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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 ___SIMULATE_1POS__
#define ___SIMULATE_1POS__
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "sequenceContainer.h"
#include "alphabet.h"
#include "threeStateModel.h"
#include "oneTwoMoreModel.h"
using namespace std;
/******************************************************************
Simulate one position using the 3stateLGT stochastic process
*******************************************************************/
class simulateOnePos{
public:
//simulateOnePos();
simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile
, MDOUBLE sumGainLoss, MDOUBLE theta
, bool is3states=false, stochasticProcess* sp=NULL, tree* pTree=NULL
, Vdouble* init_cpN_vals=NULL, Vdouble* freq_cpN=NULL);
virtual ~simulateOnePos();
VVint getChangesForBranch(int nodeID);
sequenceContainer getSequenceContainer(){return _sc;};
MDOUBLE getOccurFraction(){return _occurFraction;};
private:
void init(string strTree);
void init(tree* pTree);
void simulateOnePosLGT(stochasticProcess* sp, string strOutFile);
void simulateOnePos_cpN_Model(string strOutFile);
void printTreeWithNodeIdBPStyle(ostream &out) const;
void recursivePrintTree(ostream &out,const tree::nodeP &myNode) const;
private:
tree _tree;
stochasticProcess *_sp;
sequenceContainer _sc; // as simulated
int _simNum;
MDOUBLE _sumGainLoss;
MDOUBLE _theta;
MDOUBLE _occurFraction;
alphabet* _pAlph;
vector<int> _alphVecDist;
ostream *_simulatedEvents;
ostream *_resFile;
bool _simulateNullModel;
bool _is3states;
Vdouble* _init_cpN_vals;
Vdouble* _freq_cpN;
string _rootAt;
VVVint _changesOccurred; // number of times changes from i to j occurred , for each branch
};
#endif
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