libbpp-seq-dev 2.1.0-1 / usr / include / Bpp / Seq / Container / CompressedVectorSiteContainer.h

//
// File: CompressedVectorSiteContainer.h
// Created by: Julien Dutheil
// Created on: Wed Dec  16 12:08 2009
//

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

   This software is a computer program whose purpose is to provide classes
   for sequences 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 _COMPRESSEDVECTORSITECONTAINER_H_
#define _COMPRESSEDVECTORSITECONTAINER_H_

#include "../Site.h"
#include "SiteContainer.h"
#include "AbstractSequenceContainer.h"
#include "AlignedSequenceContainer.h"
#include "OrderedSequenceContainer.h"
#include <Bpp/Numeric/VectorTools.h>

// From the STL library:
#include <string>
#include <vector>
#include <iostream>

namespace bpp
{
/**
 * @brief A low memory, yet restricted, version of the VectorSiteContainer class.
 *
 * This implementation is very similar to VectorSiteContainer, but identical sites
 * are stored only once, which significantly reduce memory usage in the case of
 * containers where the number of sites is large compared to the number of sequences.
 * site access is as fast as in the standard VectorSiteContainer class, but site
 * addition takes more time, as the new site must be first compared to the existing set.
 * A major restriction of this container is that you can't add or remove sequences.
 * The number of sequences is fixed after the first site has been added.
 *
 * @warning Since the data is compressed, the sites given as input are modified. The
 * major pratical consequence is that the 'position' attribute of sites will be lost.
 * Instead, the position will correspond to the position in the compressed container.
 * In addition, this container may lead to unexpected behavior if used with derived
 * classes of Site. Use with care then...
 *
 * @see Sequence, Site, VectorSiteContainer
 */
class CompressedVectorSiteContainer :
  public AbstractSequenceContainer,
  // This container implements the SequenceContainer interface
  // and use the AbstractSequenceContainer adapter.
  public virtual SiteContainer        // This container is a SiteContainer.
{
protected:
  std::vector<Site*> sites_; //A set of unique sites.
  std::vector<size_t> index_; //For all sites, give the actual position in the set.
  std::vector<std::string> names_;
  std::vector<Comments*> comments_; // Sequences comments.
  mutable std::vector<Sequence*> sequences_; // To store pointer toward sequences retrieved (cf. AlignedSequenceContainer).

public:
  /**
   * @brief Build a new container from a set of sites.
   *
   * @param vs A std::vector of sites.
   * @param alpha The common alphabet for all sites.
   * @throw Exception If sites differ in size or in alphabet.
   */
  CompressedVectorSiteContainer(const std::vector<const Site*>& vs, const Alphabet* alpha) throw (Exception);
  /**
   * @brief Build a new empty container with specified size.
   *
   * @param size Number of sequences in the container.
   * @param alpha The alphabet for this container.
   */
  CompressedVectorSiteContainer(size_t size, const Alphabet* alpha);
  /**
   * @brief Build a new empty container with specified sequence names.
   *
   * @param names Sequence names. This will set the number of sequences in the container.
   * @param alpha The alphabet for this container.
   */
  CompressedVectorSiteContainer(const std::vector<std::string>& names, const Alphabet* alpha);

  /**
   * @brief Build a new empty container.
   *
   * @param alpha The alphabet for this container.
   */
  CompressedVectorSiteContainer(const Alphabet* alpha);

  CompressedVectorSiteContainer(const CompressedVectorSiteContainer& vsc);
  CompressedVectorSiteContainer(const SiteContainer& sc);

  CompressedVectorSiteContainer& operator=(const CompressedVectorSiteContainer& vsc);
  CompressedVectorSiteContainer& operator=(const SiteContainer& sc);

  virtual ~CompressedVectorSiteContainer() { clear(); }

public:
  /**
   * @name The Clonable interface.
   *
   * @{
   */
  CompressedVectorSiteContainer* clone() const { return new CompressedVectorSiteContainer(*this); }
  /** @} */

