Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignmentPanelTest	37	40	5	12	0.7333333573.3%	Show methods

Class AlignmentPanelTest

Class AlignmentPanelTest	Line # 37	Total Statements 40	Complexity 5	Uncovered Elements 12	TOTAL Coverage 0.7333333573.3%
setUp() : void   setUp() : void	133133	7.07	3.03	3.03	0.6666667 0.666666766.7%
TestSetScrollValues() : void   TestSetScrollValues() : void	166166	25.025	1.01	0.00	1.0 1.0100%
TestUpdateLayout_endRes() : void   TestUpdateLayout_endRes() : void	227227	8.08	1.01	8.08	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5777778	jalview.gui.AlignmentPanelTest.TestSetScrollValuesjalview.gui.AlignmentPanelTest.TestSetScrollValues	1PASS
	0.2	jalview.gui.AlignmentPanelTest.TestUpdateLayout_endResjalview.gui.AlignmentPanelTest.TestUpdateLayout_endRes	3FAIL

 

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.gui;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertNotEquals;
25
26		import jalview.bin.Cache;
27		import jalview.bin.Jalview;
28		import jalview.datamodel.Sequence;
29		import jalview.datamodel.SequenceI;
30		import jalview.io.DataSourceType;
31		import jalview.io.FileLoader;
32		import jalview.viewmodel.ViewportRanges;
33
34		import org.testng.annotations.BeforeMethod;
35		import org.testng.annotations.Test;
36
		73.3% Uncovered Elements: 12 (45) Complexity: 5 Complexity Density: 0.12
37		public class AlignmentPanelTest
38		{
39		SequenceI seq1 = new Sequence(
40		"Seq1",
41		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
42
43		SequenceI seq2 = new Sequence(
44		"Seq2",
45		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
46
47		SequenceI seq3 = new Sequence(
48		"Seq3",
49		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
50
51		SequenceI seq4 = new Sequence(
52		"Seq4",
53		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
54
55		SequenceI seq5 = new Sequence(
56		"Seq5",
57		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
58
59		SequenceI seq6 = new Sequence(
60		"Seq6",
61		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
62
63		SequenceI seq7 = new Sequence(
64		"Seq7",
65		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
66
67		SequenceI seq8 = new Sequence(
68		"Seq8",
69		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
70
71		SequenceI seq9 = new Sequence(
72		"Seq9",
73		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
74
75		SequenceI seq10 = new Sequence(
76		"Seq10",
77		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
78
79		SequenceI seq11 = new Sequence(
80		"Seq11",
81		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
82
83		SequenceI seq12 = new Sequence(
84		"Seq12",
85		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
86
87		SequenceI seq13 = new Sequence(
88		"Seq13",
89		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
90
91		SequenceI seq14 = new Sequence(
92		"Seq14",
93		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
94
95		SequenceI seq15 = new Sequence(
96		"Seq15",
97		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
98
99		SequenceI seq16 = new Sequence(
100		"Seq16",
101		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
102
103		SequenceI seq17 = new Sequence(
104		"Seq17",
105		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
106
107		SequenceI seq18 = new Sequence(
108		"Seq18",
109		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
110
111		SequenceI seq19 = new Sequence(
112		"Seq19",
113		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
114
115		SequenceI seq20 = new Sequence(
116		"Seq20",
117		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
118
119		SequenceI seq21 = new Sequence(
120		"Seq21",
121		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
122
123		SequenceI seq22 = new Sequence(
124		"Seq22",
125		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
126
127		SequenceI seq23 = new Sequence(
128		"Seq23",
129		"ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
130
131		AlignFrame af;
132
