libpappsomspp
Library for mass spectrometry
peptidenaturalisotopeaverage.h
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1 /*******************************************************************************
2  * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
3  *
4  * This file is part of the PAPPSOms++ library.
5  *
6  * PAPPSOms++ is free software: you can redistribute it and/or modify
7  * it under the terms of the GNU General Public License as published by
8  * the Free Software Foundation, either version 3 of the License, or
9  * (at your option) any later version.
10  *
11  * PAPPSOms++ is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14  * GNU General Public License for more details.
15  *
16  * You should have received a copy of the GNU General Public License
17  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
18  *
19  * Contributors:
20  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
21  *implementation
22  ******************************************************************************/
23 
24 #pragma once
25 
26 
27 #include <vector>
28 
29 #include "../exportinmportconfig.h"
30 #include "peptidenaturalisotope.h"
31 
32 namespace pappso
33 {
34 
35 class PeptideNaturalIsotopeList;
36 
37 class PeptideNaturalIsotopeAverage;
38 
39 typedef std::shared_ptr<const PeptideNaturalIsotopeAverage>
41 
43 {
44  public:
45  /** @brief fast constructor
46  * simple isotope build, not computing isotope ratio
47  */
49  unsigned int isotopeNumber,
50  unsigned int charge,
51  PrecisionPtr precision);
52 
54  unsigned int askedIsotopeRank,
55  unsigned int isotopeLevel,
56  unsigned int charge,
57  PrecisionPtr precision);
59  unsigned int askedIsotopeRank,
60  unsigned int isotopeLevel,
61  unsigned int charge,
62  PrecisionPtr precision);
63 
66 
67  PeptideNaturalIsotopeAverageSp makePeptideNaturalIsotopeAverageSp() const;
68  pappso_double getMz() const;
69  pappso_double getIntensityRatio() const;
70  unsigned int getCharge() const;
71  unsigned int getIsotopeNumber() const;
72  unsigned int getIsotopeRank() const;
73  const std::vector<PeptideNaturalIsotopeSp> &getComponents() const;
74  const PeptideInterfaceSp &getPeptideInterfaceSp() const;
75  PrecisionPtr getPrecision() const;
76  virtual bool matchPeak(pappso_double peak_mz) const final;
77  bool isEmpty() const;
78  virtual QString toString() const;
79 
80  private:
81  void recursiveDepletion(std::vector<PeptideNaturalIsotopeSp> &v_isotope_list,
82  unsigned int rank);
83 
84 
85  private:
87  std::vector<PeptideNaturalIsotopeSp> m_peptideNaturalIsotopeSpList;
88 
91  unsigned int m_isotopeLevel;
92  unsigned int m_isotopeRank = 1;
93  unsigned int m_z;
94  PrecisionPtr mp_precision = nullptr;
95 };
96 } // namespace pappso
std::vector< PeptideNaturalIsotopeSp > m_peptideNaturalIsotopeSpList
#define PMSPP_LIB_DECL
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
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp
peptide natural isotope model