void embPropCalcFragments(const char *s, ajint n,
AjPList *l, AjPList *pa,
AjBool unfavoured, AjBool overlap,
AjBool allpartials, ajint *ncomp, ajint *npart,
AjPStr *rname, AjBool nterm, AjBool cterm,
AjBool dorag, EmbPPropMolwt const *mwdata,
AjBool mono)
{
static const char *PROPENZReagent[]=
{
"Trypsin","Lys-C","Arg-C","Asp-N","V8-bicarb","V8-phosph",
"Chymotrypsin","CNBr"
};
static const char *PROPENZSite[]=
{
"KR","K","R","D","E","DE","FYWLM","M"
};
static const char *PROPENZAminoCarboxyl[]=
{
"CC","C","C","N","C","CC","CCCCC","C"
};
static const char *PROPENZUnfavoured[]=
{
"KRIFLP","P","P","","KREP","P","P",""
};
ajint i;
ajint j;
ajint lim;
ajint len;
AjPList t;
EmbPPropFrag fr;
ajint *begsa = NULL;
ajint *endsa = NULL;
double molwt;
double *molwtsa = NULL;
AjBool *afrag = NULL;
ajint mark;
ajint bwp;
ajint ewp;
ajint *ival;
ajint defcnt;
ajint it;
ajint st = 0;
ajint mt = 0;
ajint et = 0;
ajStrAssignC(rname,PROPENZReagent[n]);
defcnt = 0;
len = (ajint) strlen(s);
t = ajListNew(); /* Temporary list */
/* First get all potential cut points */
for(i=0;i<len;++i)
{
if(!strchr(PROPENZSite[n],s[i]))
continue;
if(len==i+1)
continue;
if(strchr(PROPENZUnfavoured[n],s[i+1])
&& !unfavoured)
continue;
AJNEW0(ival);
*ival = i;
ajListPushAppend(t,(void *)ival);
++defcnt;
}
if(defcnt)
{
AJCNEW(begsa,(defcnt+1));
AJCNEW(endsa,(defcnt+1));
AJCNEW(molwtsa,(defcnt+1));
AJCNEW(afrag,(defcnt+1));
}
for(i=0;i<defcnt;++i) /* Pop them into a temporary array */
{
ajListPop(t,(void **)&ival);
endsa[i] = *ival;
AJFREE(ival);
}
mark = 0;
for(i=0;i<defcnt;++i) /* Work out true starts, ends and molwts */
{
bwp = mark;
ewp = endsa[i];
if(strchr(PROPENZAminoCarboxyl[n],'N'))
--ewp;
molwt=embPropCalcMolwt(s,bwp,ewp,mwdata,mono);
if(n==PROPENZCNBR)
molwt -= (17.045 + 31.095);
begsa[i] = mark;
endsa[i] = ewp;
molwtsa[i] = molwt;
afrag[i] = ajFalse;
mark = ewp+1;
}
if(defcnt) /* Special treatment for last fragment */
{
molwt = embPropCalcMolwt(s,mark,len-1,mwdata,mono);
if(n==PROPENZCNBR)
molwt -= (17.045 + 31.095);
begsa[i] = mark;
endsa[i] = len-1;
molwtsa[i] = molwt;
afrag[i] = ajFalse;
++defcnt;
}
/* Push the hits */
for(i=0;i<defcnt;++i)
{
if(dorag)
{
st = begsa[i];
et = endsa[i];
for(it=st+RAG_MINPEPLEN-1; it < et; ++it)
{
AJNEW0(fr);
fr->start = st;
fr->end = it;
fr->molwt = embPropCalcMolwt(s,st,it,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
AJNEW0(fr);
fr->start = begsa[i];
fr->end = endsa[i];
fr->molwt = molwtsa[i];
fr->isfrag = afrag[i];
ajListPush(*l,(void *) fr);
if(dorag && nterm)
for(it=st+1; it < et-RAG_MINPEPLEN+2; ++it)
{
AJNEW0(fr);
fr->start = it;
fr->end = et;
