/dports/biology/seaview/seaview/csrc/ |
H A D | dnapars.c | 422 endsite = 0; in makeweights() 425 endsite++; in makeweights() 427 for (i = 1; i <= endsite; i++) in makeweights() 432 for (i = 0; i < endsite; i++) { in makeweights() 437 for (i = 0; i < endsite; i++) in makeweights() 530 for (i = 0; i < endsite; i++) { in evaluate() 578 sumnsteps2(tempsum, temp, p->back, endsite+1, endsite, threshwt); in tryadd() 580 multisumnsteps(temp, temp1, endsite+1, endsite, threshwt); in tryadd() 594 sumnsteps2(temp, item, p, endsite+1, endsite, threshwt); in tryadd() 596 sumnsteps(temp1, item, p, endsite+1, endsite); in tryadd() [all …]
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H A D | seq.c | 73 zeronumnuc(*temp, endsite); in alloctemp() 260 for (j = 0; j < endsite; j++) in allocx() 289 for (j = 0; j < endsite; j++) in prot_allocx() 706 for (j = 0; j < endsite; j++) { in makevalues() 805 for (k = 0; k < endsite; k++) { in makevalues2() 952 for (i = 0; i < endsite; i++) in fillin() 991 for (i = 0; i < endsite; i++) { in multifillin() 1497 zeronumnuc(p, endsite); in postorder() 2016 for (i = 0; i < endsite; i++) in moresteps() 3374 for (i = 0; i < endsite; i++) in copynode() [all …]
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H A D | phylip.c | 1969 void zeronumnuc(node *p, long endsite) in zeronumnuc() argument 1973 for (i = 0; i < endsite; i++) in zeronumnuc() 1983 for (i = 0; i < endsite; i++) in zerodiscnumnuc() 2002 zeronumnuc(p, endsite); in allocnontip() 2019 zerodiscnumnuc(p, endsite); in allocdiscnontip() 2032 long endsite) in allocdiscnode() argument 2050 zeronumnuc(*p, endsite); in gnutreenode() 2052 allocnode(p, zeros, endsite); in gnutreenode() 2075 zerodiscnumnuc(*p, endsite); in gnudisctreenode() 2330 for (i = 0; i < endsite; i++) in malloc_pheno() [all …]
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H A D | seq.h | 82 extern long nonodes, endsite, outgrno, nextree, which;
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/ |
H A D | seq.cpp | 79 zeronumnuc(*temp, endsite); in alloctemp() 266 for (j = 0; j < endsite; j++) in allocx() 295 for (j = 0; j < endsite; j++) in prot_allocx() 713 for (j = 0; j < endsite; j++) { in makevalues() 812 for (k = 0; k < endsite; k++) { in makevalues2() 959 for (i = 0; i < endsite; i++) in fillin() 1504 zeronumnuc(p, endsite); in postorder() 2023 for (i = 0; i < endsite; i++) in moresteps() 2559 for (i = 0; i < endsite; i++) in hypstates() 3380 for (i = 0; i < endsite; i++) in copynode() [all …]
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H A D | phylip.cpp | 2018 void zeronumnuc(node *p, long endsite) in zeronumnuc() argument 2022 for (i = 0; i < endsite; i++) in zeronumnuc() 2032 for (i = 0; i < endsite; i++) in zerodiscnumnuc() 2051 zeronumnuc(p, endsite); in allocnontip() 2068 zerodiscnumnuc(p, endsite); in allocdiscnontip() 2081 long endsite) in allocdiscnode() argument 2099 zeronumnuc(*p, endsite); in gnutreenode() 2101 allocnode(p, zeros, endsite); in gnutreenode() 2124 zerodiscnumnuc(*p, endsite); in gnudisctreenode() 2379 for (i = 0; i < endsite; i++) in malloc_pheno() [all …]
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H A D | dnadist.cpp | 698 endsite = 0; in makeweights() 701 endsite++; in makeweights() 703 for (i = 1; i <= endsite; i++) in makeweights() 727 for (j = 0; j < endsite; j++) in dnadist_makevalues() 730 for (k = 0; k < endsite; k++) { in dnadist_makevalues() 857 for (j = 0; j < endsite; j++) { in dnadist_empiricalfreqs() 1011 for (i = 0; i < endsite; i++) { in makev() 1068 for (i = 0; i < endsite; i++) { in makev() 1144 for (i = 0; i < endsite; i++) { in makev() 1231 for (i = 0; i < endsite; i++) { in makev() [all …]
