/dports/biology/fluctuate/fluctuate1.4/ |
H A D | getdata.c | 282 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 …]
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H A D | fluctuate.c | 43 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()
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H A D | fluctuate.h | 283 double freqa, freqc, freqg, freqt, freqr, freqy, freqar, freqcy, member
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/dports/biology/migrate/migrate-3.6.11/src/ |
H A D | sequence.c | 216 *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 …]
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H A D | tree.c | 3078 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 …]
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H A D | sequence.h | 40 extern void initfreqs (MYREAL *freqa, MYREAL *freqc, MYREAL *freqg,
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H A D | migration.h | 192 MYREAL freqa, freqt, freqg, freqc; //!< base frequencies member 550 MYREAL freqc; member
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/ |
H A D | dnadist.cpp | 848 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 …]
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H A D | protdist.cpp | 141 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()
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H A D | dnadist.h | 22 extern double xi, xv, ttratio, ttratio0, freqa, freqc, freqg, freqt, freqr, freqy,
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H A D | seq.cpp | 393 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 …]
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H A D | DistanceMatrix.cpp | 102 …getbasefreqs(freqa, freqc, freqg, freqt, &freqr, &freqy, &freqar, &freqcy, &freqgr, &freqty, &ttra… in calculateOutOfAlignment()
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H A D | phylip.cpp | 1052 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()
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/dports/audio/sc3-plugins/sc3-plugins-Version-3.9.0/source/AYUGens/sc/HelpSource/Classes/ |
H A D | AY.schelp | 111 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),
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/dports/biology/recombine/recombine1.41/ |
H A D | getdata.c | 1153 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 …]
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H A D | recombine.c | 116 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 …]
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H A D | recombine.h | 385 double freqa, freqc, freqg, freqt, freqr, freqy, freqar, freqcy, member
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/dports/biology/pear-merger/pear-0.9.6-src/src/ |
H A D | emp.h | 21 unsigned long freqc; /**< @brief Frequency of C */ member
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H A D | pear-pt.c | 2656 ++ 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()
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/dports/games/SRB2/SRB2-SRB2_release_2.2.9/src/ |
H A D | g_game.h | 141 mapsearchfreq_t **freqp, INT32 *freqc); 142 void G_FreeMapSearch(mapsearchfreq_t *freq, INT32 freqc);
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H A D | g_game.c | 4939 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 …]
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/dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
H A D | dlmodel.cpp | 849 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 …]
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/dports/biology/fastdnaml/fastDNAml_1.2.2/source/ |
H A D | fastDNAml.c | 1017 & 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 …]
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H A D | fastDNAml.h | 111 double freqa, freqc, freqg, freqt, /* base frequencies */ member
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/dports/biology/seaview/seaview/csrc/ |
H A D | seq.c | 387 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 …]
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