int main(int argc, char **argv) { /* Variable Declarations */ AjPStr code = NULL; AjPFile mfptr = NULL; AjPFile wfptr = NULL; AjPFile outf = NULL; EmbPPropMolwt *mwdata; EmbPPropAmino *aadata; float *dhstat = NULL; char code1; AjPStr code3 = NULL; ajint idx = 0; ajuint i; ajuint iend; AjPStr propstr = NULL; float charge; char csign; /* ACD File Processing */ embInit("inforesidue", argc, argv); code = ajAcdGetString("code"); mfptr = ajAcdGetDatafile("aadata"); wfptr = ajAcdGetDatafile("mwdata"); outf = ajAcdGetOutfile("outfile"); aadata = embPropEaminoRead(mfptr); mwdata = embPropEmolwtRead(wfptr); if(!embReadAminoDataFloatC(DAYHOFF_FILE,&dhstat,(float)0.001)) ajFatal("Set the EMBOSS_DATA environment variable"); /* Application logic */ ajStrFmtUpper(&code); iend = ajStrGetLen(code); ajFmtPrintF(outf, "%-4s %-5s %-20s %6s %9s %-30s %s\n", "Code", "Short", "Mnemonic", "Charge", "MolWt", "Properties", "Ambiguity"); for(i=0; i<iend; i++) { code1=ajStrGetCharPos(code,i); if(ajResidueExistsChar(code1)) { idx = ajBasecodeToInt(code1); ajResidueToTriplet(code1, &code3); ajStrFmtTitle(&code3); if(!embPropGetProperties(aadata[idx], &propstr)) ajStrAssignC(&propstr, "(none)"); charge = embPropGetCharge(aadata[idx]); if(charge > 0.0) csign = '+'; else if(charge < 0.0) csign = '-'; else csign = ' '; ajFmtPrintF(outf, "%-4c %-5S %-20S %3c%3.1f %9.4f %-30S %S\n", code1, code3, ajResidueGetMnemonic(code1), csign, fabs(charge), embPropMolwtGetMolwt(mwdata[idx]), propstr, ajResidueGetCodes(code1)); } else { ajFmtPrintF(outf, "%-4c %-5s %-20s %6s %9s %-30s %s\n", code1, ".", "invalid", ".", ".", ".", "."); } } /* Memory management and exit */ ajStrDel(&code); ajStrDel(&code3); ajStrDel(&propstr); ajFileClose(&outf); ajFileClose(&mfptr); ajFileClose(&wfptr); ajFileClose(&outf); embPropAminoDel(&aadata); embPropMolwtDel(&mwdata); AJFREE(dhstat); embExit(); return 0; }
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; }