Searched refs:RateHeterotachy (Results 1 – 6 of 6) sorted by relevance
/dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
H A D | rateheterotachyinvar.cpp | 11 : 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() [all …]
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H A D | rateheterotachy.cpp | 12 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() [all …]
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H A D | rateheterotachyinvar.h | 14 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()
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H A D | rateheterotachy.h | 20 class RateHeterotachy: virtual public RateHeterogeneity { 31 RateHeterotachy(int ncat, string params, PhyloTree *tree); 36 virtual ~RateHeterotachy();
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H A D | modelfactory.cpp | 795 site_rate = new RateHeterotachy(num_rate_cats, heterotachy_params, tree); in ModelFactory()
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/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | phylotree.h | 330 friend class RateHeterotachy; variable
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