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H A D | NeighborJoinWidget.cpp | 149 const qint64 endsite = msa->getLength(); in checkMemoryEstimation() local 151 …const qint64 minMemoryForDistanceMatrixMb = (qint64)(spp * endsite * 32 + endsite * 4) / (1024 * 1… in checkMemoryEstimation()
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H A D | seq.h | 83 extern long nonodes, endsite, outgrno, nextree, which;
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H A D | DistanceMatrix.cpp | 289 for (int j = 0; j < endsite; j++) { in ~DistanceMatrix()
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/dports/biology/migrate/migrate-3.6.11/src/ |
H A D | sequence.c | 492 world->data->seq[0]->endsite = 1; in makeweights() 506 seq->endsite = i; in makeweights() 508 for (i = 1; i <= seq->endsite; i++) in makeweights() 969 long endsite = world->data->seq[0]->endsite; in make_invarsites() local 978 for (k = endsite; k < endsite + 4; k++) in make_invarsites() 995 long endsite = world->data->seq[0]->endsite; in make_invarsites_unlinked() local 1006 for (k = endsite * 5; k < endsite * 5 + 4; k++) in make_invarsites_unlinked() 1023 for (k = endsite * 5; k < endsite * 5 + 4; k++) in make_invarsites_unlinked() 1731 for (i = endsite; i < endsite + 4; i++) in snp_invariants_original() 1764 for (i = seq->endsite - seq->addon ; i < seq->endsite; i++) in snp_invariants() [all …]
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H A D | heating.c | 440 long endsite = seq->endsite; in reset_weight() local 441 long heated_end = (long) (endsite - endsite * 1./world->heat); in reset_weight() 443 memcpy(seq->aliasweight, seq->savealiasweight, sizeof(long)*endsite); in reset_weight()
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H A D | tree.c | 2002 long endsite = world->data->seq[0]->endsite; in alloc_seqx() local 3054 const long endsite = world->data->seq[0]->endsite; in nuview_sequence() local 3244 const long endsite = world->data->seq[0]->endsite; in nuview_sequence_slow() local 3492 const long endsite = world->data->seq[0]->endsite; in nuview_ancestral() local 3586 const long endsite = proposal->world->data->seq[0]->endsite; in pseudonu_seq() local 3786 const long endsite = proposal->world->data->seq[0]->endsite; in pseudonu_seq_slow() local 4125 const long endsite = proposal->world->data->seq[0]->endsite; in pseudo_tl_anc() local 4258 const long endsite = world->data->seq[0]->endsite; in pseudo_tl_snp() local 4360 const long endsite = world->data->seq[0]->endsite; in pseudo_tl_snp_unlinked() local 4415 const long endsite = world->data->seq[0]->endsite; in treelike_anc() local [all …]
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H A D | mcmc1.c | 515 (*proposal)->endsite = world->data->seq[0]->endsite; in new_proposal() 539 (*proposal)->mf = (MYREAL *) mycalloc (2* (*proposal)->endsite, sizeof (MYREAL)); in new_proposal() 540 (*proposal)->mt = (*proposal)->mf + (*proposal)->endsite; in new_proposal() 544 allocate_xseq(&(*proposal)->xf, world->data->seq[0]->endsite, world->options->rcategs); in new_proposal() 545 allocate_xseq(&(*proposal)->xt, world->data->seq[0]->endsite, world->options->rcategs); in new_proposal() 608 (*proposal)->endsite = world->data->seq[0]->endsite; in set_new_proposal() 629 (*proposal)->mf = (MYREAL *) mycalloc (2* (*proposal)->endsite, sizeof (MYREAL)); in set_new_proposal() 630 (*proposal)->mt = (*proposal)->mf + (*proposal)->endsite; in set_new_proposal() 633 allocate_xseq(&(*proposal)->xf, world->data->seq[0]->endsite, world->options->rcategs); in set_new_proposal() 634 allocate_xseq(&(*proposal)->xt, world->data->seq[0]->endsite, world->options->rcategs); in set_new_proposal() [all …]
