AlphabetTools.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Text/TextTools.h>
 
#include "AlphabetTools.h"
 
using namespace bpp;
 
// From the STL:
#include <ctype.h>
#include <iostream>
#include <memory>
 
using namespace std;
 
/**********************************************************************************************/
shared_ptr<const DNA> AlphabetTools::DNA_ALPHABET = make_shared<const DNA>();
shared_ptr<const RNA> AlphabetTools::RNA_ALPHABET = make_shared<const RNA>();
shared_ptr<const CodonAlphabet> AlphabetTools::DNA_CODON_ALPHABET = make_shared<const CodonAlphabet>(dynamic_pointer_cast<const NucleicAlphabet>(DNA_ALPHABET));
shared_ptr<const CodonAlphabet> AlphabetTools::RNA_CODON_ALPHABET = make_shared<const CodonAlphabet>(dynamic_pointer_cast<const NucleicAlphabet>(RNA_ALPHABET));
shared_ptr<const ProteicAlphabet> AlphabetTools::PROTEIN_ALPHABET = make_shared<const ProteicAlphabet>();
shared_ptr<const DefaultAlphabet> AlphabetTools::DEFAULT_ALPHABET = make_shared<const DefaultAlphabet>();
 
/**********************************************************************************************/
 
int AlphabetTools::getType(char state)
{
  if (state == '-')
    return -1;
  state = static_cast<char>(toupper(static_cast<int>(state))); // toupper works on int
  bool d = DNA_ALPHABET->isCharInAlphabet(TextTools::toString(state));
  bool r = RNA_ALPHABET->isCharInAlphabet(TextTools::toString(state));
  bool p = PROTEIN_ALPHABET->isCharInAlphabet(TextTools::toString(state));
 
  if (!d && !r && !p)
    return 0; // Unknown character
  else if (d && !r && !p)
    return 1; // DNA specific
  else if (!d && r && !p)
    return 2; // RNA specific
  else if (!d && !r && p)
    return 3; // Protein specific
  else if (d && r && !p)
    return 4; // Nucleotide specific
  else if (d && !r && p)
    return 5; // DNA or Protein specific
  else if (!d && r && p)
    return 6; // RNA or Protein specific
  else
    return 7; // Non-specific character
}
 
/**********************************************************************************************/
 
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet& alphabet)
{
  if (alphabet.getNumberOfChars() == 0)
    return true; // Will this really happen?
  size_t size = alphabet.intToChar(0).size();
 
  for (size_t i = 1; i < alphabet.getNumberOfTypes(); ++i)
  {
    if (alphabet.intToChar(alphabet.getStateAt(i).getNum()).size() != size)
      return false;
  }
  return true;
}
 
/**********************************************************************************************/
 
bool AlphabetTools::checkAlphabetCodingSize(const Alphabet* alphabet)
{
  return checkAlphabetCodingSize(*alphabet);
}
 
/**********************************************************************************************/
 
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet& alphabet)
{
  if (!checkAlphabetCodingSize(alphabet))
    throw AlphabetException("Bad alphabet in function Alphabet::getAlphabetCodingSize().", &alphabet);
  return static_cast<unsigned int>(alphabet.intToChar(0).size());
}
 
/**********************************************************************************************/
 
unsigned int AlphabetTools::getAlphabetCodingSize(const Alphabet* alphabet)
{
  return getAlphabetCodingSize(*alphabet);
}