GCC Code Coverage Report

Line	Branch	Exec	Source
1			// ./tests/catch2-tests [section] -s
2
3
4			/////////////////////// Qt includes
5			#include <QDebug>
6			#include <QString>
7			#include <QDir>
8
9
10			/////////////////////// IsoSpec
11			#include <IsoSpec++/isoSpec++.h>
12			#include <IsoSpec++/element_tables.h>
13
14
15			/////////////////////// Catch2 includes
16			#include <catch2/catch_test_macros.hpp>
17			#include <catch2/matchers/catch_matchers_floating_point.hpp>
18
19
20			/////////////////////// Local includes
21			// #include "tests-config.h"
22			#include "TestUtils.hpp"
23			#include <libXpertMass/CalcOptions.hpp>
24			#include <libXpertMass/Coordinates.hpp>
25			#include <libXpertMass/Monomer.hpp>
26			#include <libXpertMass/globals.hpp>
27
28			namespace MsXpS
29			{
30
31			namespace libXpertMass
32			{
33
34
35		16	SCENARIO("Polymer_s are created in the context of a PolChemDef")
36			{
37	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	TestUtils test_utils;
38
39	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	test_utils.initializeXpertmassLibrary();
40
41	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	test_utils.m_polChemDefName = "protein-1-letter";
42	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	test_utils.m_polChemDefDirName = "protein-1-letter";
43	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
44
45	7/14 ✓ 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 16 times. ✗ Branch 24 not taken.	16	WHEN("A polymer chemistry definition is loaded from disk")
46			{
47	1/2 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken.	16	PolChemDefCstSPtr pol_chem_def_csp = test_utils.initializePolChemDef();
48	5/14 ✓ 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 17 taken 16 times. ✗ Branch 18 not taken. ✗ Branch 23 not taken. ✗ Branch 24 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken.	16	REQUIRE(pol_chem_def_csp != nullptr);
49
50			QString chicken_telokin_file_path =
51	2/4 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken.	32	QString("%1/chicken-telokin.mxp").arg(test_utils.m_testsInputPolSeqsDir);
52
53	6/16 ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 16 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 16 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 16 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 16 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 16 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	16	REQUIRE(pol_chem_def_csp->codeLength() == 1);
54	6/16 ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 16 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 16 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 16 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 16 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	16	REQUIRE(pol_chem_def_csp->monomerList().size() == 21);
55	6/16 ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 16 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 16 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 16 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 16 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	16	REQUIRE(pol_chem_def_csp->modifList().size() == 26);
56	6/16 ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 16 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 16 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 16 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 16 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	16	REQUIRE(pol_chem_def_csp->crossLinkerList().size() == 2);
57	6/16 ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 16 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 16 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 16 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 16 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	16	REQUIRE(pol_chem_def_csp->cleaveSpecList().size() == 8);
58	6/16 ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 16 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 16 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 16 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 16 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	16	REQUIRE(pol_chem_def_csp->fragSpecList().size() == 7);
59
60	8/14 ✓ Branch 1 taken 16 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 16 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 16 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 16 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 16 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 16 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 12 times.	16	AND_WHEN(
61			"A new Polymer instance is created with default arguments to the "
62			"constructor")
63			{
64
65	4/8 ✓ 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 11 taken 4 times. ✗ Branch 12 not taken.	4	Polymer polymer_1(pol_chem_def_csp);
66
67	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_WHEN("The setters are used to configure it")
68			{
69	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setName("PolymerName");
70	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setCode("PolymerCode");
71	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setAuthor("PolymerAuthor");
72
73	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 member data are set accordingly")
74			{
75	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(polymer_1.name().toStdString() == "PolymerName");
76	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(polymer_1.code().toStdString() == "PolymerCode");
77	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(polymer_1.author().toStdString() == "PolymerAuthor");
78		4	}
79		4	}
80		20	}
81
82	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_WHEN(
83			"A new Polymer instance is created with specified arguments to the "
84			"constructor")
85			{
86			Polymer polymer_1(
87	4/8 ✓ 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 11 taken 12 times. ✗ Branch 12 not taken.	12	pol_chem_def_csp, "PolymerName", "PolymerCode", "PolymerAuthor");
88
89	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 member data are set accordingly")
90			{
91	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(polymer_1.name().toStdString() == "PolymerName");
92	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(polymer_1.code().toStdString() == "PolymerCode");
93	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(polymer_1.author().toStdString() == "PolymerAuthor");
94		12	}
95
96	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 8 times. ✓ Branch 24 taken 4 times.	12	AND_WHEN("The file path is set")
97			{
98	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	polymer_1.setFilePath(chicken_telokin_file_path);
99
100	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("It can be checked")
101			{
102	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(polymer_1.filePath().toStdString() ==
103			chicken_telokin_file_path.toStdString());
104		8	}
105
106	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 polymer sequence file is loaded")
107			{
108	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	bool result = polymer_1.renderXmlPolymerFile();
109
110	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 file should have loaded fine and the size should check ok")
111			{
112	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);
113	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(polymer_1.size() ==
114			test_utils.m_telokinSequenceMonomerCount);
115		4	}
116		8	}
117		12	}
118		28	}
119		32	}
120		16	}
121
122		8	SCENARIO("Polymer_s can be modified on monomers")
123			{
124	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	TestUtils test_utils;
