GCC Code Coverage Report

Line	Branch	Exec	Source
1			// ./tests/catch2-tests [section] -s
2
3
4			/////////////////////// Stdlib includes
5			#include <cassert>
6
7			/////////////////////// Qt includes
8			#include <QDebug>
9			#include <QString>
10			#include <QDir>
11
12
13			/////////////////////// IsoSpec
14			#include <IsoSpec++/isoSpec++.h>
15			#include <IsoSpec++/element_tables.h>
16
17
18			/////////////////////// Catch2 includes
19			#include <catch2/catch_test_macros.hpp>
20			#include <catch2/matchers/catch_matchers_floating_point.hpp>
21
22
23			/////////////////////// Local includes
24			#include "tests-config.h"
25			#include <libXpertMass/globals.hpp>
26			#include <libXpertMass/IsotopicData.hpp>
27			#include <libXpertMass/PolChemDefSpec.hpp>
28			#include <libXpertMass/PolChemDef.hpp>
29
30			namespace MsXpS
31			{
32
33			namespace libXpertMass
34			{
35
36			// In the tests below, we do not use TestUtils because we want
37			// more granularity that what is -by design- offered by TestUtils.
38		20	SCENARIO(
39			"PolChemDef instantiated using the specification in a PolChemDefSpec "
40			"instance")
41			{
42	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	PolChemDefSpec pol_chem_def_spec;
43	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	PolChemDef pol_chem_def;
44
45			// We use polymer chemistry definitions copied to the
46			// tests/data/polymer-chemistry-definitions directory.
47			QString test_pol_chem_defs_dir =
48	3/6 ✓ 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.	40	QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
49
50	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString pol_chem_def_name = "protein-1-letter";
51			QString pol_chem_def_file_base_name =
52	2/4 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken.	40	QString("%1.xml").arg(pol_chem_def_name);
53
54			// Relative is to one of the polChemDefs directory (in system or user
55			// directory)
56	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString pol_chem_def_relative_dir_path = "protein-1-letter";
57
58			QString pol_chem_def_relative_file_path =
59	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2")
60	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(pol_chem_def_relative_dir_path)
61	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	.arg(pol_chem_def_file_base_name);
62
63			QString pol_chem_def_absolute_dir_path =
64	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2")
65	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(test_pol_chem_defs_dir)
66	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	.arg(pol_chem_def_relative_dir_path);
67
68			QString pol_chem_def_absolute_file_path =
69	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2")
70	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(pol_chem_def_absolute_dir_path)
71	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	.arg(pol_chem_def_file_base_name);
72
73
74	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	GIVEN("Constructing an empty PolChemDefSpec")
75			{
76
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78			{
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81		4	}
82		20	}
83
84	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 16 times. ✓ Branch 24 taken 4 times.	20	AND_GIVEN("Set name and file path")
85			{
86	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	pol_chem_def_spec.setName(pol_chem_def_file_base_name);
87	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	pol_chem_def_spec.setFilePath(pol_chem_def_relative_file_path);
88
89	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("The name and file path are set to the member data")
90			{
91	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 28 taken 4 times. ✗ Branch 29 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken. ✗ Branch 39 not taken. ✗ Branch 40 not taken.	4	REQUIRE(pol_chem_def_spec.name().toStdString() ==
92			pol_chem_def_file_base_name.toStdString());
93	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(pol_chem_def_spec.getFilePath().toStdString() ==
94			pol_chem_def_relative_file_path.toStdString());
95		16	}
96
97	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 12 times. ✓ Branch 24 taken 4 times.	16	AND_GIVEN("That PolChemDefSpec, allocate a PolChemDef")
98			{
99	1/2 ✓ Branch 1 taken 12 times. ✗ Branch 2 not taken.	12	PolChemDef pol_chem_def(pol_chem_def_spec);
100
101	8/14 ✓ Branch 1 taken 12 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 12 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 12 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 12 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 12 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 12 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 8 times.	12	THEN("The PolChemDef name is set to the PolChemDefSpec name")
