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//
// rateheterotachy.hpp
// iqtree
//
// Created by Minh Bui on 11/8/16.
//
//
#ifndef rateheterotachy_hpp
#define rateheterotachy_hpp
#include "rateheterogeneity.h"
class PhyloTree;
/**
rate-heterotachy model, allowing for mixed branch lengths
*/
class RateHeterotachy: virtual public RateHeterogeneity {
friend class ModelFactoryMixlen;
public:
/**
constructor
@param ncat number of rate categories
@param sorted_rates TRUE to sort the rate in increasing order
@param tree associated phylogenetic tree
*/
RateHeterotachy(int ncat, string params, PhyloTree *tree);
/**
destructor
*/
virtual ~RateHeterotachy();
/**
@return TRUE if this is a heterotachy model, default: FALSE
*/
virtual bool isHeterotachy() { return true; }
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
* @return model name with parameters in form of e.g. GTR{a,b,c,d,e,f}
*/
virtual string getNameParams();
/**
fix parameters, so that no optimization done
@param mode some input mode
*/
virtual int getFixParams() { return fix_params; }
/**
fix parameters, so that no optimization done
@param mode some input mode
*/
virtual void setFixParams(int mode) { fix_params = mode; }
/**
return the number of dimensions
*/
virtual int getNDim();
/**
@return the number of rate categories
*/
virtual int getNRate() { return ncategory; }
/**
get the number of rate categories for site-specific category model
@return the number of rate categories
*/
virtual int getNDiscreteRate() { return ncategory; }
/**
@param category category ID from 0 to #category-1
@return the rate of the specified category
*/
virtual double getRate(int category) {
return 1.0;
}
/**
get the proportion of sites under a specified category.
@param category category ID from 0 to #category-1
@return the proportion of the specified category
*/
virtual double getProp(int category) { return prop[category]; }
/**
set the proportion of a specified category.
@param category category ID from 0 to #category-1
@return the proportion of the specified category
*/
virtual void setProp(int category, double value) { prop[category] = value; }
/**
set number of optimization steps
@param opt_steps number of optimization steps
*/
virtual void setOptimizeSteps(int optimize_steps) { this->optimize_steps = optimize_steps; }
/**
optimize parameters. Default is to optimize gamma shape
@return the best likelihood
*/
virtual double optimizeParameters(double gradient_epsilon);
/**
optimize rate parameters using EM algorithm
@return log-likelihood of optimized parameters
*/
double optimizeWithEM();
/**
write information
@param out output stream
*/
virtual void writeInfo(ostream &out);
/**
write parameters, used with modeltest
@param out output stream
*/
virtual void writeParameters(ostream &out);
/**
set number of rate categories
@param ncat #categories
*/
virtual void setNCategory(int ncat);
protected:
/**
number of rate categories
*/
int ncategory;
/**
* proportion of sites for each rate categories
*/
double *prop;
/** TRUE to fix parameters */
int fix_params;
/** number of optimization steps, default: ncategory*2 */
int optimize_steps;
};
#endif /* rateheterotachy_hpp */
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