125
126	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.initializeXpertmassLibrary();
127
128	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefName = "protein-1-letter";
129	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefDirName = "protein-1-letter";
130	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
131
132	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	test_utils.initializePolChemDef();
133		8	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
134
135			QString chicken_telokin_file_path =
136	2/4 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 8 times. ✗ Branch 5 not taken.	16	QString("%1/chicken-telokin.mxp").arg(test_utils.m_testsInputPolSeqsDir);
137
138	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);
139	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);
140	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);
141	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);
142	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);
143	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);
144
145	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 new Polymer instance created by loading a file with no modification")
146			{
147			Polymer polymer_1(
148	4/8 ✓ 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 11 taken 8 times. ✗ Branch 12 not taken.	8	pol_chem_def_csp, "PolymerName", "PolymerCode", "PolymerAuthor");
149	7/18 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 8 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 8 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	8	REQUIRE(polymer_1.name().toStdString() == "PolymerName");
150	7/18 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 8 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 8 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	8	REQUIRE(polymer_1.code().toStdString() == "PolymerCode");
151	7/18 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 8 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 8 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	8	REQUIRE(polymer_1.author().toStdString() == "PolymerAuthor");
152
153	1/2 ✓ Branch 1 taken 8 times. ✗ Branch 2 not taken.	8	polymer_1.setFilePath(chicken_telokin_file_path);
154	8/20 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 8 times. ✗ Branch 20 not taken. ✓ Branch 22 taken 8 times. ✗ Branch 23 not taken. ✓ Branch 29 taken 8 times. ✗ Branch 30 not taken. ✗ Branch 38 not taken. ✗ Branch 39 not taken. ✗ Branch 41 not taken. ✗ Branch 42 not taken.	8	REQUIRE(polymer_1.filePath().toStdString() ==
155			chicken_telokin_file_path.toStdString());
156
157	7/18 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 8 times. ✗ Branch 20 not taken. ✓ Branch 24 taken 8 times. ✗ Branch 25 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	8	REQUIRE(polymer_1.renderXmlPolymerFile() == true);
158	6/16 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 8 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	8	REQUIRE(polymer_1.size() == test_utils.m_telokinSequenceMonomerCount);
159
160	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("There are no modified monomers")
161			{
162	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(polymer_1.hasModifiedMonomer(
163			0, test_utils.m_telokinSequenceMonomerCount - 1) == false);
164		8	}
165
166	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("Modifying one monomer at a specified index")
167			{
168		4	int index = 4; // the Ser
169
170	3/8 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 5 taken 4 times. ✗ Branch 6 not taken. ✓ Branch 9 taken 4 times. ✗ Branch 10 not taken. ✗ Branch 17 not taken. ✗ Branch 18 not taken.	4	Modif *modif_p = new Modif(pol_chem_def_csp, "NOT_SET");
171
172	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 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(polymer_1.getPolChemDefCstSPtr()->referenceModifByName(
173			"Phosphorylation", modif_p) == true);
174
175	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Monomer monomer_p = const_cast<Monomer >(polymer_1.at(index));
176		4	QStringList errorList;
177	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(monomer_p->modify(modif_p, false, errorList) == true);
178
179	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("There should be a modified monomer, this time")
180			{
181	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(polymer_1.hasModifiedMonomer(
182			0, test_utils.m_telokinSequenceMonomerCount - 1) == true);
183		4	}
184		12	}
185		16	}
186		8	}
187
188		20	SCENARIO("Polymer_s can be modified on their own left and right ends")
189			{
190	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	TestUtils test_utils;
191
192	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.initializeXpertmassLibrary();
193
194
195	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.m_polChemDefName = "protein-1-letter";
196	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.m_polChemDefDirName = "protein-1-letter";
197	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
198
199	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	test_utils.initializePolChemDef();
200		20	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
201
202			QString chicken_telokin_file_path =
203	2/4 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken.	40	QString("%1/chicken-telokin.mxp").arg(test_utils.m_testsInputPolSeqsDir);
204
205	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);
206	6/16 ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 20 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 20 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 20 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 20 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 20 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	20	REQUIRE(pol_chem_def_csp->monomerList().size() == 21);
207	6/16 ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 20 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 20 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 20 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 20 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 20 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	20	REQUIRE(pol_chem_def_csp->modifList().size() == 26);
208	6/16 ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 20 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 20 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 20 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 20 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 20 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	20	REQUIRE(pol_chem_def_csp->crossLinkerList().size() == 2);
209	6/16 ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 20 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 20 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 20 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 20 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 20 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	20	REQUIRE(pol_chem_def_csp->cleaveSpecList().size() == 8);
210	6/16 ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 20 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 20 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 20 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 20 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 20 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	20	REQUIRE(pol_chem_def_csp->fragSpecList().size() == 7);
211
212
213	7/14 ✓ 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 20 times. ✗ Branch 24 not taken.	20	GIVEN("A new Polymer instance created by loading a file with no modification")
214			{
215			Polymer polymer_1(
