VectorSequenceContainer.h

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//
// File VectorSequenceContainer.h
// Created by: Guillaume Deuchst
//             Julien Dutheil
//

/*
Copyright or © or Copr. CNRS, (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 _VECTORSEQUENCECONTAINER_H_
#define _VECTORSEQUENCECONTAINER_H_

#include "../Alphabet/Alphabet.h"
#include "../Sequence.h"
#include "AbstractSequenceContainer.h"
#include <Bpp/Exceptions.h>

// From the STL:
#include <algorithm>
#include <vector>

namespace bpp
{

class VectorSequenceContainer:
  public AbstractSequenceContainer
{
  private:

    mutable std::vector<Sequence*> sequences_;
        
  public:
    
    VectorSequenceContainer(
      const std::vector<const Sequence*>& vs, const Alphabet* alpha)
      throw (AlphabetMismatchException);
  
    VectorSequenceContainer(const Alphabet* alpha): AbstractSequenceContainer(alpha), sequences_() {}
    
    VectorSequenceContainer(const VectorSequenceContainer& vsc);
    
    VectorSequenceContainer(const OrderedSequenceContainer& osc);

    VectorSequenceContainer(const SequenceContainer& osc);

    VectorSequenceContainer& operator=(const VectorSequenceContainer& vsc);

    VectorSequenceContainer& operator=(const OrderedSequenceContainer& osc);
  
    VectorSequenceContainer& operator=(const SequenceContainer& osc);

    virtual ~VectorSequenceContainer() { clear(); }

  public:
    
    Clonable* clone() const { return new VectorSequenceContainer(*this); }
    bool hasSequence(const std::string& name) const;
  
    const Sequence& getSequence(const std::string& name) const throw (SequenceNotFoundException);

    void setSequence(const std::string& name, const Sequence& sequence, bool checkName = true) throw (Exception)
    {
      setSequence(getSequencePosition(name), sequence, checkName);
    }

    Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException)
    {
      return removeSequence(getSequencePosition(name));
    }

    void deleteSequence(const std::string& name) throw (SequenceNotFoundException)
    {
      deleteSequence(getSequencePosition(name));
    }
    
    size_t getNumberOfSequences() const { return sequences_.size(); }
    
    std::vector<std::string> getSequencesNames() const;
    void setSequencesNames(const std::vector<std::string>& names, bool checkNames = true) throw (Exception);
    void clear();
    VectorSequenceContainer * createEmptyContainer() const;
    
    int& valueAt(const std::string& sequenceName, size_t elementIndex) throw (SequenceNotFoundException, IndexOutOfBoundsException)
    {
      return getSequence_(sequenceName)[elementIndex];
    }

    const int& valueAt(const std::string& sequenceName, size_t elementIndex) const throw (SequenceNotFoundException, IndexOutOfBoundsException)
    {
      return getSequence(sequenceName)[elementIndex]; 
    }

    int& operator()(const std::string& sequenceName, size_t elementIndex)
    {
      return getSequence_(sequenceName)[elementIndex];
    }

    const int& operator()(const std::string& sequenceName, size_t elementIndex) const
    {
      return getSequence(sequenceName)[elementIndex]; 
    }
    
    int& valueAt(size_t sequenceIndex, size_t elementIndex) throw (IndexOutOfBoundsException)
    {
      return getSequence_(sequenceIndex)[elementIndex];
    }

    const int& valueAt(size_t sequenceIndex, size_t elementIndex) const throw (IndexOutOfBoundsException)
    {
      return getSequence(sequenceIndex)[elementIndex];
    }

    int& operator()(size_t sequenceIndex, size_t elementIndex)
    {
      return getSequence_(sequenceIndex)[elementIndex];
    }
    const int & operator()(size_t sequenceIndex, size_t elementIndex) const
    {
      return getSequence(sequenceIndex)[elementIndex];
    } 
    void setComments(const std::string & name, const Comments& comments) throw (SequenceNotFoundException)
    {
      AbstractSequenceContainer::setComments(name, comments);
    }

    void setComments(size_t sequenceIndex, const Comments& comments) throw (IndexOutOfBoundsException);
    size_t getSequencePosition(const std::string& name) const throw (SequenceNotFoundException);
    const Sequence& getSequence(size_t sequenceIndex) const throw (IndexOutOfBoundsException);
    void  setSequence(size_t sequenceIndex, const Sequence& sequence, bool checkName = true) throw (Exception);
    Sequence* removeSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
    void deleteSequence(size_t sequenceIndex) throw (IndexOutOfBoundsException);
    virtual void addSequence(const Sequence& sequence, bool checkName = true) throw (Exception);

    virtual void addSequence(const Sequence& sequence, size_t sequenceIndex, bool checkName = true) throw (Exception);

  protected:

    Sequence& getSequence_(size_t i) throw (IndexOutOfBoundsException);
    Sequence& getSequence_(const std::string& name) throw (SequenceNotFoundException);
};

} //end of namespace bpp.

#endif // _VECTORSEQUENCECONTAINER_H_