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/*
Copyright (C) 2011 Tal Pupko TalP@tauex.tau.ac.il.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ___SITE_SPECIFIC_GL__
#define ___SITE_SPECIFIC_GL__
#include "definitions.h"
#include "likelihoodComputation.h"
#include "seqContainerTreeMap.h"
// per all sites computation
void computeEB_EXP_siteSpecificGL(Vdouble & GainLossV,
Vdouble & stdV,
Vdouble & lowerBoundV,
Vdouble & upperBoundV,
VVdouble & posteriorsV,
const sequenceContainer& sc,
const vector<vector<stochasticProcess*> >& sp,
const tree& tr,
const distribution * gainDist,
const distribution * lossDist,
const distribution * distPrim,
const MDOUBLE alphaConf,
VVVdouble & postProbPerSpPerCatPerPos, //2 fill (*postProbPerSpPerCatPerPos)[sp][pos]
unObservableData* unObservableData_p);
// per one site
void computeEB_EXP_siteSpecificGL(int pos,
const sequenceContainer& sc,
const vector<vector<stochasticProcess*> >& sp,
//const computePijGam& cpg,
const tree &tr,
const distribution * gainDist,
const distribution * lossDist,
const distribution * distPrim,
Vdouble & posteriorV,
MDOUBLE& GainLossExpectation,
MDOUBLE & stdForce,
MDOUBLE & lowerConf,
MDOUBLE & upperConf,
const MDOUBLE alphaConf,
VVVdouble & postProbPerSpPerCatPerPos, //2 fill (*postProbPerSpPerCatPerPos)[sp][pos]
unObservableData* unObservableData_p);
#endif
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