216	4/8 ✓ 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 11 taken 20 times. ✗ Branch 12 not taken.	20	pol_chem_def_csp, "PolymerName", "PolymerCode", "PolymerAuthor");
217	7/18 ✓ 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 13 taken 20 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 20 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 20 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 20 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	20	REQUIRE(polymer_1.name().toStdString() == "PolymerName");
218	7/18 ✓ 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 13 taken 20 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 20 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 20 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 20 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	20	REQUIRE(polymer_1.code().toStdString() == "PolymerCode");
219	7/18 ✓ 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 13 taken 20 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 20 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 20 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 20 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	20	REQUIRE(polymer_1.author().toStdString() == "PolymerAuthor");
220
221	1/2 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken.	20	polymer_1.setFilePath(chicken_telokin_file_path);
222	8/20 ✓ 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 13 taken 20 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 20 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 20 times. ✗ Branch 20 not taken. ✓ Branch 22 taken 20 times. ✗ Branch 23 not taken. ✓ Branch 29 taken 20 times. ✗ Branch 30 not taken. ✗ Branch 38 not taken. ✗ Branch 39 not taken. ✗ Branch 41 not taken. ✗ Branch 42 not taken.	20	REQUIRE(polymer_1.filePath().toStdString() ==
223			chicken_telokin_file_path.toStdString());
224
225	7/18 ✓ 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 13 taken 20 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 20 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 20 times. ✗ Branch 20 not taken. ✓ Branch 24 taken 20 times. ✗ Branch 25 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	20	REQUIRE(polymer_1.renderXmlPolymerFile() == true);
226	6/16 ✓ 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 13 taken 20 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 20 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 20 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	20	REQUIRE(polymer_1.size() == test_utils.m_telokinSequenceMonomerCount);
227
228	8/14 ✓ Branch 1 taken 20 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 20 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 20 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 20 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 20 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 20 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 16 times.	20	THEN("There are no modified ends")
229			{
230	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(polymer_1.isLeftEndModified() == false);
231	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(polymer_1.isRightEndModified() == false);
232		20	}
233
234	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 8 times. ✓ Branch 24 taken 12 times.	20	WHEN("The left end is modified according to one method")
235			{
236	7/18 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 8 times. ✗ Branch 20 not taken. ✓ Branch 24 taken 8 times. ✗ Branch 25 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken. ✗ Branch 34 not taken. ✗ Branch 35 not taken.	8	REQUIRE(polymer_1.setLeftEndModif("Acetylation") == true);
237
238	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 modification should be set")
239			{
240	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(polymer_1.isLeftEndModified() == true);
241	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif left_end_modif = polymer_1.leftEndModif();
242	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(left_end_modif.name().toStdString() == "Acetylation");
243		12	}
244
245	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 right end is modified")
246			{
247	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(polymer_1.setRightEndModif("AmidationGlu") == true);
248
249	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 modification should be set")
250			{
251	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(polymer_1.isRightEndModified() == true);
252	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif right_end_modif = polymer_1.rightEndModif();
253	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(right_end_modif.name().toStdString() == "AmidationGlu");
254		8	}
255		8	}
256		20	}
257
258	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 8 times. ✓ Branch 24 taken 12 times.	20	WHEN("The left end is modified according to another method")
259			{
260	6/16 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 8 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	8	REQUIRE(polymer_1.isLeftEndModified() == false);
261	6/16 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 8 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	8	REQUIRE(polymer_1.isRightEndModified() == false);
262
263	2/4 ✓ Branch 2 taken 8 times. ✗ Branch 3 not taken. ✓ Branch 6 taken 8 times. ✗ Branch 7 not taken.	8	Modif left_end_modif(pol_chem_def_csp, "Formylation");
264
265	6/16 ✓ 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 16 taken 8 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 8 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	8	REQUIRE(polymer_1.setLeftEndModif(left_end_modif) == true);
266
267	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 modification should be set")
268			{
269	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(polymer_1.isLeftEndModified() == true);
270	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif left_end_modif = polymer_1.leftEndModif();
271	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(left_end_modif.name().toStdString() == "Formylation");
272		12	}
273
274	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 right end is modified")
275			{
276	2/4 ✓ Branch 2 taken 4 times. ✗ Branch 3 not taken. ✓ Branch 6 taken 4 times. ✗ Branch 7 not taken.	4	Modif right_end_modif(pol_chem_def_csp, "AmidationGlu");
277	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	polymer_1.setRightEndModif(right_end_modif);
278
279	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 modification should be set")
280			{
281	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(polymer_1.isRightEndModified() == true);
282	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif right_end_modif = polymer_1.rightEndModif();
283	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(right_end_modif.name().toStdString() == "AmidationGlu");
284		8	}
285		12	}
286		28	}
287		40	}
288		20	}
289
290		32	SCENARIO(
291			"Polymer_s have masses that can be calculated in various ways for whole "
292			"sequence")
293			{
294	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	TestUtils test_utils;
295
296	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.initializeXpertmassLibrary();
297
298	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.m_polChemDefName = "protein-1-letter";
299	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.m_polChemDefDirName = "protein-1-letter";
300	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
301
302	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	test_utils.initializePolChemDef();
303		32	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
304	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);
