReadlineTrim(primerFile, &rdline))
{
primdata = NULL;
if (ajStrGetCharFirst(rdline) == '#')
continue;
if (ajStrSuffixC(rdline, ".."))
continue;
AJNEW(primdata);
primdata->Name = NULL;
primersearch_initialise_pguts(&primdata->forward);
primersearch_initialise_pguts(&primdata->reverse);
primdata->hitlist = ajListNew();
handle = ajStrTokenNewC(rdline, " \t");
ajStrTokenNextParse(&handle, &primdata->Name);
ajStrTokenNextParse(&handle, &primdata->forward->patstr);
ajStrFmtUpper(&primdata->forward->patstr);
ajStrTokenNextParse(&handle, &primdata->reverse->patstr);
ajStrFmtUpper(&primdata->reverse->patstr);
ajStrTokenDel(&handle);
/* copy patterns for Henry Spencer code */
ajStrAssignC(&primdata->forward->origpat,
ajStrGetPtr(primdata->forward->patstr));
ajStrAssignC(&primdata->reverse->origpat,
ajStrGetPtr(primdata->reverse->patstr));
/* set the mismatch level */
primdata->forward->mm = (ajint)
(ajStrGetLen(primdata->forward->patstr)*mmp)/100;
primdata->reverse->mm = (ajint)
(ajStrGetLen(primdata->reverse->patstr)*mmp)/100;
if(primersearch_classify_and_compile(&primdata))
{
ajListPushAppend(*primerList, primdata);
nprimers++;
}
else /* there was something funny about the primer sequences */
{
ajUser("Cannot use %s\n", ajStrGetPtr(primdata->Name));
primersearch_free_pguts(&primdata->forward);
primersearch_free_pguts(&primdata->reverse);
ajStrDel(&primdata->Name);
ajListFree(&primdata->hitlist);
ajListFree(&primdata->hitlist);
AJFREE(primdata);
}
}
ajStrDel(&rdline);
return;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPFile primfile;
AjPStr rdline = NULL;
Primer primdata;
AjPStrTok handle = NULL;
AjPList primList = NULL;
embInit("stssearch", argc, argv);
primfile = ajAcdGetInfile("infile");
out = ajAcdGetOutfile("outfile");
seqall = ajAcdGetSeqall("seqall");
while(ajReadlineTrim(primfile, &rdline))
{
if(ajStrGetCharFirst(rdline) == '#')
continue;
if(ajStrSuffixC(rdline, ".."))
continue;
AJNEW(primdata);
primdata->Name = NULL;
primdata->Oligoa = NULL;
primdata->Oligob = NULL;
handle = ajStrTokenNewC(rdline, " \t");
ajStrTokenNextParse(&handle, &primdata->Name);
if(!(nprimers % 1000))
ajDebug("Name [%d]: '%S'\n", nprimers, primdata->Name);
ajStrTokenNextParse(&handle, &primdata->Oligoa);
ajStrFmtUpper(&primdata->Oligoa);
primdata->Prima = ajRegComp(primdata->Oligoa);
ajStrTokenNextParse(&handle, &primdata->Oligob);
ajStrFmtUpper(&primdata->Oligob);
primdata->Primb = ajRegComp(primdata->Oligob);
ajStrTokenDel(&handle);
if(!nprimers)
primList = ajListNew();
ajListPushAppend(primList, primdata);
nprimers++;
}
if(!nprimers)
ajFatal("No primers read\n");
ajDebug("%d primers read\n", nprimers);
