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52 lines
2.6 KiB
C++
52 lines
2.6 KiB
C++
#ifndef ___SIMULATE_CODONS_JUMPS__
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#define ___SIMULATE_CODONS_JUMPS__
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#include "simulateJumpsAbstract.h"
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#include "codon.h"
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using namespace std;
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/******************************************************************
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This class implements simulateJumpsAbstract for small alphabets: (tested so far up to 3)
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*******************************************************************/
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class simulateCodonsJumps:public simulateJumpsAbstract {
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public:
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simulateCodonsJumps(const tree& inTree, const stochasticProcess& sp, const int alphabetSize);
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virtual ~simulateCodonsJumps();
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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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MDOUBLE getExpectation(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId);
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MDOUBLE getExpectation(const string& nodeName, int terminalStart, int terminalEnd, codonUtility::replacementType substitutionType);
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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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MDOUBLE getProb(const string& nodeName, int terminalStart, int terminalEnd, int fromId, int toId);
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MDOUBLE getProb(const string& nodeName, int terminalStart, int terminalEnd, codonUtility::replacementType substitutionType);
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private:
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void init();
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void runOneIter(int state);
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void computeExpectationsAndPosterior();
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private:
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//_node2Jumps: maps a node name (which specify a branch length) to
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//the expected number of synonymous and nonsynonymous jumps between any two characters along the branch leading from the father to this node
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//given the terminal characters of this branch.
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//We use a "combined alphabet" to make access easier. see getCombinedState() for details
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//The dimension of the vector is the combined terminal state and the pair elements are: synonymous and non-synonymous jumps, respectively.
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map<string, vector<pair<MDOUBLE,MDOUBLE> > > _nodes2JumpsExp;
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//_node2JumpsProb: maps a node name (which specify a branch length) to
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//the probability of a synonymous and non-synonymous jump between any two characters along the branch leading from the father to this node
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//given the terminal characters of this branch.
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//We use a "combined alphabet" to make access easier. see getCombinedState() for details
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//The dimension of the vector is the combined terminal state and the pair elements are: synonymous and non-synonymous jumps, respectively
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map<string, vector<pair<MDOUBLE,MDOUBLE> > > _nodes2JumpsProb;
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};
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#endif
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