Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureMappingTest	37	60	2	0.00%	Show methods

Class StructureMappingTest

Class StructureMappingTest	Line # 37	Total Statements 60	Complexity 2	TOTAL Coverage 0.00%
testGetPDBResNumRanges() : void   testGetPDBResNumRanges() : void	3939	23.023	1.01	0.0 0.00%
testEquals() : void   testEquals() : void	7373	37.037	1.01	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.structure;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertTrue;
26
27		import jalview.datamodel.Mapping;
28		import jalview.datamodel.Sequence;
29		import jalview.datamodel.SequenceI;
30		import jalview.util.MapList;
31
32		import java.util.HashMap;
33		import java.util.List;
34
35		import org.testng.annotations.Test;
36
		0% Uncovered Elements: 62 (62) Complexity: 2 Complexity Density: 0.03
37		public class StructureMappingTest
38		{
		0% Uncovered Elements: 23 (23) Complexity: 1 Complexity Density: 0.04 4-
39	0	@Test(groups = "Functional")...
40		public void testGetPDBResNumRanges()
41		{
42	0	HashMap<Integer, int[]> map = new HashMap<>();
43
44	0	StructureMapping mapping = new StructureMapping(null, null, null, null,
45		map, null);
46
47	0	List<int[]> ranges = mapping.getPDBResNumRanges(1, 2);
48	0	assertTrue(ranges.isEmpty());
49
50	0	map.put(1, new int[] { 12, 20 }); // 1 maps to 12
51	0	ranges = mapping.getPDBResNumRanges(2, 3);
52	0	assertTrue(ranges.isEmpty());
53	0	ranges = mapping.getPDBResNumRanges(1, 2);
54	0	assertEquals(ranges.size(), 1);
55	0	assertEquals(ranges.get(0)[0], 12);
56	0	assertEquals(ranges.get(0)[1], 12);
57
58	0	map.put(2, new int[] { 13, 20 }); // 2 maps to 13
59	0	ranges = mapping.getPDBResNumRanges(1, 2);
60	0	assertEquals(ranges.size(), 1);
61	0	assertEquals(ranges.get(0)[0], 12);
62	0	assertEquals(ranges.get(0)[1], 13);
63
64	0	map.put(3, new int[] { 15, 20 }); // 3 maps to 15 - break
65	0	ranges = mapping.getPDBResNumRanges(1, 5);
66	0	assertEquals(ranges.size(), 2);
67	0	assertEquals(ranges.get(0)[0], 12);
68	0	assertEquals(ranges.get(0)[1], 13);
69	0	assertEquals(ranges.get(1)[0], 15);
70	0	assertEquals(ranges.get(1)[1], 15);
71		}
72
		0% Uncovered Elements: 37 (37) Complexity: 1 Complexity Density: 0.03 4-
73	0	@Test(groups = "Functional")...
74		public void testEquals()
75		{
76	0	SequenceI seq1 = new Sequence("seq1", "ABCDE");
77	0	SequenceI seq2 = new Sequence("seq1", "ABCDE");
78	0	String pdbFile = "a/b/file1.pdb";
79	0	String pdbId = "1a70";
80	0	String chain = "A";
81	0	String mappingDetails = "these are the mapping details, honest";
82	0	HashMap<Integer, int[]> map = new HashMap<>();
83
84	0	Mapping seqToPdbMapping = new Mapping(seq1,
85		new MapList(new int[]
86		{ 1, 5 }, new int[] { 2, 6 }, 1, 1));
87	0	StructureMapping sm1 = new StructureMapping(seq1, pdbFile, pdbId, chain,
88		map, mappingDetails, seqToPdbMapping);
89	0	assertFalse(sm1.equals(null));
90	0	assertFalse(sm1.equals("x"));
91
92	0	StructureMapping sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain,
93		map, mappingDetails, seqToPdbMapping);
94	0	assertTrue(sm1.equals(sm2));
95	0	assertTrue(sm2.equals(sm1));
96	0	assertEquals(sm1.hashCode(), sm2.hashCode());
97
98		// with different sequence
99	0	sm2 = new StructureMapping(seq2, pdbFile, pdbId, chain, map,
100		mappingDetails, seqToPdbMapping);
101	0	assertFalse(sm1.equals(sm2));
102	0	assertFalse(sm2.equals(sm1));
103
104		// with different file
105	0	sm2 = new StructureMapping(seq1, "a/b/file2.pdb", pdbId, chain, map,
106		mappingDetails, seqToPdbMapping);
107	0	assertFalse(sm1.equals(sm2));
108	0	assertFalse(sm2.equals(sm1));
109
110		// with different pdbid (case sensitive)
111	0	sm2 = new StructureMapping(seq1, pdbFile, "1A70", chain, map,
112		mappingDetails, seqToPdbMapping);
113	0	assertFalse(sm1.equals(sm2));
114	0	assertFalse(sm2.equals(sm1));
115
116		// with different chain
117	0	sm2 = new StructureMapping(seq1, pdbFile, pdbId, "B", map,
118		mappingDetails, seqToPdbMapping);
119	0	assertFalse(sm1.equals(sm2));
120	0	assertFalse(sm2.equals(sm1));
121
122		// map is ignore for this test
123	0	sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain, null,
124		mappingDetails, seqToPdbMapping);
125	0	assertTrue(sm1.equals(sm2));
126	0	assertTrue(sm2.equals(sm1));
127
128		// with different mapping details
129	0	sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain, map,
130		"different details!", seqToPdbMapping);
131	0	assertFalse(sm1.equals(sm2));
132	0	assertFalse(sm2.equals(sm1));
133
134		// with different seq to pdb mapping
135	0	Mapping map2 = new Mapping(seq1,
136		new MapList(new int[]
137		{ 1, 5 }, new int[] { 3, 7 }, 1, 1));
138	0	sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain, map,
139		mappingDetails, map2);
140	0	assertFalse(sm1.equals(sm2));
141	0	assertFalse(sm2.equals(sm1));
142		}
143		}