libpappsomspp
Library for mass spectrometry
mzintegrationparams.h
Go to the documentation of this file.
1/* BEGIN software license
2 *
3 * msXpertSuite - mass spectrometry software suite
4 * -----------------------------------------------
5 * Copyright(C) 2009,...,2018 Filippo Rusconi
6 *
7 * http://www.msxpertsuite.org
8 *
9 * This file is part of the msXpertSuite project.
10 *
11 * The msXpertSuite project is the successor of the massXpert project. This
12 * project now includes various independent modules:
13 *
14 * - massXpert, model polymer chemistries and simulate mass spectrometric data;
15 * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
16 *
17 * This program is free software: you can redistribute it and/or modify
18 * it under the terms of the GNU General Public License as published by
19 * the Free Software Foundation, either version 3 of the License, or
20 * (at your option) any later version.
21 *
22 * This program is distributed in the hope that it will be useful,
23 * but WITHOUT ANY WARRANTY; without even the implied warranty of
24 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 * GNU General Public License for more details.
26 *
27 * You should have received a copy of the GNU General Public License
28 * along with this program. If not, see <http://www.gnu.org/licenses/>.
29 *
30 * END software license
31 */
32
33
34#pragma once
35
36
37#include <map>
38
39#include "../../precision.h"
40#include "../../massspectrum/massspectrum.h"
41
42
43namespace pappso
44{
45
46//! Type of binning when performing integrations to a mass spectrum
47enum class BinningType
48{
49 //! < no binning
50 NONE = 0,
51
52 //! binning based on mass spectral data
54
55 //! binning based on arbitrary bin size value
57
58 LAST,
59};
60
61extern std::map<BinningType, QString> binningTypeMap;
62
63
64//! The MzIntegrationParams class provides the parameters definining how m/z !
65// integrations must be performed.
66/*!
67 * Depending on the various mass spectrometer vendors, the mass spectrometry
68 * data files are structured in different ways and the software for mass data
69 * format conversion from raw files to mzML or mzXML produce mass data
70 * characterized by different behaviours.
71 *
72 * The different characteristics of mass spectrometry data set are:
73 *
74 * The size of the various mass spectra in the file is constant or variable;
75 *
76 * The first m/z value of the various spectra is identical or not (that is,
77 * the spectra are root in a constant or variable root m/z value);
78 *
79 * The m/z delta between two consecutive m/z values of a given spectrum are
80 * constant or variable;
81 *
82 * The spectra contain or not 0-value m/z data points;
83
84*/
86{
87 public:
88 Q_INVOKABLE MzIntegrationParams();
91 BinningType binningType,
92 int decimalPlaces,
93 pappso::PrecisionPtr precisionPtr,
94 bool applyMzShift,
96 bool removeZeroValDataPoints);
97
98 Q_INVOKABLE MzIntegrationParams(const MzIntegrationParams &other);
99
100 virtual ~MzIntegrationParams();
101
102 MzIntegrationParams &operator=(const MzIntegrationParams &other);
103
104 Q_INVOKABLE void setSmallestMz(pappso::pappso_double value);
105 Q_INVOKABLE void updateSmallestMz(pappso::pappso_double value);
106 pappso::pappso_double getSmallestMz() const;
107
108 Q_INVOKABLE void setGreatestMz(pappso::pappso_double value);
109 Q_INVOKABLE void updateGreatestMz(pappso::pappso_double value);
110 Q_INVOKABLE pappso::pappso_double getGreatestMz() const;
111
112 Q_INVOKABLE void setBinningType(BinningType binningType);
113 Q_INVOKABLE BinningType getBinningType() const;
114
115 Q_INVOKABLE void setDecimalPlaces(int decimal_places);
116 Q_INVOKABLE int getDecimalPlaces() const;
117
118 Q_INVOKABLE void setPrecision(pappso::PrecisionPtr precisionPtr);
119 Q_INVOKABLE pappso::PrecisionPtr getPrecision() const;
120
121 Q_INVOKABLE void setApplyMzShift(bool applyMzShift);
122 Q_INVOKABLE bool isApplyMzShift() const;
123
124 Q_INVOKABLE void setMzShift(double value);
125 Q_INVOKABLE double getMzShift() const;
126
127 Q_INVOKABLE void setRemoveZeroValDataPoints(bool removeOrNot = true);
128 Q_INVOKABLE bool isRemoveZeroValDataPoints() const;
129
130 Q_INVOKABLE void reset();
131
132 Q_INVOKABLE bool isValid() const;
133
134 Q_INVOKABLE bool hasValidMzRange() const;
135
136 Q_INVOKABLE std::vector<pappso::pappso_double> createBins();
137 Q_INVOKABLE std::vector<pappso::pappso_double>
138 createBins(pappso::MassSpectrumCstSPtr mass_spectrum_csp);
139
140 Q_INVOKABLE QString toString(int offset = 0,
141 const QString &spacer = QString()) const;
142
143 private:
144 // That smallest value needs to be set to max, because it will be necessary
145 // compare any new m/z valut to it.
146 pappso::pappso_double m_smallestMz = std::numeric_limits<double>::max();
147
148 // That greatest value needs to be set to min, because it will be necessary
149 // compare any new m/z valut to it.
150 pappso::pappso_double m_greatestMz = std::numeric_limits<double>::min();
151
153
154 int m_decimalPlaces = -1;
155
156 // This should actually be called "bin size" as it describes the width of
157 // the bins.
158 pappso::PrecisionPtr mp_precision =
160 bool m_applyMzShift = false;
162 bool m_removeZeroValDataPoints = true;
163
164 std::vector<double> createArbitraryBins();
165 std::vector<double>
166 createDataBasedBins(pappso::MassSpectrumCstSPtr massSpectrum);
167};
168
169
170} // namespace pappso
171
174
177
The MzIntegrationParams class provides the parameters definining how m/z !
static PrecisionPtr getDaltonInstance(pappso_double value)
get a Dalton precision pointer
Definition: precision.cpp:130
#define PMSPP_LIB_DECL
int mzIntegrationParamsMetaTypeId
Q_DECLARE_METATYPE(pappso::MzIntegrationParams)
int mzIntegrationParamsPtrMetaTypeId
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
BinningType
Type of binning when performing integrations to a mass spectrum.
@ DATA_BASED
binning based on mass spectral data
@ ARBITRARY
binning based on arbitrary bin size value
@ NONE
< no binning
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::map< BinningType, QString > binningTypeMap
Map relating the BinningType to a textual representation.