Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
PairwiseAlignmentPanelTest	16	20	2	0	1.0100%	Show methods

Class PairwiseAlignmentPanelTest

Class PairwiseAlignmentPanelTest	Line # 16	Total Statements 20	Complexity 2	Uncovered Elements 0	TOTAL Coverage 1.0100%
testConstructor_withSelectionGroup() : void   testConstructor_withSelectionGroup() : void	1818	13.013	1.01	0.00	1.0 1.0100%
testConstructor_noSelectionGroup() : void   testConstructor_noSelectionGroup() : void	5555	7.07	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.6363636	jalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroup	1PASS
	0.36363637	jalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroup	1PASS

 

Source view

1		package jalview.gui;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.datamodel.AlignmentI;
6		import jalview.datamodel.SequenceGroup;
7		import jalview.io.DataSourceType;
8		import jalview.io.FileLoader;
9
10		import javax.swing.JTextArea;
11
12		import junit.extensions.PA;
13
14		import org.testng.annotations.Test;
15
		100% Uncovered Elements: 0 (22) Complexity: 2 Complexity Density: 0.1
16		public class PairwiseAlignmentPanelTest
17		{
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
18	1	@Test(groups = "Functional")...
19		public void testConstructor_withSelectionGroup()
20		{
21	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
22		"examples/uniref50.fa", DataSourceType.FILE);
23	1	AlignViewport viewport = af.getViewport();
24	1	AlignmentI al = viewport.getAlignment();
25
26		/*
27		* select columns 29-36 of sequences 4 and 5 for alignment
28		* Q93XJ9_SOLTU/23-29 L-KAISNV
29		* FER1_PEA/26-32 V-TTTKAF
30		*/
31	1	SequenceGroup sg = new SequenceGroup();
32	1	sg.addSequence(al.getSequenceAt(3), false);
33	1	sg.addSequence(al.getSequenceAt(4), false);
34	1	sg.setStartRes(28);
35	1	sg.setEndRes(35);
36	1	viewport.setSelectionGroup(sg);
37
38	1	PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
39
40	1	String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
41	1	String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
42		+ "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
43		+ "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
44		+ " FER1_PEA/29-32 TKAF\n" + " ||.\n"
45		+ "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n";
46	1	assertEquals(text, expected);
47		}
48
49		/**
50		* This test aligns the same sequences as testConstructor_withSelectionGroup
51		* but as a complete alignment (no selection). Note that in fact the user is
52		* currently required to make a selection in order to calculate pairwise
53		* alignments, so this case does not arise.
54		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
55	1	@Test(groups = "Functional")...
56		public void testConstructor_noSelectionGroup()
57		{
58	1	String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n";
59	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
60		DataSourceType.PASTE);
61	1	AlignViewport viewport = af.getViewport();
62
63	1	PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
64
65	1	String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
66	1	String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
67		+ "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
68		+ "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
69		+ " FER1_PEA/29-32 TKAF\n" + " ||.\n"
70		+ "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n";
71	1	assertEquals(text, expected);
72		}
73		}