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 "TestUtils.hpp"
22			#include <libXpertMass/Monomer.hpp>
23
24			namespace MsXpS
25			{
26
27			namespace libXpertMass
28			{
29
30
31		12	SCENARIO("Sequence_s exist as text")
32			{
33	1/2 ✓ Branch 1 taken 12 times. ✗ Branch 2 not taken.	12	TestUtils test_utils;
34	1/2 ✓ Branch 1 taken 12 times. ✗ Branch 2 not taken.	12	test_utils.initializeXpertmassLibrary();
35
36	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	GIVEN("A newly empty allocated sequence")
37			{
38	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	Sequence sequence_1;
39
40	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	WHEN("Setting sequence as 1-letter code text")
41			{
42	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	sequence_1.setMonomerText(test_utils.m_telokinAsMonomerText1Letter);
43
44	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 sequence can be checked")
45			{
46	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(sequence_1.monomerText()->toStdString() ==
47			test_utils.m_telokinAsMonomerText1Letter.toStdString());
48
49	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	AND_THEN("Asking for next code starting at index 0 should work")
50			{
51		4	QString next_code;
52		4	int last_parsed_code_char_index = 0;
53		4	QString error;
54			// All the monomer codes are 1-letter-long.
55			int parsed_code_length =
56	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	sequence_1.nextCode(&next_code,
57			&last_parsed_code_char_index,
58			&error,
59			/* code length */ 1);
60
61	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 21 taken 4 times. ✗ Branch 22 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	4	REQUIRE(next_code.toStdString() == "M");
62			// The very first index will be returned because we have a 1-letter
63			// code string and the very first code is at index 0..
64	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(parsed_code_length == 1);
65	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(last_parsed_code_char_index == 0);
66	4/12 ✓ 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 19 not taken. ✗ Branch 20 not taken. ✗ Branch 22 not taken. ✗ Branch 23 not taken.	4	REQUIRE(!error.size());
67
68	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	AND_THEN(
69			"Asking for next code using and incremented index, should work")
70			{
71			int parsed_code_length =
72		8	sequence_1.nextCode(&next_code,
73	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	&++last_parsed_code_char_index,
74			&error,
75			/* code length */ 1);
76
77	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 21 taken 4 times. ✗ Branch 22 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	4	REQUIRE(next_code.toStdString() == "A");
78	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(parsed_code_length == 1);
79	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(last_parsed_code_char_index == 1);
80	4/12 ✓ 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 19 not taken. ✗ Branch 20 not taken. ✗ Branch 22 not taken. ✗ Branch 23 not taken.	4	REQUIRE(!error.size());
81		4	}
82		8	}
83		4	}
84		4	}
85		16	}
86
87	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	GIVEN("A newly empty allocated sequence")
88			{
89	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	Sequence sequence_1;
90
91	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	WHEN("Setting sequence as 3-letter code text")
92			{
93	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	sequence_1.setMonomerText(test_utils.m_telokinAsMonomerText3Letters);
94
95	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 sequence can be checked")
96			{
97	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(sequence_1.monomerText()->toStdString() ==
98			test_utils.m_telokinAsMonomerText3Letters.toStdString());
99
100	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	AND_THEN("Asking for next code starting at index 0 should work")
101			{
102		4	QString next_code;
103		4	int last_parsed_code_char_index = 0;
104		4	QString error;
105			// All the monomer codes are 3-letter-long.
106			int parsed_code_length =
107	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	sequence_1.nextCode(&next_code,
108			&last_parsed_code_char_index,
109			&error,
110			/* code length */ 3);
111
112	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 21 taken 4 times. ✗ Branch 22 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	4	REQUIRE(next_code.toStdString() == "Met");
113			// The very first index will be returned because we have a 1-letter
114			// code string and the very first code is at index 0..
