NucleicAlphabet.h

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//
// File: NucleicAlphabet.h
// Authors: Guillaume Deuchst
//          Julien Dutheil
//          Sylvain Gaillard
// 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 _NUCLEICALPHABET_H_
#define _NUCLEICALPHABET_H_

#include "LetterAlphabet.h"
#include "NucleicAlphabetState.h"

#include <map>
#include <iostream>
#include <typeinfo>

namespace bpp
{

  class NucleicAlphabet :
    public LetterAlphabet
  {
  private:
    std::map<int, size_t> binCodes_;
    void updateBinMaps_(size_t pos, const NucleicAlphabetState& st) {
      if (binCodes_.find(st.getBinaryCode()) == binCodes_.end())
        binCodes_[st.getBinaryCode()] = pos;
    }

  public:
    NucleicAlphabet(): LetterAlphabet(), binCodes_() {}

    NucleicAlphabet(const NucleicAlphabet& bia) : LetterAlphabet(bia), binCodes_(bia.binCodes_) {}

    NucleicAlphabet& operator=(const NucleicAlphabet& bia)
    {
      LetterAlphabet::operator=(bia);
      binCodes_ = bia.binCodes_;
      return *this;
    }

#ifndef NO_VIRTUAL_COV
    virtual NucleicAlphabet* clone() const = 0;
#endif

    virtual ~NucleicAlphabet() {}

  protected:
    void registerState(AlphabetState* st) throw (Exception) {
      NucleicAlphabetState* nst = dynamic_cast<NucleicAlphabetState*>(st);
      if (!nst)
        throw Exception("NucleicAlphabet::registerState. Incorrect alphabet type.");
      LetterAlphabet::registerState(nst);
      updateBinMaps_(getNumberOfChars(), *nst);
    }

    void setState(size_t pos, AlphabetState* st) throw (Exception, IndexOutOfBoundsException) {
      NucleicAlphabetState* nst = dynamic_cast<NucleicAlphabetState*>(st);
      if (!nst)
        throw Exception("NucleicAlphabet::setState. Incorrect alphabet type.");
      LetterAlphabet::setState(pos, nst);
      updateBinMaps_(pos, *nst);
    }

  public:
    const NucleicAlphabetState& getStateAt(size_t stateIndex) const
      throw (IndexOutOfBoundsException) {
      return dynamic_cast<const NucleicAlphabetState&>(
        AbstractAlphabet::getStateAt(stateIndex)
        );
    }
    NucleicAlphabetState& getStateAt(size_t stateIndex)
      throw (IndexOutOfBoundsException) {
      return dynamic_cast<NucleicAlphabetState&>(
        AbstractAlphabet::getStateAt(stateIndex)
        );
    }
    const NucleicAlphabetState& getState(const std::string& letter) const
      throw (BadCharException) {
      return dynamic_cast<const NucleicAlphabetState&>(
        AbstractAlphabet::getState(letter)
        );
    }
    const NucleicAlphabetState& getState(int num) const
      throw (BadIntException) {
      return dynamic_cast<const NucleicAlphabetState&>(
        AbstractAlphabet::getState(num)
        );
    }
    const NucleicAlphabetState& getStateByBinCode(int code) const
      throw (BadIntException) {
      std::map<int, size_t>::const_iterator it = binCodes_.find(code);
      if (it == binCodes_.end())
        throw BadIntException(code, "NucleicAlphabet::getState(unsigned char): Binary code not in alphabet", this);
      return getStateAt(it->second);
    }

    int subtract(int s1, int s2) const throw (BadIntException) {
      return getStateByBinCode(getState(s1).getBinaryCode() & ~ getState(s2).getBinaryCode()).getNum();
    }

    std::string subtract(const std::string& s1, const std::string& s2) const throw (BadCharException) {
      return intToChar(subtract(charToInt(s1), charToInt(s2)));
    }

    int getOverlap(int s1, int s2) const throw (BadIntException) {
      return getStateByBinCode(getState(s1).getBinaryCode() & getState(s2).getBinaryCode()).getNum();
    }

    std::string getOverlap(const std::string& s1, const std::string& s2) const throw (BadCharException) {
      return intToChar(getOverlap(charToInt(s1), charToInt(s2)));
    }

  public:
    // return 4 : A, C, G, T (or U)
    unsigned int getSize() const { return 4; }

    // return 15 : gap isn't included, generic unresolved bases (N, X, ?, O, 0) count for one
    unsigned int getNumberOfTypes() const { return 15; }
    
    int getUnknownCharacterCode() const { return 14; }

    bool isUnresolved(int state) const { return state > 3; }
    bool isUnresolved(const std::string& state) const { return charToInt(state) > 3; }

  };

} //end of namespace bpp.

#endif // _NUCLEICALPHABET_H_