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//
// partitionmodelplen.h
// iqtree
//
// Created by Olga on 04/05/17.
//
//
#ifndef iqtree_partitionmodelplen_h
#define iqtree_partitionmodelplen_h
#include "tree/phylosupertreeplen.h"
#include "model/partitionmodel.h"
class PartitionModelPlen : public PartitionModel
{
public:
PartitionModelPlen();
/**
constructor
create partition 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 super-tree
*/
PartitionModelPlen(Params ¶ms, PhyloSuperTreePlen *tree, ModelsBlock *models_block);
~PartitionModelPlen();
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
* @param brlen_type either BRLEN_OPTIMIZE, BRLEN_FIX or BRLEN_SCALE
* @return #parameters of the model + # branches
*/
virtual int getNParameters(int brlen_type);
virtual int getNDim();
/**
write information
@param out output stream
*/
virtual void writeInfo(ostream &out);
/**
optimize model parameters and tree branch lengths
NOTE 2016-08-20: refactor the semantic of fixed_len
@param fixed_len 0: optimize branch lengths, 1: fix branch lengths, 2: scale branch lengths
@param write_info TRUE to write model parameters every optimization step, FALSE to only print at the end
@param logl_epsilon log-likelihood epsilon to stop
@param gradient_epsilon gradient (derivative) epsilon to stop
@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);
/**
* optimize model parameters and tree branch lengths for the +I+G model
* using restart strategy.
* @param fixed_len TRUE to fix branch lengths, default is false
* @return the best likelihood
*/
virtual double optimizeParametersGammaInvar(int fixed_len = BRLEN_OPTIMIZE, bool write_info = true, double logl_epsilon = 0.1, double gradient_epsilon = 0.0001);
double optimizeGeneRate(double tol);
// virtual double targetFunk(double x[]);
// virtual void getVariables(double *variables);
// virtual void setVariables(double *variables);
/** partition ID currently under optimization of of its rate */
// int optimizing_part;
/**
compute the likelihood for a partition under rate optimization (optimizing_rate).
Used for the ML optimization of gene rate
@param value x-value of the function
@return log-likelihood
*/
// virtual double computeFunction(double value);
};
#endif
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