115	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(parsed_code_length == 3);
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118
119	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	AND_THEN(
120			"Asking for next code using and incremented index, should work")
121			{
122			int parsed_code_length =
123		8	sequence_1.nextCode(&next_code,
124	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	&++last_parsed_code_char_index,
125			&error,
126			/* code length */ 3);
127
128	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 21 taken 4 times. ✗ Branch 22 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	4	REQUIRE(next_code.toStdString() == "Ala");
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132		4	}
133		8	}
134		4	}
135		4	}
136		16	}
137
138	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	GIVEN("A newly empty allocated sequence")
139			{
140	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	Sequence sequence_1;
141
142	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	WHEN("Setting sequence as 1-letter code text with spaces, tab, newlines")
143			{
144	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	sequence_1.setMonomerText(
145			test_utils.m_telokinAsMonomerText1LetterWithSpaces);
146
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148			{
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150			sequence_1.monomerText()->toStdString() ==
151			test_utils.m_telokinAsMonomerText1LetterWithSpaces.toStdString());
152
153	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	sequence_1.unspacifyMonomerText();
154
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156			{
157			// qDebug() << *sequence_1.monomerText();
158			// qDebug() << test_utils.m_telokinAsMonomerText1Letter;
159
160	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(sequence_1.monomerText()->toStdString() ==
161			test_utils.m_telokinAsMonomerText1Letter.toStdString());
162		4	}
163		4	}
164		4	}
165		16	}
166		12	}
167
168		20	SCENARIO("Sequence_s exist as text and also as a list of Monomer_s")
169			{
170	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	TestUtils test_utils;
171
172	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.m_polChemDefName = "protein-1-letter";
173	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.m_polChemDefDirName = "protein-1-letter";
174	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
175
176	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.initializePolChemDef();
177		20	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
178
179	6/16 ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 20 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 20 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 20 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 20 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 20 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	20	REQUIRE(pol_chem_def_csp->codeLength() == 1);
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185
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187			{
188	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	Sequence sequence_1(test_utils.m_telokinAsMonomerText1Letter);
189
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191			{
192		20	QList<int> error_list;
193
194	1/2 ✓ Branch 2 taken 20 times. ✗ Branch 3 not taken.	20	int monomer_count = sequence_1.makeMonomerList(
195			pol_chem_def_csp, /* reset */ false, &error_list);
196
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198			{
199	6/16 ✓ 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 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(monomer_count == sequence_1.monomerText()->size());
200		20	}
201
202	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_WHEN(
203			"On the basis of the Monomer list, the monomer text is asked for")
204			{
205	6/16 ✓ 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 13 taken 16 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 16 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 16 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	16	REQUIRE(sequence_1.makeMonomerText() == monomer_count);
206
207	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 monomer text should be identical to what it was before")
208			{
209	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(sequence_1.monomerText()->toStdString() ==
210			test_utils.m_telokinAsMonomerText1Letter.toStdString());
211		16	}
212
213	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_THEN("The isInBound() function might be tested")
214			{
215	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(sequence_1.isInBound(0) == true);
216	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(sequence_1.isInBound(monomer_count - 1) == true);
217	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(sequence_1.isInBound(monomer_count) == false);
218		16	}
219
220	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_THEN("The 1-letter-code text size and the list size are equal")
221			{
222	7/18 ✓ 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 15 taken 4 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 4 times. ✗ Branch 19 not taken. ✓ Branch 21 taken 4 times. ✗ Branch 22 not taken. ✓ Branch 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	4	REQUIRE(sequence_1.monomerText()->size() ==
223			sequence_1.monomerList().size());
224		16	}
225
226	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_THEN("The sequence can be validated successfully")
227			{
228	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 22 taken 4 times. ✗ Branch 23 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken. ✗ Branch 32 not taken. ✗ Branch 33 not taken.	4	REQUIRE(sequence_1.validate(pol_chem_def_csp) == true);
229		16	}
230		20	}
231		40	}
232		40	}
233		20	}
234
235		8	SCENARIO("Sequence_s can be copied and compared")
236			{
237	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	TestUtils test_utils;
238
239	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefName = "protein-1-letter";
240	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefDirName = "protein-1-letter";
241	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
242
243	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.initializePolChemDef();
244		8	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
245
246	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 8 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 8 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 8 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 8 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	8	REQUIRE(pol_chem_def_csp->codeLength() == 1);
247	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->monomerList().size() == 21);