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H A D | mcmc2.c | 459 sizeof (MYREAL) * proposal->endsite); in target_oback() 501 sizeof (MYREAL) * proposal->endsite); in target_ocousin() 510 sizeof (MYREAL) * proposal->endsite); in target_ocousin() 573 sizeof (MYREAL) * proposal->endsite); in target_rbcoa() 607 sizeof (MYREAL) * proposal->endsite); in target_rbcoa() 649 sizeof (MYREAL) * proposal->endsite); in target_obbcoa() 677 sizeof (MYREAL) * proposal->endsite); in target_obbcoa() 792 sizeof (MYREAL) * proposal->endsite); in target_stancoa() 889 sizeof (MYREAL) * proposal->endsite); in t_s_upper() 1502 long endsite = proposal->endsite; in copy_x() local [all …]
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H A D | mutationmodel.c | 199 mumod->numpatterns = world->data->seq[0]->endsite; // number unique patterns in finish_mutationmodel() 200 mumod->numsites = world->data->seq[0]->endsite; // number of sites in finish_mutationmodel()
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H A D | migration.h | 197 long endsite; //!< number of site patterns member 235 long endsite; //!< number of site patterns member 1364 long endsite; member
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/dports/biology/recombine/recombine1.41/ |
H A D | recombine.h | 352 long startsite, endsite; member 553 long startsite, long endsite); 555 long startsite, long endsite); 558 long indexsite, long startsite, long endsite); 560 long indexsite, long startsite, long endsite);
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H A D | recombine.c | 3896 long indexsite, long startsite, long endsite) in nuview_micro() argument 3921 for(i = startsite; i <= endsite; i++) { in nuview_micro() 3967 long startsite, long endsite) in nuview() argument 4014 calcrange(op,data,p,q,r,indexsite,startsite,endsite,op->categs); in nuview() 4161 long indexsite, long startsite, long endsite) in localsmooth() argument 4170 localsmooth(op,data,p->next->back,indexsite,startsite,endsite); in localsmooth() 4177 endsite); in localsmooth() 4186 nuview_micro(op,data,p,indexsite,startsite,endsite); in localsmooth() 4190 nuview(op,data,p,indexsite,startsite,endsite); in localsmooth() 4205 long indexsite, long startsite, long endsite) in snpsmooth() argument [all …]
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/dports/biology/fastdnaml/fastDNAml_1.2.2/source/ |
H A D | fastDNAml.c | 1863 cdta->endsite = i; in sitecombcrunch() 1864 if (cdta->aliaswgt[i] > 0) cdta->endsite++; in sitecombcrunch() 1894 for (j = 0; j < cdta->endsite; j++) { in makevalues() 1899 for (j = 0; j < cdta->endsite; j++) { in makevalues() 1928 for (j = 0; j < cdta->endsite; j++) { in empiricalfreqs() 2190 for (i = 0; i < tr->cdta->endsite; i++) { in newview() 2412 tr->log_f_valid = tr->cdta->endsite; in evaluate() 2417 for (i = 0; i < tr->cdta->endsite; i++) { in evaluate() 2424 for (i = 0; i < tr->cdta->endsite; i++) { in evaluate() 2516 for (i = 0; i < tr->cdta->endsite; i++) { in makenewz() [all …]
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H A D | fastDNAml.h | 126 int endsite; /* # of sequence patterns */ member
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