TreeLikelihood.h

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//
// File: TreeLikelihood.h
// Created by: Julien Dutheil
// Created on: Fri Oct 17 17:36:44 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 _TREELIKELIHOOD_H_
#define _TREELIKELIHOOD_H_

#include "../Node.h"
#include "../Tree.h"
#include "../Model/SubstitutionModel.h"
#include "TreeLikelihoodData.h"

#include <Bpp/Numeric/ParameterList.h>
#include <Bpp/Numeric/Parametrizable.h>
#include <Bpp/Numeric/Function/Functions.h>
#include <Bpp/Numeric/VectorTools.h>

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

namespace bpp
{

class TreeLikelihood:
  public virtual DerivableSecondOrder
{
  public:
    class BranchIterator
    {
      public:
        virtual ~BranchIterator() {}

      public:
        virtual int next() throw (Exception) = 0;
        virtual bool hasNext() const = 0;
    };

    class SiteIterator
    {
      public:
        virtual ~SiteIterator() {}

      public:
        virtual size_t next() throw (Exception) = 0;
        virtual bool hasNext() const = 0;
    };

    class ConstBranchModelDescription
    {
      public:
        virtual ~ConstBranchModelDescription() {}

      public:
        virtual const SubstitutionModel* getModel() const = 0;
        virtual SiteIterator* getNewSiteIterator() const = 0;
    };

    class ConstBranchModelIterator
    {
      public:
        virtual ~ConstBranchModelIterator() {}

      public:
        virtual ConstBranchModelDescription* next() throw (Exception) = 0;
        virtual bool hasNext() const = 0;
    };

    class ConstSiteModelDescription
    {
      public:
        virtual ~ConstSiteModelDescription() {}

      public:
        virtual const SubstitutionModel* getModel() const = 0;
        virtual BranchIterator* getNewBranchIterator() const = 0;
    };

    class ConstSiteModelIterator
    {
      public:
        virtual ~ConstSiteModelIterator() {}

      public:
        virtual ConstSiteModelDescription* next() throw (Exception) = 0;
        virtual bool hasNext() const = 0;
    };

  public:
    TreeLikelihood() {}
    virtual ~TreeLikelihood() {}

#ifndef NO_VIRTUAL_COV
    TreeLikelihood* clone() const = 0;
#endif

  public:

    virtual void setData(const SiteContainer& sites) = 0;
    
    virtual const SiteContainer* getData() const = 0;

    virtual void initialize() throw (Exception) = 0;

    virtual bool isInitialized() const = 0;

    virtual TreeLikelihoodData* getLikelihoodData() = 0;

    virtual const TreeLikelihoodData* getLikelihoodData() const = 0;

    virtual double getLikelihoodForASite(size_t site) const = 0;

    virtual double getLogLikelihoodForASite(size_t site) const = 0;

    virtual double getLikelihoodForASiteForAState(size_t site, int state) const = 0;

    virtual double getLogLikelihoodForASiteForAState(size_t site, int state) const = 0;

    virtual Vdouble getLikelihoodForEachSite() const = 0;

    virtual Vdouble getLogLikelihoodForEachSite() const = 0;

    virtual VVdouble getLikelihoodForEachSiteForEachState() const = 0;

    virtual VVdouble getLogLikelihoodForEachSiteForEachState() const = 0;
    
    virtual double getLikelihood() const = 0;

    virtual double getLogLikelihood() const = 0;
  
    virtual const Tree& getTree() const = 0;

    virtual size_t getNumberOfSites() const = 0;

    virtual size_t getNumberOfStates() const = 0;
    
    virtual int getAlphabetStateAsInt(size_t i) const = 0;
  
    virtual std::string getAlphabetStateAsChar(size_t i) const = 0;
 
    virtual const std::vector<int>& getAlphabetStates() const = 0;
  
    virtual const Alphabet* getAlphabet() const = 0;
   
    virtual ParameterList getBranchLengthsParameters() const = 0;
    
    virtual ParameterList getSubstitutionModelParameters() const = 0;

    virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0;

    virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0;

    virtual VVdouble getTransitionProbabilities(int nodeId, size_t siteIndex) const = 0;

    virtual ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const = 0;

    virtual ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const = 0;

    virtual size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) = 0;

    virtual const std::vector<double>& getRootFrequencies(size_t siteIndex) const = 0;
    
    virtual void enableDerivatives(bool yn) = 0;

    virtual ParameterList getDerivableParameters() const = 0;

    virtual ParameterList getNonDerivableParameters() const = 0;

};

} //end of namespace bpp.

#endif  //_TREELIKELIHOOD_H_