102			{
103	9/22 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✓ Branch 32 taken 4 times. ✗ Branch 33 not taken. ✗ Branch 41 not taken. ✗ Branch 42 not taken. ✗ Branch 44 not taken. ✗ Branch 45 not taken.	4	REQUIRE(pol_chem_def.name().toStdString() ==
104			pol_chem_def_spec.name().toStdString());
105		12	}
106
107	8/14 ✓ Branch 1 taken 12 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 12 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 12 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 12 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 12 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 12 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 8 times.	12	AND_THEN("The file path is set also")
108			{
109	9/22 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✓ Branch 33 taken 4 times. ✗ Branch 34 not taken. ✗ Branch 43 not taken. ✗ Branch 44 not taken. ✗ Branch 46 not taken. ✗ Branch 47 not taken.	4	REQUIRE(pol_chem_def.getXmlDataFilePath().toStdString() ==
110			pol_chem_def_spec.getFilePath().toStdString());
111		12	}
112
113	8/14 ✓ Branch 1 taken 12 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 12 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 12 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 12 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 12 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 12 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 8 times.	12	AND_THEN("Code length value is 1")
114			{
115	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(pol_chem_def.codeLength() == 1);
116		12	}
117		28	}
118		20	}
119		20	}
120
121
122		20	SCENARIO("PolChemDef instantiated empty")
123			{
124	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	PolChemDef pol_chem_def;
125		20	PolChemDefSPtr pol_chem_def_sp = nullptr;
126
127			// We use polymer chemistry definitions copied to the
128			// tests/data/polymer-chemistry-definitions directory.
129			QString test_pol_chem_defs_dir =
130	3/6 ✓ 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.	40	QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
131
132	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString pol_chem_def_name = "protein-1-letter";
133			QString pol_chem_def_file_base_name =
134	2/4 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken.	40	QString("%1.xml").arg(pol_chem_def_name);
135
136			// Relative is to one of the polChemDefs directory (in system or user
137			// directory)
138	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString pol_chem_def_relative_dir_path = "protein-1-letter";
139
140			QString pol_chem_def_relative_file_path =
141	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2")
142	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(pol_chem_def_relative_dir_path)
143	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	.arg(pol_chem_def_file_base_name);
144
145			QString pol_chem_def_isotopic_data_relative_file_path =
146	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2/%3")
147	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(pol_chem_def_relative_dir_path)
148	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(pol_chem_def_file_base_name)
149	2/4 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken.	20	.arg("isotopic-data.dat");
150
151			QString pol_chem_def_absolute_dir_path =
152	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2")
153	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(test_pol_chem_defs_dir)
154	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	.arg(pol_chem_def_relative_dir_path);
155
156			// qDebug() << "The dir: " << pol_chem_def_absolute_dir_path.toStdString()
157			// << std::endl;
158
159			QString pol_chem_def_absolute_file_path =
160	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2")
161	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(pol_chem_def_absolute_dir_path)
162	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	.arg(pol_chem_def_file_base_name);
163
164			QString pol_chem_def_isotopic_data_absolute_file_path =
165	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	QString("%1/%2")
166	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	40	.arg(pol_chem_def_absolute_dir_path)
167	2/4 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken.	20	.arg("isotopic-data.dat");
168
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170			{
171
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173			{
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176		4	}
177		20	}
178