305	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);
306	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);
307	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);
308	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);
309	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);
310
311			QString chicken_telokin_file_path =
312	2/4 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken.	64	QString("%1/chicken-telokin.mxp").arg(test_utils.m_testsInputPolSeqsDir);
313
314	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 new Polymer instance created by loading a file with no modification")
315			{
316			Polymer polymer_1(
317	4/8 ✓ 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 11 taken 32 times. ✗ Branch 12 not taken.	32	pol_chem_def_csp, "PolymerName", "PolymerCode", "PolymerAuthor");
318	7/18 ✓ 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 16 taken 32 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 32 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 32 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	32	REQUIRE(polymer_1.name().toStdString() == "PolymerName");
319	7/18 ✓ 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 16 taken 32 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 32 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 32 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	32	REQUIRE(polymer_1.code().toStdString() == "PolymerCode");
320	7/18 ✓ 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 16 taken 32 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 32 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 32 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	32	REQUIRE(polymer_1.author().toStdString() == "PolymerAuthor");
321
322	1/2 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken.	32	polymer_1.setFilePath(chicken_telokin_file_path);
323	8/20 ✓ 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 16 taken 32 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 32 times. ✗ Branch 20 not taken. ✓ Branch 22 taken 32 times. ✗ Branch 23 not taken. ✓ Branch 29 taken 32 times. ✗ Branch 30 not taken. ✗ Branch 38 not taken. ✗ Branch 39 not taken. ✗ Branch 41 not taken. ✗ Branch 42 not taken.	32	REQUIRE(polymer_1.filePath().toStdString() ==
324			chicken_telokin_file_path.toStdString());
325
326	2/4 ✓ Branch 1 taken 32 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 32 times. ✗ Branch 5 not taken.	32	bool result = polymer_1.renderXmlPolymerFile();
327	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(result == true);
328	6/16 ✓ 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 16 taken 32 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 32 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	32	REQUIRE(polymer_1.size() == test_utils.m_telokinSequenceMonomerCount);
329
330	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
331			"Masses are calculated: full sequence, no deep-calc, no caps, no "
332			"modifs, various ionization levels")
333			{
334			CalcOptions calc_options(false,
335			MassType::MASS_BOTH,
336			CAP_NONE,
337			MONOMER_CHEMENT_NONE,
338	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
339			// calc_options.setSelectionType(
340			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
341
342	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
343	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
344	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
345	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
346
347	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
348			true);
349
350	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_THAT(polymer_1.mono(),
351			Catch::Matchers::WithinAbs(17307.781794, 0.000001));
352	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_THAT(polymer_1.avg(),
353			Catch::Matchers::WithinAbs(17318.813085, 0.000001));
354
355			// The polymer is not ionized at this moment
356	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(polymer_1.isIonized() == false);
357
358	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 32 not taken. ✗ Branch 33 not taken. ✗ Branch 35 not taken. ✗ Branch 36 not taken.	4	REQUIRE(test_utils.m_h1IonizeRule.validate(
359			pol_chem_def_csp->getIsotopicDataCstSPtr()) == true);
360
361	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(polymer_1.isIonized() == false);
362	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(polymer_1.ionize(test_utils.m_h1IonizeRule) == 1);
363
364			// Now it is.
365	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(polymer_1.isIonized() == true);
366
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 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_THAT(polymer_1.mono(),
368			Catch::Matchers::WithinAbs(17308.789619, 0.000001));
369	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_THAT(polymer_1.avg(),
370			Catch::Matchers::WithinAbs(17319.821026, 0.000001));
371
372	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 32 not taken. ✗ Branch 33 not taken. ✗ Branch 35 not taken. ✗ Branch 36 not taken.	4	REQUIRE(test_utils.m_h20IonizeRule.validate(
373			pol_chem_def_csp->getIsotopicDataCstSPtr()) == true);
374
375	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(polymer_1.ionize(test_utils.m_h20IonizeRule) == 1);
376
377	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_THAT(polymer_1.mono(),
378			Catch::Matchers::WithinAbs(866.396915, 0.000001));
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 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_THAT(polymer_1.avg(),
380			Catch::Matchers::WithinAbs(866.948596, 0.000001));
381
382	7/18 ✓ 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 25 taken 4 times. ✗ Branch 26 not taken. ✗ Branch 32 not taken. ✗ Branch 33 not taken. ✗ Branch 35 not taken. ✗ Branch 36 not taken.	4	REQUIRE(test_utils.m_mg2IonizeRule.validate(
383			pol_chem_def_csp->getIsotopicDataCstSPtr()) == true);
384
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(polymer_1.ionize(test_utils.m_mg2IonizeRule) == 1);
386
387	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_THAT(polymer_1.mono(),
388			Catch::Matchers::WithinAbs(4338.937969, 0.000001));
389	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_THAT(polymer_1.avg(),
390			Catch::Matchers::WithinAbs(4341.855819, 0.000001));
391		36	}
392
393	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
394			"Masses are calculated: full sequence, no deep-calc, left cap, no "
395			"modifs")
396			{
397			CalcOptions calc_options(false,
398			MassType::MASS_BOTH,
399			CAP_LEFT,
400			MONOMER_CHEMENT_NONE,
401	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
402			// calc_options.setSelectionType(
403			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
404
405	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
406	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
407	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
408	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
409
410	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
411			true);
412
413	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_THAT(polymer_1.mono(),
414			Catch::Matchers::WithinAbs(17308.789619, 0.000001));
415	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_THAT(polymer_1.avg(),
416			Catch::Matchers::WithinAbs(17319.821026, 0.000001));
417		36	}
418
419	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
420			"Masses are calculated: full sequence, no deep-calc, right cap, no "
421			"modifs")
422			{
423			CalcOptions calc_options(false,
424			MassType::MASS_BOTH,
425			CAP_RIGHT,
426			MONOMER_CHEMENT_NONE,
427	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