while(ajSeqallNext(seqall, &seq))
{
ajSeqFmtUpper(seq);
ajStrAssignS(&seqstr, ajSeqGetSeqS(seq));
ajStrAssignS(&revstr, ajSeqGetSeqS(seq));
ajSeqstrReverse(&revstr);
ajDebug("Testing: %s\n", ajSeqGetNameC(seq));
ntests = 0;
ajListMap(primList, stssearch_primTest, NULL);
}
ajFileClose(&out);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajFileClose(&out);
ajStrDel(&revstr);
ajStrDel(&seqstr);
ajFileClose(&primfile);
ajListMap(primList, stssearch_primDel, NULL);
ajListFree(&primList);
ajStrDel(&rdline);
embExit();
return 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 ajint silent_restr_read(AjPList *relist,const AjPStr enzymes)
{
EmbPPatRestrict rptr = NULL;
AjPFile fin = NULL;
AjPStr refilename = NULL;
register ajint RStotal = 0;
PRinfo rinfo = NULL;
AjBool isall = ajFalse;
ajint ne = 0;
ajint i;
AjPStr *ea = NULL;
refilename = ajStrNewC("REBASE/embossre.enz");
rptr = embPatRestrictNew();
*relist = ajListNew();
fin = ajDatafileNewInNameS(refilename);
if(!fin)
ajFatal("Aborting...restriction file '%S' not found", refilename);
/* Parse the user-selected enzyme list */
if(!enzymes)
isall = ajTrue;
else
{
ne = ajArrCommaList(enzymes,&ea);
for(i=0;i<ne;++i)
ajStrRemoveWhite(&ea[i]);
if(ajStrMatchCaseC(ea[0],"all"))
isall = ajTrue;
else
isall = ajFalse;
}
while(!ajFileIsEof(fin))
{
if(!embPatRestrictReadEntry(rptr,fin))
continue;
if(!isall)
{
for(i=0;i<ne;++i)
if(ajStrMatchCaseS(ea[i],rptr->cod))
break;
if(i==ne)
continue;
}
AJNEW(rinfo);
/* reading in RE info into rinfo from EmbPPatRestrict structure */
rinfo->code = ajStrNewC(ajStrGetPtr(rptr->cod));
rinfo->site = ajStrNewC(ajStrGetPtr(rptr->pat));
rinfo->ncuts = rptr->ncuts;
rinfo->cut1 = rptr->cut1;
rinfo->cut2 = rptr->cut2;
rinfo->cut3 = rptr->cut3;
rinfo->cut4 = rptr->cut4;
ajListPush(*relist,(void *)rinfo);
RStotal++;
}
for(i=0;i<ne;++i)
ajStrDel(&ea[i]);
AJFREE(ea);
embPatRestrictDel(&rptr);
ajFileClose(&fin);
ajStrDel(&refilename);
return RStotal;
}
int main(int argc, char **argv)
{
AjPFile outf = NULL;
AjPSeq sequence = NULL;
AjPStr substr = NULL;
AjPStr seqstr = NULL;
AjPStr revstr = NULL;
AjPStr p1;
AjPStr p2;
PPrimer eric = NULL;
PPrimer fred = NULL;
PPrimer f;
PPrimer r;
PPair pair;
AjPList forlist = NULL;
AjPList revlist = NULL;
AjPList pairlist = NULL;
AjBool targetrange;
AjBool isDNA = ajTrue;
AjBool dolist = ajFalse;
ajint primerlen = 0;
ajint minprimerlen = 0;
ajint maxprimerlen = 0;
ajint minprodlen = 0;
ajint maxprodlen = 0;
ajint prodlen = 0;
ajint seqlen = 0;
ajint stepping_value = 1;
ajint targetstart = 0;
ajint targetend = 0;
ajint limit = 0;
ajint limit2 = 0;
ajint lastpos = 0;
ajint startpos = 0;
ajint endpos = 0;