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180			{
181	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	pol_chem_def.setName(pol_chem_def_file_base_name);
182	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	pol_chem_def.setXmlDataFilePath(pol_chem_def_absolute_file_path);
183
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185			{
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187			pol_chem_def_file_base_name.toStdString());
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189			pol_chem_def_absolute_file_path.toStdString());
190	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(pol_chem_def.getXmlDataDirPath().toStdString() ==
191			pol_chem_def_absolute_dir_path.toStdString());
192		16	}
193
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195			{
196			QString isotopic_data_file_path =
197	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	pol_chem_def.deduceIsotopicDataFilePath();
198
199	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(isotopic_data_file_path.toStdString() ==
200			pol_chem_def_isotopic_data_absolute_file_path.toStdString());
201		20	}
202
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204			{
205
206			// REQUIRE(pol_chem_def.name().toStdString() ==
207			// pol_chem_def_file_base_name.toStdString());
208			// REQUIRE(pol_chem_def.getXmlDataFilePath().toStdString() ==
209			// pol_chem_def_absolute_file_path.toStdString());
210			// REQUIRE(pol_chem_def.getXmlDataDirPath().toStdString() ==
211			// pol_chem_def_absolute_dir_path.toStdString());
212
213	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	pol_chem_def_sp = std::make_shared<PolChemDef>(pol_chem_def);
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216
217	1/2 ✓ Branch 3 taken 8 times. ✗ Branch 4 not taken.	8	std::size_t isotope_count = PolChemDef::loadIsotopicData(pol_chem_def_sp);
218
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220			{
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222			// qDebug() << "Loaded " << isotope_count << " isotopes" << std::endl;
223		8	}
224
225	8/14 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 8 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 8 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 4 times.	8	WHEN("Loading the polymer chemistry definition using static function")
226			{
227	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(pol_chem_def_sp != nullptr);
228
229	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	bool result = PolChemDef::renderXmlPolChemDefFile(pol_chem_def_sp);
230
231	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("That should not fail")
232			{
233
234	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(result == true);
235		4	}
236		8	}
237		16	}
238		20	}
239		20	}
240
241		36	SCENARIO("Loading a PolChemDef")
242			{
243	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	PolChemDef pol_chem_def;
244		36	PolChemDefSPtr pol_chem_def_sp = nullptr;
245
246			// We use polymer chemistry definitions copied to the
247			// tests/data/polymer-chemistry-definitions directory.
248			QString test_pol_chem_defs_dir =
249	3/6 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken.	72	QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
250
251	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	QString pol_chem_def_name = "protein-1-letter";
252			QString pol_chem_def_file_base_name =
253	2/4 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken.	72	QString("%1.xml").arg(pol_chem_def_name);
254
255			// Relative is to one of the polChemDefs directory (in system or user
256			// directory)
257	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	QString pol_chem_def_relative_dir_path = "protein-1-letter";
258
259			QString pol_chem_def_relative_file_path =
260	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	QString("%1/%2")
261	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	72	.arg(pol_chem_def_relative_dir_path)
262	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	.arg(pol_chem_def_file_base_name);
263
264			QString pol_chem_def_isotopic_data_relative_file_path =
265	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	QString("%1/%2/%3")
266	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	72	.arg(pol_chem_def_relative_dir_path)
267	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	72	.arg(pol_chem_def_file_base_name)
268	2/4 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken.	36	.arg("isotopic-data.dat");
269
270			QString pol_chem_def_absolute_dir_path =
271	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	QString("%1/%2")
272	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	72	.arg(test_pol_chem_defs_dir)
