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// $Id: fromCountTableComponentToDistance.cpp 4471 2008-07-17 15:38:50Z cohenofi $
#include "fromCountTableComponentToDistancefixRoot.h"
#include "likeDistfixRoot.h"
#include <cassert>
fromCountTableComponentToDistancefixRoot::fromCountTableComponentToDistancefixRoot(
const vector<countTableComponentGam>& ctc,
const stochasticProcess &sp,
const MDOUBLE toll,
const MDOUBLE brLenIntialGuess,
unObservableData* unObservableData_p)
: _sp(sp), _ctc(ctc) {
_distance =brLenIntialGuess ;//0.03;
_toll = toll;
_unObservableData_p = unObservableData_p;
}
void fromCountTableComponentToDistancefixRoot::computeDistance() {
MDOUBLE maxPairwiseDistance = 5.0; // The default
MDOUBLE minPairwiseDistance = 0.0000001; // The default
likeDistfixRoot likeDist1(_sp,_toll,maxPairwiseDistance,minPairwiseDistance,_unObservableData_p);
MDOUBLE initGuess = _distance;
_distance = likeDist1.giveDistance(_ctc,_likeDistance,initGuess); // each ctc is per node, and include all letterAtRoot
assert(_distance>=0);
}
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