ajint begin;
ajint end;
ajint v1;
ajint v2;
ajint overlap;
float minpmGCcont = 0.;
float maxpmGCcont = 0.;
float minprodGCcont = 0.;
float maxprodGCcont = 0.;
float prodTm;
float prodGC;
ajint i;
ajint j;
ajint neric=0;
ajint nfred=0;
ajint npair=0;
float minprimerTm = 0.0;
float maxprimerTm = 0.0;
float saltconc = 0.0;
float dnaconc = 0.0;
embInit ("prima", argc, argv);
substr = ajStrNew();
forlist = ajListNew();
revlist = ajListNew();
pairlist = ajListNew();
p1 = ajStrNew();
p2 = ajStrNew();
sequence = ajAcdGetSeq("sequence");
outf = ajAcdGetOutfile("outfile");
minprimerlen = ajAcdGetInt("minprimerlen");
maxprimerlen = ajAcdGetInt("maxprimerlen");
minpmGCcont = ajAcdGetFloat("minpmGCcont");
maxpmGCcont = ajAcdGetFloat("maxpmGCcont");
minprimerTm = ajAcdGetFloat("mintmprimer");
maxprimerTm = ajAcdGetFloat("maxtmprimer");
minprodlen = ajAcdGetInt("minplen");
maxprodlen = ajAcdGetInt("maxplen");
minprodGCcont = ajAcdGetFloat("minpgccont");
maxprodGCcont = ajAcdGetFloat("maxpgccont");
saltconc = ajAcdGetFloat("saltconc");
dnaconc = ajAcdGetFloat("dnaconc");
targetrange = ajAcdGetToggle("targetrange");
targetstart = ajAcdGetInt("targetstart");
targetend = ajAcdGetInt("targetend");
overlap = ajAcdGetInt("overlap");
dolist = ajAcdGetBoolean("list");
seqstr = ajSeqGetSeqCopyS(sequence);
ajStrFmtUpper(&seqstr);
begin = ajSeqGetBegin(sequence);
end = ajSeqGetEnd(sequence);
seqlen = end-begin+1;
ajStrAssignSubC(&substr,ajStrGetPtr(seqstr),begin-1,end-1);
revstr = ajStrNewC(ajStrGetPtr(substr));
ajSeqstrReverse(&revstr);
AJCNEW0(entropy, seqlen);
AJCNEW0(enthalpy, seqlen);
AJCNEW0(energy, seqlen);
/* Initialise Tm calculation arrays */
ajMeltTempSave(ajStrGetPtr(substr),0,seqlen,saltconc,dnaconc,1,
&entropy, &enthalpy, &energy);
ajFmtPrintF(outf, "\n\nINPUT SUMMARY\n");
ajFmtPrintF(outf, "*************\n\n");
if(targetrange)
ajFmtPrintF
(outf, "Prima of %s from positions %d to %d bps\n",
ajSeqGetNameC(sequence),targetstart, targetend);
else
ajFmtPrintF(outf, "Prima of %s\n", ajSeqGetNameC(sequence));
ajFmtPrintF(outf, "PRIMER CONSTRAINTS:\n");
ajFmtPrintF
(outf, "PRIMA DOES NOT ALLOW PRIMER SEQUENCE AMBIGUITY OR ");
ajFmtPrintF(outf,"DUPLICATE PRIMER ENDPOINTS\n");
ajFmtPrintF(outf,
"Primer size range is %d-%d\n",minprimerlen,maxprimerlen);
ajFmtPrintF(outf,
"Primer GC content range is %.2f-%.2f\n",minpmGCcont,
maxpmGCcont);
ajFmtPrintF(outf,"Primer melting Temp range is %.2f - %.2f C\n",
minprimerTm, maxprimerTm);
ajFmtPrintF (outf, "PRODUCT CONSTRAINTS:\n");
ajFmtPrintF(outf,"Product GC content range is %.2f-%.2f\n",
minprodGCcont, maxprodGCcont);
ajFmtPrintF(outf, "Salt concentration is %.2f (mM)\n", saltconc);
