aacode.h

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/**
 * \file pappsomspp/amino_acid/aacode.h
 * \date 03/05/2023
 * \author Olivier Langella
 * \brief give an integer code to each amino acid
 */
 
/*******************************************************************************
 * Copyright (c) 2023 Olivier Langella <Olivier.Langella@u-psud.fr>.
 *
 * This file is part of PAPPSOms-tools.
 *
 *     PAPPSOms-tools is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     PAPPSOms-tools is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with PAPPSOms-tools.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/
 
#pragma once
 
#include "pappsomspp/export-import-config.h"
#include "pappsomspp/core/precision.h"
#include <vector>
#include "pappsomspp/core/amino_acid/aa.h"
 
namespace pappso
{
/**
 * @brief collection of integer code for each amino acid
 * 0 => null
 * 1 to 20 => amino acid sorted by there mass (lower to higher). Leucine is
 * replaced by Isoleucine
 */
class PMSPP_LIB_DECL AaCode
{
  public:
  /**
   * Default constructor
   */
  AaCode();
 
  /**
   * Default copy constructor
   */
  AaCode(const AaCode &other);
 
  /**
   * Destructor
   */
  ~AaCode();
 
  /** @brief get the integer code of an amino acid with the one letter code
   * @return integer 1 to 20, 0 if not found
   */
  uint8_t getAaCode(char aa_letter) const;
 
  /** @brief get the integer code of an amino acid enum
   * @return integer 1 to 20, 0 if not found
   */
  uint8_t getAaCode(pappso::Enums::AminoAcidChar aa) const;
 
 
  /** @brief get the integer code of an amino acid given a mass and a precision
   * @return integer 1 to 20, 0 if not found
   */
  uint8_t getAaCodeByMass(double mass, PrecisionPtr precision) const;
 
  /** @brief get the Aa object from the one letter code
   */
  const Aa &getAa(char aa_letter) const;
 
  /** @brief get the Aa object from the amino acid integer code
   */
  const Aa &getAa(uint8_t aa_code) const;
 
 
  /** @brief get the mass of the amino acid given its integer code
   * the amino acid can bear some modification (if addAaModification function was used)
   */
  double getMass(uint8_t aa_code) const;
  double getMass(char aa_letter) const;
 
  /** @brief add a modification on an amino acid
   * for example carbamido on C
   */
  void addAaModification(char aa_letter, AaModificationP aaModification);
 
  std::size_t getSize() const;
 
  const std::vector<Aa> &getAaCollection() const;
 
  private:
  /** @brief give a number (the code) to each amino acid sorted by mass
   */
  void updateNumbers();
  /** @brief update mass cache
   */
  void updateMass();
 
  private:
  std::vector<uint8_t> m_asciiTable;
 
  std::vector<Aa> m_aaCollection;
  std::vector<double> m_massCollection;
 
  pappso::Aa m_leucine = Aa('L');
};
} // namespace pappso