CodonSiteTools.h

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//
// File CodonSiteTools.h
// Author : Sylvain Glémin
// Last modification : November 2005
//

/*
Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)

This software is a computer program whose purpose is to provide classes
for sequences 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 _CODONSITETOOLS_H_
#define _CODONSITETOOLS_H_

#include "SymbolListTools.h"
#include "Site.h"
#include "Alphabet/CodonAlphabet.h"
#include "GeneticCode/GeneticCode.h"

#include <Bpp/Exceptions.h>

// From the STL:
#include <map>

namespace bpp
{

class CodonSiteTools:
  public SymbolListTools
{
  public:
    CodonSiteTools() {}
    virtual ~CodonSiteTools() {}

  public:

    static bool hasGapOrStop(const Site& site, const GeneticCode& gCode) throw (AlphabetException);

    static bool hasStop(const Site& site, const GeneticCode& gCode) throw (AlphabetException);

    static bool isMonoSitePolymorphic(const Site& site) throw (AlphabetException, EmptySiteException);

    static bool isSynonymousPolymorphic(const Site& site, const GeneticCode& gCode)
        throw (AlphabetException, AlphabetMismatchException, EmptySiteException);

    static Site* generateCodonSiteWithoutRareVariant(const Site& site, const GeneticCode& gCode, double freqmin)
        throw(AlphabetException, EmptySiteException);


    static size_t numberOfDifferences(int i, int j, const CodonAlphabet& ca);

    static double numberOfSynonymousDifferences(int i, int j, const GeneticCode& gCode, bool minchange=false);

    static double piSynonymous(const Site& site, const GeneticCode& gCode, bool minchange = false)
        throw (AlphabetException, AlphabetMismatchException, EmptySiteException);

    static double piNonSynonymous(const Site& site, const GeneticCode& gCode, bool minchange = false)
        throw (AlphabetException, AlphabetMismatchException, EmptySiteException);


    static double numberOfSynonymousPositions(int i, const GeneticCode& gCode,  double ratio = 1.0) throw (Exception);

    static double meanNumberOfSynonymousPositions(const Site& site, const GeneticCode& gCode, double ratio = 1)
        throw (AlphabetException, AlphabetMismatchException, EmptySiteException);

    static size_t numberOfSubsitutions(const Site& site, const GeneticCode& gCode, double freqmin = 0.)
        throw(AlphabetException, EmptySiteException);

    static size_t numberOfNonSynonymousSubstitutions(const Site& site, const GeneticCode& gCode, double freqmin = 0.)
        throw (AlphabetException, AlphabetMismatchException, EmptySiteException);

    static std::vector<size_t> fixedDifferences(const Site& siteIn, const Site& siteOut, int i, int j, const GeneticCode& gCode)
        throw (AlphabetException, AlphabetMismatchException, EmptySiteException);
    
    static bool isFourFoldDegenerated(const Site& site, const GeneticCode& gCode);

};

} //end of namespace bpp.

#endif  //_CONDONSITETOOLS_H_