mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 03:20:25 +08:00
128 lines
3.6 KiB
C++
128 lines
3.6 KiB
C++
// $Id: bestAlphaManyTrees.h 962 2006-11-07 15:13:34Z privmane $
|
|
|
|
#ifndef ___BEST_ALPHA_MANY_TREES
|
|
#define ___BEST_ALPHA_MANY_TREES
|
|
|
|
#include "definitions.h"
|
|
#include "computePijComponent.h"
|
|
#include "sequenceContainer.h"
|
|
#include "bblEM.h"
|
|
#include "gammaDistribution.h"
|
|
#include "likelihoodComputation.h"
|
|
#include "logFile.h"
|
|
|
|
using namespace likelihoodComputation;
|
|
|
|
//#define VERBOS
|
|
namespace bestAlpha {
|
|
/* void optimizeAlpha1G_EM( tree& et,
|
|
const sequenceContainer& sc,
|
|
const stochasticProcess& sp,
|
|
const Vdouble * weights,
|
|
MDOUBLE & bestAlpha,
|
|
MDOUBLE & likelihoodScore,
|
|
const int maxIterations=1000,
|
|
const MDOUBLE epsilon=0.05);
|
|
*/
|
|
void optimizeAlphaNG_EM_SEP(vector<tree>& et,
|
|
vector<sequenceContainer>& sc,
|
|
vector<stochasticProcess> &sp,
|
|
const vector<Vdouble *> * weights,
|
|
MDOUBLE & bestAlpha,
|
|
MDOUBLE & likelihoodScore,
|
|
const int maxIterations=1000,
|
|
const MDOUBLE epsilon=0.05);
|
|
void optimizeAlphaNG_EM_PROP(tree& et,// 1 alpha for all trees!
|
|
vector<sequenceContainer>& sc,
|
|
vector<stochasticProcess>& sp,
|
|
const vector<Vdouble *> * weights,
|
|
MDOUBLE & bestAlpha,
|
|
MDOUBLE & likelihoodScore,
|
|
const int maxIterations=1000,
|
|
const MDOUBLE epsilon=0.05);
|
|
void optimizeAlphaNG_EM_PROP_n_alpha(tree& et,// alpha for each trees!
|
|
vector<sequenceContainer>& sc,
|
|
vector<stochasticProcess>& sp,
|
|
const vector<Vdouble *> * weights,
|
|
vector<MDOUBLE> & bestAlpha,
|
|
MDOUBLE & likelihoodScore,
|
|
const int maxIterations=1000,
|
|
const MDOUBLE epsilon=0.05);
|
|
};
|
|
|
|
#include <iostream>// for debugging
|
|
using namespace std; // for debugging
|
|
|
|
class C_evalAlphaManyTrees{
|
|
public:
|
|
C_evalAlphaManyTrees(tree& et,
|
|
vector<sequenceContainer>& sc,
|
|
vector<stochasticProcess>& sp,
|
|
const vector<Vdouble *> * weights)
|
|
: _et(et),_sc(sc),_sp(sp),_weights(weights) {};
|
|
private:
|
|
const tree& _et;
|
|
const vector<sequenceContainer>& _sc;
|
|
vector<stochasticProcess>& _sp;
|
|
const vector<Vdouble *> * _weights;
|
|
public:
|
|
MDOUBLE operator() (MDOUBLE alpha) {
|
|
#ifdef VERBOS
|
|
LOG(5,<<"trying alpha: "<<alpha<<endl);
|
|
#endif
|
|
MDOUBLE res=0;
|
|
for (int i=0; i < _sc.size();++i) {
|
|
|
|
if (_sp[i].categories() == 1) {
|
|
errorMsg::reportError(" one category when trying to optimize alpha");
|
|
}
|
|
(static_cast<gammaDistribution*>(_sp[i].distr()))->setAlpha(alpha);
|
|
res += likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_et,_sc[i],_sp[i],_weights?(*_weights)[i]:NULL);
|
|
}
|
|
#ifdef VERBOS
|
|
LOG(5,<<"likelihood = "<<-res<<endl);
|
|
#endif
|
|
return -res;
|
|
}
|
|
};
|
|
|
|
class C_evalAlphaManyTreesSep{ // separate model, 1 gamma
|
|
public:
|
|
C_evalAlphaManyTreesSep(vector<tree>& et,
|
|
vector<sequenceContainer>& sc,
|
|
vector<stochasticProcess>& sp,
|
|
const vector<Vdouble *> * weights)
|
|
: _et(et),_sc(sc),_sp(sp),_weights(weights) {};
|
|
private:
|
|
const vector<tree>& _et;
|
|
const vector<sequenceContainer>& _sc;
|
|
vector<stochasticProcess>& _sp;
|
|
const vector<Vdouble *> * _weights;
|
|
public:
|
|
MDOUBLE operator() (MDOUBLE alpha) {
|
|
//LOG(5,<<"trying alpha: "<<alpha<<endl);
|
|
MDOUBLE res=0;
|
|
for (int i=0; i < _sc.size();++i) {
|
|
|
|
if (_sp[i].categories() == 1) {
|
|
errorMsg::reportError(" one category when trying to optimize alpha");
|
|
}
|
|
(static_cast<gammaDistribution*>(_sp[i].distr()))->setAlpha(alpha);
|
|
res += likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_et[i],_sc[i],_sp[i],_weights?(*_weights)[i]:NULL);
|
|
}
|
|
// LOG(5,<<" with alpha = "<<alpha<<" logL = "<<res<<endl);
|
|
return -res;
|
|
}
|
|
};
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
#endif
|
|
|
|
|