ajFmtPrintF(outf, "DNA concentration is %.2f (nM)\n", dnaconc);
if(targetrange)
ajFmtPrintF(outf, "Targeted range to amplify is from %d to %d\n",
targetstart,targetend);
else
{
ajFmtPrintF(outf,"Considering all suitable Primer pairs with ");
ajFmtPrintF(outf,"Product length ranges %d to %d\n\n\n", minprodlen,
maxprodlen);
}
ajFmtPrintF(outf, "\n\nPRIMER/PRODUCT PAIR CALCULATIONS & OUTPUT\n");
ajFmtPrintF(outf, "*****************************************\n\n");
if(seqlen-minprimerlen < 0)
ajFatal("Sequence too short");
if(targetrange)
{
ajStrAssignSubC(&p1,ajStrGetPtr(substr),targetstart-begin,targetend-begin);
prodGC = ajMeltGC(substr,seqlen);
prodTm = ajMeltTempProd(prodGC,saltconc,seqlen);
if(prodGC<minprodGCcont || prodGC>maxprodGCcont)
{
ajFmtPrintF(outf,
"Product GC content [%.2f] outside acceptable range\n",
prodGC);
embExitBad();
return 0;
}
prima_testtarget(substr, revstr, targetstart-begin, targetend-begin,
minprimerlen, maxprimerlen,
seqlen, minprimerTm, maxprimerTm, minpmGCcont,
maxpmGCcont, minprodGCcont, maxprodGCcont, saltconc,
dnaconc, pairlist, &npair);
}
if(!targetrange)
{
limit = seqlen-minprimerlen-minprodlen+1;
lastpos = seqlen-minprodlen;
limit2 = maxprodlen-minprodlen;
/* Outer loop selects all possible product start points */
for(i=minprimerlen; i<limit; ++i)
{
startpos = i;
ajDebug("Position in sequence %d\n",startpos);
endpos = i+minprodlen-1;
/* Inner loop selects all possible product lengths */
for(j=0; j<limit2; ++j, ++endpos)
{
if(endpos>lastpos)
break;
v1 = endpos-startpos+1;
ajStrAssignSubC(&p1,ajStrGetPtr(substr),startpos,endpos);
prodGC = ajMeltGC(p1,v1);
prodTm = ajMeltTempProd(prodGC,saltconc,v1);
if(prodGC<minprodGCcont || prodGC>maxprodGCcont)
continue;
/* Only accept primers with acceptable Tm and GC */
neric = 0;
nfred = 0;
prima_testproduct(substr, startpos, endpos, primerlen,
minprimerlen, maxprimerlen,minpmGCcont,
maxpmGCcont, minprimerTm, maxprimerTm,
minprodlen, maxprodlen, prodTm, prodGC, seqlen,
&eric,&fred,forlist,revlist,&neric,&nfred,
stepping_value, saltconc,dnaconc, isDNA, begin);
if(!neric)
continue;
/* Now reject those primers with self-complementarity */
prima_reject_self(forlist,revlist,&neric,&nfred);
if(!neric)
continue;
/* Reject any primers that could bind elsewhere in the
sequence */
prima_test_multi(forlist,revlist,&neric,&nfred,substr,revstr,
seqlen);
/* Now select the least complementary pair (if any) */
prima_best_primer(forlist, revlist, &neric, &nfred);
if(!neric)
continue;
AJNEW(pair);
ajListPop(forlist,(void **)&f);
ajListPop(revlist,(void **)&r);
pair->f = f;
pair->r = r;
++npair;
ajListPush(pairlist,(void *)pair);
