WordAlphabet.h

Go to the documentation of this file.

//
// File: WordAlphabet.h
// Created by: Laurent Gueguen
// Created on: Sun Dec 28 2008
//

/*
   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 _WORDALPHABET_H_
#define _WORDALPHABET_H_

#include "AbstractAlphabet.h"

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

#include "../Sequence.h"

namespace bpp
{
class WordAlphabet :
  public AbstractAlphabet
{
protected:
  std::vector<const Alphabet* > vAbsAlph_;

public:
  // Constructor and destructor.
  WordAlphabet(const std::vector<const Alphabet*>& vAlpha);

  WordAlphabet(const Alphabet* pAlpha, unsigned int num);

  WordAlphabet(const WordAlphabet& bia) : AbstractAlphabet(bia), vAbsAlph_(bia.vAbsAlph_) {}

  WordAlphabet& operator=(const WordAlphabet& bia)
  {
    AbstractAlphabet::operator=(bia);
    vAbsAlph_=bia.vAbsAlph_;
    return *this;
  }

  WordAlphabet* clone() const
  {
    return new WordAlphabet(*this);
  }

  virtual ~WordAlphabet() {}

public:
  std::string getName(const std::string& state) const throw (BadCharException);

  int charToInt(const std::string& state) const throw (BadCharException)
  {
    if (state.size() != vAbsAlph_.size())
      throw BadCharException(state, "WordAlphabet::charToInt", this);
    if (containsUnresolved(state))
      return static_cast<int>(getSize());
    if (containsGap(state))
      return -1;
    else return AbstractAlphabet::charToInt(state);
  }

  unsigned int getSize() const
  {
    return getNumberOfChars() - 2;
  }

  bool hasUniqueAlphabet() const;

  unsigned int getLength() const
  {
    return static_cast<unsigned int>(vAbsAlph_.size());
  }


  unsigned int getNumberOfTypes() const
  {
    return getNumberOfChars() - 1;
  }

  std::string getAlphabetType() const;

  int getUnknownCharacterCode() const
  {
    return static_cast<int>(getSize());
  }

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

  std::vector<int> getAlias(int state) const throw (BadIntException);
  std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
  int getGeneric(const std::vector<int>& states) const throw (BadIntException);
  std::string getGeneric(const std::vector<std::string>& states) const throw (BadCharException);

private:
  bool containsUnresolved(const std::string& state) const throw (BadCharException);
  bool containsGap(const std::string& state) const throw (BadCharException);
  void build_();
public:
  const Alphabet* getNAlphabet(size_t n) const
  {
    if (n >= vAbsAlph_.size())
      throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());

    return vAbsAlph_[n];
  }

  virtual int getWord(const std::vector<int>& vint, size_t pos = 0) const throw (IndexOutOfBoundsException);

  virtual std::string getWord(const std::vector<std::string>& vpos, size_t pos = 0) const throw (IndexOutOfBoundsException, BadCharException);

  int getNPosition(int word, size_t n) const throw (BadIntException)
  {
    if (n >= vAbsAlph_.size())
      throw IndexOutOfBoundsException("WordAlphabet::getNPosition", n, 0, vAbsAlph_.size());

    std::string s = intToChar(word);
    return vAbsAlph_[n]->charToInt(s.substr(n, 1));
  }

  std::vector<int> getPositions(int word) const throw (BadIntException)
  {
    std::string s = intToChar(word);
    std::vector<int> positions;
    for (size_t i = 0; i < s.size(); i++)
    {
      positions.push_back(vAbsAlph_[i]->charToInt(s.substr(i, 1)));
    }

    return positions;
  }
  std::string getNPosition(const std::string& word, size_t n) const throw (BadCharException)
  {
    if (n > vAbsAlph_.size())
      throw BadCharException("", "WordAlphabet::getNPosition", this);
    // Test:
    charToInt(word);

    return "" + word.substr(n, 1);
  }


  std::vector<std::string> getPositions(const std::string& word) const throw (BadCharException)
  {
    charToInt(word);
    std::vector<std::string> positions;
    for (size_t i = 0; i < word.size(); i++)
    {
      positions.push_back(word.substr(i, 1));
    }

    return positions;
  }

  Sequence* translate(const Sequence &sequence, size_t = 0) const throw (AlphabetMismatchException, Exception);

  Sequence* reverse(const Sequence& sequence) const throw (AlphabetMismatchException, Exception);

  unsigned int getStateCodingSize() const { return static_cast<unsigned int>(vAbsAlph_.size()); }
};
} // end of namespace bpp.

#endif  // _WORDALPHABET_H_