GCC Code Coverage Report

Line	Branch	Exec	Source
1			// ./tests/catch2-tests [section] -s
2
3
4			/////////////////////// Qt includes
5			#include <QDebug>
6			#include <QString>
7			#include <QDir>
8
9
10			/////////////////////// IsoSpec
11			#include <IsoSpec++/isoSpec++.h>
12			#include <IsoSpec++/element_tables.h>
13
14
15			/////////////////////// Catch2 includes
16			#include <catch2/catch_test_macros.hpp>
17			#include <catch2/matchers/catch_matchers_floating_point.hpp>
18
19
20			/////////////////////// Local includes
21			#include "tests-config.h"
22			#include "TestUtils.hpp"
23			#include <libXpertMass/Modif.hpp>
24
25			namespace MsXpS
26			{
27
28			namespace libXpertMass
29			{
30
31
32		44	SCENARIO("Modif_s are created in the context of a PolChemDef")
33			{
34	1/2 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken.	44	TestUtils test_utils;
35	1/2 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken.	44	test_utils.m_polChemDefName = "protein-1-letter";
36	1/2 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken.	44	test_utils.m_polChemDefDirName = "protein-1-letter";
37	1/2 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken.	44	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
38
39	1/2 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken.	44	test_utils.initializePolChemDef();
40		44	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
41
42	6/16 ✓ Branch 4 taken 44 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 44 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 44 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 44 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 44 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 44 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	44	REQUIRE(pol_chem_def_csp->codeLength() == 1);
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45	6/16 ✓ Branch 4 taken 44 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 44 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 44 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 44 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 44 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 44 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	44	REQUIRE(pol_chem_def_csp->crossLinkerList().size() == 2);
46	6/16 ✓ Branch 4 taken 44 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 44 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 44 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 44 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 44 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 44 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	44	REQUIRE(pol_chem_def_csp->cleaveSpecList().size() == 8);
47	6/16 ✓ Branch 4 taken 44 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 44 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 44 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 44 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 44 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 44 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	44	REQUIRE(pol_chem_def_csp->fragSpecList().size() == 7);
48
49	8/14 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 44 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 44 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 44 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 44 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 44 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 16 times. ✓ Branch 24 taken 28 times.	44	GIVEN("An allocated polymer chemistry definition")
50			{
51
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53			{
54			Modif modif_1 = Modif(
55	2/4 ✓ Branch 2 taken 16 times. ✗ Branch 3 not taken. ✓ Branch 6 taken 16 times. ✗ Branch 7 not taken.	16	pol_chem_def_csp, "Acetylation", test_utils.m_acetylationFormulaString);
56
57	8/14 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 16 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 16 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 16 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 12 times.	16	THEN("Checks can be performed")
58			{
59	8/20 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 4 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 4 times. ✗ Branch 20 not taken. ✓ Branch 22 taken 4 times. ✗ Branch 23 not taken. ✓ Branch 29 taken 4 times. ✗ Branch 30 not taken. ✗ Branch 38 not taken. ✗ Branch 39 not taken. ✗ Branch 41 not taken. ✗ Branch 42 not taken.	4	REQUIRE(modif_1.formula().toStdString() ==
60			test_utils.m_acetylationFormulaString.toStdString());
61
62	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 4 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	4	REQUIRE(modif_1.isNameKnown() != -1);
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64			pol_chem_def_csp->modifList()) != -1);
65	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 4 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	4	REQUIRE(modif_1.validate() == true);
66		16	}
67
68	8/14 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 16 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 16 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 16 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 12 times.	16	AND_WHEN("setTargets is called")
69			{
70	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	modif_1.setTargets("K");
71
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73
74			{
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76		4	}
77		16	}
78
79	8/14 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 16 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 16 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 16 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 12 times.	16	AND_WHEN("calculateMasses() has not been called")
80			{
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82			{
83		4	double mono = 0;
84		4	double avg = 0;
85
86	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 4 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	4	REQUIRE(modif_1.accountMasses(&mono, &avg) == true);
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89		4	}
90		16	}
91
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93			{
94	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 4 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	4	REQUIRE(modif_1.calculateMasses() == true);
95
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97			{
98			// qDebug() << "The formula: " << modif_1.formula().toStdString();
99
100		4	double mono = 0;
101		4	double avg = 0;
102
103	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 4 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	4	REQUIRE(modif_1.accountMasses(&mono, &avg) == true);
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105			Catch::Matchers::WithinAbs(42.0105646847, 0.0000000001));
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107			Catch::Matchers::WithinAbs(42.0369401545, 0.0000000001));
108
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110			{
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112		4	}
113		4	}
114		16	}
115		32	}
116		44	}
117
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119			{
120
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122			{
123			Modif modif_1 = Modif(
124	2/4 ✓ Branch 2 taken 20 times. ✗ Branch 3 not taken. ✓ Branch 6 taken 20 times. ✗ Branch 7 not taken.	20	pol_chem_def_csp, "Acetylation", test_utils.m_acetylationFormulaString);
125
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127			{
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129
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131			"A copy-constructed Modif can be allocated and tested for equality")
132			{