428			// calc_options.setSelectionType(
429			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
430
431	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
432	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
433	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
434	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
435
436	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
437			true);
438
439	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_THAT(polymer_1.mono(),
440			Catch::Matchers::WithinAbs(17324.784534, 0.000001));
441	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_THAT(polymer_1.avg(),
442			Catch::Matchers::WithinAbs(17335.820435, 0.000001));
443		36	}
444
445	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
446			"Masses are calculated: full sequence, no deep-calc, both caps, no "
447			"modifs")
448			{
449			CalcOptions calc_options(false,
450			MassType::MASS_BOTH,
451			CAP_BOTH,
452			MONOMER_CHEMENT_NONE,
453	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
454			// calc_options.setSelectionType(
455			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
456
457	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
458	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
459	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
460	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
461
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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
463			true);
464
465	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_THAT(polymer_1.mono(),
466			Catch::Matchers::WithinAbs(17325.792359, 0.000001));
467	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_THAT(polymer_1.avg(),
468			Catch::Matchers::WithinAbs(17336.828376, 0.000001));
469		36	}
470
471	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
472			"Masses are calculated: full sequence, no deep-calc, both caps, LE_MODIF")
473			{
474			CalcOptions calc_options(false,
475			MassType::MASS_BOTH,
476			CAP_BOTH,
477			MONOMER_CHEMENT_NONE,
478	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_LEFT_END_MODIF);
479			// calc_options.setSelectionType(
480			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
481
482	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
483	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
484	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
485	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
486
487	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setLeftEndModif("Acetylation");
488
489	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(polymer_1.isLeftEndModified() == true);
490	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif left_end_modif = polymer_1.leftEndModif();
491	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(left_end_modif.name().toStdString() == "Acetylation");
492
493	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setRightEndModif("AmidationGlu");
494	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(polymer_1.isRightEndModified() == true);
495	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif right_end_modif = polymer_1.rightEndModif();
496	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(right_end_modif.name().toStdString() == "AmidationGlu");
497
498	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
499			true);
500
501	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_THAT(polymer_1.mono(),
502			Catch::Matchers::WithinAbs(17367.802924, 0.000001));
503	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_THAT(polymer_1.avg(),
504			Catch::Matchers::WithinAbs(17378.865317, 0.000001));
505		36	}
506
507	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
508			"Masses are calculated: full sequence, no deep-calc, both caps, RE_MODIF")
509			{
510			CalcOptions calc_options(false,
511			MassType::MASS_BOTH,
512			CAP_BOTH,
513			MONOMER_CHEMENT_NONE,
514	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_RIGHT_END_MODIF);
515			// calc_options.setSelectionType(
516			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
517
518	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
519	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
520	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
521	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
522
523	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setLeftEndModif("Acetylation");
524
525	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(polymer_1.isLeftEndModified() == true);
526	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif left_end_modif = polymer_1.leftEndModif();
527	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(left_end_modif.name().toStdString() == "Acetylation");
528
529	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setRightEndModif("AmidationGlu");
530	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(polymer_1.isRightEndModified() == true);
531	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	Modif right_end_modif = polymer_1.rightEndModif();
532	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(right_end_modif.name().toStdString() == "AmidationGlu");
533
534	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
535			true);
536
537	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_THAT(polymer_1.mono(),
538			Catch::Matchers::WithinAbs(17324.808344, 0.000001));
539	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_THAT(polymer_1.avg(),
540			Catch::Matchers::WithinAbs(17335.843614, 0.000001));
541		36	}
542
543	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
544			"Masses are calculated: full sequence, no deep-calc, both caps, "
545			"BOTH_END_MODIFS")
546			{
547			CalcOptions calc_options(false,
548			MassType::MASS_BOTH,
549			CAP_BOTH,
550			MONOMER_CHEMENT_NONE,
551	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_BOTH_END_MODIF);
552			// calc_options.setSelectionType(
553			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
554
555	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
556	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
557	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
558	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
559
560	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(polymer_1.setLeftEndModif("Acetylation") == true);
561	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(polymer_1.isLeftEndModified() == true);
562	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
563
564	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(polymer_1.setRightEndModif("AmidationGlu") == true);
565	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(polymer_1.isRightEndModified() == true);
566	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
567
568	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
569			true);
570
571	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_THAT(polymer_1.mono(),
572			Catch::Matchers::WithinAbs(17366.818908, 0.000001));
573	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_THAT(polymer_1.avg(),
574			Catch::Matchers::WithinAbs(17377.880555, 0.000001));
575		36	}
576
577	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 4 times. ✓ Branch 24 taken 28 times.	32	THEN(
578			"Masses are calculated: full sequence, deep-calc, both caps, "
579			"BOTH_END_MODIFS and monomer modif Ser-phos")
580			{
581			CalcOptions calc_options(true,
582			MassType::MASS_BOTH,
583			CAP_BOTH,
584			MONOMER_CHEMENT_MODIF,
585	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_BOTH_END_MODIF);
586			// calc_options.setSelectionType(
587			// SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
588