248	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->modifList().size() == 26);
249	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->crossLinkerList().size() == 2);
250	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->cleaveSpecList().size() == 8);
251	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->fragSpecList().size() == 7);
252
253	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 newly allocated sequence with a string sequence during construction")
254			{
255	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	Sequence sequence_1(test_utils.m_telokinAsMonomerText1Letter);
256
257	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	WHEN("A new Sequence is either copy-constructed or assigned")
258			{
259	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	Sequence sequence_2(sequence_1);
260	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	Sequence sequence_3(sequence_1);
261
262	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	THEN("The two Sequence objects should be identical (monomer text-wise)")
263			{
264	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(sequence_2 == sequence_1);
265	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(sequence_2 != sequence_1);
266
267	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(sequence_3 == sequence_1);
268	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(sequence_3 != sequence_1);
269		8	}
270
271	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("The monomer list is crafted in both sequences")
272			{
273	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	sequence_1.makeMonomerList(pol_chem_def_csp);
274	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	sequence_2.makeMonomerList(pol_chem_def_csp);
275	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	sequence_3.makeMonomerList(pol_chem_def_csp);
276
277	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(
278			"The two Sequence objects should be identical (monomer text and "
279			"list-wise)")
280			{
281	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(sequence_1 == sequence_2);
282	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(sequence_1 != sequence_2);
283
284	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(sequence_3 == sequence_2);
285	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(sequence_3 != sequence_2);
286		4	}
287		8	}
288		16	}
289		16	}
290		8	}
291
292
293		8	SCENARIO("A motif can be searched in a Sequence")
294			{
295
296	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	TestUtils test_utils;
297
298	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.initializeXpertmassLibrary();
299	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefName = "protein-1-letter";
300	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefDirName = "protein-1-letter";
301	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
302
303	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.initializePolChemDef();
304		8	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
305
306	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 8 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 8 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 8 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 8 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	8	REQUIRE(pol_chem_def_csp->codeLength() == 1);
307	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->monomerList().size() == 21);
308	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->modifList().size() == 26);
309	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->crossLinkerList().size() == 2);
310	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->cleaveSpecList().size() == 8);
311	6/16 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 8 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	8	REQUIRE(pol_chem_def_csp->fragSpecList().size() == 7);
312
313	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 newly allocated sequence with a string sequence during construction")
314			{
315	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	Sequence sequence_1(test_utils.m_telokinAsMonomerText1Letter);
316
317		8	QList<int> errorList;
318	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	int result = sequence_1.makeMonomerList(pol_chem_def_csp, true, &errorList);
319	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	const QString *monomer_text_p = sequence_1.monomerText();
320	5/14 ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 8 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 8 times. ✗ Branch 15 not taken. ✓ Branch 18 taken 8 times. ✗ Branch 19 not taken. ✗ Branch 24 not taken. ✗ Branch 25 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken.	8	REQUIRE(result == monomer_text_p->size());
321
322		8	int search_index_1 = 0;
323		8	int search_index_2 = 0;
324		8	int search_index_3 = 0;
325		8	int search_index_4 = 0;
326		8	int search_index_5 = 0;
327		8	int search_index_6 = 0;
328		8	int search_index_7 = 0;
329
330	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	8	Sequence motif_sequence_1_occurrence("MAMISGM");
331	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	motif_sequence_1_occurrence.makeMonomerList(pol_chem_def_csp);
332
333	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	8	Sequence motif_sequence_6_occurrences("EE");
334	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	motif_sequence_6_occurrences.makeMonomerList(pol_chem_def_csp);
335
336	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	WHEN("A single-copy existing motif is searched")
337			{
338	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	int result_1 = sequence_1.findForwardMotif(
339			&motif_sequence_1_occurrence, pol_chem_def_csp, &search_index_1);
340
341	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	search_index_2 = search_index_1 + motif_sequence_1_occurrence.size();
342	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	int result_2 = sequence_1.findForwardMotif(
343			&motif_sequence_1_occurrence, pol_chem_def_csp, &search_index_2);
344
345	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	THEN("The motif should be found only once")
346			{
347	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_1 == 1);
348	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(search_index_1 == 0);
349	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_2 == 0);
350		8	}
351
352	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("A a seven-copy existing motif is searched")
353			{
354		4	search_index_1 = 0;
355		4	search_index_2 = 0;
356
357			// qDebug() << "search_index_1: " << search_index_1 << std::endl;
358			// qDebug() << "search_index_2: " << search_index_2 << std::endl;
359
