libpappsomspp
Library for mass spectrometry
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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
36#include "../../mzrange.h"
38
39namespace 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.
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
basic mass spectrum
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:432
std::shared_ptr< const Peptide > PeptideSp
PeptideDirection
Definition peptide.h:46
double pappso_double
A type definition for doubles.
Definition types.h:50
peptide ion model