DataSet.h

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//
// File DataSet.h
// Author : Sylvain Gaillard
// Last modification : April 4, 2008
//

/*
   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 _DATASET_H_
#define _DATASET_H_

// From the STL
#include <algorithm>
#include <vector>
#include <map>
#include <string>

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

// From PopGenLib (local)
#include "Group.h"
#include "Individual.h"
#include "Locality.h"
#include "GeneralExceptions.h"
#include "AnalyzedLoci.h"
#include "AnalyzedSequences.h"
#include "PolymorphismMultiGContainer.h"
#include "PolymorphismSequenceContainer.h"

namespace bpp
{
class DataSet
{
private:
  AnalyzedLoci* analyzedLoci_;
  AnalyzedSequences* analyzedSequences_;
  std::vector<Locality<double>*> localities_;
  std::vector<Group*> groups_;

public:
  // Constructor and destructor
  DataSet();

  ~DataSet();

  DataSet(const DataSet& ds);

  DataSet& operator=(const DataSet& ds);

public:
  // Methodes
// ** Locality manipulation ***************************************************/
  void addLocality(Locality<double>& locality) throw (BadIdentifierException);

  size_t getLocalityPosition(const std::string& name) const throw (LocalityNotFoundException);

  const Locality<double>& getLocalityAtPosition(size_t locality_position) const throw (IndexOutOfBoundsException);

  const Locality<double>& getLocalityByName(const std::string& name) const throw (LocalityNotFoundException);

  void deleteLocalityAtPosition(size_t locality_position) throw (IndexOutOfBoundsException);

  void deleteLocalityByName(const std::string& name) throw (LocalityNotFoundException);

  size_t getNumberOfLocalities() const;

  bool hasLocality() const;

  // ** Group manipulation ******************************************************/
  void addGroup(const Group& group) throw (BadIdentifierException);

  void addEmptyGroup(size_t group_id) throw (BadIdentifierException);

  const Group& getGroupById(size_t group_id) const throw (GroupNotFoundException);

  size_t getGroupPosition(size_t group_id) const throw (GroupNotFoundException);

  std::string getGroupName(size_t group_id) const throw (GroupNotFoundException);
  void setGroupName(size_t group_id, const std::string& group_name) const throw (GroupNotFoundException);

  const Group& getGroupAtPosition(size_t group_position) const throw (IndexOutOfBoundsException);

  void deleteGroupAtPosition(size_t group_position) throw (IndexOutOfBoundsException);

  size_t getNumberOfGroups() const;

  void mergeTwoGroups(size_t source_id, size_t target_id) throw (GroupNotFoundException);

  void mergeGroups(std::vector<size_t>& group_ids) throw (GroupNotFoundException);

  void splitGroup(size_t group_id, std::vector<size_t> individuals_selection) throw (Exception);

  // ** Individuals manipulation ************************************************/
  void addIndividualToGroup(size_t group_position, const Individual& individual) throw (Exception);

  void addEmptyIndividualToGroup(size_t group_position, const std::string& individual_id) throw (Exception);

  size_t getNumberOfIndividualsInGroup(size_t group_position) const
  throw (IndexOutOfBoundsException);

  size_t getIndividualPositionInGroup(size_t group_position, const std::string& individual_id) const
  throw (Exception);
  const Individual* getIndividualAtPositionFromGroup(size_t group_position, size_t individual_position) const
  throw (IndexOutOfBoundsException);

  const Individual* getIndividualByIdFromGroup(size_t group_position, const std::string& individual_id) const
  throw (Exception);

  void deleteIndividualAtPositionFromGroup(size_t group_position, size_t individual_position)
  throw (IndexOutOfBoundsException);

  void deleteIndividualByIdFromGroup(size_t group_position, const std::string& individual_id)
  throw (Exception);

  void setIndividualSexInGroup(size_t group_position, size_t individual_position, const unsigned short sex)
  throw (IndexOutOfBoundsException);

  unsigned short getIndividualSexInGroup(size_t group_position, size_t individual_position) const
  throw (IndexOutOfBoundsException);