360	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_1 = sequence_1.findForwardMotif(
361			&motif_sequence_6_occurrences, pol_chem_def_csp, &search_index_1);
362
363	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	search_index_2 = search_index_1 + motif_sequence_6_occurrences.size();
364	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_2 = sequence_1.findForwardMotif(
365			&motif_sequence_6_occurrences, pol_chem_def_csp, &search_index_2);
366
367	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	search_index_3 = search_index_2 + motif_sequence_6_occurrences.size();
368	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_3 = sequence_1.findForwardMotif(
369			&motif_sequence_6_occurrences, pol_chem_def_csp, &search_index_3);
370
371	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	search_index_4 = search_index_3 + motif_sequence_6_occurrences.size();
372	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_4 = sequence_1.findForwardMotif(
373			&motif_sequence_6_occurrences, pol_chem_def_csp, &search_index_4);
374
375	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	search_index_5 = search_index_4 + motif_sequence_6_occurrences.size();
376	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_5 = sequence_1.findForwardMotif(
377			&motif_sequence_6_occurrences, pol_chem_def_csp, &search_index_5);
378
379	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	search_index_6 = search_index_5 + motif_sequence_6_occurrences.size();
380	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_6 = sequence_1.findForwardMotif(
381			&motif_sequence_6_occurrences, pol_chem_def_csp, &search_index_6);
382
383	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	search_index_7 = search_index_6 + motif_sequence_6_occurrences.size();
384	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_7 = sequence_1.findForwardMotif(
385			&motif_sequence_6_occurrences, pol_chem_def_csp, &search_index_7);
386
387	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 motif should be found seven times")
388			{
389	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_1 == 1);
390	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(search_index_1 == 33);
391
392	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_2 == 1);
393	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(search_index_2 == 37);
394
395	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_3 == 1);
396	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(search_index_3 == 96);
397
398	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_4 == 1);
399	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(search_index_4 == 148);
400
401	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_5 == 1);
402	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(search_index_5 == 151);
403
404	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_6 == 1);
405	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(search_index_6 == 153);
406
407	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_7 == 1);
408	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(search_index_7 == 155);
409		4	}
410		8	}
411		8	}
412		16	}
413		8	}
414
415		4	SCENARIO("A number of checks might be performed on a Sequence")
416			{
417
418	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	TestUtils test_utils;
419
420	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	test_utils.initializeXpertmassLibrary();
421	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	test_utils.m_polChemDefName = "protein-1-letter";
422	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	test_utils.m_polChemDefDirName = "protein-1-letter";
423	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
424
425	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	test_utils.initializePolChemDef();
426		4	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
427
428	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_csp->codeLength() == 1);
429	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_csp->monomerList().size() == 21);
430	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_csp->modifList().size() == 26);
431	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_csp->crossLinkerList().size() == 2);
432	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_csp->cleaveSpecList().size() == 8);
433	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_csp->fragSpecList().size() == 7);
434
435	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	GIVEN("A newly allocated sequence with a string sequence during construction")
436			{
437	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Sequence sequence_1(test_utils.m_telokinAsMonomerText1Letter);
438	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	const QString *monomer_text_p = sequence_1.monomerText();
439	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(monomer_text_p->size() == test_utils.m_telokinSequenceMonomerCount);
440
441		4	QList<int> errorList;
442	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result = sequence_1.makeMonomerList(pol_chem_def_csp, true, &errorList);
443
444			bool all_correct =
445	3/6 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken. ✓ Branch 6 taken 4 times. ✗ Branch 7 not taken.	4	(result == monomer_text_p->size() && sequence_1.size() == result);
446	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(all_correct == true);
447
448		4	int tested_index = 0;
449
450
451	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("It is possible to check if an index is inbound or not")
452			{
453	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(sequence_1.isInBound(tested_index) == true);
454
455		4	tested_index = result / 2;
456	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(sequence_1.isInBound(tested_index) == true);
457
458		4	tested_index = result - 1;
459	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(sequence_1.isInBound(tested_index) == true);
460
461		4	tested_index = result;
462	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(sequence_1.isInBound(tested_index) == false);
463		4	}
464		8	}
465		4	}
466
467		32	SCENARIO("Monomers can be added or removed from a Sequence")
468			{
469	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	TestUtils test_utils;
470
471	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.initializeXpertmassLibrary();
472	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.m_polChemDefName = "protein-1-letter";
473	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.m_polChemDefDirName = "protein-1-letter";
474	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
475
476	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.initializePolChemDef();
477		32	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
478
