libpappsomspp
Library for mass spectrometry
peptideinterface.h
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1 
2 /*******************************************************************************
3  * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
4  *
5  * This file is part of the PAPPSOms++ library.
6  *
7  * PAPPSOms++ is free software: you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation, either version 3 of the License, or
10  * (at your option) any later version.
11  *
12  * PAPPSOms++ is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
19  *
20  * Contributors:
21  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
22  *implementation
23  ******************************************************************************/
24 
25 #pragma once
26 
27 #include <memory>
28 #include "ion.h"
29 #include <QString>
30 #include "../amino_acid/atomnumberinterface.h"
31 #include "../mzrange.h"
32 #include "../exportinmportconfig.h"
33 
34 
35 namespace pappso
36 {
37 
38 class PeptideInterface;
39 typedef std::shared_ptr<const PeptideInterface> PeptideInterfaceSp;
40 
41 
43 {
44  public:
45  /** @brief amino acid sequence without modification
46  * */
47  virtual const QString getSequence() const = 0;
48 
49 
50  /** @brief tells if the peptide sequence is a palindrome
51  */
52  virtual bool isPalindrome() const = 0;
53 
54  /** @brief amino acid sequence without modification where L are replaced by I
55  * */
56  virtual const QString getSequenceLi() const;
57 
58  virtual unsigned int size() const = 0;
59  virtual const QString
60  getName() const
61  {
62  return QString("unknown");
63  };
64 
65  virtual const QString getFormula(unsigned int charge) const final;
66 
67  virtual bool
69  pappso_double peak_mz,
70  unsigned int charge) const final
71  {
72  return (MzRange((getMass() + (MHPLUS * charge)) / charge, precision)
73  .contains(peak_mz));
74  }
75 
76  // virtual int getNumberOfIsotope(Isotope isotope) const override = 0;
77 };
78 } // namespace pappso
virtual const QString getName() const
virtual const QString getSequence() const =0
amino acid sequence without modification
virtual bool matchPeak(PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
virtual bool isPalindrome() const =0
tells if the peptide sequence is a palindrome
virtual unsigned int size() const =0
#define PMSPP_LIB_DECL
ion interface
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const PeptideInterface > PeptideInterfaceSp
const pappso_double MHPLUS(1.007276466879)
double pappso_double
A type definition for doubles.
Definition: types.h:49