Bpp/Seq/SequenceWithAnnotation.h

Go to the documentation of this file.

//
// File: SequenceWithAnnotation.h
// Created by: Julien Dutheil
// Created on: Mon Jul 19 2010
//

/*
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 _SEQUENCEWITHANNOTATION_H_
#define _SEQUENCEWITHANNOTATION_H_

#include "Sequence.h"

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

namespace bpp
{

class SequenceWithAnnotation;

class SequenceAnnotation :
  public virtual SymbolListListener
{
  public:
    virtual SequenceAnnotation* clone() const = 0;

    virtual void init(const Sequence& seq) = 0;

    virtual const std::string& getType() const = 0;

    virtual bool isValidWith(const SequenceWithAnnotation& sequence, bool throwException = true) const = 0;

    virtual bool merge(const SequenceAnnotation& anno) = 0;

    virtual SequenceAnnotation* getPartAnnotation(size_t pos, size_t len) const throw (Exception) = 0;
};

class SequenceWithAnnotation :
  public Sequence,
  public EdSymbolList
{
  private:

    std::string name_;

    Comments comments_;

  public:

    SequenceWithAnnotation(const Alphabet* alpha);

    SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
  
    SequenceWithAnnotation(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
  
    SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
    
    SequenceWithAnnotation(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
  
    SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
    
    SequenceWithAnnotation(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);

    SequenceWithAnnotation(const Sequence& s);
   
    SequenceWithAnnotation(const SequenceWithAnnotation& s);
 
    SequenceWithAnnotation& operator=(const Sequence& s);
   
    SequenceWithAnnotation& operator=(const SequenceWithAnnotation& s);

    virtual ~SequenceWithAnnotation() {}

  public:
  
    SequenceWithAnnotation* clone() const { return new SequenceWithAnnotation(*this); }
    const std::string& getName() const { return name_; }
    
    void setName(const std::string& name) { name_ = name; }
    
    const Comments& getComments() const { return comments_; }
    
    void setComments(const Comments& comments) { comments_ = comments; }
    
    virtual void setContent(const std::string& sequence) throw (BadCharException);
    void setContent(const std::vector<int>& list) throw (BadIntException)
    {
      EdSymbolList::setContent(list);
    }
    void setContent(const std::vector<std::string>& list) throw (BadCharException)
    {
      EdSymbolList::setContent(list);
    }


    virtual void setToSizeR(size_t newSize);
    
    virtual void setToSizeL(size_t newSize);

    void append(const std::vector<int>& content) throw (BadIntException);

    void append(const std::vector<std::string>& content) throw (BadCharException);

    void append(const std::string& content) throw (BadCharException);

    virtual void addAnnotation(SequenceAnnotation* anno) throw (Exception)
    {
      anno->isValidWith(*this);
      addSymbolListListener(anno);
    }
 
    virtual bool hasAnnotation(const std::string& type) const
    {
      for (size_t i = 0; i < getNumberOfListeners(); ++i) {
        const SymbolListListener* listener = &getListener(i);
        const SequenceAnnotation* anno = dynamic_cast<const SequenceAnnotation*>(listener);
        if (anno && anno->getType() == type) return true;
      }
      return false;
    }

   
    virtual const SequenceAnnotation& getAnnotation(const std::string& type) const
    {
      for (size_t i = 0; i < getNumberOfListeners(); ++i) {
        const SymbolListListener* listener = &getListener(i);
        const SequenceAnnotation* anno = dynamic_cast<const SequenceAnnotation*>(listener);
        if (anno && anno->getType() == type) return *anno;
      }
      throw Exception("SequenceWithAnnotation::getAnnotation. No annotation found with type '" + type + "'.");
    }
    
    virtual SequenceAnnotation& getAnnotation(const std::string& type)
    {
      for (size_t i = 0; i < getNumberOfListeners(); ++i) {
        SymbolListListener* listener = &getListener(i);
        SequenceAnnotation* anno = dynamic_cast<SequenceAnnotation*>(listener);
        if (anno && anno->getType() == type) return *anno;
      }
      throw Exception("SequenceWithAnnotation::getAnnotation. No annotation found with type '" + type + "'.");
    }

    virtual std::vector<std::string> getAnnotationTypes() const;

    virtual void merge(const SequenceWithAnnotation& swa)
        throw (AlphabetMismatchException, Exception);


};

} //end of namespace bpp.

#endif // _SEQUENCEWITHANNOTATION_H_