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