479	6/16 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 32 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 32 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 32 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 32 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 32 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	32	REQUIRE(pol_chem_def_csp->codeLength() == 1);
480	6/16 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 32 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 32 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 32 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 32 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	32	REQUIRE(pol_chem_def_csp->monomerList().size() == 21);
481	6/16 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 32 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 32 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 32 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 32 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	32	REQUIRE(pol_chem_def_csp->modifList().size() == 26);
482	6/16 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 32 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 32 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 32 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 32 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	32	REQUIRE(pol_chem_def_csp->crossLinkerList().size() == 2);
483	6/16 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 32 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 32 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 32 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 32 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	32	REQUIRE(pol_chem_def_csp->cleaveSpecList().size() == 8);
484	6/16 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 32 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 32 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 32 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 32 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	32	REQUIRE(pol_chem_def_csp->fragSpecList().size() == 7);
485
486	7/14 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 32 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 32 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 32 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 32 times. ✗ Branch 24 not taken.	32	GIVEN("A newly allocated sequence with a string sequence during construction")
487			{
488	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	Sequence sequence_1(test_utils.m_telokinAsMonomerText1Letter);
489	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	const QString *monomer_text_p = sequence_1.monomerText();
490	5/14 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 32 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 32 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 32 times. ✗ Branch 15 not taken. ✓ Branch 18 taken 32 times. ✗ Branch 19 not taken. ✗ Branch 24 not taken. ✗ Branch 25 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken.	32	REQUIRE(monomer_text_p->size() == test_utils.m_telokinSequenceMonomerCount);
491
492		32	QList<int> errorList;
493	1/2 ✓ Branch 2 taken 32 times. ✗ Branch 3 not taken.	32	int result = sequence_1.makeMonomerList(pol_chem_def_csp, true, &errorList);
494
495			bool all_correct =
496	3/6 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 6 taken 32 times. ✗ Branch 7 not taken.	32	(result == monomer_text_p->size() && sequence_1.size() == result);
497	5/14 ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 32 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 32 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 32 times. ✗ Branch 14 not taken. ✓ Branch 17 taken 32 times. ✗ Branch 18 not taken. ✗ Branch 23 not taken. ✗ Branch 24 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken.	32	REQUIRE(all_correct == true);
498
499	8/14 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 32 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 32 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 32 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 8 times. ✓ Branch 24 taken 24 times.	32	WHEN("A monomer is inserted at the beginining of the sequence")
500			{
501	4/10 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 5 taken 8 times. ✗ Branch 6 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✗ Branch 22 not taken. ✗ Branch 23 not taken.	8	Monomer *monomer_1_p = new Monomer(pol_chem_def_csp, "Tryptophan", "W");
502
503	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	sequence_1.insertMonomerAt(monomer_1_p, 0);
504
505	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	THEN("That monomer has to be found there")
506			{
507	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(sequence_1.at(0)->code().toStdString() == "W");
508
509			// sequence_1.makeMonomerText();
510			// qDebug() << "Sequence: " << *sequence_1.monomerText();
511		8	}
512
513	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("When searching for a motif comprising that monomer")
514			{
515	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Sequence motif_sequence_1_occurrence("WMAMISGMSGR");
516	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	motif_sequence_1_occurrence.makeMonomerList(pol_chem_def_csp);
517		4	int search_index_1 = 0;
518
519	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_1 = sequence_1.findForwardMotif(
520			&motif_sequence_1_occurrence, pol_chem_def_csp, &search_index_1);
521
522	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 search is successful")
523			{
524	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_1 == true);
525	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(search_index_1 == 0);
526		4	}
527		12	}
528		32	}
529
530	8/14 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 32 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 32 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 32 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 8 times. ✓ Branch 24 taken 24 times.	32	WHEN("A monomer is inserted at the end of the sequence")
531			{
532	4/10 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 5 taken 8 times. ✗ Branch 6 not taken. ✓ Branch 8 taken 8 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 8 times. ✗ Branch 13 not taken. ✗ Branch 22 not taken. ✗ Branch 23 not taken.	8	Monomer *monomer_1_p = new Monomer(pol_chem_def_csp, "Tryptophan", "W");
533
534	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	sequence_1.insertMonomerAt(monomer_1_p,
535			test_utils.m_telokinSequenceMonomerCount);
536
537	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	THEN("That monomer has to be found there")
538			{
