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64 lines
3.5 KiB
C++
64 lines
3.5 KiB
C++
// $Id: ssrvDistanceSeqs2Tree.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___SSRV_DISTANCE_SEQS2TREE
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#define ___SSRV_DISTANCE_SEQS2TREE
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#include "distanceBasedSeqs2Tree.h"
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#include "tree.h"
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/* class ssrvDistanceSeqs2Tree
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A type of distance-based tree reconstruction method like the iterative
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method commonAlphaDistanceSeqs2Tree, but using a model with SSRV
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(Site-Specific Rate Variation, AKA covarion model). Compared to
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commonAlphaDistanceSeqs2Tree, we change the distance method to use an
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SSRV model, and in the optimizations we estimate ni in addition to
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alpha.
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*/
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class ssrvDistanceSeqs2Tree : public iterativeDistanceSeqs2Tree {
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public:
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// Given likeDist is assumed to hold a gamma-distribution, SSRV stochasticProcess
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ssrvDistanceSeqs2Tree(likeDist &distM, distances2Tree &dist2et, const Vdouble *weights = NULL,
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const MDOUBLE epsilonLikelihoodImprovement = 0.001,
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const MDOUBLE epsilonLikelihoodImprovement4paramOptimiz = 0.001,
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const MDOUBLE epsilonLikelihoodImprovement4BBL = 0.001,
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const int maxIterationsBBL = 50)
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: iterativeDistanceSeqs2Tree(distM, dist2et, weights, epsilonLikelihoodImprovement, epsilonLikelihoodImprovement4paramOptimiz, epsilonLikelihoodImprovement4BBL, maxIterationsBBL) {}
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virtual ~ssrvDistanceSeqs2Tree () {}
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// Datastruct for handling side info for the SSRV model (used as return value)
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struct alphaAndNu {
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MDOUBLE alpha;
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MDOUBLE nu;
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alphaAndNu(){}
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alphaAndNu(MDOUBLE setAlpha, MDOUBLE setNu) : alpha(setAlpha), nu(setNu) {}
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};
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// NOTE! This version calls ITERATIVE seqs2Tree because side info is not given by the user, so we have to generate and optimize it
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virtual tree seqs2Tree(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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// NOTE! This version is a NON-ITERATIVE version that uses the side info supplied by the user
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tree seqs2Tree(const sequenceContainer &sc, MDOUBLE alpha, MDOUBLE nu, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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// Does one bootstrap iteration
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tree seqs2TreeBootstrap(const sequenceContainer &sc, const MDOUBLE alpha, MDOUBLE nu, const Vdouble *weights, const tree* constraintTreePtr=NULL);
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// Explicitly ask for iterations
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virtual tree seqs2TreeIterative(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); // homogenous rates will be used for first iteration
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tree seqs2TreeIterative(const sequenceContainer &sc, MDOUBLE initAlpha, MDOUBLE initNu, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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virtual tree seqs2TreeIterative(const sequenceContainer &sc, const tree &initTree, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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virtual tree seqs2TreeIterative(const sequenceContainer &sc, const tree &initTree, MDOUBLE initAlpha, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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tree seqs2TreeIterative(const sequenceContainer &sc, const tree &initTree, MDOUBLE initAlpha, MDOUBLE initNu, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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// handling side info
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virtual MDOUBLE optimizeSideInfo(const sequenceContainer &sc, tree &et);
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virtual MDOUBLE calcSideInfoGivenTreeAndAlpha(const sequenceContainer &sc, const tree &et, MDOUBLE alpha);
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virtual void acceptSideInfo();
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virtual void utilizeSideInfo();
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virtual void printSideInfo(ostream& out) const;
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void setSideInfo(const MDOUBLE alpha, MDOUBLE nu);
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alphaAndNu getSideInfo() const;
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protected:
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MDOUBLE _nu;
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MDOUBLE _newNu;
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};
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#endif
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