273	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	.arg(pol_chem_def_relative_dir_path);
274
275			// qDebug() << "The dir: " << pol_chem_def_absolute_dir_path.toStdString()
276			// << std::endl;
277
278			QString pol_chem_def_absolute_file_path =
279	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	QString("%1/%2")
280	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	72	.arg(pol_chem_def_absolute_dir_path)
281	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	.arg(pol_chem_def_file_base_name);
282
283			QString pol_chem_def_isotopic_data_absolute_file_path =
284	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	QString("%1/%2")
285	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	72	.arg(pol_chem_def_absolute_dir_path)
286	2/4 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken.	36	.arg("isotopic-data.dat");
287
288	1/2 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken.	36	pol_chem_def_sp = std::make_shared<PolChemDef>(pol_chem_def);
289
290	1/2 ✓ Branch 2 taken 36 times. ✗ Branch 3 not taken.	36	pol_chem_def_sp->setName(pol_chem_def_file_base_name);
291	1/2 ✓ Branch 2 taken 36 times. ✗ Branch 3 not taken.	36	pol_chem_def_sp->setXmlDataFilePath(pol_chem_def_absolute_file_path);
292
293	7/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 36 times. ✗ Branch 24 not taken.	36	GIVEN("Loading isotopic data and polymer chemistry definition")
294			{
295	1/2 ✓ Branch 3 taken 36 times. ✗ Branch 4 not taken.	36	std::size_t isotope_count = PolChemDef::loadIsotopicData(pol_chem_def_sp);
296	1/2 ✓ Branch 2 taken 36 times. ✗ Branch 3 not taken.	36	bool result = PolChemDef::renderXmlPolChemDefFile(pol_chem_def_sp);
297
298	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	THEN(
299			"Count the isotopes that have been loaded and check PolChemDef load was "
300			"successful")
301			{
302	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(isotope_count > 0);
303			// qDebug() << "Loaded " << isotope_count << " isotopes" << std::endl;
304	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(result == true);
305		36	}
306	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	AND_THEN("The singular chemical entities are checked (end cap chemistry")
307			{
308	8/20 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 4 times. ✗ Branch 8 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 4 times. ✗ Branch 18 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✓ Branch 23 taken 4 times. ✗ Branch 24 not taken. ✓ Branch 30 taken 4 times. ✗ Branch 31 not taken. ✗ Branch 39 not taken. ✗ Branch 40 not taken. ✗ Branch 42 not taken. ✗ Branch 43 not taken.	4	REQUIRE(pol_chem_def_sp->name().toStdString() ==
309			pol_chem_def_name.toStdString());
310	8/20 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 4 times. ✗ Branch 18 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✓ Branch 23 taken 4 times. ✗ Branch 24 not taken. ✓ Branch 29 taken 4 times. ✗ Branch 30 not taken. ✗ Branch 37 not taken. ✗ Branch 38 not taken. ✗ Branch 40 not taken. ✗ Branch 41 not taken.	4	REQUIRE(pol_chem_def_sp->leftCap().toString().toStdString() ==
311			"\"N-term amine\" +H");
312	8/20 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 4 times. ✗ Branch 18 not taken. ✓ Branch 20 taken 4 times. ✗ Branch 21 not taken. ✓ Branch 23 taken 4 times. ✗ Branch 24 not taken. ✓ Branch 29 taken 4 times. ✗ Branch 30 not taken. ✗ Branch 37 not taken. ✗ Branch 38 not taken. ✗ Branch 40 not taken. ✗ Branch 41 not taken.	4	REQUIRE(pol_chem_def_sp->rightCap().toString().toStdString() ==
313			"\"C-term carboxylic acid\" +OH");
314		36	}
315
316	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	AND_THEN("And the ionization rule is checked")
317			{
318	2/4 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken. ✓ Branch 5 taken 4 times. ✗ Branch 6 not taken.	4	IonizeRule ionize_rule = pol_chem_def_sp->ionizeRule();
319	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(ionize_rule.formula().toStdString() == "+H");
320	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(ionize_rule.charge() == 1);
321	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(ionize_rule.level() == 1);
322		40	}
323
324	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	AND_THEN("And the code length is checked")
325			{
326	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 4 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 4 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	4	REQUIRE(pol_chem_def_sp->codeLength() == 1);
327		36	}
328
329	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	AND_THEN("The Monomer_s are checked")
330			{
331		4	Monomer *monomer_p = nullptr;
332
333			// Because of diaminopimelic acid, not 20, but 21.
