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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 "../mzrange.h"
#include "../exportinmportconfig.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 QString getFormula(unsigned int charge) const final;
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(Isotope isotope) const override = 0;
};
} // namespace pappso
pappso::AtomNumberInterface
Definition atomnumberinterface.h:31
pappso::Ion
Definition ion.h:40
pappso::MzRange
Definition mzrange.h:46
pappso::PeptideInterface
Definition peptideinterface.h:43
pappso::PeptideInterface::getName
virtual const QString getName() const
Definition peptideinterface.h:60
pappso::PeptideInterface::getSequence
virtual const QString getSequence() const =0
amino acid sequence without modification
pappso::PeptideInterface::matchPeak
virtual bool matchPeak(PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
Definition peptideinterface.h:68
pappso::PeptideInterface::isPalindrome
virtual bool isPalindrome() const =0
tells if the peptide sequence is a palindrome
pappso::PeptideInterface::size
virtual unsigned int size() const =0
pappso::PrecisionBase
Definition precision.h:44
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition exportinmportconfig.h:14
ion.h
ion interface
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::PeptideInterfaceSp
std::shared_ptr< const PeptideInterface > PeptideInterfaceSp
Definition peptideinterface.h:39
pappso::MHPLUS
const pappso_double MHPLUS(1.007276466879)
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:50