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

  const Date* getIndividualDateInGroup(size_t group_position, size_t individual_position) const
  throw (Exception);

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

  const Point2D<double>* getIndividualCoordInGroup(size_t group_position, size_t individual_position) const
  throw (Exception);

  void setIndividualLocalityInGroupByName(size_t group_position, size_t individual_position, const std::string& locality_name)
  throw (Exception);

  const Locality<double>* getIndividualLocalityInGroup(size_t group_position, size_t individual_position) const
  throw (Exception);

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

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

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

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

  void deleteIndividualSequenceAtPositionInGroup(size_t group_position, size_t individual_position, size_t sequence_position)
  throw (Exception);

  std::vector<std::string> getIndividualSequencesNamesInGroup(size_t group_position, size_t individual_position) const
  throw (Exception);

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

  size_t getIndividualNumberOfSequencesInGroup(size_t group_position, size_t individual_position) const
  throw (Exception);

  void setIndividualGenotypeInGroup(size_t group_position, size_t individual_position, const MultilocusGenotype& genotype)
  throw (Exception);

  void initIndividualGenotypeInGroup(size_t group_position, size_t individual_position)
  throw (Exception);

  void deleteIndividualGenotypeInGroup(size_t group_position, size_t individual_position)
  throw (IndexOutOfBoundsException);

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

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

  void setIndividualMonolocusGenotypeByAlleleIdInGroup(size_t group_position, size_t individual_position, size_t locus_position, const std::vector<std::string> allele_id)
  throw (Exception);

  const MonolocusGenotype* getIndividualMonolocusGenotypeInGroup(size_t group_position, size_t individual_position, size_t locus_position) const
  throw (Exception);

  // ** AnalyzedSequences manipulation ******************************************/
  void setAlphabet(const Alphabet* alpha);

  void setAlphabet(const std::string& alpha_type);

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

  std::string getAlphabetType() const throw (NullPointerException);

  // ** AnalyzedLoci manipulation ***********************************************/
  void setAnalyzedLoci(const AnalyzedLoci& analyzedLoci) throw (Exception);

  void initAnalyzedLoci(size_t number_of_loci) throw (Exception);

  const AnalyzedLoci* getAnalyzedLoci() const throw (NullPointerException);

  void deleteAnalyzedLoci();

  void setLocusInfo(size_t locus_position, const LocusInfo& locus)
  throw (Exception);

  const LocusInfo& getLocusInfoByName(const std::string& locus_name) const
  throw (Exception);

  const LocusInfo& getLocusInfoAtPosition(size_t locus_position) const
  throw (Exception);

  void addAlleleInfoByLocusName(const std::string& locus_name, const AlleleInfo& allele)
  throw (Exception);

  void addAlleleInfoByLocusPosition(size_t locus_position, const AlleleInfo& allele)
  throw (Exception);

  size_t getNumberOfLoci() const throw (NullPointerException);

  size_t getPloidyByLocusName(const std::string& locus_name) const throw (Exception);

  size_t getPloidyByLocusPosition(size_t locus_position) const throw (Exception);

  // ** Container extraction ***************************************************/
  PolymorphismMultiGContainer* getPolymorphismMultiGContainer() const;

  PolymorphismMultiGContainer* getPolymorphismMultiGContainer(const std::map<size_t, std::vector<size_t> >& selection) const throw (Exception);

  PolymorphismSequenceContainer* getPolymorphismSequenceContainer(const std::map<size_t, std::vector<size_t> >& selection, size_t sequence_position) const throw (Exception);

  // ** General tests **********************************************************/
  bool hasSequenceData() const;

  bool hasAlleleicData() const;
};
} // end of namespace bpp;

#endif // _DATASET_H_