libpappsomspp
Library for mass spectrometry
xtandemhyperscore.h
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1 /**
2  * \file pappsomspp/psm/xtandem/xtandemhyperscore.h
3  * \date 19/3/2015
4  * \author Olivier Langella
5  * \brief computation of the X!Tandem hyperscore
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  * Contributors:
27  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
31 
32 #pragma once
33 
34 
35 #include "../../massspectrum/massspectrum.h"
36 #include "../../mzrange.h"
37 #include "../../peptide/peptidefragmention.h"
38 
39 namespace pappso
40 {
41 
43 {
44  public:
45  using AaFactorMap = std::map<char, pappso_double>;
46  XtandemHyperscore(const MassSpectrum &spectrum,
47  pappso::PeptideSp peptideSp,
48  unsigned int parent_charge,
49  PrecisionPtr precision,
50  std::list<PeptideIon> ion_list,
51  bool refine_spectrum_synthesis);
54 
55  pappso_double getHyperscore() const;
56  unsigned int getMatchedIons(PeptideIon ion_type) const;
57 
58  private:
60 
61  unsigned int
62  getXtandemPredictedIonIntensityFactor(const QString &sequence,
63  PeptideDirection ion_direction,
64  unsigned int ion_size) const;
65 
67  std::map<PeptideIon, unsigned int> _ion_count;
68 
71 };
72 
73 
74 } // namespace pappso
Class to represent a mass spectrum.
Definition: massspectrum.h:71
static AaFactorMap _aa_ion_factor_y
std::map< char, pappso_double > AaFactorMap
static AaFactorMap _aa_ion_factor_b
std::map< PeptideIon, unsigned int > _ion_count
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:386
std::shared_ptr< const Peptide > PeptideSp
PeptideDirection
Definition: peptide.h:46
double pappso_double
A type definition for doubles.
Definition: types.h:49