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120 lines
3.6 KiB
C++
120 lines
3.6 KiB
C++
// $Id: mainSemphy.h 2324 2007-08-08 13:55:45Z privmane $
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// This comment is a test for a problem with SVN commit
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#ifndef ___MAIN_SEMPHY
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#define ___MAIN_SEMPHY
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#include "aaJC.h"
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#include "alphabet.h"
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#include "amino.h"
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#include "chebyshevAccelerator.h"
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#include "clustalFormat.h"
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#include "definitions.h"
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#include "distanceMethod.h"
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#include "fastaFormat.h"
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#include "gammaDistribution.h"
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#include "hky.h"
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#include "maseFormat.h"
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#include "molphyFormat.h"
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#include "nucJC.h"
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#include "nucleotide.h"
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#include "phylipFormat.h"
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#include "readDatMatrix.h"
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#include "sequenceContainer.h"
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#include "semphy_cmdline.h"
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#include "stochasticProcess.h"
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#include "tree.h"
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#include "trivialAccelerator.h"
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#include "uniDistribution.h"
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#include "cmdline2EvolObjs.h"
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#include "distanceBasedSeqs2TreeFactory.h"
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#include <iostream>
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#include <vector>
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#include <string>
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using namespace std;
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class mainSemphy {
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public:
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explicit mainSemphy(int argc, char* argv[]);
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explicit mainSemphy(const gengetopt_args_info& gn);
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virtual ~mainSemphy();
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void compute(bool doBootstrapOneIteration=false);
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enum AlgorithmType {DO_DEFAULT = 0, DO_SEMPHY=1, DO_BBL=2, DO_LIKELIHOOD=4, DO_PERPOS_LIKELIHOOD=8, DO_NJ=16};
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tree getTree() const {return *_etPtr;}
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const stochasticProcess& getStochasticProcess() const {return *_spP;}
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MDOUBLE getLikelihood() const { return _treeLogLikelihood;}
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void setWeights(const Vdouble& weights);
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sequenceContainer getSequenceContainer() const { return _sc;}
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void setGlobalRate(MDOUBLE rate) {_spP->setGlobalRate(rate);};
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void output() const;
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ostream& out() const {return *_outPtr;}
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void setTree(const tree& inEtPtr);
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void nullifyTree();
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void semphyCorrectToCanonialForm(void);
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void initializeFromArgsInfo();
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void computeNJtree(bool doBootstrapOneIteration=false);
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void extractPosteriorProb(VVdoubleRep & posteriorProbVV) const;
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void optimizeBranchLengths();
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void computeSemphyTree();
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void optimizeAlphaOnly(); // NOTE: If an SSRV model is used this method also optimizes the Nu parameter
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void optimizeGlobalRate();
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void computeLikelihoodAndLikelihoodPerPosition();
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void computeLikelihoodAndLikelihoodPerPositionAndPosterior();
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void printLikelihoodAndLikelihoodPerPosition() const;
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void printPosterior() const;
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void printTree(const int logLvl=3) const;
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void printTreeToTreeFile() const;
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void computeTree(bool doBootstrapOneIteration=false);
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void optimizeParameters();
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void getDistanceTableAndNames(VVdouble& disTable,
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vector<string> & vNames,
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const distanceMethod* cd) const;
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void computeNJtreeFromDisTableAndNames(const VVdouble& disTable,
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const vector<string> & vNames);
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gengetopt_args_info _args_info; // the information form the command line
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cmdline2EvolObjs<gengetopt_args_info> _evolObj;
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private:
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void printSemphyTitle(ostream & out);
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void readCommandLineInformation(int argc, char* argv[]);
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void initializeRandomSeed() const;
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void initializeLogFile() const;
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void initializeAlphabet();
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void takeCareOfGaps();
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void readTreeFile();
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void readConstraintTreeFile();
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void initializeStochaticProcess();
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void initializeSequenceContainer();
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void initializeOutputStream();
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void argsConsistencyCheck() const;
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void constraintTreeConsistencyCheck() const;
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tree* _etPtr;
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tree* _constraintTreePtr;
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ostream* _outPtr;
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Vdouble* _weights;
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distanceBasedSeqs2Tree* _s2tPtr;
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int _numberOfRandomStart;
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VVdoubleRep _posterior; // per position posterior of rates
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VdoubleRep _llpp; // log likelihood per position
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MDOUBLE _treeLogLikelihood; // log likelihood of the tree
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stochasticProcess *_spP;
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sequenceContainer _sc;
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alphabet* _alphP;
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VVdoubleRep _posteriorRates;
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};
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#endif
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