/usr/include/libphylo/simulateJumps.h is in rate4site 3.0.0-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | #ifndef ___SIMULATE_JUMPS__
#define ___SIMULATE_JUMPS__
#include "simulateJumpsAbstract.h"
using namespace std;
/******************************************************************
This class implements simulateJumpsAbstract for small alphabets: (tested so far up to 3)
*******************************************************************/
class simulateJumps:public simulateJumpsAbstract {
public:
simulateJumps(const tree& inTree, const stochasticProcess& sp, const int alphabetSize);
virtual ~simulateJumps();
//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);
//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);
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 jumps between any two characters along the branch leading from the father to this node
//given the terminal characters of this branch.
//The matrix is 2D and not 4D because we use a "combined alphabet" to make access easier. see getCombinedState() for details
//The first dimension is the combined terminal state and the second dimension is the combined jump state
map<string, VVdouble> _nodes2JumpsExp;
//_node2JumpsProb: maps a node name (which specify a branch length) to
//the probability of a jump between any two characters along the branch leading from the father to this node
//given the terminal characters of this branch.
//The matrix is 2D and not 4D because we use a "combined alphabet" to make access easier. see getCombinedState() for details
//The first dimension is the combined terminal state and the second dimension is the combined jump state
map<string, VVdouble> _nodes2JumpsProb;
};
#endif
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