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196 lines
12 KiB
C++
196 lines
12 KiB
C++
// $Id: distanceBasedSeqs2Tree.h 5989 2009-03-19 09:27:26Z privmane $
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#ifndef ___DISTANCE_BASED_SEQS2TREE
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#define ___DISTANCE_BASED_SEQS2TREE
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#include "distanceMethod.h"
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#include "sequenceContainer.h"
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#include "stochasticProcess.h"
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#include "likeDist.h"
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#include "distances2Tree.h"
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#include "givenRatesMLDistance.h"
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#include "posteriorDistance.h"
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#include "float.h"
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// NOTE: These modules take sequenceContainer as argument, and do not
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// manipulate it. If you want to take care of gaps do it yourself!
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class distanceBasedSeqs2Tree {
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public:
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distanceBasedSeqs2Tree(distanceMethod &distM, distances2Tree &dist2et, const Vdouble *weights = NULL)
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: _distM(distM.clone()), _dist2et(dist2et.clone()), _weights(weights), _treeLogLikelihood(VERYBIG) {}
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virtual ~distanceBasedSeqs2Tree() {delete (_distM);delete (_dist2et);}
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virtual tree seqs2Tree(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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// Does one bootstrap iteration
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virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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virtual MDOUBLE getLogLikelihood() {return _treeLogLikelihood;}
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protected:
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distanceMethod *_distM;
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distances2Tree *_dist2et;
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const Vdouble * _weights;
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MDOUBLE _treeLogLikelihood;
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const tree* _constraintTreePtr;
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};
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class iterativeDistanceSeqs2Tree : public distanceBasedSeqs2Tree {
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public:
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iterativeDistanceSeqs2Tree(likeDist &distM, distances2Tree &dist2et, const Vdouble *weights = NULL,
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const MDOUBLE epsilonLikelihoodImprovement = 0.001,
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const MDOUBLE epsilonLikelihoodImprovement4alphaOptimiz = 0.001,
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const MDOUBLE epsilonLikelihoodImprovement4BBL = 0.001,
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const int maxIterationsBBL = 10);
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virtual ~iterativeDistanceSeqs2Tree() {}
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virtual tree seqs2Tree(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL) = 0; // iterative
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virtual tree seqs2TreeIterative(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL) = 0;
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// Start from optimization of branch length and side info for a given initial topology
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virtual tree seqs2TreeIterative(const sequenceContainer &sc, const tree &initTree, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL) = 0;
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// Start from calculating side info for a given tree and alpha
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virtual tree seqs2TreeIterative(const sequenceContainer &sc, const tree &initTree, MDOUBLE initAlpha, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL) = 0;
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// Does one bootstrap iteration
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virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL);
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tree getTree() {return _et;}
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// *** handling side info ***
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// Optimize nj tree (optimize alpha, branch lengths, etc.) and produce
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// side info based on the optimized tree
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virtual MDOUBLE optimizeSideInfo(const sequenceContainer &sc, tree &et) = 0;
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// Calculate side info without changing the given tree and alpha
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// (Optimization should be done in here for side info that includes other optimizable parameters
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// e.g. ML rates, Nu...)
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virtual MDOUBLE calcSideInfoGivenTreeAndAlpha(const sequenceContainer &sc, const tree &et, MDOUBLE alpha) = 0;
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// Copy new side info (based on the new tree) to the "current" side info variable, before the next iteration
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virtual void acceptSideInfo() = 0;
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// Apply the optimized side info into _optimizedSp
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virtual void utilizeSideInfo() = 0;
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virtual void printSideInfo(ostream& out) const = 0;
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MDOUBLE getAlpha() const { return _alpha; }
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protected:
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tree seqs2TreeIterativeInternal(const sequenceContainer &sc, bool initSideInfoGiven=false);
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tree seqs2TreeIterativeInternalInitTreeGiven(const sequenceContainer &sc, const tree &initTree);
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tree seqs2TreeIterativeInternalInitTreeGiven(const sequenceContainer &sc, bool initSideInfoGiven, const tree &initTree, MDOUBLE initAlpha);
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void seqs2TreeOneIterationInternal(const sequenceContainer &sc, const bool sideInfoSet);
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MDOUBLE _newTreeLogLikelihood;
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MDOUBLE _epsilonLikelihoodImprovement;
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MDOUBLE _epsilonLikelihoodImprovement4alphaOptimiz;
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MDOUBLE _epsilonLikelihoodImprovement4BBL;
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int _maxIterationsBBL;
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MDOUBLE _alpha;
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MDOUBLE _newAlpha;
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stochasticProcess *_spPtr;
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tree _et, _newTree;
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};
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class commonAlphaDistanceSeqs2Tree : public iterativeDistanceSeqs2Tree {
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public:
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// Given likeDist is assumed to hold a gamma-distribution stochasticProcess
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commonAlphaDistanceSeqs2Tree(likeDist &distM, distances2Tree &dist2et, const Vdouble *weights = NULL,
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const MDOUBLE epsilonLikelihoodImprovement = 0.001,
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const MDOUBLE epsilonLikelihoodImprovement4alphaOptimiz = 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, epsilonLikelihoodImprovement4alphaOptimiz, epsilonLikelihoodImprovement4BBL, maxIterationsBBL) {}
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virtual ~commonAlphaDistanceSeqs2Tree() {}
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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, 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, 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, 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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// 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);
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MDOUBLE getSideInfo() const;
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};
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class rate4siteDistanceSeqs2Tree : public iterativeDistanceSeqs2Tree {
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public:
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rate4siteDistanceSeqs2Tree(givenRatesMLDistance &distM, distances2Tree &dist2et, const Vdouble *weights = NULL,
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const MDOUBLE epsilonLikelihoodImprovement = 0.001,
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const MDOUBLE epsilonLikelihoodImprovement4alphaOptimiz = 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, epsilonLikelihoodImprovement4alphaOptimiz, epsilonLikelihoodImprovement4BBL, maxIterationsBBL) {}
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virtual ~rate4siteDistanceSeqs2Tree() {}
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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, const Vdouble &rates, 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 Vdouble &rates, 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, const Vdouble &initRates, 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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// 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 Vdouble &rates);
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const Vdouble& getSideInfo() const;
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private:
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Vdouble _rates;
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Vdouble _newRates;
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};
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class posteriorDistanceSeqs2Tree : public iterativeDistanceSeqs2Tree {
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public:
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posteriorDistanceSeqs2Tree(posteriorDistance &distM, distances2Tree &dist2et, const Vdouble *weights = NULL,
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const MDOUBLE epsilonLikelihoodImprovement = 0.001,
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const MDOUBLE epsilonLikelihoodImprovement4alphaOptimiz = 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, epsilonLikelihoodImprovement4alphaOptimiz, epsilonLikelihoodImprovement4BBL, maxIterationsBBL) {}
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virtual ~posteriorDistanceSeqs2Tree() {}
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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, const VVdoubleRep &posterior, 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 VVdoubleRep &posterior, const Vdouble *weights=NULL, 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, const VVdoubleRep &initPosterior, 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, const VVdoubleRep &initPosterior, 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 VVdoubleRep &posterior);
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const VVdoubleRep& getSideInfo() const;
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private:
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VVdoubleRep _posterior;
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VVdoubleRep _newPosterior;
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};
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#endif
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