fr->molwt = embPropCalcMolwt(s,it,et,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
if(!dorag)
ajListSort(*l, &propFragCompare);
*ncomp = defcnt;
/* Now deal with overlaps */
*npart = 0;
lim = defcnt -1;
if(overlap && !allpartials)
{
for(i=0;i<lim;++i)
{
if(dorag)
{
st = begsa[i];
mt = endsa[i];
et = endsa[i+1];
if(cterm)
for(it=mt+1; it < et; ++it)
{
AJNEW0(fr);
fr->start = st;
fr->end = it;
fr->molwt = embPropCalcMolwt(s,st,it,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
AJNEW0(fr);
fr->isfrag = ajTrue;
fr->molwt = embPropCalcMolwt(s,begsa[i],endsa[i+1],mwdata,mono);
if(n==PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->start = begsa[i];
fr->end = endsa[i+1];
ajListPush(*pa,(void *)fr);
++(*npart);
if(dorag && nterm)
for(it=st+1; it<mt; ++it)
{
AJNEW0(fr);
fr->start = it;
fr->end = et;
fr->molwt = embPropCalcMolwt(s,it,et,mwdata,mono);
if(n == PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->isfrag = ajTrue;
ajListPush(*l,(void *)fr);
}
}
if(*npart) /* Remove complete sequence */
{
--(*npart);
ajListPop(*pa,(void **)&fr);
}
if(!dorag)
ajListSort(*pa, &propFragCompare);
}
if(allpartials)
{
lim = defcnt;
for(i=0;i<lim;++i)
for(j=i+1;j<lim;++j)
{
AJNEW0(fr);
fr->isfrag = ajTrue;
fr->molwt = embPropCalcMolwt(s,begsa[i],endsa[j],mwdata,mono);
if(n==PROPENZCNBR)
fr->molwt -= (17.045 + 31.095);
fr->start = begsa[i];
fr->end = endsa[j];
ajListPush(*pa,(void *)fr);
++(*npart);
}
if(*npart) /* Remove complete sequence */
{
--(*npart);
ajListPop(*pa,(void **)&fr);
}
if(!dorag)
ajListSort(*pa, &propFragCompare);
}
if(defcnt)
{
AJFREE(molwtsa);
AJFREE(endsa);
AJFREE(begsa);
AJFREE(afrag);
}
ajListFree(&t);
return;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq a;
AjPStr substr;
AjPStr rname;
ajint be;
ajint en;
ajint len;
AjBool unfavoured;
AjBool overlap;
AjBool allpartials;
AjPStr menu;
AjPStr rag;
ajint n = 0;
ajint r = 0;
AjPFile outf = NULL;
AjPReport report = NULL;
AjPFeattable TabRpt = NULL;
AjPStr tmpStr = NULL;
AjPList l;
AjPList pa;
AjPFile mfptr = NULL;
AjBool nterm = ajFalse;
AjBool cterm = ajFalse;
AjBool dorag = ajFalse;
ajint ncomp;
ajint npart;
EmbPPropMolwt *mwdata = NULL;
AjBool mono;
embInit("digest", argc, argv);
seqall = ajAcdGetSeqall("seqall");
menu = ajAcdGetListSingle("menu");
dorag = ajAcdGetBoolean("ragging");
rag = ajAcdGetListSingle("termini");
unfavoured = ajAcdGetBoolean("unfavoured");
overlap = ajAcdGetBoolean("overlap");
allpartials = ajAcdGetBoolean("allpartials");
report = ajAcdGetReport("outfile");
mfptr = ajAcdGetDatafile("mwdata");
mono = ajAcdGetBoolean("mono");
/* obsolete. Can be uncommented in acd file and here to reuse */