133	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	Modif modif_2(modif_1);
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136
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138			{
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140
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143		16	}
144
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146			{
147			// qDebug() << "The formula: " << modif_2.formula().toStdString();
148	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	modif_2.setMasses(120, 130);
149
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152		16	}
153
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155			"If the Modif name is changed, the tests results must negate")
156			{
157			// qDebug() << "The formula: " << modif_2.formula().toStdString();
158	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	modif_2.setName("Phosphorylation");
159
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162		16	}
163
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165			"If the Modif targets is changed, the tests results must negate")
166			{
167			// qDebug() << "The formula: " << modif_2.formula().toStdString();
168	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	modif_2.setTargets("S;T;Y");
169
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172		16	}
173		36	}
174
175	8/14 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 20 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 20 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 20 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 20 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 16 times.	20	THEN(
176			"An operator= assignment-constructed Modif can be allocated and "
177			"tested for equality")
178			{
179	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Modif modif_3 = modif_1;
180	5/14 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 17 taken 4 times. ✗ Branch 18 not taken. ✗ Branch 23 not taken. ✗ Branch 24 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken.	4	REQUIRE(modif_3 == modif_1);
181	6/16 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 4 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 4 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	4	REQUIRE_FALSE(modif_3 != modif_1);
182		24	}
183		20	}
184		40	}
185		44	}
186
187	8/14 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 44 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 44 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 44 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 44 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 44 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 40 times.	44	GIVEN("An allocated polymer chemistry definition")
188			{
189
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191			{
192			Modif modif_1 = Modif(
193	2/4 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken. ✓ Branch 6 taken 4 times. ✗ Branch 7 not taken.	4	pol_chem_def_csp, "Acetylation", test_utils.m_acetylationFormulaString);
194	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	modif_1.setTargets("K");
195
196	7/14 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 4 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 4 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 4 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✗ Branch 24 not taken.	4	THEN("The Modif might be printed out as an XML string")
197			{
198	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	QString expected_string = "<mdf>\n";
199	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	expected_string += " <name>Acetylation</name>\n";
200	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	expected_string += " <formula>-H2O+CH3COOH</formula>\n";
201	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	expected_string += " <targets>;K;</targets>\n";
202	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	expected_string += " <maxcount>1</maxcount>\n";
203	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	expected_string += "</mdf>\n";
204
205			QString *formatted_xml_element_string_p =
206	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	modif_1.formatXmlMdfElement(0, " ");
207
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209			expected_string.toStdString());
210		8	}
211		8	}
212		44	}
213
214	8/14 ✓ Branch 1 taken 44 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 44 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 44 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 44 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 44 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 44 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 40 times.	44	GIVEN("An allocated polymer chemistry definition and a QDomDocument")
215			{
216	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	QDomDocument document;
217
218	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomElement mdf_element = document.createElement("mdf");
219
220
221	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomElement name_element = document.createElement("name");
222	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomText name_text = document.createTextNode("Acetylation");
223	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	name_element.appendChild(name_text);
224
225	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomElement formula_element = document.createElement("formula");
226			QDomText formula_text =
227	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	document.createTextNode(test_utils.m_acetylationFormulaString);
228	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	formula_element.appendChild(formula_text);
229
230	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomElement targets_element = document.createElement("targets");
231	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomText targets_text = document.createTextNode("K");
232	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	targets_element.appendChild(targets_text);
233
234	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomElement maxcount_element = document.createElement("maxcount");
235	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	QDomText maxcount_text = document.createTextNode("1");
236	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	maxcount_element.appendChild(maxcount_text);
237
238	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	mdf_element.appendChild(name_element);
239	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	mdf_element.appendChild(formula_element);
240	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	mdf_element.appendChild(targets_element);
241	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	mdf_element.appendChild(maxcount_element);
242
243	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	document.appendChild(mdf_element);
244
245	4/8 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken. ✓ Branch 5 taken 4 times. ✗ Branch 6 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken.	4	qDebug() << "The document:" << document.toString();
246
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248			document.toString().toStdString() ==
249			"<mdf>\n <name>Acetylation</name>\n <formula>-H2O+CH3COOH</formula>\n "
250			"<targets>K</targets>\n <maxcount>1</maxcount>\n</mdf>\n");
251
252
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254			{
255	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	Modif modif_1 = Modif(pol_chem_def_csp, mdf_element, 1);
256
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258			{
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263		4	}
264		8	}
265		48	}
266		44	}
267
268			} // namespace libXpertMass
269			} // namespace MsXpS
270