libpappsomspp
Library for mass spectrometry
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xtandemhyperscorebis.h
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1/**
2 * \file pappsomspp/psm/xtandem/xtandemhyperscorebis.h
3 * \date 8/9/2016
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#pragma once
32
33
34#include "../../massspectrum/massspectrum.h"
35#include "../../peptide/peptide.h"
36
37namespace pappso
38{
39
41{
42 using AaFactorMap = std::map<char, pappso_double>;
43
44 private:
45 unsigned int getXtandemPredictedIonIntensityFactor(const QString &sequence,
46 PeptideIon ion_type,
47 unsigned int size) const;
50 std::vector<PeptideIon> m_ionList;
51
52 unsigned int m_totalMatchedIons = 0;
54
55
57
60
61 public:
62 XtandemHyperscoreBis(bool refine_spectrum_synthesis,
63 PrecisionPtr precision,
64 const std::vector<PeptideIon> &ion_list);
66
68 unsigned int getMatchedIons(PeptideIon ion_type) const;
69
70
71 void reset();
72
73 bool computeXtandemHyperscore(const MassSpectrum &spectrum,
74 const Peptide &peptide,
75 unsigned int parent_charge);
76 unsigned int getTotalMatchedIons() const;
77};
78
79
80} // namespace pappso
Class to represent a mass spectrum.
unsigned int getXtandemPredictedIonIntensityFactor(const QString &sequence, PeptideIon ion_type, unsigned int size) const
std::map< char, pappso_double > AaFactorMap
bool computeXtandemHyperscore(const MassSpectrum &spectrum, const Peptide &peptide, unsigned int parent_charge)
unsigned int m_ionCount[PEPTIDE_ION_TYPE_COUNT]
std::vector< PeptideIon > m_ionList
unsigned int getMatchedIons(PeptideIon ion_type) const
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
double pappso_double
A type definition for doubles.
Definition types.h:50
#define PEPTIDE_ION_TYPE_COUNT
only useful for internal use DO not change this value : it is used to define static array size
Definition types.h:452