libpappsomspp
Library for mass spectrometry
massspectrumwidget.h
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1/**
2 * \file pappsomspp/widget/massspectrumwidget/massspectrumwidget.h
3 * \date 22/12/2017
4 * \author Olivier Langella
5 * \brief plot a sectrum and annotate with peptide
6 */
7
8
9/*******************************************************************************
10 * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
11 *
12 * This file is part of the PAPPSOms++ library.
13 *
14 * PAPPSOms++ is free software: you can redistribute it and/or modify
15 * it under the terms of the GNU General Public License as published by
16 * the Free Software Foundation, either version 3 of the License, or
17 * (at your option) any later version.
18 *
19 * PAPPSOms++ is distributed in the hope that it will be useful,
20 * but WITHOUT ANY WARRANTY; without even the implied warranty of
21 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22 * GNU General Public License for more details.
23 *
24 * You should have received a copy of the GNU General Public License
25 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26 *
27 * Contributors:
28 * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
29 *implementation
30 ******************************************************************************/
31
32
33#pragma once
34
35
36#include "../../massspectrum/qualifiedmassspectrum.h"
37#include "../../peptide/peptide.h"
38#include "../../peptide/peptidefragmentionlistbase.h"
39#include "../../peptide/peptidenaturalisotopeaverage.h"
40#include "../../psm/peptideisotopespectrummatch.h"
41#include "../graphicdevicewidget.h"
42#include "qcpspectrum.h"
43
44namespace pappso
45{
46
48{
49 Q_OBJECT
50 public:
51 MassSpectrumWidget(QWidget *parent = 0);
53
54 void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum);
55 void setMsLevel(unsigned int ms_level);
56 void setMassSpectrumCstSPtr(const MassSpectrumCstSPtr &spectrum);
57 void setPeptideSp(const PeptideSp &peptide_sp);
58 void plot();
59 void rescale();
60
61 void setPeptideCharge(unsigned int parent_ion_charge);
62 void setMaximumIsotopeNumber(unsigned int max_isotope_number);
63 void setMaximumIsotopeRank(unsigned int max_isotope_rank);
64 // void setIsolationWindow(PrecisionPtr precision);
65 void setIonList(const std::list<PeptideIon> &ion_list);
66 void setMs1Precision(PrecisionPtr precision);
67 void setMs2Precision(PrecisionPtr precision);
68
69 bool savePdf(const QString &fileName, int width = 0, int height = 0);
70 void toQPaintDevice(QPaintDevice *device, const QSize &size) override;
71 void highlightPrecursorPeaks();
72 // void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp>
73 // & isotope_mass_list);
74
75
76 signals:
77 void mzChanged(double mz) const;
78 void peakChanged(pappso::DataPointCstSPtr peak_match) const;
80
81 protected:
82 friend class QCPSpectrum;
83 void mzChangeEvent(pappso_double mz) const;
84 void peakChangeEvent(const DataPoint *p_peak_match);
85
86 private:
87 void peptideAnnotate();
88 void setVisibleMassDelta(bool visible);
89 void clearData();
90 void computeIsotopeMassList();
91
92 private:
93 unsigned int _tag_nmost_intense = 10;
94 unsigned int _max_isotope_number = 0;
95 unsigned int _max_isotope_rank = 1;
99 unsigned int _peptide_charge = 3;
100 unsigned int _ms_level;
102 std::list<PeptideIon> _ion_list;
103
104 std::list<PeakIonIsotopeMatch> _peak_ion_isotope_match_list;
105
106 /** @brief list of isotope precursors
107 */
108 std::vector<pappso::PeptideNaturalIsotopeAverageSp> _isotope_mass_list;
109
110 QCPSpectrum *_custom_plot = nullptr;
112
113 const DataPoint *_p_mouse_peak = nullptr;
114};
115
116
117} // namespace pappso
std::vector< pappso::PeptideNaturalIsotopeAverageSp > _isotope_mass_list
list of isotope precursors
void peakChanged(pappso::DataPointCstSPtr peak_match) const
std::list< PeakIonIsotopeMatch > _peak_ion_isotope_match_list
MassSpectrumCstSPtr _spectrum_sp
void mzChanged(double mz) const
void ionChanged(pappso::PeakIonIsotopeMatchCstSPtr ion) const
std::list< PeptideIon > _ion_list
static PrecisionPtr getDaltonInstance(pappso_double value)
get a Dalton precision pointer
Definition: precision.cpp:130
Class representing a fully specified mass spectrum.
#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 Peptide > PeptideSp
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::shared_ptr< const PeakIonIsotopeMatch > PeakIonIsotopeMatchCstSPtr
std::shared_ptr< const DataPoint > DataPointCstSPtr
Definition: datapoint.h:18