539	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(sequence_1.at(test_utils.m_telokinSequenceMonomerCount)
540			->code()
541			.toStdString() == "W");
542
543			// sequence_1.makeMonomerText();
544			// qDebug() << "Sequence: " << *sequence_1.monomerText();
545		8	}
546
547	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("When searching for a motif comprising that monomer")
548			{
549	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Sequence motif_sequence_1_occurrence("EEEEEEW");
550	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	motif_sequence_1_occurrence.makeMonomerList(pol_chem_def_csp);
551		4	int search_index_1 = 0;
552
553	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_1 = sequence_1.findForwardMotif(
554			&motif_sequence_1_occurrence, pol_chem_def_csp, &search_index_1);
555
556	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 search is successful")
557			{
558	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_1 == true);
559	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(search_index_1 == 151);
560		4	}
561		12	}
562		32	}
563
564	8/14 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 32 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 32 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 32 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 32 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 16 times. ✓ Branch 24 taken 16 times.	32	WHEN("A monomer is inserted in the middle of the sequence")
565			{
566	4/10 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken. ✓ Branch 5 taken 16 times. ✗ Branch 6 not taken. ✓ Branch 8 taken 16 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 16 times. ✗ Branch 13 not taken. ✗ Branch 22 not taken. ✗ Branch 23 not taken.	16	Monomer *monomer_1_p = new Monomer(pol_chem_def_csp, "Tryptophan", "W");
567
568		16	int floor = std::floor(result / 2);
569			// qDebug() << "The floor:" << floor;
570
571	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	sequence_1.insertMonomerAt(monomer_1_p, floor);
572
573	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("That monomer has to be found there")
574			{
575	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(sequence_1.at(floor)->code().toStdString() == "W");
576
577			// sequence_1.makeMonomerText();
578			// qDebug() << "Sequence: " << *sequence_1.monomerText();
579		16	}
580
581	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 8 times. ✓ Branch 24 taken 8 times.	16	AND_WHEN("When searching for a motif comprising that monomer")
582			{
583	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	8	Sequence motif_sequence_1_occurrence("DPEVMWWYKDDQ");
584	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	motif_sequence_1_occurrence.makeMonomerList(pol_chem_def_csp);
585		8	int search_index_1 = 0;
586
587	1/2 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken.	8	int result_1 = sequence_1.findForwardMotif(
588			&motif_sequence_1_occurrence, pol_chem_def_csp, &search_index_1);
589
590	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	THEN("The search is successful")
591			{
592	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_1 == true);
593	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(search_index_1 == 72);
594		8	}
595
596	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("That monomer is removed back")
597			{
598	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	sequence_1.removeMonomerAt(floor);
599
600			// sequence_1.makeMonomerText();
601			// qDebug() << "Sequence: " << *sequence_1.monomerText();
602
603	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 sequence with the inserted monomer cannot be found anymore")
604			{
605		4	search_index_1 = 0;
606
607	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	result_1 = sequence_1.findForwardMotif(
608			&motif_sequence_1_occurrence, pol_chem_def_csp, &search_index_1);
609
610
611	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_1 == 0);
612	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(search_index_1 == 0);
613
614	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	AND_THEN("The original sequence can be found again")
615			{
616
617	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	motif_sequence_1_occurrence.setMonomerText("DPEVMWYKDDQ");
618		4	QList<int> errorList;
619	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	motif_sequence_1_occurrence.makeMonomerList(
620			pol_chem_def_csp, true, &errorList);
621		4	search_index_1 = 0;
622
623			result_1 =
624	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	sequence_1.findForwardMotif(&motif_sequence_1_occurrence,
625			pol_chem_def_csp,
626			&search_index_1);
627
628	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_1 == 1);
629	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(search_index_1 == 72);
630		8	}
631		4	}
632		8	}
633		24	}
634
635	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	WHEN("A monomer sequence text is appended to the Sequence")
636			{
637	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	sequence_1.appendMonomerText("THISTEQST");
638		4	QList<int> errorList;
639	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	sequence_1.makeMonomerList(pol_chem_def_csp, true, &errorList);
640
641
642	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("Searching for it should return the right index")
643			{
644	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Sequence motif_sequence_1_occurrence("EEEEEETHISTEQST");
645	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	motif_sequence_1_occurrence.makeMonomerList(pol_chem_def_csp);
646		4	int search_index_1 = 0;
647
648	1/2 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken.	4	int result_1 = sequence_1.findForwardMotif(
649			&motif_sequence_1_occurrence, pol_chem_def_csp, &search_index_1);
650
651	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_1 == true);
652	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(search_index_1 == 151);
653		8	}
654		20	}
655		32	}
656		64	}
657		32	}
658
659			} // namespace libXpertMass
660			} // namespace MsXpS
661

Function (Line)	Call count	Block coverage
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_0() (line 31)	called 12 times, returned 12 times	48.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_16() (line 168)	called 20 times, returned 20 times	49.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_26() (line 235)	called 8 times, returned 8 times	49.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_33() (line 293)	called 8 times, returned 8 times	48.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_40() (line 415)	called 4 times, returned 4 times	50.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_44() (line 467)	called 32 times, returned 32 times	48.0%