589	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Coordinates coord(0, test_utils.m_telokinSequenceMonomerCount - 1);
590	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	CoordinateList coord_list("TEST");
591	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	coord_list.setCoordinates(coord);
592	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
593
594	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setLeftEndModif("Acetylation");
595
596	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(polymer_1.isLeftEndModified() == true);
597	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
598
599	2/4 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 4 times. ✗ Branch 5 not taken.	4	polymer_1.setRightEndModif("AmidationGlu");
600	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(polymer_1.isRightEndModified() == true);
601	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
602
603			// Phosphorylate Ser at index 4
604		4	int index = 4; // the Ser
605	3/8 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 5 taken 4 times. ✗ Branch 6 not taken. ✓ Branch 9 taken 4 times. ✗ Branch 10 not taken. ✗ Branch 17 not taken. ✗ Branch 18 not taken.	4	Modif *modif_p = new Modif(pol_chem_def_csp, "NOT_SET");
606	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 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(polymer_1.getPolChemDefCstSPtr()->referenceModifByName(
607			"Phosphorylation", modif_p) == true);
608	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Monomer monomer_p = const_cast<Monomer >(polymer_1.at(index));
609		4	QStringList errorList;
610	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(monomer_p->modify(modif_p, false, errorList) == true);
611
612	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
613			true);
614
615	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_THAT(polymer_1.mono(),
616			Catch::Matchers::WithinAbs(17446.785239, 0.000001));
617	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_THAT(polymer_1.avg(),
618			Catch::Matchers::WithinAbs(17457.860484, 0.000001));
619		36	}
620		64	}
621		32	}
622
623		40	SCENARIO(
624			"Polymer_s have masses that can be calculated in various ways for selections")
625			{
626	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	TestUtils test_utils;
627
628	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	test_utils.initializeXpertmassLibrary();
629
630	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	test_utils.m_polChemDefName = "protein-1-letter";
631	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	test_utils.m_polChemDefDirName = "protein-1-letter";
632	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	test_utils.m_polChemDefFileBaseName = "protein-1-letter.xml";
633
634	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	test_utils.initializePolChemDef();
635		40	PolChemDefCstSPtr pol_chem_def_csp = test_utils.m_polChemDefSPtr;
636	6/16 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 40 times. ✗ Branch 9 not taken. ✓ Branch 11 taken 40 times. ✗ Branch 12 not taken. ✓ Branch 14 taken 40 times. ✗ Branch 15 not taken. ✓ Branch 17 taken 40 times. ✗ Branch 18 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✗ Branch 27 not taken. ✗ Branch 28 not taken. ✗ Branch 30 not taken. ✗ Branch 31 not taken.	40	REQUIRE(pol_chem_def_csp->codeLength() == 1);
637	6/16 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 40 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 40 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 40 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 40 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	40	REQUIRE(pol_chem_def_csp->monomerList().size() == 21);
638	6/16 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 40 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 40 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 40 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 40 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	40	REQUIRE(pol_chem_def_csp->modifList().size() == 26);
639	6/16 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 40 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 40 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 40 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 40 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	40	REQUIRE(pol_chem_def_csp->crossLinkerList().size() == 2);
640	6/16 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 40 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 40 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 40 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 40 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	40	REQUIRE(pol_chem_def_csp->cleaveSpecList().size() == 8);
641	6/16 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 8 taken 40 times. ✗ Branch 9 not taken. ✓ Branch 12 taken 40 times. ✗ Branch 13 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 18 taken 40 times. ✗ Branch 19 not taken. ✓ Branch 22 taken 40 times. ✗ Branch 23 not taken. ✗ Branch 28 not taken. ✗ Branch 29 not taken. ✗ Branch 31 not taken. ✗ Branch 32 not taken.	40	REQUIRE(pol_chem_def_csp->fragSpecList().size() == 7);
642
643			QString chicken_telokin_file_path =
644	2/4 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken.	80	QString("%1/chicken-telokin.mxp").arg(test_utils.m_testsInputPolSeqsDir);
645
646	7/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 40 times. ✗ Branch 24 not taken.	40	GIVEN("A new Polymer instance created by loading a file with no modification")
647			{
648			Polymer polymer_1(
649	4/8 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 11 taken 40 times. ✗ Branch 12 not taken.	40	pol_chem_def_csp, "PolymerName", "PolymerCode", "PolymerAuthor");
650	7/18 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 40 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 40 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 40 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 40 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	40	REQUIRE(polymer_1.name().toStdString() == "PolymerName");
651	7/18 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 40 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 40 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 40 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 40 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	40	REQUIRE(polymer_1.code().toStdString() == "PolymerCode");
652	7/18 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 40 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 40 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 40 times. ✗ Branch 20 not taken. ✓ Branch 25 taken 40 times. ✗ Branch 26 not taken. ✗ Branch 33 not taken. ✗ Branch 34 not taken. ✗ Branch 36 not taken. ✗ Branch 37 not taken.	40	REQUIRE(polymer_1.author().toStdString() == "PolymerAuthor");
653
654	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	polymer_1.setFilePath(chicken_telokin_file_path);
655	8/20 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 40 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 40 times. ✗ Branch 17 not taken. ✓ Branch 19 taken 40 times. ✗ Branch 20 not taken. ✓ Branch 22 taken 40 times. ✗ Branch 23 not taken. ✓ Branch 29 taken 40 times. ✗ Branch 30 not taken. ✗ Branch 38 not taken. ✗ Branch 39 not taken. ✗ Branch 41 not taken. ✗ Branch 42 not taken.	40	REQUIRE(polymer_1.filePath().toStdString() ==
656			chicken_telokin_file_path.toStdString());
657
658	2/4 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken.	40	bool result = polymer_1.renderXmlPolymerFile();
659	5/14 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 40 times. ✗ Branch 14 not taken. ✓ Branch 17 taken 40 times. ✗ Branch 18 not taken. ✗ Branch 23 not taken. ✗ Branch 24 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken.	40	REQUIRE(result == true);
