CaseMaskedAlphabet.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Text/TextTools.h>
 
#include "CaseMaskedAlphabet.h"
 
using namespace bpp;
 
// From the STL:
#include <vector>
#include <iostream>
 
using namespace std;
 
CaseMaskedAlphabet::CaseMaskedAlphabet(std::shared_ptr<const LetterAlphabet> nocaseAlphabet) :
  LetterAlphabet(true),
  nocaseAlphabet_(nocaseAlphabet)
{
  vector<string> chars = nocaseAlphabet_->getSupportedChars();
  for (size_t i = 0; i < chars.size(); ++i)
  {
    AlphabetState* state = nocaseAlphabet_->getState(chars[i]).clone();
    registerState(state);
    char c = *chars[i].c_str();
    if (isalpha(c))
    {
      if (isupper(c))
      {
        registerState(new AlphabetState(state->getNum() + 100, TextTools::toLower(state->getLetter()), string("Masked ") + state->getName()));
      }
    }
  }
}
 
int CaseMaskedAlphabet::getMaskedEquivalentState(int state) const
{
  if (!isIntInAlphabet(state))
    throw BadIntException(state, "CaseMaskedAlphabet::getMaskedEquivalentState. Unsupported state code.", this);
  if (state >= 100)
    return state;
  else
  {
    state += 100;
    if (!isIntInAlphabet(state))
      throw BadIntException(state, "CaseMaskedAlphabet::getMaskedEquivalentState. State has masked equivalent.", this);
    return state;
  }
}
 
const string CaseMaskedAlphabet::getMaskedEquivalentState(const string& state) const
{
  if (!isCharInAlphabet(state))
    throw BadCharException(state, "CaseMaskedAlphabet::getMaskedEquivalentState. Unsupported state code.", this);
  int code = charToInt(state);
  if (code >= 100)
    return state;
  else
  {
    code += 100;
    if (!isIntInAlphabet(code))
      throw BadIntException(code, "CaseMaskedAlphabet::getMaskedEquivalentState. State has masked equivalent.", this);
    return intToChar(code);
  }
}