peptideinterface.h

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/*******************************************************************************
 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
 *
 * This file is part of the PAPPSOms++ library.
 *
 *     PAPPSOms++ 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++ 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++.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
 *implementation
 ******************************************************************************/
 
#pragma once
 
#include <memory>
#include "ion.h"
#include <QString>
#include "../amino_acid/atomnumberinterface.h"
#include "../amino_acid/chemicalformula.h"
#include "pappsomspp/core/mzrange.h"
#include "pappsomspp/export-import-config.h"
 
 
namespace pappso
{
 
class PeptideInterface;
typedef std::shared_ptr<const PeptideInterface> PeptideInterfaceSp;
 
 
class PMSPP_LIB_DECL PeptideInterface : public Ion, public AtomNumberInterface
{
  public:
  /** @brief amino acid sequence without modification
   * */
  virtual const QString getSequence() const = 0;
 
 
  /** @brief tells if the peptide sequence is a palindrome
   */
  virtual bool isPalindrome() const = 0;
 
  /** @brief amino acid sequence without modification where L are replaced by I
   * */
  virtual const QString getSequenceLi() const;
 
  virtual unsigned int size() const = 0;
  virtual const QString
  getName() const
  {
    return QString("unknown");
  };
 
  virtual const ChemicalFormula getChemicalFormulaCharge(unsigned int charge) const;
  virtual const QString getFormula(unsigned int charge) const final;
 
 
  /** @brief tells if the peptide m/z matches a given experimental mass
   */
  virtual bool
  matchPeak(PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
  {
    return (MzRange((getMass() + (MHPLUS * charge)) / charge, precision).contains(peak_mz));
  };
 
  // virtual int getNumberOfIsotope(Enums::Isotope isotope) const override = 0;
};
} // namespace pappso