  /**
   * @name The SiteContainer interface implementation:
   *
   * @{
   */
  const Site& getSite(size_t siteIndex) const throw (IndexOutOfBoundsException);
  void        setSite(size_t siteIndex, const Site& site, bool checkPosition = false) throw (Exception);
  Site*    removeSite(size_t siteIndex) throw (IndexOutOfBoundsException);
  void     deleteSite(size_t siteIndex) throw (IndexOutOfBoundsException);
  void    deleteSites(size_t siteIndex, size_t length) throw (IndexOutOfBoundsException);
  void        addSite(const Site& site,                                       bool checkPosition = false) throw (Exception);
  void        addSite(const Site& site,                         int position, bool checkPosition = false) throw (Exception)
  {
    addSite(site, checkPosition);
  }
  void        addSite(const Site& site, size_t siteIndex,               bool checkPosition = false) throw (Exception);
  void        addSite(const Site& site, size_t siteIndex, int position, bool checkPosition = false) throw (Exception)
  {
    addSite(site, siteIndex, checkPosition);
  }
  size_t getNumberOfSites() const { return index_.size(); }
  void reindexSites();
  Vint getSitePositions() const;
  /** @} */

  // Theses methods are implemented for this class:

  /**
   * @name The SequenceContainer interface.
   *
   * @{
   */
  void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);

  // Method to get a sequence object from sequence container
  const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
  const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);
  bool hasSequence(const std::string& name) const;

  // Methods to get position of a sequence in sequence container from his name
  // This method is used by delete and remove methods
  size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);

  Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::removeSequence.");
  }

  Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::removeSequence.");
  }

  void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::deleteSequence.");
  }

  void deleteSequence(const std::string& name) throw (SequenceNotFoundException, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::deleteSequence.");
  }

  size_t getNumberOfSequences() const { return names_.size(); }

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

  void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);

  void clear();

  CompressedVectorSiteContainer* createEmptyContainer() const;

  int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
  {
    if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(std::string, size_t).", elementIndex, 0, getNumberOfSites() - 1);
    return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
  }
  const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
  {
    if (elementIndex >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(std::string, size_t).", elementIndex, 0, getNumberOfSites() - 1);
    return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
  }
  int& operator()(const std::string& sequenceName, size_t elementIndex)
  {
    return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
  }
  const int& operator()(const std::string& sequenceName, size_t elementIndex) const
  {
    return (*sites_[index_[elementIndex]])[getSequencePosition(sequenceName)];
  }

  int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
  {
    if (sequenceIndex >= getNumberOfSequences()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", sequenceIndex, 0, getNumberOfSequences() - 1);
    if (elementIndex  >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", elementIndex, 0, getNumberOfSites() - 1);
    return (*sites_[index_[elementIndex]])[sequenceIndex];
  }
  const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
  {
    if (sequenceIndex >= getNumberOfSequences()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", sequenceIndex, 0, getNumberOfSequences() - 1);
    if (elementIndex  >= getNumberOfSites()) throw IndexOutOfBoundsException("VectorSiteContainer::operator(size_t, size_t).", elementIndex, 0, getNumberOfSites() - 1);
    return (*sites_[index_[elementIndex]])[sequenceIndex];
  }
  int& operator()(size_t sequenceIndex, size_t elementIndex)
  {
    return (*sites_[index_[elementIndex]])[sequenceIndex];
  }
  const int& operator()(size_t sequenceIndex, size_t elementIndex) const
  {
    return (*sites_[index_[elementIndex]])[sequenceIndex];
  }
  /** @} */

  void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::addSequence.");
  }
  
  void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::addSequence.");
  }

  void setSequence(const std::string& name, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::setSequence.");
  }

  void setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName) throw (Exception, NotImplementedException)
  {
    //Implementing this function would involve (partially) decompressing the data...
    throw NotImplementedException("CompressedVectorSiteContainer::setSequence.");
  }

protected:
  /**
   * @return The position of the site in the compressed set. If the site is not found,
   * this will return the number of sites in the compressed set.
   */
  size_t getSiteIndex_(const Site& site);
};

} // end of namespace bpp.

#endif  // _COMPRESSEDVECTORSITECONTAINER_H_