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// $Id: replacementModelSSRV.cpp 4165 2008-06-04 09:19:48Z osnatz $
#include "replacementModelSSRV.h"
#include "logFile.h"
#include <iomanip>
#include <iostream>
replacementModelSSRV::replacementModelSSRV(const distribution* dist, const replacementModel* baseRM, MDOUBLE rateOfRate /*= 1 */) :
_dist(dist->clone()),
_baseRM(baseRM->clone()),
_rateOfRate(rateOfRate)
{
if (_dist->categories() == 0)
errorMsg::reportError("replacementModelSSRV::replacementModelSSRV : number of categories == 0");
updateFreq();
updateQ();
}
//// similar to goldmanYangModel.cpp
//replacementModelSSRV::replacementModelSSRV(const replacementModelSSRV& other) :
//_dist(other._dist->clone()),
//_baseRM(other._baseRM->clone()),
//_rateOfRate(other._rateOfRate)
//{
// int size = alphabetSize();
// _Q.resize(size);
// for (int z=0; z < _Q.size();++z)
// _Q[z].resize(size,0);
// updateFreq();
// updateQ();
//}
// Instead of calling updateQ here, like in goldmanYangModel.cpp,
// this method uses the copy constructor of q2pt and also copies _freq and _Q
replacementModelSSRV::replacementModelSSRV(const replacementModelSSRV& other) :
_dist(other._dist->clone()),
_baseRM(other._baseRM->clone()),
_rateOfRate(other._rateOfRate),
_q2pt(other._q2pt),
_freq(other._freq),
_Q(other._Q)
{
}
replacementModelSSRV::~replacementModelSSRV()
{
if (_dist) delete (_dist);
if (_baseRM) delete (_baseRM);
}
replacementModelSSRV& replacementModelSSRV::operator=(const replacementModelSSRV &other)
{
if (_dist) delete (_dist);
if (_baseRM) delete (_baseRM);
_dist = other._dist->clone();
_baseRM = other._baseRM->clone();
_rateOfRate = other._rateOfRate;
_q2pt = other._q2pt; //@@@@ why doesn't this work ? explicit ?
// _q2pt.fillFromRateMatrix(other._freq,other._Q);
_freq = other._freq;
_Q = other._Q;
return (*this);
}
const int replacementModelSSRV::alphabetSize() const
{
return (_baseRM->alphabetSize() * _dist->categories());
}
// The freq of each mulCharacter is its freq in the _baseRM * the freq of the rate-category
void replacementModelSSRV::updateFreq()
{
_freq.clear();
int size = alphabetSize();
int numCategories = _dist->categories();
_freq.resize(size);
int idInCategory;
for(idInCategory=0; idInCategory < _baseRM->alphabetSize() ; ++idInCategory)
{
for (int categoryNumber=0; categoryNumber < numCategories; ++categoryNumber)
_freq[categoryNumber*_baseRM->alphabetSize() + idInCategory] =
_baseRM->freq(idInCategory) * _dist->ratesProb(categoryNumber);
}
}
void replacementModelSSRV::updateQ()
{
if (_rateOfRate < EPSILON) _rateOfRate = EPSILON; // Temporary - to overcome a bug in QL algorithm, when _rateOfRate == 0
_Q.clear();
int size = alphabetSize();
_Q.resize(size);
for (int z=0; z < _Q.size();++z)
_Q[z].resize(size,0.0);
// fill Q
int _BaseRM_alphabetSize = _baseRM->alphabetSize();
int numCategories = _dist->categories();
// i,j : go over all the base-alphabet.
// z,w : go over all the categories.
for (int i=0; i < _BaseRM_alphabetSize; ++i)
{
for (int j=0; j < _BaseRM_alphabetSize; ++j)
{
for (int z=0; z < numCategories; ++z)
{
for (int w=0; w < numCategories; ++w)
{
if (i!=j)
{
// different alphabet, same rate category
if (z==w)
_Q[z*_BaseRM_alphabetSize + i][z*_BaseRM_alphabetSize+j]
= _dist->rates(z) * _baseRM->dPij_dt(i,j,0);
}
else
{
// same alphabet, different rate category
if (z!=w)
{
_Q[z*_BaseRM_alphabetSize+i][w*_BaseRM_alphabetSize+i] = _rateOfRate * _dist->ratesProb(w);
}
// same alphabet, same rate category
else
_Q[z*_BaseRM_alphabetSize+i][z*_BaseRM_alphabetSize+i] =
_dist->rates(z) * _baseRM->dPij_dt(i,j,0)
- ( _rateOfRate * (1.0 - _dist->ratesProb(z)));
}
}
}
}
}
// // check OZ
// LOG(4, <<"THE Q MATRIX IS: "<<endl ) ;
// VVdouble::iterator itr1 = _Q.begin();
// Vdouble::iterator itr2;
// for (; itr1 != _Q.end(); ++itr1)
// {
// for (itr2 = itr1->begin(); itr2 != itr1->end(); ++itr2)
// LOG(4,<< setprecision(3) << setw(5) << *itr2 <<'\t');
// LOG(4,<<endl);
// }
// LOG (4,<<endl);
//// end of check
_q2pt.fillFromRateMatrix(_freq,_Q);
}
void replacementModelSSRV::setDistribution(const distribution* dist)
{
if (dist->categories() == 0)
errorMsg::reportError("replacementModelSSRV::setDistribution : number of categories == 0");
if (_dist) delete (_dist);
_dist=dist->clone();
updateQ();
}
MDOUBLE replacementModelSSRV::sumPijQij() const{
MDOUBLE sum=0.0;
for (int i=0; i < _Q.size(); ++i) {
sum -= _Q[i][i]*_freq[i];
}
return sum;
}
//void replacementModelSSRV::norm(MDOUBLE scale){
//
// for (int i=0; i < _Q.size(); ++i) {
// for (int j=0; j < _Q.size(); ++j) {
// _Q[i][j]*=scale;
// }
// }
//
// _q2pt.fillFromRateMatrix(_freq,_Q);
//}
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