mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 01:20:24 +08:00
56 lines
2.8 KiB
C++
56 lines
2.8 KiB
C++
#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
|