SiteTools.h

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//
// File SiteTools.h
// Author: Julien Dutheil
//         Guillaume Deuchst
// Last modification : Friday August 8 2003
//

/*
   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 _SITETOOLS_H_
#define _SITETOOLS_H_

#include "SymbolListTools.h"
#include "Site.h"
#include <Bpp/Exceptions.h>

// From the STL:
#include <map>

namespace bpp
{
class SiteTools :
  public SymbolListTools
{
public:
  SiteTools() {}
  virtual ~SiteTools() {}

public:
  static bool hasGap(const Site& site);

  static bool isGapOnly(const Site& site);

  static bool isGapOrUnresolvedOnly(const Site& site);

  static bool hasUnknown(const Site& site);

  static bool isComplete(const Site& site);

  static bool isConstant(const Site& site, bool ignoreUnknown = false, bool unresolvedRaisesException = true) throw (EmptySiteException);

  static bool areSitesIdentical(const Site& site1, const Site& site2);

  static double variabilityShannon(const Site& site, bool resolveUnknowns) throw (EmptySiteException);

  static double variabilityFactorial(const Site& site) throw (EmptySiteException);

  static double mutualInformation(const Site& site1, const Site& site2, bool resolveUnknowns) throw (DimensionException,EmptySiteException);

  static double entropy(const Site& site, bool resolveUnknowns) throw (EmptySiteException) {
    return variabilityShannon(site, resolveUnknowns); 
  }


  static double jointEntropy(const Site& site1, const Site& site2, bool resolveUnknowns) throw (DimensionException,EmptySiteException);

  static double heterozygosity(const Site& site) throw (EmptySiteException);

  static size_t getNumberOfDistinctCharacters(const Site& site) throw (EmptySiteException);

  static bool hasSingleton(const Site& site) throw (EmptySiteException);

  static bool isParsimonyInformativeSite(const Site& site) throw (EmptySiteException);


  static bool isTriplet(const Site& site) throw (EmptySiteException);
};
} // end of namespace bpp.

#endif  // _SITETOOLS_H_