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Searched refs:endsite (Results 1 – 21 of 21) sorted by relevance

/dports/biology/seaview/seaview/csrc/
H A Ddnapars.c422 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()
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H A Dseq.c73 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()
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H A Dphylip.c1969 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()
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H A Dseq.h82 extern long nonodes, endsite, outgrno, nextree, which;
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/
H A Dseq.cpp79 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()
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H A Dphylip.cpp2018 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()
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H A Ddnadist.cpp698 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()
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H A DNeighborJoinWidget.cpp149 const qint64 endsite = msa->getLength(); in checkMemoryEstimation() local
151 …const qint64 minMemoryForDistanceMatrixMb = (qint64)(spp * endsite * 32 + endsite * 4) / (1024 * 1… in checkMemoryEstimation()
H A Dseq.h83 extern long nonodes, endsite, outgrno, nextree, which;
H A DDistanceMatrix.cpp289 for (int j = 0; j < endsite; j++) { in ~DistanceMatrix()
/dports/biology/migrate/migrate-3.6.11/src/
H A Dsequence.c492 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()
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H A Dheating.c440 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()
H A Dtree.c2002 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
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H A Dmcmc1.c515 (*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()
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H A Dmcmc2.c459 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
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H A Dmutationmodel.c199 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()
H A Dmigration.h197 long endsite; //!< number of site patterns member
235 long endsite; //!< number of site patterns member
1364 long endsite; member
/dports/biology/recombine/recombine1.41/
H A Drecombine.h352 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);
H A Drecombine.c3896 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
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/dports/biology/fastdnaml/fastDNAml_1.2.2/source/
H A DfastDNAml.c1863 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()
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H A DfastDNAml.h126 int endsite; /* # of sequence patterns */ member