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// $Id: simulateTree.h 8507 2010-08-12 15:20:59Z rubi $
#ifndef ___SIMULATE_TREE
#define ___SIMULATE_TREE
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "sequenceContainer.h"
//class sequenceData; // to be able to go to simulate data.
class simulateTree {
public:
explicit simulateTree(const tree& _inEt,const stochasticProcess& sp,
const alphabet* alph);
void generate_seq(int seqLength);
// This function generates the sequences not using the discrete gamma, but rather,
// the rates are sampled from the continuous distribution.
// It assumes the Gamma distribution has mean 1 (alpha = beta).
void generate_seq_continuous_gamma(int seqLength);
void generate_seqWithRateVector(const Vdouble& simRates, const int seqLength);
//these function do the same simulation as above but check that no stop codon is created.
//applicable only when the stochasticProcess is based on nucleotides
void generate_seqWithRateVectorNoStopCodon(const Vdouble& simRates, int seqLength);
tree gettree() {return _et;}
virtual ~simulateTree();
sequenceContainer toSeqData();
sequenceContainer toSeqDataWithoutInternalNodes();
void generate_rates_continuous_gamma(const int seqLength,const MDOUBLE alpha,Vdouble rates);
MDOUBLE getAvgSub() {return _avgSubtitutionsPerSite;}
private:
void generateRootSeq(int seqLength);
void recursiveGenerateSpecificSeq(const Vdouble& rateVec, int seqLength, tree::nodeP myNode);
int giveRandomChar() const;
int giveRandomChar(const int letterInFatherNode, const MDOUBLE length,const int pos) const;
int getRandCategory(const int pos) const;
vector<sequence> _simulatedSequences; // the sequences (nodes * seqLen)
tree _et;
const stochasticProcess& _sp;
const alphabet* _alph;
MDOUBLE _avgSubtitutionsPerSite;
};
#endif
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