PhylogeneticsApplicationTools.h

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//
// File: PhylogeneticsApplicationTools.h
// Created by: Julien Dutheil
// Created on: Fri Oct 21 16:49 2005
// from old file ApplicationTools.h created on Sun Dec 14 09:36:26 2003
//

/*
  Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

  This software is a computer program whose purpose is to provide classes
  for phylogenetic data analysis.

  This software is governed by the CeCILL  license under French law and
  abiding by the rules of distribution of free software.  You can  use, 
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info". 

  As a counterpart to the access to the source code and  rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty  and the software's author,  the holder of the
  economic rights,  and the successive licensors  have only  limited
  liability. 

  In this respect, the user's attention is drawn to the risks associated
  with loading,  using,  modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean  that it is complicated to manipulate,  and  that  also
  therefore means  that it is reserved for developers  and  experienced
  professionals having in-depth computer knowledge. Users are therefore
  encouraged to load and test the software's suitability as regards their
  requirements in conditions enabling the security of their systems and/or 
  data to be ensured and,  more generally, to use and operate it in the 
  same conditions as regards security. 

  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL license and that you accept its terms.
*/

#ifndef _PHYLOGENETICSAPPLICATIONTOOLS_H_
#define _PHYLOGENETICSAPPLICATIONTOOLS_H_

#include "../Tree.h"
#include "../Model/SubstitutionModel.h"
#include "../Model/SubstitutionModelSet.h"
#include "../Model/MixedSubstitutionModelSet.h"
#include "../Model/MarkovModulatedSubstitutionModel.h"
#include "../Likelihood/HomogeneousTreeLikelihood.h"
#include "../Likelihood/ClockTreeLikelihood.h"
#include "../Mapping/SubstitutionCount.h"
#include <Bpp/Text/TextTools.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Io/OutputStream.h>
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/Prob/MultipleDiscreteDistribution.h>
#include <Bpp/Numeric/Function/Optimizer.h>

// From SeqLib:
#include <Bpp/Seq/Container/SiteContainer.h>
#include <Bpp/Seq/Container/VectorSiteContainer.h>

// From the STL:
#include <string>
#include <map>

namespace bpp
{


  class PhylogeneticsApplicationTools
  {
  
  public:
    PhylogeneticsApplicationTools();
    virtual ~PhylogeneticsApplicationTools();
  

    static Tree* getTree(
        std::map<std::string, std::string>& params,
        const std::string& prefix = "input.",
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1) throw (Exception);
 
    static std::vector<Tree*> getTrees(
        std::map<std::string, std::string>& params,
        const std::string& prefix = "input.",
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1) throw (Exception);
  
    static SubstitutionModel* getSubstitutionModel(
        const Alphabet* alphabet,
        const GeneticCode* gCode,
        const SiteContainer* data, 
        std::map<std::string, std::string>& params,
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1) throw (Exception);
  

    static void setSubstitutionModelParametersInitialValuesWithAliases(
                                                                       SubstitutionModel& model,
                                                                       std::map<std::string, std::string>& unparsedParameterValues,
                                                                       size_t modelNumber,
                                                                       const SiteContainer* data,
                                                                       std::map<std::string, double>& existingParams,
                                                                       std::map<std::string, std::string>& sharedParams,
                                                                       bool verbose) throw (Exception);

    static FrequenciesSet* getRootFrequenciesSet(
        const Alphabet* alphabet,
        const GeneticCode* gCode,
        const SiteContainer* data, 
        std::map<std::string, std::string>& params,
        const std::vector<double>& rateFreqs,
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1) throw (Exception);

    static FrequenciesSet* getFrequenciesSet(
        const Alphabet* alphabet,
        const GeneticCode* gCode,
        const std::string& freqDescription,
        const SiteContainer* data, 
        const std::vector<double>& rateFreqs,
        bool verbose = true,
        int warn = 1)
      throw (Exception);

     static SubstitutionModelSet* getSubstitutionModelSet(
         const Alphabet* alphabet,
         const GeneticCode* gcode,
         const SiteContainer* data, 
         std::map<std::string, std::string>& params,
         const std::string& suffix = "",
         bool suffixIsOptional = true,
         bool verbose = true,
         int warn = 1);    

    static void setSubstitutionModelSet(
        SubstitutionModelSet& modelSet,
        const Alphabet* alphabet,
        const GeneticCode* gcode,
        const SiteContainer* data, 
        std::map<std::string, std::string>& params,
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1);
    
    static void completeMixedSubstitutionModelSet(
        MixedSubstitutionModelSet& mixedModelSet,
        const Alphabet* alphabet,
        const SiteContainer* data, 
        std::map<std::string, std::string>& params,
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1);

    static MultipleDiscreteDistribution* getMultipleDistributionDefaultInstance(
        const std::string& distDescription,
        std::map<std::string, std::string>& unparsedParameterValues,
        bool verbose = true);

    static DiscreteDistribution* getRateDistribution(
        std::map<std::string, std::string>& params,
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true)
      throw (Exception);
      
    static TreeLikelihood* optimizeParameters(
        TreeLikelihood* tl,
        const ParameterList& parameters,
        std::map<std::string, std::string>& params,
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1)
      throw (Exception);
    
    static void optimizeParameters(
        DiscreteRatesAcrossSitesClockTreeLikelihood* tl,
        const ParameterList& parameters,
        std::map<std::string, std::string>& params,
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        int warn = 1)
      throw (Exception);
    
    static void checkEstimatedParameters(const ParameterList& pl);

    static SubstitutionCount* getSubstitutionCount(
        const Alphabet* alphabet,
        const SubstitutionModel* model,
        map<string, string>& params,
        string suffix = "",
        bool verbose = true,
        int warn = 1);
   
    static void writeTree(
        const TreeTemplate<Node>& tree,
        std::map<std::string, std::string>& params,
        const std::string& prefix = "output.",
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        bool checkOnly = false,
        int warn = 1) throw (Exception);
    
    static void writeTrees(
        const std::vector<Tree*>& trees,
        std::map<std::string, std::string>& params,
        const std::string& prefix = "output.",
        const std::string& suffix = "",
        bool suffixIsOptional = true,
        bool verbose = true,
        bool checkOnly = false,
        int warn = 1) throw (Exception);


    
    static void printParameters(const SubstitutionModel* model, OutputStream& out,int warn = 1);



    static void printParameters(const SubstitutionModelSet* modelSet, OutputStream& out, int warn = 1);



    static void printParameters(const DiscreteDistribution* rDist, OutputStream& out);

  };

} //end of namespace bpp.

#endif  //_PHYLOGENETICSAPPLICATIONTOOLS_H_