Home
last modified time | relevance | path

Searched refs:freqc (Results 1 – 25 of 28) sorted by relevance

12

/dports/biology/fluctuate/fluctuate1.4/
H A Dgetdata.c282 dna->freqc = 0.25; in empiricalfreqs()
294 temp += dna->freqc * curtree->nodep[i]->x[j][0][baseC]; in empiricalfreqs()
298 sumc += w * dna->freqc * curtree->nodep[i]->x[j][0][baseC] / temp; in empiricalfreqs()
305 dna->freqc = sumc / temp; in empiricalfreqs()
321 fprintf(outfile, " C %10.5f\n", dna->freqc); in getbasefreqs()
325 dna->freqy = dna->freqc + dna->freqt; in getbasefreqs()
327 dna->freqcy = dna->freqc / dna->freqy; in getbasefreqs()
332 dna->freqa * dna->freqg - dna->freqc * dna->freqt; in getbasefreqs()
333 bb = dna->freqa * dna->freqgr + dna->freqc * dna->freqty; in getbasefreqs()
347 2 * dna->freqc * dna->freqty) + in getbasefreqs()
[all …]
H A Dfluctuate.c43 double locus_ttratio, freqa, freqc, freqg, freqt, variable
661 freqc = (double)atof(strtok(NULL,";")); in booleancheck()
1042 scanf("%lf%lf%lf%lf", &freqa, &freqc, &freqg, &freqt); in getoptions()
1401 dna->freqc = freqc; in getinput()
1659 term[j] = dna->freqa * x1[baseA] + dna->freqc * x1[baseC] + in evaluate()
1761 sum1 = yy1 * (dna->freqa * xx1[baseA] + dna->freqc * xx1[baseC] + in nuview()
1763 sum2 = yy2 * (dna->freqa * xx2[baseA] + dna->freqc * xx2[baseC] + in nuview()
H A Dfluctuate.h283 double freqa, freqc, freqg, freqt, freqr, freqy, freqar, freqcy, member
/dports/biology/migrate/migrate-3.6.11/src/
H A Dsequence.c216 *freqc /= summ; in initfreqs()
434 freqc = seq->basefrequencies[NUC_C]; in getbasefreqs()
452 freqc * freqt; in getbasefreqs()
464 freqc * freqt) / ((freqr) * (freqy)); in getbasefreqs()
476 freqc * in getbasefreqs()
477 freqc - in getbasefreqs()
1416 options->freqc = 0.25; in empiricalfreqs()
1442 options->freqc = sumc / summ; in empiricalfreqs()
1724 freqc = seq->basefrequencies[NUC_C]; in snp_invariants_original()
1754 freqc = seq->basefrequencies[NUC_C]; in snp_invariants()
[all …]
H A Dtree.c3078 freqc = seq->basefrequencies[NUC_C]; in nuview_sequence()
3271 freqc = seq->basefrequencies[NUC_C]; in nuview_sequence_slow()
3608 freqc = seq->basefrequencies[NUC_C]; in pseudonu_seq()
3649 tc = freqc * xx1t1; in pseudonu_seq()
3659 ttc = freqc * xx2t1; in pseudonu_seq()
3812 freqc = seq->basefrequencies[NUC_C]; in pseudonu_seq_slow()
3851 tc = freqc * xx1t1; in pseudonu_seq_slow()
3861 ttc = freqc * xx2t1; in pseudonu_seq_slow()
3948 tc = freqc * xx1t1; in pseudonu_seq_slow()
3958 ttc = freqc * xx2t1; in pseudonu_seq_slow()
[all …]
H A Dsequence.h40 extern void initfreqs (MYREAL *freqa, MYREAL *freqc, MYREAL *freqg,
H A Dmigration.h192 MYREAL freqa, freqt, freqg, freqc; //!< base frequencies member
550 MYREAL freqc; member
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/
H A Ddnadist.cpp848 freqc = 0.25; in dnadist_empiricalfreqs()
860 sum += freqc * nodep[i]->x[j][0][(long)C - (long)A]; in dnadist_empiricalfreqs()
871 freqc = sumc / sum; in dnadist_empiricalfreqs()
885 freqc = 0.25; in getinput()
894 freqc = 0.999999*freqc; in getinput()
898 if (freqc < 0.00000001) { in getinput()
900 freqc = 0.000001; in getinput()
906 freqc = 0.999999*freqc; in getinput()
912 freqc = 0.999999*freqc; in getinput()
1148 xx1freqc = xx1[(long)C - (long)A] * freqc; in makev()
