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#ifndef ___SIMULATE_CODONS_JUMPS__
#define ___SIMULATE_CODONS_JUMPS__
#include "simulateJumpsAbstract.h"
#include "codon.h"
using namespace std;
/******************************************************************
This class implements simulateJumpsAbstract for small alphabets: (tested so far up to 3)
*******************************************************************/
class simulateCodonsJumps:public simulateJumpsAbstract {
public:
simulateCodonsJumps(const tree& inTree, const stochasticProcess& sp, const int alphabetSize);
virtual ~simulateCodonsJumps();
//for a branch length specified by a nodeName:
//give the expected number of jumps (changes) from fromId to toId that occured along the specified branh length,
//in which the starting character is terminalStart and the terminal character is terminalEnd
MDOUBLE getExpectation(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId);
MDOUBLE getExpectation(const string& nodeName, int terminalStart, int terminalEnd, codonUtility::replacementType substitutionType);
//same as above, except here we return the probability of a jump from fromId to toId given
//terminal states terminalStart, terminalEnd in this branch
MDOUBLE getProb(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId);
MDOUBLE getProb(const string& nodeName, int terminalStart, int terminalEnd, codonUtility::replacementType substitutionType);
private:
void init();
void runOneIter(int state);
void computeExpectationsAndPosterior();
private:
//_node2Jumps: maps a node name (which specify a branch length) to
//the expected number of synonymous and nonsynonymous jumps between any two characters along the branch leading from the father to this node
//given the terminal characters of this branch.
//We use a "combined alphabet" to make access easier. see getCombinedState() for details
//The dimension of the vector is the combined terminal state and the pair elements are: synonymous and non-synonymous jumps, respectively.
map<string, vector<pair<MDOUBLE,MDOUBLE> > > _nodes2JumpsExp;
//_node2JumpsProb: maps a node name (which specify a branch length) to
//the probability of a synonymous and non-synonymous jump between any two characters along the branch leading from the father to this node
//given the terminal characters of this branch.
//We use a "combined alphabet" to make access easier. see getCombinedState() for details
//The dimension of the vector is the combined terminal state and the pair elements are: synonymous and non-synonymous jumps, respectively
map<string, vector<pair<MDOUBLE,MDOUBLE> > > _nodes2JumpsProb;
};
#endif
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