334	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 4 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 4 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 4 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	4	REQUIRE(pol_chem_def_sp->monomerList().size() == 21);
335
336	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	monomer_p = pol_chem_def_sp->monomerList().at(0);
337	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->name().toStdString() == "Glycine");
338	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->code().toStdString() == "G");
339	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->formula().toStdString() == "C2H3N1O1");
340
341	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	monomer_p = pol_chem_def_sp->monomerList().at(4);
342	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->name().toStdString() == "DiaminoPimelic");
343	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->code().toStdString() == "O");
344	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->formula().toStdString() == "C7H12N2O3");
345
346	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	monomer_p = pol_chem_def_sp->monomerList().at(12);
347	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->name().toStdString() == "Aspartate");
348	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->code().toStdString() == "D");
349	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->formula().toStdString() == "C4H5N1O3");
350
351	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	monomer_p = pol_chem_def_sp->monomerList().at(20);
352	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->name().toStdString() == "Proline");
353	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->code().toStdString() == "P");
354	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(monomer_p->formula().toStdString() == "C5H7N1O1");
355		36	}
356
357	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	AND_THEN("The Modif_s are checked")
358			{
359		4	Modif *modif_p = nullptr;
360
361	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 4 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 4 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 4 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	4	REQUIRE(pol_chem_def_sp->modifList().size() == 26);
362
363	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	modif_p = pol_chem_def_sp->modifList().at(0);
364	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Acetylation");
365	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->formula().toStdString() == "C2H2O1");
366	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->targets().toStdString() == ";K;");
367	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_p->maxCount() == 1);
368
369	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	modif_p = pol_chem_def_sp->modifList().at(5);
370	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "CarboxyMethylation");
371	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->formula().toStdString() == "C2H2O2");
372	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->targets().toStdString() == ";C;");
373	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_p->maxCount() == 1);
374
375	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	modif_p = pol_chem_def_sp->modifList().at(8);
376	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Chromo-H3");
377	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->formula().toStdString() == "-H3");
378	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->targets().toStdString() == ";Y;F;W;");
379	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_p->maxCount() == 1);
380
381	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	modif_p = pol_chem_def_sp->modifList().at(12);
382	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Formylation");
383	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->formula().toStdString() == "C1O1");
384	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->targets().toStdString() == "*");
385	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_p->maxCount() == 1);
386
387	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	modif_p = pol_chem_def_sp->modifList().at(15);
388	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Glycylation");
389	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->formula().toStdString() == "C2H3N1O1");
390	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->targets().toStdString() == ";E;");
391	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_p->maxCount() == 34);
392
393	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	modif_p = pol_chem_def_sp->modifList().at(20);
394	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Phosphorylation");
395	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->formula().toStdString() == "H1O3P1");
396	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->targets().toStdString() == ";S;T;Y;");
397	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_p->maxCount() == 1);
398		36	}
399
400	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	AND_THEN("The CrossLinker_s are checked")
401			{
402		4	CrossLinker *crossLinker_p = nullptr;
403		4	QList<Modif *> modifList;
404		4	Modif *modif_p = nullptr;
405
406	6/16 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 4 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 4 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 4 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	4	REQUIRE(pol_chem_def_sp->crossLinkerList().size() == 2);
407
408	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	crossLinker_p = pol_chem_def_sp->crossLinkerList().at(0);
409	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(crossLinker_p->name().toStdString() == "CFP-chromophore");
410	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(crossLinker_p->formula().toStdString() == "");
411
412	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	modifList = crossLinker_p->modifList();
413	5/14 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✗ Branch 24 not taken. ✗ Branch 25 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken.	4	REQUIRE(modifList.size() == 3);
