Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SeqsetUtilsTest	40	20	2	1.0100%	Show methods

Class SeqsetUtilsTest

Class SeqsetUtilsTest	Line # 40	Total Statements 20	Complexity 2	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4343	2.02	1.01	1.0 1.0100%
testSeqFeatureAddition() : void   testSeqFeatureAddition() : void	5454	18.018	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8636364	jalview.analysis.SeqsetUtilsTest.testSeqFeatureAdditionjalview.analysis.SeqsetUtilsTest.testSeqFeatureAddition	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.analysis;
22
23		import jalview.datamodel.Alignment;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.Sequence;
26		import jalview.datamodel.SequenceFeature;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.JvOptionPane;
29
30		import java.util.Hashtable;
31
32		import org.testng.Assert;
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.Test;
35
36		/**
37		* @author jprocter
38		*
39		*/
		100% Uncovered Elements: 0 (22) Complexity: 2 Complexity Density: 0.1
40		public class SeqsetUtilsTest
41		{
42
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
43	1	@BeforeClass(alwaysRun = true)...
44		public void setUpJvOptionPane()
45		{
46	1	JvOptionPane.setInteractiveMode(false);
47	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48		}
49
50		/**
51		* test for JAL-2046 bug - duplication of sequence features on reconstructed
52		* alignment
53		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
54	1	@Test(groups = { "Functional" })...
55		public void testSeqFeatureAddition()
56		{
57	1	SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"),
58		new Sequence("Aseq2", "AREALSEQ") };
59
60	1	AlignmentI al = new Alignment(sqset);
61	1	al.setDataset(null);
62	1	AlignmentI ds = al.getDataset();
63	1	SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
64	1	SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
65	1	ds.getSequenceAt(0).addSequenceFeature(sf1);
66	1	Hashtable unq = SeqsetUtils.uniquify(sqset, true);
67	1	SequenceI[] sqset2 = new SequenceI[] {
68		new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
69		new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
70	1	Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
71	1	Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
72	1	ds.getSequenceAt(0).addSequenceFeature(sf2);
73	1	Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
74	1	SeqsetUtils.deuniquify(unq, sqset2);
75		// explicitly test that original sequence features still exist because they
76		// are on the shared dataset sequence
77	1	Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
78	1	Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
79	1	Assert.assertSame(sqset[0].getSequenceFeatures().get(0),
80		sqset2[0].getSequenceFeatures().get(0));
81	1	Assert.assertSame(sqset[0].getSequenceFeatures().get(1),
82		sqset2[0].getSequenceFeatures().get(1));
83		}
84		}