Alphabet.h

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//
// File: Alphabet.h
// Created by: Guillaume Deuchst
//             Julien Dutheil
// Created on: Tue Jul 22 2003
//

/*
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 _ALPHABET_H_
#define _ALPHABET_H_

#include <string>
#include <vector>

#include "AlphabetExceptions.h"
#include "AlphabetState.h"

#include <Bpp/Clonable.h>

namespace bpp
{

  class Alphabet:
    public virtual Clonable
{
  public:
    Alphabet() {}
    virtual ~Alphabet() {}

#ifndef NO_VIRTUAL_COV
  Alphabet* clone() const = 0;
#endif
  
  public:
    
    virtual std::string getName(int state) const throw (BadIntException)  = 0;
        
    virtual std::string getName(const std::string& state) const throw (BadCharException) = 0;

    virtual int getIntCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;

    virtual const std::string& getCharCodeAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;

    virtual size_t getStateIndex(int state) const throw (BadIntException) = 0;
    
    virtual size_t getStateIndex(const std::string& state) const throw (BadCharException) = 0;

    virtual bool isIntInAlphabet(int state) const = 0;
    
    virtual bool isCharInAlphabet(const std::string& state) const = 0;
    virtual const AlphabetState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException) = 0;

    virtual const AlphabetState& getState(int state) const throw (BadIntException) = 0;

    virtual const AlphabetState& getState(const std::string& state) const throw (BadCharException) = 0;

    virtual std::string intToChar(int state) const throw (BadIntException) = 0;
        
    virtual int charToInt(const std::string& state) const throw (BadCharException) = 0;
    virtual size_t getNumberOfStates() const = 0;
   
    virtual unsigned int getNumberOfChars() const = 0;
        
    virtual unsigned int getNumberOfTypes() const = 0;
        
    virtual unsigned int getSize() const = 0;
    
    virtual std::vector<int> getAlias(int state) const throw (BadIntException) = 0;
    
    virtual std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException) = 0;

    virtual int getGeneric(const std::vector<int>& states) const throw (BadIntException) = 0;

    virtual std::string getGeneric(const std::vector<std::string>& states) const throw (AlphabetException) = 0;

    virtual const std::vector<int>& getSupportedInts() const = 0;
    
    virtual const std::vector<std::string>& getSupportedChars() const = 0;
    
    virtual int getUnknownCharacterCode() const = 0;

    virtual int getGapCharacterCode() const = 0;

    virtual bool isGap(int state) const = 0;

    virtual bool isGap(const std::string& state) const = 0;

    virtual bool isUnresolved(int state) const = 0;

    virtual bool isUnresolved(const std::string& state) const = 0;

    virtual std::string getAlphabetType() const = 0;

    virtual unsigned int getStateCodingSize() const = 0;

    virtual bool equals(const Alphabet& alphabet) const = 0;
};

} //end of namespace bpp.

#endif // _ALPHABET_H_