Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureViewerTest	39	38	3	1.0100%	Show methods

Class StructureViewerTest

Class StructureViewerTest	Line # 39	Total Statements 38	Complexity 3	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4242	2.02	1.01	1.0 1.0100%
testGetSequencesForPdbs() : void   testGetSequencesForPdbs() : void	4949	36.036	2.02	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.9285714	jalview.gui.StructureViewerTest.testGetSequencesForPdbsjalview.gui.StructureViewerTest.testGetSequencesForPdbs	1PASS

 

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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.gui;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNull;
26		import static org.testng.Assert.assertSame;
27		import static org.testng.Assert.assertTrue;
28
29		import jalview.datamodel.PDBEntry;
30		import jalview.datamodel.PDBEntry.Type;
31		import jalview.datamodel.Sequence;
32		import jalview.datamodel.SequenceI;
33
34		import java.util.Map;
35
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.Test;
38
		100% Uncovered Elements: 0 (42) Complexity: 3 Complexity Density: 0.08
39		public class StructureViewerTest
40		{
41
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
42	1	@BeforeClass(alwaysRun = true)...
43		public void setUpJvOptionPane()
44		{
45	1	JvOptionPane.setInteractiveMode(false);
46	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47		}
48
		100% Uncovered Elements: 0 (38) Complexity: 2 Complexity Density: 0.06 1PASS
49	1	@Test(groups = "Functional")...
50		public void testGetSequencesForPdbs()
51		{
52	1	StructureViewer sv = new StructureViewer(null);
53
54	1	assertNull(sv.getSequencesForPdbs(null, null));
55
56	1	PDBEntry pdbe1 = new PDBEntry("1A70", "A", Type.PDB, "path1");
57	1	PDBEntry pdbe2 = new PDBEntry("3A6S", "A", Type.PDB, "path2");
58	1	PDBEntry pdbe3 = new PDBEntry("1A70", "B", Type.PDB, "path1");
59	1	PDBEntry pdbe4 = new PDBEntry("1GAQ", "A", Type.PDB, null);
60	1	PDBEntry pdbe5 = new PDBEntry("3A6S", "B", Type.PDB, "path2");
61	1	PDBEntry pdbe6 = new PDBEntry("1GAQ", "B", Type.PDB, null);
62	1	PDBEntry pdbe7 = new PDBEntry("1FOO", "Q", Type.PDB, null);
63
64	1	PDBEntry[] pdbs = new PDBEntry[] { pdbe1, pdbe2, pdbe3, pdbe4, pdbe5,
65		pdbe6, pdbe7 };
66
67		/*
68		* seq1 ... seq6 associated with pdbe1 ... pdbe6
69		*/
70	1	SequenceI[] seqs = new SequenceI[pdbs.length];
71	8	for (int i = 0; i < seqs.length; i++)
72		{
73	7	seqs[i] = new Sequence("Seq" + i, "abc");
74		}
75
76		/*
77		* pdbe3/5/6 should get removed as having a duplicate file path
78		*/
79	1	Map<PDBEntry, SequenceI[]> uniques = sv.getSequencesForPdbs(pdbs, seqs);
80	1	assertTrue(uniques.containsKey(pdbe1));
81	1	assertTrue(uniques.containsKey(pdbe2));
82	1	assertFalse(uniques.containsKey(pdbe3));
83	1	assertTrue(uniques.containsKey(pdbe4));
84	1	assertFalse(uniques.containsKey(pdbe5));
85	1	assertFalse(uniques.containsKey(pdbe6));
86	1	assertTrue(uniques.containsKey(pdbe7));
87
88		// 1A70 associates with seq1 and seq3
89	1	SequenceI[] ss = uniques.get(pdbe1);
90	1	assertEquals(ss.length, 2);
91	1	assertSame(seqs[0], ss[0]);
92	1	assertSame(seqs[2], ss[1]);
93
94		// 3A6S has seq2 and seq5
95	1	ss = uniques.get(pdbe2);
96	1	assertEquals(ss.length, 2);
97	1	assertSame(seqs[1], ss[0]);
98	1	assertSame(seqs[4], ss[1]);
99
100		// 1GAQ has seq4 and seq6
101	1	ss = uniques.get(pdbe4);
102	1	assertEquals(ss.length, 2);
103	1	assertSame(seqs[3], ss[0]);
104	1	assertSame(seqs[5], ss[1]);
105
106		// 1FOO has seq7
107	1	ss = uniques.get(pdbe7);
108	1	assertEquals(ss.length, 1);
109	1	assertSame(seqs[6], ss[0]);
110		}
111		}