Individual.h

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//
// File Individual.h
// Author : Sylvain Gaillard
// Last modification : Tuesday August 03 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 _INDIVIDUAL_H_
#define _INDIVIDUAL_H_

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

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

// From SeqLib
#include <Bpp/Seq/Sequence.h>
#include <Bpp/Seq/SequenceExceptions.h>
#include <Bpp/Seq/Container/OrderedSequenceContainer.h>
#include <Bpp/Seq/Container/MapSequenceContainer.h>

// From PopGenLib
#include "Locality.h"
#include "Date.h"
#include "MultilocusGenotype.h"
#include "GeneralExceptions.h"

namespace bpp
{
class Individual
{
protected:
  std::string id_;
  unsigned short sex_;
  std::auto_ptr<Date> date_;
  std::auto_ptr< Point2D<double> > coord_;
  const Locality<double>* locality_;
  std::auto_ptr<MapSequenceContainer> sequences_;
  std::auto_ptr<MultilocusGenotype> genotype_;

public:
  // Constructors and destructor :
  Individual();

  Individual(const std::string& id);

  Individual(const std::string& id,
             const Date& date,
             const Point2D<double>& coord,
             Locality<double>* locality,
             const unsigned short sex);

  Individual(const Individual& ind);

  virtual ~Individual();

public:
  // Methods
  Individual& operator=(const Individual& ind);

  void setId(const std::string& id);

  const std::string& getId() const { return id_; }

  void setSex(const unsigned short sex);

  unsigned short getSex() const { return sex_; }

  void setDate(const Date& date);

  const Date& getDate() const throw (NullPointerException);

  bool hasDate() const;

  void setCoord(const Point2D<double>& coord);

  void setCoord(const double x, const double y);

  const Point2D<double>& getCoord() const throw (NullPointerException);

  bool hasCoord() const;

  void setX(const double x) throw (NullPointerException);

  void setY(const double y) throw (NullPointerException);

  double getX() const throw (NullPointerException);

  double getY() const throw (NullPointerException);

  void setLocality(const Locality<double>* locality);

  const Locality<double>* getLocality() const throw (NullPointerException);

  bool hasLocality() const;

  void addSequence(size_t sequence_key, const Sequence& sequence)
  throw (Exception);

  const Sequence& getSequenceByName(const std::string& sequence_name)
  const throw (Exception);

  const Sequence& getSequenceAtPosition(const size_t sequence_position)
  const throw (Exception);

  void deleteSequenceByName(const std::string& sequence_name) throw (Exception);

  void deleteSequenceAtPosition(size_t sequence_position) throw (Exception);

  bool hasSequences() const;

  bool hasSequenceAtPosition(size_t position) const;

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

  std::vector<std::string> getSequencesNames() const throw (NullPointerException);

  std::vector<size_t> getSequencesPositions() const throw (NullPointerException);

  size_t getSequencePosition(const std::string& sequence_name) const throw (Exception);

  size_t getNumberOfSequences() const;

  void setSequences(const MapSequenceContainer& msc);

  const OrderedSequenceContainer& getSequences() const throw (NullPointerException);

  void setGenotype(const MultilocusGenotype& genotype);

  void initGenotype(size_t loci_number) throw (Exception);

  const MultilocusGenotype& getGenotype() const throw (NullPointerException);

  void deleteGenotype();

  bool hasGenotype() const;

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

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

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

  const MonolocusGenotype& getMonolocusGenotype(size_t locus_position) throw (Exception);

  size_t countNonMissingLoci() const throw (NullPointerException);

  size_t countHomozygousLoci() const throw (NullPointerException);

  size_t countHeterozygousLoci() const throw (NullPointerException);
};
} // end of namespace bpp;

#endif // _INDIVIDUAL_H_