[all …]
H A Dprotdist.cpp141 freqc = 0.25; in prot_getoptions()
522 freqy = freqc + freqt; in transition()
525 aa = ttratio * freqr * freqy - freqa * freqg - freqc * freqt; in transition()
526 bb = freqa * freqgr + freqc * freqty; in transition()
1163 f[1] = freqc; in maketrans()
1166 g[0] = freqc + freqt; in maketrans()
1167 g[1] = freqc + freqt; in maketrans()
H A Ddnadist.h22 extern double xi, xv, ttratio, ttratio0, freqa, freqc, freqg, freqt, freqr, freqy,
H A Dseq.cpp393 fprintf(outfile, " C %10.5f\n", freqc); in getbasefreqs()
399 *freqy = freqc + freqt; in getbasefreqs()
401 *freqcy = freqc / *freqy; in getbasefreqs()
406 bb = freqa * (*freqgr) + freqc * (*freqty); in getbasefreqs()
420 if (freqc <= 0.0) in getbasefreqs()
421 freqc = 0.000001; in getbasefreqs()
427 (*xv) * (1.0 - freqa * freqa - freqc * freqc - freqg * freqg in getbasefreqs()
441 *freqc = 0.25; in empiricalfreqs()
464 *freqc = sumc / sum; in empiricalfreqs()
470 if (*freqc <= 0.0) in empiricalfreqs()
[all …]
H A DDistanceMatrix.cpp102 …getbasefreqs(freqa, freqc, freqg, freqt, &freqr, &freqy, &freqar, &freqcy, &freqgr, &freqty, &ttra… in calculateOutOfAlignment()
H A Dphylip.cpp1052 void initfreqs(double *freqa, double *freqc, double *freqg, double *freqt) in initfreqs() argument
1062 scanned = sscanf(input,"%lf%lf%lf%lf%*[^\n]", freqa, freqc, freqg, freqt); in initfreqs()
/dports/audio/sc3-plugins/sc3-plugins-Version-3.9.0/source/AYUGens/sc/HelpSource/Classes/
H A DAY.schelp111 SynthDef(\ay1, { | freqa=440, freqb=550, freqc=660, vola=15, volb=0, volc=0, chink=1, wobbly=1, pan…
118 # freqa, freqb, freqc = [freqa, freqb, freqc] * [1, wobblyenv, wobblyenv] * chinkenv;
119 ay = AY.ar(AY.freqtotone(freqa), AY.freqtotone(freqb), AY.freqtotone(freqc),
/dports/biology/recombine/recombine1.41/
H A Dgetdata.c1153 dna->freqc = 0.25; in empiricaldnafreqs()
1164 temp += dna->freqc * curtree->nodep[i]->x->s[j][0][0][baseC]; in empiricaldnafreqs()
1168 sumc += w * dna->freqc * curtree->nodep[i]->x->s[j][0][0][baseC] / temp; in empiricaldnafreqs()
1175 dna->freqc = sumc / temp; in empiricaldnafreqs()
1192 fprintf(outfile, " C %10.5f\n", dna->freqc); in getbasednafreqs()
1196 dna->freqy = dna->freqc + dna->freqt; in getbasednafreqs()
1198 dna->freqcy = dna->freqc / dna->freqy; in getbasednafreqs()
1203 dna->freqa * dna->freqg - dna->freqc * dna->freqt; in getbasednafreqs()
1204 bb = dna->freqa * dna->freqgr + dna->freqc * dna->freqty; in getbasednafreqs()
1218 2 * dna->freqc * dna->freqty) + in getbasednafreqs()
[all …]
H A Drecombine.c116 double freqa, freqc, freqg, freqt; /* dna freqs */ variable
1252 freqc = (double)atof(strtok(NULL,";")); in booleancheck()
1470 freqa, freqc, freqg, freqt); in rec_parmfilewrite()
1986 scanf("%lf%lf%lf%lf", &freqa, &freqc, &freqg, &freqt); in workmenu2()
2408 data->dnaptr->freqc = freqc; in locusinit()
3496 dna->freqc * x1[baseC] + dna->freqg * x1[baseG] + in snp_eval_calcrange()
3599 dna->freqc * x1[k][baseC] + dna->freqg * x1[k][baseG] + in panel_eval_calcrange()
3623 invarterm += dna->freqa * x1[k][baseA] + dna->freqc * in panel_eval_calcrange()
3700 term[j] = dna->freqa * x1[baseA] + dna->freqc * x1[baseC] + in eval_calcrange()
4096 dna->freqc * xx1[k][baseC] + in calcrange()
[all …]
