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78 lines
3.5 KiB
C++
78 lines
3.5 KiB
C++
#ifndef ___SIMULATE_JUMPS_ABSTRACT_
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#define ___SIMULATE_JUMPS_ABSTRACT_
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#include "definitions.h"
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#include "tree.h"
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#include "stochasticProcess.h"
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#include "alphabet.h"
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#include <map>
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#include <vector>
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using namespace std;
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/******************************************************************
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This is an abstract class to various implementations of simulateJumps.
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It was created to be a father class to the generic (original) implementation of
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simulateJumps class simulateJumps (working on alphabets of either 0,1,2 or 0,1
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and class simulateCodonsJumps which is a variant simulateJumps that can handle the
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61 sized alphabet without memory limitations.
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The simulateJumps algorithm simulates jumps (events) along differing branch lengths (according to a
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given tree), with the aim of giving the expectation of the number of jumps
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from state a to state b given that the terminal states at the end of the branch are
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x and y.
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*******************************************************************/
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class simulateJumpsAbstract {
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public:
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simulateJumpsAbstract(const tree& inTree, const stochasticProcess& sp, const int alphabetSize);
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virtual ~simulateJumpsAbstract(){}
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virtual void runSimulation(int iterNum = 10000);
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//for a branch length specified by a nodeName:
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//give the expected number of jumps (changes) from fromId to toId that occured along the specified branh length,
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//in which the starting character is terminalStart and the terminal character is terminalEnd
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virtual MDOUBLE getExpectation(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId) = 0;
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//same as above, except here we return the probability of a jump from fromId to toId given
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//terminal states terminalStart, terminalEnd in this branch
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virtual MDOUBLE getProb(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId) = 0;
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virtual int getTotalTerminal(const string& nodeName, int terminalStart, int terminalEnd){
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map<string, Vdouble>::iterator iterTerm = _totalTerminals.find(nodeName);
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return (int)iterTerm->second[getCombinedState(terminalStart,terminalEnd)];
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}
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protected:
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virtual int getCombinedState(int terminalStart, int terminalEnd) const;
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virtual int getCombinedAlphabetSize() const {return _alphabetSize*_alphabetSize;}
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virtual int getStartId(int combinedState) const;
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virtual int getEndId(int combinedState) const;
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virtual void init() = 0;
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virtual void runOneIter(int state) = 0;
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virtual void computeExpectationsAndPosterior() = 0;
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// a comparison function to be used in sort init
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static bool compareDist(tree::nodeP node1, tree::nodeP node2){ return (node1->dis2father() < node2->dis2father());}
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protected:
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tree _tree;
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stochasticProcess _sp;
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const int _alphabetSize;
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Vdouble _waitingTimeParams;//each entry is the lambda parameter of the exponential distribution modeling the waiting time for "getting out" of state i
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//_jumpProbs[i][j] is the probability of jumping from state i to state j (given that a change has ocured).
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VVdouble _jumpProbs;
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//the number of times we reached a certain combination of terminal states for each branch lengths
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//e.g. the number of times we observed 0,1 at terminal states given branch length 0.03
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//this is used to to afterwards normalize (i.e. compute the expectation) the _nodes2JumpsExp values
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map<string, Vdouble> _totalTerminals;
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vector<tree::nodeP> _orderNodesVec; //internal use: the branch are sorted in ascending order
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};
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#endif
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