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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 ___SANKOFF__GL__H
#define ___SANKOFF__GL__H
#include "tree.h"
#include "logFile.h"
#include "someUtil.h"
#include "definitions.h"
#include "stochasticProcess.h"
#include "sequenceContainer.h"
#include "gainLossUtils.h"
#include <map>
class sankoffReconstructGL {
public:
explicit sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent);
virtual ~sankoffReconstructGL() ;
void traverseUpMP(VVdouble &upCosts, vector <VVint> &backtrack); // input as empty vector to be filled
MDOUBLE traverseDownMP(VVdouble &upCosts, vector <VVint> &backtrack, VVint &transitionTypeCount, VVdouble &totalCosts); // input as already filled vector
Vdouble getGainMPPerPos(){return _gainMPPerPos;}
Vdouble getLossMPPerPos(){return _lossMPPerPos;}
VVVdouble getMPPerPos(){return _MPPerPos;}
VVVdouble getMPPerBranch(){return _MPPerBranch;}
VVVVdouble getMPPerPosPerNode(){return _MPPerPosPerNode;}
int getNumOfGainEvnetsMP(){return _numOfGains;}
int getNumOfLossEvnetsMP(){return _numOfLosses;}
private:
void initialize();
void run();
void startTree();
void startSequenceContainer();
void startCostMatrix();
MDOUBLE runPosition(int pos, ofstream& gainLossMPPerPosPerBranchStream, ofstream& MPprints, ofstream& gainLossMPAncestralReconstructStream);
void preparePrintData(Vstring &data);//prepares the data to be printed as BP data on the tree
void printMPPerBranch(ostream& out);
void printMPPerPos(ostream& out);
public:
private:
VVdouble _costMatrix;
Vint _states; // the vector with the states of the leaves, to be filled with reconstructed states
alphabet * _alph;
tree _tr;
sequenceContainer _sc;
MDOUBLE _costOfTree;
int _numOfGains;
int _numOfLosses;
Vdouble _lossMPPerPos;
Vdouble _gainMPPerPos;
VVVdouble _MPPerPos;
VVVdouble _MPPerBranch;
VVVVdouble _MPPerPosPerNode;
MDOUBLE _distanceFromRootForRecent;
MDOUBLE _costMatrixGainLossRatio;
string _outDir;
};
#endif
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