}
}
}
if(!targetrange)
{
/* Get rid of primer pairs nearby the top scoring ones */
prima_TwoSortscorepos(&pairlist);
prima_prune_nearby(pairlist, &npair, maxprimerlen-1);
ajListSort(pairlist,prima_PosCompare);
prima_check_overlap(pairlist,&npair,overlap);
}
if(npair)
{
if(!targetrange)
ajFmtPrintF(outf,"%d pairs found\n\n",npair);
else
ajFmtPrintF(outf,
"Closest primer pair to specified product is:\n\n");
if((maxprimerlen<26 && seqlen<999999 && !dolist))
ajFmtPrintF(outf,"\n\t\tForward\t\t\t\t\tReverse\n\n");
}
for(i=0;i<npair;++i)
{
if(!targetrange)
ajFmtPrintF(outf,"[%d]\n",i+1);
ajListPop(pairlist,(void **)&pair);
prodlen = pair->r->start - (pair->f->start + pair->f->primerlen);
if((maxprimerlen<26 && seqlen<999999 && !dolist))
{
v1 = pair->f->start;
v2 = v1 + pair->f->primerlen -1;
ajStrAssignSubS(&p1,substr,v1,v2);
ajFmtPrintF(outf,"%6d %-25.25s %d\t", v1+begin, ajStrGetPtr(p1),
v2+begin);
v1 = pair->r->start;
v2 = v1 + pair->r->primerlen -1;
ajStrAssignSubS(&p2,substr,v1,v2);
ajSeqstrReverse(&p2);
ajFmtPrintF(outf,
"%6d %-25.25s %d\n", v1+begin, ajStrGetPtr(p2), v2+begin);
ajFmtPrintF(outf," Tm %.2f C (GC %.2f%%)\t\t ",
pair->f->primerTm,pair->f->primGCcont*100.);
ajFmtPrintF(outf,"Tm %.2f C (GC %.2f%%)\n",
pair->r->primerTm,pair->r->primGCcont*100.);
ajFmtPrintF(outf," Length: %-32dLength: %d\n",
pair->f->primerlen,pair->r->primerlen);
ajFmtPrintF(outf," Tma: %.2f C\t\t\t",
ajAnneal(pair->f->primerTm,pair->f->prodTm));
ajFmtPrintF(outf," Tma: %.2f C\n\n\n",
ajAnneal(pair->r->primerTm,pair->f->prodTm));
ajFmtPrintF(outf," Product GC: %.2f%%\n",
pair->f->prodGC * 100.0);
ajFmtPrintF(outf," Product Tm: %.2f C\n",
pair->f->prodTm);
ajFmtPrintF(outf," Length: %d\n\n\n",prodlen);
}
else
{
ajFmtPrintF(outf," Product from %d to %d\n",pair->f->start+
pair->f->primerlen+begin,pair->r->start-1+begin);
ajFmtPrintF(outf," Tm: %.2f C GC: %.2f%%\n",
pair->f->prodTm,pair->f->prodGC*(float)100.);
ajFmtPrintF(outf," Length: %d\n\n\n",prodlen);
v1 = pair->f->start;
v2 = v1 + pair->f->primerlen -1;
ajStrAssignSubS(&p1,substr,v1,v2);
ajFmtPrintF(outf," Forward: 5' %s 3'\n",ajStrGetPtr(p1));
ajFmtPrintF(outf," Start: %d\n",v1+begin);
ajFmtPrintF(outf," End: %d\n",v2+begin);
ajFmtPrintF(outf," Tm: %.2f C\n",
pair->f->primerTm);
ajFmtPrintF(outf," GC: %.2f%%\n",
pair->f->primGCcont*(float)100.);
ajFmtPrintF(outf," Len: %d\n",
pair->f->primerlen);
ajFmtPrintF(outf," Tma: %.2f C\n\n\n",
ajAnneal(pair->f->primerTm,pair->f->prodTm));
v1 = pair->r->start;
v2 = v1 + pair->r->primerlen -1;
ajStrAssignSubS(&p2,substr,v1,v2);
ajSeqstrReverse(&p2);
ajStrAssignSubS(&p1,substr,v1,v2);
ajFmtPrintF(outf," Reverse: 5' %s 3'\n",ajStrGetPtr(p1));
