Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PairwiseAlignmentPanelTest	36	20	2	1.0100%	Show methods

Class PairwiseAlignmentPanelTest

Class PairwiseAlignmentPanelTest	Line # 36	Total Statements 20	Complexity 2	TOTAL Coverage 1.0100%
testConstructor_withSelectionGroup() : void   testConstructor_withSelectionGroup() : void	3838	13.013	1.01	1.0 1.0100%
testConstructor_noSelectionGroup() : void   testConstructor_noSelectionGroup() : void	7575	7.07	1.01	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

 

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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
25		import jalview.api.AlignViewportI;
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.SequenceGroup;
28		import jalview.io.DataSourceType;
29		import jalview.io.FileLoader;
30		import javax.swing.JTextArea;
31
32		import org.testng.annotations.Test;
33
34		import junit.extensions.PA;
35
		100% Uncovered Elements: 0 (22) Complexity: 2 Complexity Density: 0.1
36		public class PairwiseAlignmentPanelTest
37		{
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
38	1	@Test(groups = "Functional")...
39		public void testConstructor_withSelectionGroup()
40		{
41	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
42		"examples/uniref50.fa", DataSourceType.FILE);
43	1	AlignViewportI viewport = af.getViewport();
44	1	AlignmentI al = viewport.getAlignment();
45
46		/*
47		* select columns 29-36 of sequences 4 and 5 for alignment
48		* Q93XJ9_SOLTU/23-29 L-KAISNV
49		* FER1_PEA/26-32 V-TTTKAF
50		*/
51	1	SequenceGroup sg = new SequenceGroup();
52	1	sg.addSequence(al.getSequenceAt(3), false);
53	1	sg.addSequence(al.getSequenceAt(4), false);
54	1	sg.setStartRes(28);
55	1	sg.setEndRes(35);
56	1	viewport.setSelectionGroup(sg);
57
58	1	PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
59
60	1	String text = ((JTextArea) PA.getValue(testee, "textarea")).getText().replace("\r\n", "\n");
61	1	String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
62		+ "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
63		+ "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
64		+ " FER1_PEA/29-32 TKAF\n" + " ||.\n"
65		+ "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n";
66	1	assertEquals(text, expected);
67		}
68
69		/**
70		* This test aligns the same sequences as testConstructor_withSelectionGroup
71		* but as a complete alignment (no selection). Note that in fact the user is
72		* currently required to make a selection in order to calculate pairwise
73		* alignments, so this case does not arise.
74		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
75	1	@Test(groups = "Functional")...
76		public void testConstructor_noSelectionGroup()
77		{
78	1	String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n";
79	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
80		DataSourceType.PASTE);
81	1	AlignViewportI viewport = af.getViewport();
82
83	1	PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
84
85	1	String text = ((JTextArea) PA.getValue(testee, "textarea")).getText().replace("\r\n", "\n");
86	1	String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
87		+ "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
88		+ "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
89		+ " FER1_PEA/29-32 TKAF\n" + " ||.\n"
90		+ "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n";
91	1	assertEquals(text, expected);
92		}
93		}