660	6/16 ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 13 taken 40 times. ✗ Branch 14 not taken. ✓ Branch 16 taken 40 times. ✗ Branch 17 not taken. ✓ Branch 20 taken 40 times. ✗ Branch 21 not taken. ✗ Branch 26 not taken. ✗ Branch 27 not taken. ✗ Branch 29 not taken. ✗ Branch 30 not taken.	40	REQUIRE(polymer_1.size() == test_utils.m_telokinSequenceMonomerCount);
661
662			// Only left end sequence MAMISGMSGRKAS
663	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	Coordinates coord(0, 12);
664	2/4 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken.	40	CoordinateList coord_list("TEST");
665	1/2 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken.	40	coord_list.setCoordinates(coord);
666
667	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
668			"Masses are calculated: selection, no deep-calc, no caps, no "
669			"modifs")
670			{
671			CalcOptions calc_options(false,
672			MassType::MASS_BOTH,
673			CAP_NONE,
674			MONOMER_CHEMENT_NONE,
675	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
676
677	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
678			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
679
680	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
681
682	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
683			true);
684
685	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_THAT(polymer_1.mono(),
686			Catch::Matchers::WithinAbs(1307.614834, 0.000001));
687	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_THAT(polymer_1.avg(),
688			Catch::Matchers::WithinAbs(1308.600609, 0.000001));
689		44	}
690
691	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
692			"Masses are calculated: selection, no deep-calc, left cap, no "
693			"modifs")
694			{
695			CalcOptions calc_options(false,
696			MassType::MASS_BOTH,
697			CAP_LEFT,
698			MONOMER_CHEMENT_NONE,
699	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
700
701	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
702			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
703
704	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
705
706	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
707			true);
708
709	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_THAT(polymer_1.mono(),
710			Catch::Matchers::WithinAbs(1308.622659, 0.000001));
711	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_THAT(polymer_1.avg(),
712			Catch::Matchers::WithinAbs(1309.608550, 0.000001));
713		44	}
714
715	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
716			"Masses are calculated: selection, no deep-calc, right cap, no "
717			"modifs")
718			{
719			CalcOptions calc_options(false,
720			MassType::MASS_BOTH,
721			CAP_RIGHT,
722			MONOMER_CHEMENT_NONE,
723	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
724
725	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
726			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
727
728	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
729
730	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
731			true);
732
733	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_THAT(polymer_1.mono(),
734			Catch::Matchers::WithinAbs(1324.617573, 0.000001));
735	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_THAT(polymer_1.avg(),
736			Catch::Matchers::WithinAbs(1325.607959, 0.000001));
737		44	}
738
739	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
740			"Masses are calculated: selection, no deep-calc, both caps, no "
741			"modifs")
742			{
743			CalcOptions calc_options(false,
744			MassType::MASS_BOTH,
745			CAP_BOTH,
746			MONOMER_CHEMENT_NONE,
747	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_NONE);
748
749	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
750			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
751
752	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
753
754	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
755			true);
756
757	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_THAT(polymer_1.mono(),
758			Catch::Matchers::WithinAbs(1325.625398, 0.000001));
759	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_THAT(polymer_1.avg(),
760			Catch::Matchers::WithinAbs(1326.615900, 0.000001));
761		44	}
762
763	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN("Masses are calculated: selection, no deep-calc, both caps, LE_MODIF")
764			{
765			CalcOptions calc_options(false,
766			MassType::MASS_BOTH,
767			CAP_BOTH,
768			MONOMER_CHEMENT_NONE,
769	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_LEFT_END_MODIF);
770
771	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
772			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
773
774	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
775
776	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(polymer_1.setLeftEndModif("Acetylation") == true);
777	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(polymer_1.isLeftEndModified() == true);
778	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
779
780	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(polymer_1.setRightEndModif("AmidationGlu") == true);
781	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(polymer_1.isRightEndModified() == true);
782	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
783
784	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
785			true);
786
787	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_THAT(polymer_1.mono(),
788			Catch::Matchers::WithinAbs(1367.635963, 0.000001));
789	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_THAT(polymer_1.avg(),
790			Catch::Matchers::WithinAbs(1368.652841, 0.000001));
791		44	}
792
793	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
794			"Masses are calculated: selection, no deep-calc, both caps, RE_MODIF, no "
795			"force right end modif")
796			{
797			CalcOptions calc_options(false,
798			MassType::MASS_BOTH,
799			CAP_BOTH,
800			MONOMER_CHEMENT_NONE,
801	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_RIGHT_END_MODIF);
802
803	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
804			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
805
806	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
807
808	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(polymer_1.setLeftEndModif("Acetylation") == true);
809	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(polymer_1.isLeftEndModified() == true);
810	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
811
812	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(polymer_1.setRightEndModif("AmidationGlu") == true);
813	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(polymer_1.isRightEndModified() == true);
814	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
815
816	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
817			true);
818
819	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_THAT(polymer_1.mono(),
820			Catch::Matchers::WithinAbs(1325.625398, 0.000001));
821	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_THAT(polymer_1.avg(),
822			Catch::Matchers::WithinAbs(1326.615900, 0.000001));
823		44	}
824
825	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
826			"Masses are calculated: selection, no deep-calc, both caps, RE_MODIF, "
827			"force right end modif")
828			{
829			CalcOptions calc_options(false,
830			MassType::MASS_BOTH,
831			CAP_BOTH,
832			MONOMER_CHEMENT_NONE,
833			POLYMER_CHEMENT_RIGHT_END_MODIF \|
834	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_FORCE_RIGHT_END_MODIF);
835
836	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
837			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
