Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentViewTest	41	55	4	0.813559381.4%	Show methods

Class AlignmentViewTest

Class AlignmentViewTest	Line # 41	Total Statements 55	Complexity 4	TOTAL Coverage 0.813559381.4%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	1.0 1.0100%
testGetVisibleAlignmentGapChar() : void   testGetVisibleAlignmentGapChar() : void	5151	8.08	1.01	1.0 1.0100%
testGetVisibleContigMapFor() : void   testGetVisibleContigMapFor() : void	6565	10.010	1.01	0.0 0.00%
testGetVisibleContigs() : void   testGetVisibleContigs() : void	8585	35.035	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6101695	jalview.datamodel.AlignmentViewTest.testGetVisibleContigsjalview.datamodel.AlignmentViewTest.testGetVisibleContigs	1PASS
	0.15254237	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.hamcrest.MatcherAssert.assertThat;
24		import static org.hamcrest.Matchers.contains;
25		import org.hamcrest.Matchers;
26		import static org.testng.Assert.assertEquals;
27
28		import java.util.Arrays;
29		import java.util.List;
30
31		import jalview.gui.AlignFrame;
32		import jalview.gui.JvOptionPane;
33		import jalview.io.DataSourceType;
34		import jalview.io.FileLoader;
35		import jalview.viewmodel.AlignmentViewport;
36
37		import org.testng.annotations.BeforeClass;
38		import org.testng.annotations.Test;
39
40
		81.4% Uncovered Elements: 11 (59) Complexity: 4 Complexity Density: 0.07
41		public class AlignmentViewTest
42		{
43
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	1	JvOptionPane.setInteractiveMode(false);
48	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
51	1	@Test(groups = { "Functional" })...
52		public void testGetVisibleAlignmentGapChar()
53		{
54	1	SeqCigar ss = new SeqCigar(new Sequence("One", "A..CDE"));
55	1	CigarArray ca = new CigarArray(new CigarSimple[] { ss });
56	1	AlignmentView av = new AlignmentView(ca);
57	1	String dots = av.getSequenceStrings('.')[0];
58	1	assertEquals(dots, "A..CDE");
59	1	String dollars = av.getSequenceStrings('$')[0];
60	1	assertEquals(dollars, "A$$CDE");
61	1	assertEquals(av.getVisibleAlignment('$').getSequenceAt(0)
62		.getSequenceAsString(), "A$$CDE");
63		}
64
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 1PASS
65	0	@Test...
66		public void testGetVisibleContigMapFor()
67		{
68	0	AlignFrame af = new FileLoader()
69		.LoadFileWaitTillLoaded(">seq\nAAA-AAAA---AA--\n",
70		DataSourceType.PASTE);
71	0	var av = af.getViewport();
72	0	var seq = av.getAlignment().getSequenceAt(0);
73	0	var gapMap = seq.gapMap();
74	0	assertThat(Arrays.stream(gapMap).boxed().toArray(Integer[]::new),
75		Matchers.arrayContaining(0, 1, 2, 4, 5, 6, 7, 11, 12));
76
77	0	av.hideColumns(0, 1);
78	0	av.hideColumns(6, 7);
79	0	AlignmentView view = av.getAlignmentView(true);
80	0	var delMap = view.getVisibleContigMapFor(gapMap);
81	0	assertThat(Arrays.stream(delMap).boxed().toArray(Integer[]::new),
82		Matchers.arrayContaining(2, 3, 4, 7, 8));
83		}
84
		100% Uncovered Elements: 0 (35) Complexity: 1 Complexity Density: 0.03 1PASS
85	1	@Test(groups = { "Functional" })...
86		public void testGetVisibleContigs()
87		{
88	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
89		">s1\n0123456789\n", DataSourceType.PASTE);
90	1	AlignmentViewport av = af.getViewport();
91	1	AlignmentView view = av.getAlignmentView(true);
92
93		/*
94		* verify getVisibleContigs returns inclusive [start, end] ranges
95		*
96		* no columns hidden
97		*/
98	1	int[] contigs = view.getVisibleContigs();
99	1	assertEquals(contigs, new int[] { 0, 9 });
100
101		/*
102		* hide 3 internal columns
103		*/
104	1	av.hideColumns(5, 7);
105		// the old AlignmentView is now stale!
106	1	contigs = view.getVisibleContigs();
107	1	assertEquals(contigs, new int[] { 0, 9 });
108		// get a fresh AlignmentView
109	1	view = av.getAlignmentView(true);
110	1	contigs = view.getVisibleContigs();
111	1	assertEquals(contigs, new int[] { 0, 4, 8, 9 });
112
113		// hide first 2 columns
114	1	av.hideColumns(0, 1);
115	1	view = av.getAlignmentView(true);
116	1	contigs = view.getVisibleContigs();
117	1	assertEquals(contigs, new int[] { 2, 4, 8, 9 });
118
119		// hide last column
120	1	av.hideColumns(9, 9);
121	1	view = av.getAlignmentView(true);
122	1	contigs = view.getVisibleContigs();
123	1	assertEquals(contigs, new int[] { 2, 4, 8, 8 });
124
125		// unhide columns 5-7
126	1	av.showColumn(5);
127	1	view = av.getAlignmentView(true);
128	1	contigs = view.getVisibleContigs();
129	1	assertEquals(contigs, new int[] { 2, 8 });
130
131		// hide columns 2-7
132	1	av.hideColumns(2, 7);
133	1	view = av.getAlignmentView(true);
134	1	contigs = view.getVisibleContigs();
135	1	assertEquals(contigs, new int[] { 8, 8 });
136
137		// hide column 8
138	1	av.hideColumns(8, 8);
139	1	view = av.getAlignmentView(true);
140	1	contigs = view.getVisibleContigs();
141	1	assertEquals(contigs, new int[] {});
142
143		// unhide all
144	1	av.showAllHiddenColumns();
145	1	view = av.getAlignmentView(true);
146	1	contigs = view.getVisibleContigs();
147	1	assertEquals(contigs, new int[] { 0, 9 });
148		}
149		}