libpappsomspp
Library for mass spectrometry
mzintegrationparams.h
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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
42namespace pappso
43{
44
45//! Type of binning when performing integrations to a mass spectrum
46enum class BinningType
47{
48 //! < no binning
49 NONE = 0,
50
51 //! binning based on mass spectral data
53
54 //! binning based on arbitrary bin size value
56
57 LAST,
58};
59
60extern std::map<BinningType, QString> binningTypeMap;
61
62
63//! The MzIntegrationParams class provides the parameters definining how m/z !
64// integrations must be performed.
65/*!
66 * Depending on the various mass spectrometer vendors, the mass spectrometry
67 * data files are structured in different ways and the software for mass data
68 * format conversion from raw files to mzML or mzXML produce mass data
69 * characterized by different behaviours.
70 *
71 * The different characteristics of mass spectrometry data set are:
72 *
73 * The size of the various mass spectra in the file is constant or variable;
74 *
75 * The first m/z value of the various spectra is identical or not (that is,
76 * the spectra are root in a constant or variable root m/z value);
77 *
78 * The m/z delta between two consecutive m/z values of a given spectrum are
79 * constant or variable;
80 *
81 * The spectra contain or not 0-value m/z data points;
82
83*/
85{
86
87 public:
91 BinningType binningType,
92 int decimalPlaces,
93 pappso::PrecisionPtr precisionPtr,
94 bool applyMzShift,
96 bool removeZeroValDataPoints);
97
99
100 virtual ~MzIntegrationParams();
101
102 MzIntegrationParams &operator=(const MzIntegrationParams &other);
103
104 void setSmallestMz(pappso::pappso_double value);
105 void updateSmallestMz(pappso::pappso_double value);
106 pappso::pappso_double getSmallestMz() const;
107
108 void setGreatestMz(pappso::pappso_double value);
109 void updateGreatestMz(pappso::pappso_double value);
110 pappso::pappso_double getGreatestMz() const;
111
112 void setBinningType(BinningType binningType);
113 BinningType getBinningType() const;
114
115 void setDecimalPlaces(int decimal_places);
116 int getDecimalPlaces() const;
117
118 void setPrecision(pappso::PrecisionPtr precisionPtr);
119 pappso::PrecisionPtr getPrecision() const;
120
121 void setApplyMzShift(bool applyMzShift);
122 bool isApplyMzShift() const;
123
124 void setMzShift(double value);
125 double getMzShift() const;
126
127 void setRemoveZeroValDataPoints(bool removeOrNot = true);
128 bool isRemoveZeroValDataPoints() const;
129
130 void reset();
131
132 bool isValid() const;
133
134 bool hasValidMzRange() const;
135
136 std::vector<pappso::pappso_double> createBins();
137 std::vector<pappso::pappso_double>
138 createBins(pappso::MassSpectrumCstSPtr mass_spectrum_csp);
139
140 QString toString(int offset = 0, const QString &spacer = QString()) const;
141
142 private:
143 // That smallest value needs to be set to max, because it will be necessary
144 // compare any new m/z valut to it.
145 pappso::pappso_double m_smallestMz = std::numeric_limits<double>::max();
146
147 // That greatest value needs to be set to min, because it will be necessary
148 // compare any new m/z valut to it.
149 pappso::pappso_double m_greatestMz = std::numeric_limits<double>::min();
150
152
153 int m_decimalPlaces = -1;
154
155 // This should actually be called "bin size" as it describes the width of
156 // the bins.
157 pappso::PrecisionPtr mp_precision =
159 bool m_applyMzShift = false;
161 bool m_removeZeroValDataPoints = true;
162
163 std::vector<double> createArbitraryBins();
164 std::vector<double>
165 createDataBasedBins(pappso::MassSpectrumCstSPtr massSpectrum);
166};
167
168
169} // namespace pappso
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
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:48
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::map< BinningType, QString > binningTypeMap
Map relating the BinningType to a textual representation.