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/*
* modelfactorymixlen.h
*
* Created on: Sep 2, 2015
* Author: minh
*/
#include "modelfactory.h"
class ModelFactoryMixlen : public ModelFactory {
public:
/**
constructor
create substitution model with possible rate heterogeneity. Create proper class objects
for two variables: model and site_rate. It takes the following field of params into account:
model_name, num_rate_cats, freq_type, store_trans_matrix
@param params program parameters
@param tree associated phylogenetic tree
*/
ModelFactoryMixlen(Params ¶ms, string &model_name, PhyloTree *tree, ModelsBlock *models_block);
/**
optimize model parameters and tree branch lengths
@param fixed_len TRUE to fix branch lengths, default is false
@return the best likelihood
*/
virtual double optimizeParameters(int fixed_len = BRLEN_OPTIMIZE, bool write_info = true,
double logl_epsilon = 0.1, double gradient_epsilon = 0.0001);
/**
sort classes in ascending order of tree lengths
@return tree string with sorted branch lengths
*/
string sortClassesByTreeLength();
/**
* @param brlen_type either BRLEN_OPTIMIZE, BRLEN_FIX or BRLEN_SCALE
* @return #parameters of the model + # branches
*/
virtual int getNParameters(int brlen_type);
};
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