Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SeqsetUtilsTest	46	24	4	1.0100%	Show methods

Class SeqsetUtilsTest

Class SeqsetUtilsTest	Line # 46	Total Statements 24	Complexity 4	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	1.0 1.0100%
testSeqFeatureAddition() : void   testSeqFeatureAddition() : void	6060	18.018	1.01	1.0 1.0100%
sequenceAndMask() : Object[][]   sequenceAndMask() : Object[][]	9191	1.01	1.01	1.0 1.0100%
testFilterSequence(String,long,String) : void   testFilterSequence(String,long,String) : void	108108	3.03	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6785714	jalview.analysis.SeqsetUtilsTest.testSeqFeatureAdditionjalview.analysis.SeqsetUtilsTest.testSeqFeatureAddition	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS
	0.14285715	jalview.analysis.SeqsetUtilsTest.testFilterSequencejalview.analysis.SeqsetUtilsTest.testFilterSequence	1PASS

 

Source view

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 static org.hamcrest.MatcherAssert.assertThat;
31		import static org.hamcrest.Matchers.equalTo;
32
33		import java.util.BitSet;
34		import java.util.Hashtable;
35		import java.util.Map;
36
37		import org.testng.Assert;
38		import org.testng.annotations.BeforeClass;
39		import org.testng.annotations.DataProvider;
40		import org.testng.annotations.Test;
41
42		/**
43		* @author jprocter
44		*
45		*/
		100% Uncovered Elements: 0 (28) Complexity: 4 Complexity Density: 0.17
46		public class SeqsetUtilsTest
47		{
48
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
49	1	@BeforeClass(alwaysRun = true)...
50		public void setUpJvOptionPane()
51		{
52	1	JvOptionPane.setInteractiveMode(false);
53	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54		}
55
56		/**
57		* test for JAL-2046 bug - duplication of sequence features on reconstructed
58		* alignment
59		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
60	1	@Test(groups = { "Functional" })...
61		public void testSeqFeatureAddition()
62		{
63	1	SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"),
64		new Sequence("Aseq2", "AREALSEQ") };
65
66	1	AlignmentI al = new Alignment(sqset);
67	1	al.setDataset(null);
68	1	AlignmentI ds = al.getDataset();
69	1	SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
70	1	SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
71	1	ds.getSequenceAt(0).addSequenceFeature(sf1);
72	1	Map<String, SeqsetUtils.SequenceInfo> unq = SeqsetUtils.uniquify(sqset, true);
73	1	SequenceI[] sqset2 = new SequenceI[] {
74		new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
75		new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
76	1	Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
77	1	Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
78	1	ds.getSequenceAt(0).addSequenceFeature(sf2);
79	1	Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
80	1	SeqsetUtils.deuniquify(unq, sqset2);
81		// explicitly test that original sequence features still exist because they
82		// are on the shared dataset sequence
83	1	Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
84	1	Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
85	1	Assert.assertSame(sqset[0].getSequenceFeatures().get(0),
86		sqset2[0].getSequenceFeatures().get(0));
87	1	Assert.assertSame(sqset[0].getSequenceFeatures().get(1),
88		sqset2[0].getSequenceFeatures().get(1));
89		}
90
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
91	1	@DataProvider...
92		public Object[][] sequenceAndMask()
93		{
94	1	return new Object[][] {
95		{ "AAAABBBBCCCCDDDD", 0xFFFFL, "AAAABBBBCCCCDDDD" },
96		{ "AAAABBBBCCCCDDDD", 0x000FL, "AAAA" },
97		{ "---A---B---C---D", 0x8888L, "ABCD" },
98		{ "---A---B---C---D", 0x9999L, "-A-B-C-D" },
99		{ "ABCDABCDABCDABCD", 0xC5A3L, "ABBDACCD" },
100		{ "", 0xFFFFL, "" },
101		{ "AAAABBBBCCCCDDDD", 0x0000L, "" },
102		{ "AAABBBCCC", 0xFFFF, "AAABBBCCC" },
103		{ "AAAABBBB", 0xD000L, "" },
104		{ "AAAABBBB", 0xAA0AL, "AA" },
105		};
106		}
107
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
108	10	@Test(groups = {"Functional"}, dataProvider = "sequenceAndMask")...
109		public void testFilterSequence(String sequence, long mask, String expected)
110		{
111	10	BitSet bitMask = BitSet.valueOf(new long[] {mask});
112	10	var result = SeqsetUtils.filterSequence(sequence.toCharArray(), bitMask);
113	10	assertThat(result, equalTo(expected.toCharArray()));
114		}
115		}