SiteContainerTools.h

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//
// File: SiteContainerTools.h
// Created by: Julien Dutheil
// Created on: Fri Dec 12 18:55:06 2003
//

#ifndef _SITECONTAINERTOOLS_H_
#define _SITECONTAINERTOOLS_H_

/*
  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.
*/

#include "SiteContainer.h"
#include "VectorSiteContainer.h"
#include "AlignedSequenceContainer.h"
#include "../AlphabetIndex/AlphabetIndex2.h"
#include "../DistanceMatrix.h"
#include "../GeneticCode/GeneticCode.h"
#include <Bpp/Numeric/Matrix/Matrix.h>

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

namespace bpp
{

  typedef std::vector<size_t> SiteSelection;

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

  public:

    static SiteContainer* getSitesWithoutGaps(const SiteContainer& sites);

    static SiteContainer* getCompleteSites(const SiteContainer& sites);

    static SiteContainer* removeGapOnlySites(const SiteContainer& sites);

    static void removeGapOnlySites(SiteContainer& sites);

    static SiteContainer* removeGapOrUnresolvedOnlySites(const SiteContainer& sites);
    
    static void removeGapOrUnresolvedOnlySites(SiteContainer& sites);

    static SiteContainer* removeGapSites(const SiteContainer& sites, double maxFreqGaps);

    static void removeGapSites(SiteContainer& sites, double maxFreqGaps);

    static SiteContainer* removeStopCodonSites(const SiteContainer& sites, const GeneticCode& gCode) throw (AlphabetException);

    static SiteContainer* getSelectedSites(const SiteContainer& sequences, const SiteSelection& selection);

    static SiteContainer* getSelectedPositions(const SiteContainer& sequences, const SiteSelection& selection);

    static Sequence* getConsensus(const SiteContainer& sc, const std::string& name = "consensus", bool ignoreGap = true, bool resolveUnknown = false);
    
    static void changeGapsToUnknownCharacters(SiteContainer& sites);

    static void changeUnresolvedCharactersToGaps(SiteContainer& sites);

    static SiteContainer* resolveDottedAlignment(const SiteContainer& dottedAln, const Alphabet* resolvedAlphabet) throw (AlphabetException, Exception);

    static std::map<size_t, size_t> getSequencePositions(const Sequence& seq);

    static std::map<size_t, size_t> getAlignmentPositions(const Sequence& seq);

    static void getSequencePositions(const SiteContainer& sites, Matrix<size_t>& positions);
    static std::map<size_t, size_t> translateAlignment(const Sequence& seq1, const Sequence& seq2) throw (AlphabetMismatchException, Exception);

    static std::map<size_t, size_t> translateSequence(const SiteContainer& sequences, size_t i1, size_t i2);

    static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double gap) throw (AlphabetMismatchException);

    static AlignedSequenceContainer* alignNW(const Sequence& seq1, const Sequence& seq2, const AlphabetIndex2& s, double opening, double extending) throw (AlphabetMismatchException);

    static VectorSiteContainer* sampleSites(const SiteContainer& sites, size_t nbSites, std::vector<size_t>* index = 0);

    static VectorSiteContainer* bootstrapSites(const SiteContainer& sites);

    static double computeSimilarity(const Sequence& seq1, const Sequence& seq2, bool dist = false, const std::string& gapOption = SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap = true) throw (SequenceNotAlignedException, AlphabetMismatchException, Exception);

    static DistanceMatrix* computeSimilarityMatrix(const SiteContainer& sites, bool dist = false, const std::string& gapOption = SIMILARITY_NOFULLGAP, bool unresolvedAsGap = true);

    static const std::string SIMILARITY_ALL;
    static const std::string SIMILARITY_NOFULLGAP;
    static const std::string SIMILARITY_NODOUBLEGAP;
    static const std::string SIMILARITY_NOGAP;

    static void merge(SiteContainer& seqCont1, const SiteContainer& seqCont2, bool leavePositionAsIs = false) throw (AlphabetMismatchException, Exception);

    static std::vector<int> getColumnScores(const Matrix<size_t>& positions1, const Matrix<size_t>& positions2, int na = 0);
   
    static std::vector<double> getSumOfPairsScores(const Matrix<size_t>& positions1, const Matrix<size_t>& positions2, double na = 0);
  };

} //end of namespace bpp.

#endif  //_SITECONTAINERTOOLS_H_