GCC Code Coverage Report

./
File: src/XpertMass/IsotopicDataBaseHandler.cpp
Date: 2024-08-24 11:26:06
Lines:
13/31
41.9%
Functions:
4/10
40.0%
Branches:
2/18
11.1%
Line Branch Exec Source
1 /* BEGIN software license
2 *
3 * MsXpertSuite - mass spectrometry software suite
4 * -----------------------------------------------
5 * Copyright (C) 2009--2020 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 /////////////////////// Qt includes
35 #include <QDebug>
36
37
38 /////////////////////// IsoSpec
39 #include <IsoSpec++/isoSpec++.h>
40 #include <IsoSpec++/element_tables.h>
41
42
43 /////////////////////// Local includes
44 #include "globals.hpp"
45 #include "PeakCentroid.hpp"
46 #include "IsotopicDataBaseHandler.hpp"
47
48
49 namespace MsXpS
50 {
51
52 namespace libXpertMass
53 {
54
55 /*!
56 \class MsXpS::libXpertMass::IsotopicDataBaseHandler
57 \inmodule libXpertMass
58 \ingroup PolChemDefBuildingdBlocks
59 \inheaderfile IsotopicDataBaseHandler.hpp
60
61 \brief The IsotopicDataBaseHandler class features basic handling of
62 \l{IsotopicData}.
63
64 The IsotopicDataBaseHandler class provides the skeleton for derived classes
65 to handle \l{IsotopicData}.
66
67 There are different isotopic data handlers:
68
69 \list
70 \li The \l{IsotopicDataLibraryHandler} that handles isotopic data from the
71 IsoSpec element data tables directly from the library's data. These are the
72 reference, pristine \e{unmodified} isotopic data.
73 \li The \l{IsotopicDataUserConfigHandler} that handles isotopic data with the
74 exact same format of those from the IsoSpec element data tables. However, these
75 data correspond to user-modified isotopic data, \e{not} the reference, pristine
76 \e{unmodified} isotopic data.
77 \li The \l{IsotopicDataManualConfigHandler} that handles user-defined data
78 according to an entirely different format. These data are typically used when
79 the user defines new chemical elements that cannot fit in the IsoSpec element
80 data tables format.
81 \endlist
82
83 \sa IsotopicDataLibraryHandler, IsotopicDataUserConfigHandler,
84 IsotopicDataManualConfigHandler
85 */
86
87 /*!
88 \variable int MsXpS::libXpertMass::IsotopicDataBaseHandler::msp_isotopicData
89
90 \brief The msp_isotopicData is a pointer to \l{IsotopicData}.
91 */
92
93 /*!
94 \variable int MsXpS::libXpertMass::IsotopicDataBaseHandler::m_fileName
95
96 \brief The m_fileName is the filename in which to store the \l{IsotopicData}
97 for from with to load the \l{IsotopicData}.
98 */
99
100 /*!
101 \brief Constructs the \l{IsotopicDataBaseHandler} with \a file_name.
102
103 The msp_isotopicData is initialized by creating an empty IsotopicData
104 instance.
105 */
106 74 IsotopicDataBaseHandler::IsotopicDataBaseHandler(const QString &file_name)
107 74 : m_fileName(file_name)
108 {
109 // We cannot allow to have a nullptr msp_isotopicData member.
110
1/2
✓ Branch 1 taken 74 times.
✗ Branch 2 not taken.
 74 msp_isotopicData = std::make_shared<IsotopicData>();
111 74 }
112
113 /*!
114 \brief Constructs the \l{IsotopicDataBaseHandler}.
115
116 \a isotopic_data_sp Isotopic data
117
118 \a file_name File name
119 */
120 396 IsotopicDataBaseHandler::IsotopicDataBaseHandler(
121 396 IsotopicDataSPtr isotopic_data_sp, const QString &file_name)
122 396 : msp_isotopicData(isotopic_data_sp), m_fileName(file_name)
123 {
124 // We cannot allow to have a nullptr msp_isotopicData member.
125
1/2
✗ Branch 1 not taken.
✓ Branch 2 taken 396 times.
 396 if(msp_isotopicData == nullptr)
126 ✗ msp_isotopicData = std::make_shared<IsotopicData>();
127 396 }
128
129 /*!
130 \brief Destructs the \l{IsotopicDataBaseHandler}.
131 */
132 964 IsotopicDataBaseHandler::~IsotopicDataBaseHandler()
133 {
134 // qDebug();
135 964 }
136
137
138 std::size_t
139 ✗ IsotopicDataBaseHandler::loadData([[maybe_unused]] const QString &file_name)
140 {
141 ✗ qDebug() << "The base class does not load data.";
142 ✗ return 0;
143 }
144
145 std::size_t
146 ✗ IsotopicDataBaseHandler::writeData([[maybe_unused]] const QString &file_name)
147 {
148 ✗ qDebug() << "The base class does not write data.";
149 ✗ return 0;
150 }
151
152 /*!
153 \brief Sets the IsotopicData to \a isotopic_data_sp.
154 */
155 void
156 ✗ IsotopicDataBaseHandler::setIsotopicData(IsotopicDataSPtr isotopic_data_sp)
157 {
158 ✗ msp_isotopicData = isotopic_data_sp;
159 ✗ }
160
161 /*!
162 \brief Returns the IsotopicData
163 */
164 IsotopicDataSPtr
165 136 IsotopicDataBaseHandler::getIsotopicData()
166 {
167 136 return msp_isotopicData;
168 }
169
170 /*!
171 \brief Sets the file name to \a file_name
172 */
173 void
174 ✗ IsotopicDataBaseHandler::setFileName(const QString &file_name)
175 {
176 ✗ m_fileName = file_name;
177 ✗ }
178
179 /*!
180 \brief Returns the file name
181 */
182 QString
183 ✗ IsotopicDataBaseHandler::getFileName()
184 {
185 ✗ return m_fileName;
186 }
187
188
189 std::size_t
190 ✗ IsotopicDataBaseHandler::checkConsistency()
191 {
192 ✗ qDebug() << "The base class does not check consistenty.";
193 ✗ return 0;
194 }
195
196 } // namespace libXpertMass
197
198 } // namespace MsXpS
199
200
201 #if 0
202
203 Example from IsoSpec.
204
205 For water H2O
206
207 const int elementNumber = 2;
208 const int isotopeNumbers[2] = {2,3};
209
210 const int atomCounts[2] = {2,1};
211
212
213 const double hydrogen_masses[2] = {1.00782503207, 2.0141017778};
214 const double oxygen_masses[3] = {15.99491461956, 16.99913170, 17.9991610};
215
216 const double* isotope_masses[2] = {hydrogen_masses, oxygen_masses};
217
218 const double hydrogen_probs[2] = {0.5, 0.5};
219 const double oxygen_probs[3] = {0.5, 0.3, 0.2};
220
221 const double* probs[2] = {hydrogen_probs, oxygen_probs};
222
223 IsoLayeredGenerator iso(Iso(elementNumber, isotopeNumbers, atomCounts,
224 isotope_masses, probs), 0.99);
225
226 #endif
227