AbstractAlphabet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABET_ABSTRACTALPHABET_H
#define BPP_SEQ_ALPHABET_ABSTRACTALPHABET_H
 
#include <Bpp/Exceptions.h>
 
#include "Alphabet.h"
#include "AlphabetState.h"
 
// From the STL:
#include <string>
#include <vector>
#include <map>
 
namespace bpp
{
class AbstractAlphabet :
  public Alphabet
{
private:
  std::vector<AlphabetState*> alphabet_;
 
  std::map<std::string, size_t> letters_;
  std::map<int, size_t> nums_;
  void updateMaps_(size_t pos, const AlphabetState& st);
 
protected:
  mutable std::vector<std::string> charList_;
  mutable std::vector<int> intList_;
public:
  AbstractAlphabet() : alphabet_(), letters_(), nums_(), charList_(), intList_() {}
 
  AbstractAlphabet(const AbstractAlphabet& alph) : alphabet_(), letters_(alph.letters_), nums_(alph.nums_), charList_(alph.charList_), intList_(alph.intList_)
  {
    for (size_t i = 0; i < alph.alphabet_.size(); ++i)
    {
      alphabet_.push_back(alph.alphabet_[i]->clone());
    }
  }
 
  AbstractAlphabet& operator=(const AbstractAlphabet& alph)
  {
    for (size_t i = 0; i < alphabet_.size(); ++i)
    {
      delete alphabet_[i];
    }
 
    for (size_t i = 0; i < alph.alphabet_.size(); ++i)
    {
      alphabet_.push_back(alph.alphabet_[i]->clone());
    }
 
    letters_  = alph.letters_;
    nums_     = alph.nums_;
    charList_ = alph.charList_;
    intList_  = alph.intList_;
 
    return *this;
  }
 
  virtual AbstractAlphabet* clone() const = 0;
 
  virtual ~AbstractAlphabet()
  {
    for (size_t i = 0; i < alphabet_.size(); ++i)
    {
      delete alphabet_[i];
    }
  }
 
public:
  size_t getNumberOfStates() const { return alphabet_.size(); }
  unsigned int getNumberOfChars() const { return static_cast<unsigned int>(alphabet_.size()); }
  std::string getName(const std::string& state) const;
  std::string getName(int state) const;
  int charToInt(const std::string& state) const;
  std::string intToChar(int state) const;
  bool isIntInAlphabet(int state) const;
  bool isCharInAlphabet(const std::string& state) const;
  bool isResolvedIn(int state1, int state2) const;
  std::vector<int> getAlias(int state) const;
  std::vector<std::string> getAlias(const std::string& state) const;
  int getGeneric(const std::vector<int>& states) const;
  std::string getGeneric(const std::vector<std::string>& states) const;
  const std::vector<int>& getSupportedInts() const;
  const std::vector<std::string>& getSupportedChars() const;
  const std::vector<std::string>& getResolvedChars() const;
  int getGapCharacterCode() const { return -1; }
  bool isGap(int state) const { return state == -1; }
  bool isGap(const std::string& state) const { return charToInt(state) == -1; }
  virtual AlphabetState& getStateAt(size_t stateIndex);
 
  virtual const AlphabetState& getStateAt(size_t stateIndex) const;
 
  const AlphabetState& getState(const std::string& letter) const;
 
  AlphabetState& getState(const std::string& letter);
 
  const AlphabetState& getState(int num) const;
 
  AlphabetState& getState(int num);
 
  int getIntCodeAt(size_t stateIndex) const
  {
    return getStateAt(stateIndex).getNum();
  }
 
  const std::string& getCharCodeAt(size_t stateIndex) const
  {
    return getStateAt(stateIndex).getLetter();
  }
 
  size_t getStateIndex(int state) const;
 
  size_t getStateIndex(const std::string& state) const;
protected:
  virtual void registerState(AlphabetState* st);
 
  virtual void setState(size_t pos, AlphabetState* st);
 
  void resize(size_t size) { alphabet_.resize(size); }
 
  void remap()
  {
    letters_.clear();
    nums_.clear();
    for (size_t i = 0; i < alphabet_.size(); ++i)
    {
      updateMaps_(i, *alphabet_[i]);
    }
  }
 
  unsigned int getStateCodingSize() const { return 1; }
 
  bool equals(const Alphabet& alphabet) const
  {
    return getAlphabetType() == alphabet.getAlphabetType();
  }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABET_ABSTRACTALPHABET_H