ajFmtPrintF(outf," Start: %d\n",v1+begin);
ajFmtPrintF(outf," End: %d\n",v2+begin);
ajFmtPrintF(outf," Tm: %.2f C\n",
pair->r->primerTm);
ajFmtPrintF(outf," GC: %.2f%%\n",
pair->r->primGCcont*(float)100.);
ajFmtPrintF(outf," Len: %d\n",
pair->r->primerlen);
ajFmtPrintF(outf," Tma: %.2f C\n\n\n",
ajAnneal(pair->r->primerTm,pair->f->prodTm));
}
prima_PrimerDel(&pair->f);
prima_PrimerDel(&pair->r);
AJFREE(pair);
}
ajStrDel(&seqstr);
ajStrDel(&revstr);
ajStrDel(&substr);
ajStrDel(&p1);
ajStrDel(&p2);
ajListFree(&forlist);
ajListFree(&revlist);
ajListFree(&pairlist);
ajFileClose(&outf);
ajSeqDel(&sequence);
AJFREE(entropy);
AJFREE(enthalpy);
AJFREE(energy);
embExit();
return 0;
}
/* @funcstatic newcoils_read_matrix *******************************************
**
** Reads the matrix and stores in a hept_pref structure
**
** @param [u] inf [AjPFile] matrix input file
** @return [struct hept_pref*] Matrix data for heptad preference
******************************************************************************/
static struct hept_pref* newcoils_read_matrix(AjPFile inf)
{
ajint i;
ajint j;
ajint pt;
ajint aa_len;
ajint win;
float m_g;
float sd_g;
float m_cc;
float sd_cc;
float sc;
float hept[NCHEPTAD];
AjPStr buff;
const char *pbuff;
struct hept_pref *h;
buff = ajStrNew();
aa_len = strlen(NCAAs);
AJNEW(h);
AJCNEW(h->m,aa_len);
for(i=0; i<aa_len; ++i)
{
AJCNEW(h->m[i],NCHEPTAD);
for(j=0; j<NCHEPTAD; ++j)
h->m[i][j] = -1;
}
AJNEW(h->f);
h->n = 0;
h->smallest = 1.0;
while(ajReadlineTrim(inf,&buff))
{
pbuff = ajStrGetPtr(buff);
if(*pbuff != '%')
{
if((strncmp(pbuff,"uw ",3)==0) || (strncmp(pbuff,"w ",2)==0))
{
i = h->n;
if(strncmp(pbuff,"uw ",3)==0)
h->f[i].w = 0;
else
h->f[i].w = 1;
ajFmtScanS(buff,"%*s %d %f %f %f %f %f",&win,&m_cc,
&sd_cc,&m_g,&sd_g,&sc);
h->f[i].win = win;
h->f[i].m_cc = (float)m_cc;
h->f[i].sd_cc = (float)sd_cc;
h->f[i].m_g = (float)m_g;
h->f[i].sd_g = (float)sd_g;
h->f[i].sc = (float)sc;
h->n++;
AJCRESIZE(h->f,(h->n)+1);
if((h->n)>=9)
ajFatal("Too many window parms in matrix file\n");
}
else if(*pbuff>='A' && *pbuff<='Z')
{
/* AA data */
pt = (int)(pbuff[0]-'A');
if(h->m[pt][0]==-1)
{
ajFmtScanS(buff,"%*s%f%f%f%f%f%f%f",&hept[0],
&hept[1],&hept[2],&hept[3],&hept[4],
&hept[5],&hept[6]);
for(i=0; i<NCHEPTAD; ++i)
{
h->m[pt][i] = (float)hept[i];
if(h->m[pt][i]>0)
{
if(h->m[pt][i]<h->smallest)
h->smallest = h->m[pt][i];
}
else
h->m[pt][i]=-1; /* Don't permit zero values */
}
}
else
ajWarn("multiple entries for AA %c in matrix file\n",
*pbuff);
}
else
{
ajWarn("strange characters in matrix file\n");
ajWarn("Ignoring line: %S\n",buff);
}
}
}
ajStrDel(&buff);
return h;
}