838
839	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
840
841	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(polymer_1.setLeftEndModif("Acetylation") == true);
842	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(polymer_1.isLeftEndModified() == true);
843	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
844
845	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(polymer_1.setRightEndModif("AmidationGlu") == true);
846	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(polymer_1.isRightEndModified() == true);
847	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
848
849	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
850			true);
851
852	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_THAT(polymer_1.mono(),
853			Catch::Matchers::WithinAbs(1324.641383, 0.000001));
854	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_THAT(polymer_1.avg(),
855			Catch::Matchers::WithinAbs(1325.631138, 0.000001));
856		44	}
857
858	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
859			"Masses are calculated: selection, no deep-calc, both caps, "
860			"BOTH_END_MODIFS no force right end modif")
861			{
862			CalcOptions calc_options(false,
863			MassType::MASS_BOTH,
864			CAP_BOTH,
865			MONOMER_CHEMENT_NONE,
866	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_BOTH_END_MODIF);
867
868	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
869			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
870
871	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
872
873	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(polymer_1.setLeftEndModif("Acetylation") == true);
874	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(polymer_1.isLeftEndModified() == true);
875	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
876
877	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(polymer_1.setRightEndModif("AmidationGlu") == true);
878	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(polymer_1.isRightEndModified() == true);
879	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
880
881	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
882			true);
883
884	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_THAT(polymer_1.mono(),
885			Catch::Matchers::WithinAbs(1367.635963, 0.000001));
886	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_THAT(polymer_1.avg(),
887			Catch::Matchers::WithinAbs(1368.652841, 0.000001));
888		44	}
889
890	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
891			"Masses are calculated: selection, no deep-calc, both caps, "
892			"BOTH_END_MODIFS force right end modif")
893			{
894			CalcOptions calc_options(false,
895			MassType::MASS_BOTH,
896			CAP_BOTH,
897			MONOMER_CHEMENT_NONE,
898			POLYMER_CHEMENT_BOTH_END_MODIF \|
899	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_FORCE_RIGHT_END_MODIF);
900
901	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
902			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
903
904	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
905
906	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(polymer_1.setLeftEndModif("Acetylation") == true);
907	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(polymer_1.isLeftEndModified() == true);
908	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
909
910	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(polymer_1.setRightEndModif("AmidationGlu") == true);
911	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(polymer_1.isRightEndModified() == true);
912	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
913
914	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
915			true);
916
917	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_THAT(polymer_1.mono(),
918			Catch::Matchers::WithinAbs(1366.651947, 0.000001));
919	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_THAT(polymer_1.avg(),
920			Catch::Matchers::WithinAbs(1367.668078, 0.000001));
921		44	}
922
923	8/14 ✓ Branch 1 taken 40 times. ✗ Branch 2 not taken. ✓ Branch 4 taken 40 times. ✗ Branch 5 not taken. ✓ Branch 7 taken 40 times. ✗ Branch 8 not taken. ✓ Branch 10 taken 40 times. ✗ Branch 11 not taken. ✓ Branch 15 taken 40 times. ✗ Branch 16 not taken. ✓ Branch 21 taken 40 times. ✗ Branch 22 not taken. ✓ Branch 23 taken 4 times. ✓ Branch 24 taken 36 times.	40	THEN(
924			"Masses are calculated: selection, deep-calc, both caps, "
925			"BOTH_END_MODIFS force end modif and monomer modif Ser-phos")
926			{
927			CalcOptions calc_options(true,
928			MassType::MASS_BOTH,
929			CAP_BOTH,
930			MONOMER_CHEMENT_MODIF,
931			POLYMER_CHEMENT_BOTH_END_MODIF \|
932	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	POLYMER_CHEMENT_FORCE_RIGHT_END_MODIF);
933
934	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setSelectionType(
935			SelectionType::SELECTION_TYPE_RESIDUAL_CHAINS);
936
937	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	calc_options.setCoordinateList(coord_list);
938
939	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(polymer_1.setLeftEndModif("Acetylation") == true);
940	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(polymer_1.isLeftEndModified() == true);
941	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(polymer_1.leftEndModif().name().toStdString() == "Acetylation");
942
943	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(polymer_1.setRightEndModif("AmidationGlu") == true);
944	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(polymer_1.isRightEndModified() == true);
945	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(polymer_1.rightEndModif().name().toStdString() == "AmidationGlu");
946
947			// Phosphorylate Ser at index 4
948		4	int index = 4; // the Ser
949	3/8 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 5 taken 4 times. ✗ Branch 6 not taken. ✓ Branch 9 taken 4 times. ✗ Branch 10 not taken. ✗ Branch 17 not taken. ✗ Branch 18 not taken.	4	Modif *modif_p = new Modif(pol_chem_def_csp, "NOT_SET");
950	3/6 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken. ✓ Branch 5 taken 4 times. ✗ Branch 6 not taken. ✓ Branch 8 taken 4 times. ✗ Branch 9 not taken.	4	result = polymer_1.getPolChemDefCstSPtr()->referenceModifByName(
951			"Phosphorylation", modif_p);
952	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);
953	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	Monomer monomer_p = const_cast<Monomer >(polymer_1.at(index));
954		4	QStringList errorList;
955	1/2 ✓ Branch 1 taken 4 times. ✗ Branch 2 not taken.	4	result = monomer_p->modify(modif_p, false, errorList);
956	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);
957
958	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(polymer_1.calculateMasses(calc_options, /* reset */ true) ==
959			true);
960
961	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_THAT(polymer_1.mono(),
962			Catch::Matchers::WithinAbs(1446.618278, 0.000001));
963	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_THAT(polymer_1.avg(),
964			Catch::Matchers::WithinAbs(1447.648008, 0.000001));
965		44	}
966		80	}
967		40	}
968
969			} // namespace libXpertMass
970			} // namespace MsXpS
971

Function (Line)	Call count	Block coverage
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_0() (line 35)	called 16 times, returned 16 times	48.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_12() (line 122)	called 8 times, returned 8 times	47.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_18() (line 188)	called 20 times, returned 20 times	47.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_30() (line 290)	called 32 times, returned 32 times	46.0%
MsXpS::libXpertMass::CATCH2_INTERNAL_TEST_41() (line 623)	called 40 times, returned 40 times	46.0%