PolymorphismMultiGContainer.h

Go to the documentation of this file.

//
// File PolymorphismMultiGContainer.h
// Author : Sylvain Gaillard
//

/*
   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 _POLYMORPHYSMMULTIGCONTAINER_H_
#define _POLYMORPHYSMMULTIGCONTAINER_H_

// From Utils
#include <Bpp/Clonable.h>
#include <Bpp/Exceptions.h>
#include <Bpp/Utils/MapTools.h>
#include <Bpp/Text/TextTools.h>

// From popgenlib
#include "MultilocusGenotype.h"
#include "GeneralExceptions.h"

// From STL
#include <string>
#include <vector>
#include <map>
#include <set>

namespace bpp
{
class PolymorphismMultiGContainer
{
private:
  std::vector<MultilocusGenotype*> multilocusGenotypes_;
  std::vector<size_t> groups_; // group id for each multilocusgenotype
  std::map<size_t, std::string> groups_names_;

public:
  // Constructors and destructor
  PolymorphismMultiGContainer();

  PolymorphismMultiGContainer(const PolymorphismMultiGContainer& pmgc);

  ~PolymorphismMultiGContainer();

public:
  PolymorphismMultiGContainer& operator=(const PolymorphismMultiGContainer& pmgc);

  void addMultilocusGenotype(const MultilocusGenotype& mg, size_t group);

  const MultilocusGenotype* getMultilocusGenotype(size_t position) const throw (IndexOutOfBoundsException);

  MultilocusGenotype* removeMultilocusGenotype(size_t position) throw (IndexOutOfBoundsException);

  void deleteMultilocusGenotype(size_t position) throw (IndexOutOfBoundsException);

  bool isAligned() const;

  size_t getNumberOfLoci() const throw (Exception);

  size_t getGroupId(size_t position) const throw (IndexOutOfBoundsException);

  void setGroupId(size_t position, size_t group_id) throw (IndexOutOfBoundsException);

  std::set<size_t> getAllGroupsIds() const;

  std::vector<std::string> getAllGroupsNames() const;

  bool groupExists(size_t group) const;

  size_t getNumberOfGroups() const;

  size_t getGroupSize(size_t group) const;

  std::string getGroupName(size_t group_id) const throw (GroupNotFoundException);

  void setGroupName(size_t group_id, std::string name)  throw (GroupNotFoundException);

  void addGroupName(size_t group_id, std::string name);

  size_t getLocusGroupSize(size_t group, size_t locus_position) const;

  size_t size() const;

  void clear();
};
} // end of namespace bpp;

#endif // _POLYMORPHYSMMULTIGCONTAINER_H_