Group.h

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//
// File Group.h
// Author : Sylvain Gaillard
//          Khalid Belkhir
// Last modification : Thursday July 29 2004
//

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

   This software is a computer program whose purpose is to provide classes
   for population genetics 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 _GROUP_H_
#define _GROUP_H_

// From STL
#include <vector>
#include <memory>

#include <Bpp/Exceptions.h>
#include <Bpp/Graphics/Point2D.h>

// From SeqLib
#include <Bpp/Seq/Container/VectorSequenceContainer.h>
#include <Bpp/Seq/Container/VectorSiteContainer.h>
#include <Bpp/Seq/Container/SequenceContainerTools.h>

// From local
#include "Individual.h"
#include "GeneralExceptions.h"

namespace bpp
{
class Group
{
protected:
  size_t id_;
  std::string name_;
  std::vector<Individual*> individuals_;

public:
  // Constructors and destructor :
  Group(size_t group_id);

  Group(const Group& group);

  Group(const Group& group, size_t group_id);

  ~Group();

public:
  Group& operator=(const Group& group);

  void setGroupId(size_t group_id);

  const std::string& getGroupName() const { return name_; }

  void setGroupName(const std::string& group_name);

  size_t getGroupId() const { return id_; }

  void addIndividual(const Individual& ind) throw (BadIdentifierException);

  void addEmptyIndividual(const std::string& individual_id) throw (BadIdentifierException);

  size_t getNumberOfIndividuals() const;

  size_t getMaxNumberOfSequences() const;

  size_t getIndividualPosition(const std::string& individual_id) const
  throw (IndividualNotFoundException);

  const Individual& getIndividualById(const std::string& individual_id) const throw (IndividualNotFoundException);

  const Individual& getIndividualAtPosition(size_t individual_position) const
  throw (IndexOutOfBoundsException);

  std::auto_ptr<Individual> removeIndividualById(const std::string& individual_id) throw (IndividualNotFoundException);

  std::auto_ptr<Individual> removeIndividualAtPosition(size_t individual_position) throw (IndexOutOfBoundsException);

  void deleteIndividualById(const std::string& individual_id) throw (IndividualNotFoundException);

  void deleteIndividualAtPosition(size_t individual_position) throw (IndexOutOfBoundsException);

  void clear();

  // -- Dealing with Individuals -----------------------------
  void setIndividualSexAtPosition(size_t individual_position, const unsigned short sex)
  throw (IndexOutOfBoundsException);

  unsigned short getIndividualSexAtPosition(size_t individual_position) const
  throw (IndexOutOfBoundsException);

  void setIndividualDateAtPosition(size_t individual_position, const Date& date)
  throw (IndexOutOfBoundsException);

  const Date& getIndividualDateAtPosition(size_t individual_position) const
  throw (Exception);

  void setIndividualCoordAtPosition(size_t individual_position, const Point2D<double>& coord)
  throw (IndexOutOfBoundsException);

  const Point2D<double>& getIndividualCoordAtPosition(size_t individual_position) const
  throw (Exception);

  void setIndividualLocalityAtPosition(size_t individual_position, const Locality<double>* locality)
  throw (IndexOutOfBoundsException);

  const Locality<double>& getIndividualLocalityAtPosition(size_t individual_position) const
  throw (Exception);

  void addIndividualSequenceAtPosition(size_t individual_position,
                                       size_t sequence_position, const Sequence& sequence)
  throw (Exception);

  const Sequence& getIndividualSequenceByName(size_t individual_position, const std::string& sequence_name) const
  throw (Exception);

  const Sequence& getIndividualSequenceAtPosition(size_t individual_position, size_t sequence_position) const
  throw (Exception);

  void deleteIndividualSequenceByName(size_t individual_position, const std::string& sequence_name)
  throw (Exception);

  void deleteIndividualSequenceAtPosition(size_t individual_position, size_t sequence_position)
  throw (Exception);

  bool hasIndividualSequences(size_t individual_position) const throw (IndexOutOfBoundsException);

  std::vector<std::string> getIndividualSequencesNames(size_t individual_position) const throw (Exception);

  size_t getIndividualSequencePosition(size_t individual_position, const std::string& sequence_name) const
  throw (Exception);

  size_t getIndividualNumberOfSequences(size_t individual_position) const throw (Exception);

  void setIndividualSequences(size_t individual_position, const MapSequenceContainer& msc)
  throw (IndexOutOfBoundsException);

  void setIndividualGenotype(size_t individual_position, const MultilocusGenotype& genotype) throw (IndexOutOfBoundsException);

  void initIndividualGenotype(size_t individual_position, size_t loci_number)
  throw (Exception);

  void deleteIndividualGenotype(size_t individual_position) throw (IndexOutOfBoundsException);

  bool hasIndividualGenotype(size_t individual_position) const throw (IndexOutOfBoundsException);

  void setIndividualMonolocusGenotype(size_t individual_position, size_t locus_position,
                                      const MonolocusGenotype& monogen) throw (Exception);

  void setIndividualMonolocusGenotypeByAlleleKey(size_t individual_position, size_t locus_position,
                                                 const std::vector<size_t>& allele_keys) throw (Exception);

  void setIndividualMonolocusGenotypeByAlleleId(size_t individual_position, size_t locus_position,
                                                const std::vector<std::string>& allele_id, const LocusInfo& locus_info) throw (Exception);

  const MonolocusGenotype& getIndividualMonolocusGenotype(size_t individual_position,
                                                          size_t locus_position) const throw (Exception);

  bool hasSequenceData() const;

  const Alphabet* getAlphabet() const throw (NullPointerException);

  size_t getGroupSizeForLocus(size_t locus_position) const;

  size_t getGroupSizeForSequence(size_t sequence_position) const;
};
} // end of namespace bpp;

#endif // _GROUP_H_