PolymorphismSequenceContainer.h

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//
// File: PolymorphismSequenceContainer.h
// Authors: Eric Bazin
//          Sylvain Gaillard
// Created on: Wednesday August 04 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 _POLYMORPHISMSEQUENCECONTAINER_H_
#define _POLYMORPHISMSEQUENCECONTAINER_H_

#include <set>
#include <string>

#include <Bpp/Clonable.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Text/TextTools.h>

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

namespace bpp
{
class PolymorphismSequenceContainer :
  public VectorSiteContainer
{
private:
  std::vector<bool> ingroup_;
  std::vector<unsigned int> count_;
  std::vector<size_t> group_;

public:
  // Constructors and destructor
  PolymorphismSequenceContainer(const Alphabet* alpha);

  PolymorphismSequenceContainer(size_t size, const Alphabet* alpha);

  PolymorphismSequenceContainer(const OrderedSequenceContainer& sc);

  PolymorphismSequenceContainer(const SiteContainer& sc);

  PolymorphismSequenceContainer(const PolymorphismSequenceContainer& psc);

  PolymorphismSequenceContainer& operator=(const PolymorphismSequenceContainer& psc);

  virtual ~PolymorphismSequenceContainer();

  PolymorphismSequenceContainer* clone() const
  {
    return new PolymorphismSequenceContainer(*this);
  }

public:
  // Other methods
  Sequence* removeSequence(size_t index) throw (IndexOutOfBoundsException);

  Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);

  void deleteSequence(size_t index) throw (IndexOutOfBoundsException);

  void deleteSequence(const std::string& name) throw (SequenceNotFoundException);

  void addSequenceWithFrequency(const Sequence& sequence, unsigned int frequency, bool checkName = true) throw (Exception);
  void addSequenceWithFrequency(const Sequence& sequence, size_t sequenceIndex, unsigned int frequency, bool checkName = true) throw (Exception);
  void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception) {
    addSequenceWithFrequency(sequence, 1, checkName);
  }
  void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception) {
    addSequenceWithFrequency(sequence, sequenceIndex, 1, checkName);
  }

  void clear();

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

  size_t getGroupId(const std::string& name) const throw (SequenceNotFoundException);

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

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

  void setGroupId(const std::string& name, size_t group_id) throw (SequenceNotFoundException);

  size_t getNumberOfGroups() const;

  bool isIngroupMember(size_t index) const throw (IndexOutOfBoundsException);

  bool isIngroupMember(const std::string& name) const throw (SequenceNotFoundException);

  void setAsIngroupMember(size_t index) throw (IndexOutOfBoundsException);

  void setAsIngroupMember(const std::string& name) throw (SequenceNotFoundException);

  void setAsOutgroupMember(size_t index) throw (IndexOutOfBoundsException);

  void setAsOutgroupMember(const std::string& name) throw (SequenceNotFoundException);

  void setSequenceCount(size_t index, unsigned int count) throw (Exception);

  void setSequenceCount(const std::string& name, unsigned int count) throw (Exception);

  void incrementSequenceCount(size_t index) throw (IndexOutOfBoundsException);

  void incrementSequenceCount(const std::string& name) throw (SequenceNotFoundException);

  void decrementSequenceCount(size_t index) throw(IndexOutOfBoundsException, BadIntegerException);

  void decrementSequenceCount(const std::string& name) throw (SequenceNotFoundException, BadIntegerException);

  unsigned int getSequenceCount(size_t index) const throw (IndexOutOfBoundsException);

  unsigned int getSequenceCount(const std::string& name) const throw (SequenceNotFoundException);
};
} // end of namespace bpp;

#endif  // _POLYMORPHISMSEQUENCECONTAINER_H_