text: // 	$Id: distanceBasedSeqs2TreeFactory.h 1941 2007-04-15 14:17:22Z privmane $	
  #include "distanceBasedSeqs2Tree.h"
  
  #include "pairwiseGammaDistance.h"
  
  #include "nj.h"
  
  //using namespace std;
  
  #ifndef __DISTANCEBASEDSEQS2TREEFACTORY_H
  #define __DISTANCEBASEDSEQS2TREEFACTORY_H
  
  typedef enum {homogeneousRatesDTME,
  			  pairwiseGammaDTME,
  			  commonAlphaDTME,
  			  rate4siteDTME,
  			  posteriorDTME
  } distanceBasedMethod_t;
  
  
  
  distanceBasedSeqs2Tree* distanceBasedSeqs2TreeFactory(const distanceBasedMethod_t distanceBasedMethod, 
  													  stochasticProcess& sp, // may change sp (alpha)
  													  const bool   useJcDistance,
  													  const bool   optimizeAlpha,
  													  const bool   useSSRV,
  													  const double epsilonLikelihoodImprovement4iterNJ = 0.01,
  													  const double epsilonLikelihoodImprovement4pairwiseDistance = 0.0001,
  													  const double epsilonLikelihoodImprovement4alphaOptimiz = 0.01,
  													  const double epsilonLikelihoodImprovement4BBL = 0.01,
  													  const int maxIterationsBBL = 10);
  
  
  #endif
  
  
  
  
  
  