		66.7% Uncovered Elements: 3 (9) Complexity: 3 Complexity Density: 0.43
133	2	@BeforeMethod(alwaysRun = true)...
134		public void setUp()
135		{
136	2	Jalview.main(new String[] { "-nonews", "-props",
137		"test/jalview/testProps.jvprops" });
138
139	2	Cache.applicationProperties.setProperty("SHOW_IDENTITY",
140		Boolean.TRUE.toString());
141	2	af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
142		DataSourceType.FILE);
143
144		/*
145		* wait for Consensus thread to complete
146		*/
147	2	synchronized (this)
148		{
149	2	while (af.getViewport().getConsensusSeq() == null)
150		{
151	0	try
152		{
153	0	wait(50);
154		} catch (InterruptedException e)
155		{
156		}
157		}
158		}
159		}
160
161
162		/**
163		* Test side effect that end residue is set correctly by setScrollValues, with
164		* or without hidden columns
165		*/
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
166	1	@Test(groups = "Functional")...
167		public void TestSetScrollValues()
168		{
169	1	ViewportRanges ranges = af.getViewport().getRanges();
170	1	af.alignPanel.setScrollValues(0, 0);
171
172	1	int oldres = ranges.getEndRes();
173	1	af.alignPanel.setScrollValues(-1, 5);
174
175		// setting -ve x value does not change residue
176	1	assertEquals(ranges.getEndRes(), oldres);
177
178	1	af.alignPanel.setScrollValues(0, 5);
179
180		// setting 0 as x value does not change residue
181	1	assertEquals(ranges.getEndRes(), oldres);
182
183	1	af.alignPanel.setScrollValues(5, 5);
184		// setting x value to 5 extends endRes by 5 residues
185	1	assertEquals(ranges.getEndRes(), oldres + 5);
186
187		// scroll to position after hidden columns sets endres to oldres (width) +
188		// position
189	1	int scrollpos = 60;
190	1	af.getViewport().hideColumns(30, 50);
191	1	af.alignPanel.setScrollValues(scrollpos, 5);
192	1	assertEquals(ranges.getEndRes(), oldres + scrollpos);
193
194		// scroll to position within hidden columns, still sets endres to oldres +
195		// position
196		// not sure if this is actually correct behaviour but this is what Jalview
197		// currently does
198	1	scrollpos = 40;
199	1	af.getViewport().showAllHiddenColumns();
200	1	af.getViewport().hideColumns(30, 50);
201	1	af.alignPanel.setScrollValues(scrollpos, 5);
202	1	assertEquals(ranges.getEndRes(), oldres + scrollpos);
203
204		// scroll to position within <width> distance of the end of the alignment
205		// endRes should be set to width of alignment - 1
206	1	scrollpos = 130;
207	1	af.getViewport().showAllHiddenColumns();
208	1	af.alignPanel.setScrollValues(scrollpos, 5);
209	1	assertEquals(ranges.getEndRes(), af.getViewport()
210		.getAlignment().getWidth() - 1);
211
212		// now hide some columns, and scroll to position within <width>
213		// distance of the end of the alignment
214		// endRes should be set to width of alignment - 1 - the number of hidden
215		// columns
216	1	af.getViewport().hideColumns(30, 50);
217	1	af.alignPanel.setScrollValues(scrollpos, 5);
218	1	assertEquals(ranges.getEndRes(), af.getViewport()
219		.getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
220		// columns
221		}
222
223		/**
224		* Test that update layout reverts to original (unwrapped) values for endRes
225		* and endSeq when switching from wrapped to unwrapped mode (JAL-2739)
226		*/
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12 3FAIL
227	0	@Test(groups = "Functional")...
228		public void TestUpdateLayout_endRes()
229		{
230		// get details of original alignment dimensions
231	0	ViewportRanges ranges = af.getViewport().getRanges();
232	0	int endres = ranges.getEndRes();
233
234		// wrap
235	0	af.alignPanel.getAlignViewport().setWrapAlignment(true);
236	0	af.alignPanel.updateLayout();
237
238		// endRes changes
239	0	assertNotEquals(ranges.getEndRes(), endres);
240
241		// unwrap
242	0	af.alignPanel.getAlignViewport().setWrapAlignment(false);
243	0	af.alignPanel.updateLayout();
244
245		// endRes and endSeq back to original values
246	0	assertEquals(ranges.getEndRes(), endres);
247
248		}
249		}