Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GroupingTest	37	20	4	1.0100%	Show methods

Class GroupingTest

Class GroupingTest	Line # 37	Total Statements 20	Complexity 4	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	1.0 1.0100%
testMakeGroupsWithBoth() : void   testMakeGroupsWithBoth() : void	7474	18.018	3.03	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.88461536	jalview.analysis.GroupingTest.testMakeGroupsWithBothjalview.analysis.GroupingTest.testMakeGroupsWithBoth	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.ColumnSelection;
26		import jalview.datamodel.Sequence;
27		import jalview.datamodel.SequenceGroup;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.JvOptionPane;
30
31		import java.util.Arrays;
32
33		import org.testng.AssertJUnit;
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.Test;
36
		100% Uncovered Elements: 0 (26) Complexity: 4 Complexity Density: 0.2
37		public class GroupingTest
38		{
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
39	1	@BeforeClass(alwaysRun = true)...
40		public void setUpJvOptionPane()
41		{
42	1	JvOptionPane.setInteractiveMode(false);
43	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44		}
45
46		Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");
47
48		Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");
49
50		Sequence s3 = new Sequence("s3", "ACAADDEDEEEE");
51
52		Sequence s4 = new Sequence("s4", "AAAADDEDEEEE");
53
54		Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
55
56		SequenceGroup sg_12 = new SequenceGroup(
57		Arrays.asList(new SequenceI[]
58		{ s1, s2 }), "Group1", null, false, false, false, 0, 5);
59
60		SequenceGroup sg_345 = new SequenceGroup(
61		Arrays.asList(new SequenceI[]
62		{ s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
63
64		AlignmentI alignment = new Alignment(
65		new SequenceI[]
66		{ s1, s2, s3, s4, s5 });
67
68		/*
69		* test for the case where column selections are not added in
70		* left to right order
71		*/
72		int[] positions = new int[] { 7, 9, 1 };
73
		100% Uncovered Elements: 0 (22) Complexity: 3 Complexity Density: 0.17 1PASS
74	1	@Test(groups = { "Functional" })...
75		public void testMakeGroupsWithBoth()
76		{
77	1	String[] str = new String[alignment.getHeight()];
78	1	int seq = 0;
79	1	for (SequenceI s : alignment.getSequences())
80		{
81	5	StringBuilder sb = new StringBuilder();
82	5	for (int p : positions)
83		{
84	15	sb.append(s.getCharAt(p));
85		}
86	5	str[seq++] = sb.toString();
87		}
88	1	SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
89		alignment.getSequencesArray(), str,
90		Arrays.asList(new SequenceGroup[]
91		{ sg_12, sg_345 }));
92
93	1	ColumnSelection cs = new ColumnSelection();
94	1	for (int p : positions)
95		{
96	3	cs.addElement(p);
97		}
98	1	SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
99		alignment.getSequencesArray(), cs,
100		Arrays.asList(new SequenceGroup[]
101		{ sg_12, sg_345 }));
102	1	AssertJUnit.assertEquals(seqgroupsString.length,
103		seqgroupsColSel.length);
104	5	for (int p = 0; p < seqgroupsString.length; p++)
105		{
106	4	AssertJUnit.assertEquals(seqgroupsString[p].getName(),
107		seqgroupsColSel[p].getName());
108	4	AssertJUnit.assertArrayEquals(
109		seqgroupsString[p].getSequencesInOrder(alignment),
110		seqgroupsColSel[p].getSequencesInOrder(alignment));
111	4	if (seqgroupsString[p].getSequences().contains(s2))
112		{
113	1	AssertJUnit.assertTrue(seqgroupsString[p].getSize() == 2);
114		}
115		}
116		}
117
118		}