414
415		4	modif_p = modifList.at(0);
416	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Chromo-O");
417		4	modif_p = modifList.at(1);
418	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Chromo-H3");
419		4	modif_p = modifList.at(2);
420	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "Chromo-H");
421
422	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	crossLinker_p = pol_chem_def_sp->crossLinkerList().at(1);
423	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(crossLinker_p->name().toStdString() == "DisulfideBond");
424	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(crossLinker_p->formula().toStdString() == "");
425
426	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	modifList = crossLinker_p->modifList();
427	5/14 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✗ Branch 24 not taken. ✗ Branch 25 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken.	4	REQUIRE(modifList.size() == 2);
428
429		4	modif_p = modifList.at(0);
430	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "ProtonLoss");
431		4	modif_p = modifList.at(1);
432	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(modif_p->name().toStdString() == "ProtonLoss");
433		40	}
434
435	8/14 ✓ Branch 1 taken 36 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 36 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 36 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 36 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 36 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 36 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 32 times.	36	AND_THEN("The CleaveSpec_s are checked (and the CleaveRules_ if any)")
436			{
437		4	CleaveSpec *cleave_spec_p = nullptr;
438	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	QList<CleaveSpec *> cleave_spec_list = pol_chem_def_sp->cleaveSpecList();
439
440	5/14 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✗ Branch 24 not taken. ✗ Branch 25 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken.	4	REQUIRE(cleave_spec_list.size() == 8);
441
442		4	cleave_spec_p = cleave_spec_list.at(0);
443	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(cleave_spec_p->name().toStdString() == "EndoAspN+GluN");
444	7/18 ✓ 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 24 taken 4 times. ✗ Branch 25 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	4	REQUIRE(cleave_spec_p->pattern().toStdString() == "/D;/E");
445
446		4	cleave_spec_p = cleave_spec_list.at(3);
447	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(cleave_spec_p->name().toStdString() == "EndoLysC");
448	7/18 ✓ 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 24 taken 4 times. ✗ Branch 25 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	4	REQUIRE(cleave_spec_p->pattern().toStdString() == "K/");
449
450		4	cleave_spec_p = cleave_spec_list.at(6);
451	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(cleave_spec_p->name().toStdString() == "CyanogenBromide");
452	7/18 ✓ 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 24 taken 4 times. ✗ Branch 25 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	4	REQUIRE(cleave_spec_p->pattern().toStdString() == "M/");
453
454	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	CleaveRule *cleave_rule_p = cleave_spec_p->ruleList()->at(0);
455	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(cleave_rule_p->name().toStdString() == "Homoseryl");
456	7/18 ✓ 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 24 taken 4 times. ✗ Branch 25 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	4	REQUIRE(cleave_rule_p->rightCode().toStdString() == "M");
457	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 28 taken 4 times. ✗ Branch 29 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken. ✗ Branch 39 not taken. ✗ Branch 40 not taken.	4	REQUIRE(cleave_rule_p->rightFormula().toString().toStdString() ==
458			"-CH2S+O");
459		40	}
460
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462			{
463		4	FragSpec *frag_spec_p = nullptr;
464	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	QList<FragSpec *> frag_spec_list = pol_chem_def_sp->fragSpecList();
465
466	5/14 ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 4 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 4 times. ✗ Branch 15 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✗ Branch 24 not taken. ✗ Branch 25 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken.	4	REQUIRE(frag_spec_list.size() == 7);
467
468		4	frag_spec_p = frag_spec_list.at(0);
469	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(frag_spec_p->name().toStdString() == "a");
470	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(frag_spec_p->fragEnd() == FragEnd::FRAG_END_LEFT);
471	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(frag_spec_p->formula().toStdString() == "-C1O1H1");
472	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(frag_spec_p->monomerContribution() == 0);
473	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(frag_spec_p->comment().toStdString() == "");
474
475		4	frag_spec_p = frag_spec_list.at(3);
476	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(frag_spec_p->name().toStdString() == "z");
477	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(frag_spec_p->fragEnd() == FragEnd::FRAG_END_RIGHT);
478	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(frag_spec_p->formula().toStdString() == "-N1H1");
479	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(frag_spec_p->monomerContribution() == 0);
480	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	4	REQUIRE(frag_spec_p->comment().toStdString() ==
481			"Typically in ECD of protonated ions");
482		40	}
483		36	}
484		36	}
485
486		8	SCENARIO("Loading the same PolChemDef and writing it back")
487			{
488	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	PolChemDef pol_chem_def;
489		8	PolChemDefSPtr pol_chem_def_sp = nullptr;
490
491			// We use polymer chemistry definitions copied to the
492			// tests/data/polymer-chemistry-definitions directory.