/* outf = ajAcdGetOutfile("originalfile"); */
ajStrToInt(menu, &n);
--n;
ajStrToInt(rag, &r);
if(r==2 || r==4)
nterm = ajTrue;
if(r==3 || r==4)
cterm = ajTrue;
mwdata = embPropEmolwtRead(mfptr);
while(ajSeqallNext(seqall, &a))
{
substr = ajStrNew();
be = ajSeqGetBegin(a);
en = ajSeqGetEnd(a);
ajStrAssignSubC(&substr,ajSeqGetSeqC(a),be-1,en-1);
ajStrFmtUpper(&substr);
len = en-be+1;
l = ajListNew();
pa = ajListNew();
rname = ajStrNew();
TabRpt = ajFeattableNewSeq(a);
embPropCalcFragments(ajStrGetPtr(substr),n,&l,&pa,
unfavoured,overlap,
allpartials,&ncomp,&npart,&rname,
nterm, cterm, dorag, mwdata, mono);
if(outf)
ajFmtPrintF(outf,"DIGEST of %s from %d to %d Molwt=%10.3f\n\n",
ajSeqGetNameC(a),be,en,
embPropCalcMolwt(ajSeqGetSeqC(a),0,len-1,mwdata,mono));
if(!ncomp)
{
if(outf)
ajFmtPrintF(outf,
"Is not proteolytically digested using %s\n",
ajStrGetPtr(rname));
}
else
{
if(outf)
{
ajFmtPrintF(outf,"Complete digestion with %s "
"yields %d fragments:\n",
ajStrGetPtr(rname),ncomp);
digest_print_hits(l,outf,be,ajStrGetPtr(substr));
}
ajFmtPrintS(&tmpStr,
"Complete digestion with %S yields %d fragments",
rname,ncomp);
ajReportSetHeaderS(report, tmpStr);
digest_report_hits(TabRpt,l,be, ajStrGetPtr(substr));
ajReportWrite(report, TabRpt, a);
ajFeattableClear(TabRpt);
}
if(overlap && !allpartials && npart)
{
if(outf)
{
ajFmtPrintF(outf,
"\n\nPartial digest with %s yields %d extras.\n",
ajStrGetPtr(rname),npart);
ajFmtPrintF(outf,"Only overlapping partials shown:\n");
digest_print_hits(pa,outf,be,ajStrGetPtr(substr));
}
ajFmtPrintS(&tmpStr,
"\n\nPartial digest with %S yields %d extras.\n",
rname,npart);
ajFmtPrintAppS(&tmpStr,"Only overlapping partials shown:\n");
ajReportSetHeaderS(report, tmpStr);
digest_report_hits(TabRpt, pa,be,ajStrGetPtr(substr));
ajReportWrite(report, TabRpt, a);
ajFeattableClear(TabRpt);
}
if(allpartials && npart)
{
if(outf)
{
ajFmtPrintF(outf,
"\n\nPartial digest with %s yields %d extras.\n",
ajStrGetPtr(rname),npart);
ajFmtPrintF(outf,"All partials shown:\n");
digest_print_hits(pa,outf,be,ajStrGetPtr(substr));
}
ajFmtPrintS(&tmpStr,
"\n\nPartial digest with %S yields %d extras.\n",
rname,npart);
ajFmtPrintAppS(&tmpStr,"All partials shown:\n");
ajReportSetHeaderS(report, tmpStr);
digest_report_hits(TabRpt, pa,be, ajStrGetPtr(substr));
ajReportWrite(report, TabRpt, a);
ajFeattableClear(TabRpt);
}
}
embPropMolwtDel(&mwdata);
ajReportDel(&report);
ajFeattableDel(&TabRpt);
ajSeqDel(&a);
ajSeqallDel(&seqall);
ajStrDel(&rname);
ajStrDel(&substr);
ajListFree(&pa);
ajListFree(&l);
ajStrDel(&menu);
ajStrDel(&rag);
if(outf)
ajFileClose(&outf);
ajFileClose(&mfptr);
ajStrDel(&tmpStr);
embExit();
return 0;
}
