#ifndef ___SIMULATE_RATESHIFT_JUMPS__
#define ___SIMULATE_RATESHIFT_JUMPS__

#include "simulateJumpsAbstract.h"
#include "mulAlphabet.h"
using namespace std;

/******************************************************************
This class implements simulateJumpsAbstract for multiplied alphabet used for rate-shift
*******************************************************************/

class simulateRateShiftJumps:public simulateJumpsAbstract  {
public:
	simulateRateShiftJumps(const tree& inTree, const stochasticProcess& sp, const int alphabetSize);
	virtual ~simulateRateShiftJumps();
	void runSimulation(int iterNum, vector <tree::nodeP> inputNodes);
	//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, mulAlphabet::rateShiftType my_rateShiftType);
	//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, mulAlphabet::rateShiftType my_rateShiftType);
    	
private:
	void init();
	void init(vector <tree::nodeP> inputNodes);
	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;

	int _baseAlphabetSize;
	int _numRateCategories;

};

#endif