493			QString test_pol_chem_defs_dir =
494	3/6 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken.	16	QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
495
496	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString pol_chem_def_name = "protein-1-letter";
497			QString pol_chem_def_file_base_name =
498	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	16	QString("%1.xml").arg(pol_chem_def_name);
499
500			// Relative is to one of the polChemDefs directory (in system or user
501			// directory)
502	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString pol_chem_def_relative_dir_path = "protein-1-letter";
503
504			QString pol_chem_def_relative_file_path =
505	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString("%1/%2")
506	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	16	.arg(pol_chem_def_relative_dir_path)
507	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	.arg(pol_chem_def_file_base_name);
508
509			QString pol_chem_def_isotopic_data_relative_file_path =
510	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString("%1/%2/%3")
511	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	16	.arg(pol_chem_def_relative_dir_path)
512	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	16	.arg(pol_chem_def_file_base_name)
513	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	8	.arg("isotopic-data.dat");
514
515			QString pol_chem_def_absolute_dir_path =
516	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString("%1/%2")
517	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	16	.arg(test_pol_chem_defs_dir)
518	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	.arg(pol_chem_def_relative_dir_path);
519
520			// qDebug() << "The dir: " << pol_chem_def_absolute_dir_path.toStdString()
521			// << std::endl;
522
523			QString pol_chem_def_absolute_file_path =
524	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString("%1/%2")
525	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	16	.arg(pol_chem_def_absolute_dir_path)
526	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	.arg(pol_chem_def_file_base_name);
527
528			QString pol_chem_def_isotopic_data_absolute_file_path =
529	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString("%1/%2")
530	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	16	.arg(pol_chem_def_absolute_dir_path)
531	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	8	.arg("isotopic-data.dat");
532
533	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	pol_chem_def_sp = std::make_shared<PolChemDef>(pol_chem_def);
534
535	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	pol_chem_def_sp->setName(pol_chem_def_file_base_name);
536	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	pol_chem_def_sp->setXmlDataFilePath(pol_chem_def_absolute_file_path);
537
538	1/2 ✓ Branch 3 taken 8 times. ✗ Branch 4 not taken.	8	std::size_t isotope_count = PolChemDef::loadIsotopicData(pol_chem_def_sp);
539	5/14 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 8 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 8 times. ✗ Branch 14 not taken. ✓ Branch 17 taken 8 times. ✗ Branch 18 not taken. ✗ Branch 23 not taken. ✗ Branch 24 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken.	8	REQUIRE(isotope_count == 288);
540
541	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	bool result = PolChemDef::renderXmlPolChemDefFile(pol_chem_def_sp);
542	5/14 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 8 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 8 times. ✗ Branch 14 not taken. ✓ Branch 17 taken 8 times. ✗ Branch 18 not taken. ✗ Branch 23 not taken. ✗ Branch 24 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken.	8	REQUIRE(result == true);
543
544	7/14 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 8 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 8 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 8 times. ✗ Branch 24 not taken.	8	GIVEN("A fully loaded PolChemDef along with its IsotopicData")
545			{
546	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString pol_chem_def_output_dir = QString("%1/%2/%3")
547	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	16	.arg(TESTS_OUTPUT_DIR)
548	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	16	.arg("polymer-chemistry-definitions")
549	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	.arg(pol_chem_def_name);
550
551	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	QString pol_chem_def_output_file_name = QString("%1/%2")
552	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	16	.arg(pol_chem_def_output_dir)
553	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	.arg(pol_chem_def_file_base_name);
554	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	QDir dir;
555	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	bool result = dir.mkpath(pol_chem_def_output_dir);
556	5/14 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 8 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 8 times. ✗ Branch 14 not taken. ✓ Branch 17 taken 8 times. ✗ Branch 18 not taken. ✗ Branch 23 not taken. ✗ Branch 24 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken.	8	REQUIRE(result == true);
557
558	8/14 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 8 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 8 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 4 times.	8	WHEN("Writing that PolChemDef back to file")
559			{
560	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	pol_chem_def_sp->setXmlDataFilePath(pol_chem_def_output_file_name);
561	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	result = pol_chem_def_sp->writeXmlFile();
562
563	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 writing should be succesful")
564			{
565	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(result == true);
566		4	}
567		8	}
568	8/14 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 8 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 8 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 8 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 4 times.	8	AND_WHEN("Comparing original file and new one")
569			{
570	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	int result = testDiffBetweenTwoTextFiles(pol_chem_def_absolute_file_path,
571			pol_chem_def_output_file_name);
572
573	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 files should be identical")
574			{
575	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(result == 0);
576		4	}
577		8	}
578		16	}
579		8	}
580
581
582			} // namespace libXpertMass
583			} // namespace MsXpS
584

Function (Line)	Call count	Block coverage
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_0() (line 38)	called 20 times, returned 20 times	47.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_10() (line 122)	called 20 times, returned 20 times	46.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_21() (line 241)	called 36 times, returned 36 times	46.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_33() (line 486)	called 8 times, returned 8 times	48.0%