Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentViewTest	34	45	3	1.0100%	Show methods

Class AlignmentViewTest

Class AlignmentViewTest	Line # 34	Total Statements 45	Complexity 3	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3737	2.02	1.01	1.0 1.0100%
testGetVisibleAlignmentGapChar() : void   testGetVisibleAlignmentGapChar() : void	4444	8.08	1.01	1.0 1.0100%
testGetVisibleContigs() : void   testGetVisibleContigs() : void	5858	35.035	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.75	jalview.datamodel.AlignmentViewTest.testGetVisibleContigsjalview.datamodel.AlignmentViewTest.testGetVisibleContigs	1PASS
	0.1875	jalview.datamodel.AlignmentViewTest.testGetVisibleAlignmentGapCharjalview.datamodel.AlignmentViewTest.testGetVisibleAlignmentGapChar	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.datamodel;
22
23		import static org.testng.Assert.assertEquals;
24
25		import jalview.gui.AlignFrame;
26		import jalview.gui.AlignViewport;
27		import jalview.gui.JvOptionPane;
28		import jalview.io.DataSourceType;
29		import jalview.io.FileLoader;
30
31		import org.testng.annotations.BeforeClass;
32		import org.testng.annotations.Test;
33
		100% Uncovered Elements: 0 (48) Complexity: 3 Complexity Density: 0.07
34		public class AlignmentViewTest
35		{
36
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
37	1	@BeforeClass(alwaysRun = true)...
38		public void setUpJvOptionPane()
39		{
40	1	JvOptionPane.setInteractiveMode(false);
41	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
42		}
43
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
44	1	@Test(groups = { "Functional" })...
45		public void testGetVisibleAlignmentGapChar()
46		{
47	1	SeqCigar ss = new SeqCigar(new Sequence("One", "A..CDE"));
48	1	CigarArray ca = new CigarArray(new CigarSimple[] { ss });
49	1	AlignmentView av = new AlignmentView(ca);
50	1	String dots = av.getSequenceStrings('.')[0];
51	1	assertEquals(dots, "A..CDE");
52	1	String dollars = av.getSequenceStrings('$')[0];
53	1	assertEquals(dollars, "A$$CDE");
54	1	assertEquals(av.getVisibleAlignment('$').getSequenceAt(0)
55		.getSequenceAsString(), "A$$CDE");
56		}
57
		100% Uncovered Elements: 0 (35) Complexity: 1 Complexity Density: 0.03 1PASS
58	1	@Test(groups = { "Functional" })...
59		public void testGetVisibleContigs()
60		{
61	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
62		">s1\n0123456789\n", DataSourceType.PASTE);
63	1	AlignViewport av = af.getViewport();
64	1	AlignmentView view = av.getAlignmentView(true);
65
66		/*
67		* verify getVisibleContigs returns inclusive [start, end] ranges
68		*
69		* no columns hidden
70		*/
71	1	int[] contigs = view.getVisibleContigs();
72	1	assertEquals(contigs, new int[] { 0, 9 });
73
74		/*
75		* hide 3 internal columns
76		*/
77	1	av.hideColumns(5, 7);
78		// the old AlignmentView is now stale!
79	1	contigs = view.getVisibleContigs();
80	1	assertEquals(contigs, new int[] { 0, 9 });
81		// get a fresh AlignmentView
82	1	view = av.getAlignmentView(true);
83	1	contigs = view.getVisibleContigs();
84	1	assertEquals(contigs, new int[] { 0, 4, 8, 9 });
85
86		// hide first 2 columns
87	1	av.hideColumns(0, 1);
88	1	view = av.getAlignmentView(true);
89	1	contigs = view.getVisibleContigs();
90	1	assertEquals(contigs, new int[] { 2, 4, 8, 9 });
91
92		// hide last column
93	1	av.hideColumns(9, 9);
94	1	view = av.getAlignmentView(true);
95	1	contigs = view.getVisibleContigs();
96	1	assertEquals(contigs, new int[] { 2, 4, 8, 8 });
97
98		// unhide columns 5-7
99	1	av.showColumn(5);
100	1	view = av.getAlignmentView(true);
101	1	contigs = view.getVisibleContigs();
102	1	assertEquals(contigs, new int[] { 2, 8 });
103
104		// hide columns 2-7
105	1	av.hideColumns(2, 7);
106	1	view = av.getAlignmentView(true);
107	1	contigs = view.getVisibleContigs();
108	1	assertEquals(contigs, new int[] { 8, 8 });
109
110		// hide column 8
111	1	av.hideColumns(8, 8);
112	1	view = av.getAlignmentView(true);
113	1	contigs = view.getVisibleContigs();
114	1	assertEquals(contigs, new int[] {});
115
116		// unhide all
117	1	av.showAllHiddenColumns();
118	1	view = av.getAlignmentView(true);
119	1	contigs = view.getVisibleContigs();
120	1	assertEquals(contigs, new int[] { 0, 9 });
121		}
122		}