H A Drecombine.h385 double freqa, freqc, freqg, freqt, freqr, freqy, freqar, freqcy, member
/dports/biology/pear-merger/pear-0.9.6-src/src/
H A Demp.h21 unsigned long freqc; /**< @brief Frequency of C */ member
H A Dpear-pt.c2656 ++ ef->freqc; in emp_entry_point()
2816 a += ef->freqa; c += ef->freqc; g += ef->freqg; t += ef->freqt; n += ef->freqn; in main()
2821 ef->freqa = a; ef->freqc = c; ef->freqg = g; ef->freqt = t; ef->freqn = n; in main()
2823 …ef->pa = ef->freqa / ef->total; ef->pc = ef->freqc / ef->total; ef->pg = ef->freqg / ef->total; ef… in main()
2855 …ef->freqa = ef->freqc = ef->freqg = ef->freqt = ef->total = ef->pa = ef->pc = ef->pg = ef->pt = ef… in main()
/dports/games/SRB2/SRB2-SRB2_release_2.2.9/src/
H A Dg_game.h141 mapsearchfreq_t **freqp, INT32 *freqc);
142 void G_FreeMapSearch(mapsearchfreq_t *freq, INT32 freqc);
H A Dg_game.c4939 INT32 freqc; in G_FindMap() local
4950 freqc++; in G_FindMap()
4957 freqc = 0; in G_FindMap()
5003 freq[freqc].mapnum = mapnum; in G_FindMap()
5005 &freq[freqc].matchd, &freq[freqc].matchc, in G_FindMap()
5008 &freq[freqc].keywhd, &freq[freqc].keywhc, in G_FindMap()
5010 if (freq[freqc].total) in G_FindMap()
5011 freqc++; in G_FindMap()
5027 for (i = 0; i < freqc; ++i) in G_FindMap()
5047 (*freqcp) = freqc; in G_FindMap()
[all …]
/dports/biology/lamarc/lamarc-2.1.8/src/datalike/
H A Ddlmodel.cpp849 double freqa(m_basefreqs[baseA]), freqc(m_basefreqs[baseC]), in Finalize() local
853 pyr = freqc + freqt; in Finalize()
855 freqcy = freqc / pyr; in Finalize()
860 ct = freqc * freqt; in Finalize()
870 double fracchange = y * (2.0 * freqa * freqgr + 2.0 * freqc * freqty) in Finalize()
871 + x * (1.0 - freqa * freqa - freqc * freqc - freqg * freqg - freqt * freqt); in Finalize()
1316 double pyr = freqc + freqt; in SimulateMarker()
1318 double alpha = (pur * pyr * m_ttratio - freqa * freqg - freqc * freqt) / in SimulateMarker()
1323 cumprob.push_back(freqa + freqc); in SimulateMarker()
1324 cumprob.push_back(freqa + freqc + freqg); in SimulateMarker()
[all …]
/dports/biology/fastdnaml/fastDNAml_1.2.2/source/
H A DfastDNAml.c1017 & rdta->freqa, & rdta->freqc, in inputfreqs()
1426 & rdta->freqa, & rdta->freqc, in getbasefreqs()
1918 rdta->freqc = 0.25; in empiricalfreqs()
1943 rdta->freqc = sumc / sum; in empiricalfreqs()
1959 printf(" C %10.5f\n", rdta->freqc); in reportfreqs()
1966 rdta->freqy = rdta->freqc + rdta->freqt; in reportfreqs()
1993 - rdta->freqc * rdta->freqc in reportfreqs()
2427 fxpc = tr->rdta->freqc * lp->c; in evaluate()
2452 fxpc = tr->rdta->freqc * lp->c; in evaluate()
2519 fx1c = tr->rdta->freqc * lp->c; in makenewz()
[all …]
H A DfastDNAml.h111 double freqa, freqc, freqg, freqt, /* base frequencies */ member
/dports/biology/seaview/seaview/csrc/
H A Dseq.c387 fprintf(outfile, " C %10.5f\n", freqc); in getbasefreqs()
393 *freqy = freqc + freqt; in getbasefreqs()
395 *freqcy = freqc / *freqy; in getbasefreqs()
399 bb = freqa * (*freqgr) + freqc * (*freqty); in getbasefreqs()
413 if (freqc <= 0.0) in getbasefreqs()
414 freqc = 0.000001; in getbasefreqs()
420 (*xv) * (1.0 - freqa * freqa - freqc * freqc - freqg * freqg in getbasefreqs()
434 *freqc = 0.25; in empiricalfreqs()
457 *freqc = sumc / sum; in empiricalfreqs()
463 if (*freqc <= 0.0) in empiricalfreqs()
[all …]

12