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Searched refs:RateHeterotachy (Results 1 – 6 of 6) sorted by relevance

/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Drateheterotachyinvar.cpp11 : RateInvar(p_invar_sites, tree), RateHeterotachy(ncat, params, tree) in RateHeterotachyInvar()
25 RateHeterotachy::saveCheckpoint(); in saveCheckpoint()
30 RateHeterotachy::restoreCheckpoint(); in restoreCheckpoint()
39 RateHeterotachy::setNCategory(ncat); in setNCategory()
51 return RateHeterotachy::targetFunk(x); in targetFunk()
56 RateHeterotachy::writeInfo(out); in writeInfo()
66 RateHeterotachy::writeParameters(out); in writeParameters()
70 RateHeterotachy::setBounds(lower_bound, upper_bound, bound_check); in setBounds()
82 tree_lh = RateHeterotachy::optimizeParameters(gradient_epsilon); in optimizeParameters()
87 RateHeterotachy::setVariables(variables); in setVariables()
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H A Drateheterotachy.cpp12 RateHeterotachy::RateHeterotachy(int ncat, string params, PhyloTree *tree) : RateHeterogeneity() { in RateHeterotachy() function in RateHeterotachy
49 RateHeterotachy::~RateHeterotachy() { in ~RateHeterotachy()
55 void RateHeterotachy::setNCategory(int ncat) { in setNCategory()
73 void RateHeterotachy::startCheckpoint() { in startCheckpoint()
80 void RateHeterotachy::saveCheckpoint() { in saveCheckpoint()
90 void RateHeterotachy::restoreCheckpoint() { in restoreCheckpoint()
97 int RateHeterotachy::getNDim() { in getNDim()
105 string RateHeterotachy::getNameParams() { in getNameParams()
116 void RateHeterotachy::writeInfo(ostream &out) { in writeInfo()
131 void RateHeterotachy::writeParameters(ostream &out) { in writeParameters()
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H A Drateheterotachyinvar.h14 class RateHeterotachyInvar: public RateInvar, public RateHeterotachy {
43 virtual int getNDim() { return RateInvar::getNDim() + RateHeterotachy::getNDim(); } in getNDim()
63 return RateInvar::getNameParams() + RateHeterotachy::getNameParams(); in getNameParams()
H A Drateheterotachy.h20 class RateHeterotachy: virtual public RateHeterogeneity {
31 RateHeterotachy(int ncat, string params, PhyloTree *tree);
36 virtual ~RateHeterotachy();
H A Dmodelfactory.cpp795 site_rate = new RateHeterotachy(num_rate_cats, heterotachy_params, tree); in ModelFactory()
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylotree.h330 friend class RateHeterotachy; variable