/usr/include/libphylo/simulateJumpsAbstract.h is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | #ifndef ___SIMULATE_JUMPS_ABSTRACT_
#define ___SIMULATE_JUMPS_ABSTRACT_
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "alphabet.h"
#include <map>
#include <vector>
using namespace std;
/******************************************************************
This is an abstract class to various implementations of simulateJumps.
It was created to be a father class to the generic (original) implementation of
simulateJumps class simulateJumps (working on alphabets of either 0,1,2 or 0,1
and class simulateCodonsJumps which is a variant simulateJumps that can handle the
61 sized alphabet without memory limitations.
The simulateJumps algorithm simulates jumps (events) along differing branch lengths (according to a
given tree), with the aim of giving the expectation of the number of jumps
from state a to state b given that the terminal states at the end of the branch are
x and y.
*******************************************************************/
class simulateJumpsAbstract {
public:
simulateJumpsAbstract(const tree& inTree, const stochasticProcess& sp, const int alphabetSize);
virtual ~simulateJumpsAbstract(){}
virtual void runSimulation(int iterNum = 10000);
//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
virtual MDOUBLE getExpectation(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId) = 0;
//same as above, except here we return the probability of a jump from fromId to toId given
//terminal states terminalStart, terminalEnd in this branch
virtual MDOUBLE getProb(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId) = 0;
virtual int getTotalTerminal(const string& nodeName, int terminalStart, int terminalEnd){
map<string, Vdouble>::iterator iterTerm = _totalTerminals.find(nodeName);
return (int)iterTerm->second[getCombinedState(terminalStart,terminalEnd)];
}
protected:
virtual int getCombinedState(int terminalStart, int terminalEnd) const;
virtual int getCombinedAlphabetSize() const {return _alphabetSize*_alphabetSize;}
virtual int getStartId(int combinedState) const;
virtual int getEndId(int combinedState) const;
virtual void init() = 0;
virtual void runOneIter(int state) = 0;
virtual void computeExpectationsAndPosterior() = 0;
// a comparison function to be used in sort init
static bool compareDist(tree::nodeP node1, tree::nodeP node2){ return (node1->dis2father() < node2->dis2father());}
protected:
tree _tree;
stochasticProcess _sp;
const int _alphabetSize;
Vdouble _waitingTimeParams;//each entry is the lambda parameter of the exponential distribution modeling the waiting time for "getting out" of state i
//_jumpProbs[i][j] is the probability of jumping from state i to state j (given that a change has ocured).
VVdouble _jumpProbs;
//the number of times we reached a certain combination of terminal states for each branch lengths
//e.g. the number of times we observed 0,1 at terminal states given branch length 0.03
//this is used to to afterwards normalize (i.e. compute the expectation) the _nodes2JumpsExp values
map<string, Vdouble> _totalTerminals;
vector<tree::nodeP> _orderNodesVec; //internal use: the branch are sorted in ascending order
};
#endif
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