Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CommandsTest2	44	46	13	0.00%	Show methods

Class CommandsTest2

Class CommandsTest2	Line # 44	Total Statements 46	Complexity 13	TOTAL Coverage 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	4646	5.05	2.02	0.0 0.00%
resetProps() : void   resetProps() : void	5858	1.01	1.01	0.0 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	6464	2.02	1.01	0.0 0.00%
tearDown() : void   tearDown() : void	7171	1.01	1.01	0.0 0.00%
structureOpeningArgsTest(String,int,int,int) : void   structureOpeningArgsTest(String,int,int,int) : void	7777	36.036	7.07	0.0 0.00%
structureOpeningArgsParams() : Object[][]   structureOpeningArgsParams() : Object[][]	151151	1.01	1.01	0.0 0.00%

 

Contributing tests

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.bin;
22
23		import java.util.Date;
24		import java.util.List;
25
26		import org.testng.Assert;
27		import org.testng.annotations.AfterClass;
28		import org.testng.annotations.AfterMethod;
29		import org.testng.annotations.BeforeClass;
30		import org.testng.annotations.DataProvider;
31		import org.testng.annotations.Test;
32
33		import jalview.api.AlignViewportI;
34		import jalview.datamodel.AlignmentAnnotation;
35		import jalview.datamodel.AlignmentI;
36		import jalview.datamodel.SequenceI;
37		import jalview.gui.AlignFrame;
38		import jalview.gui.AlignmentPanel;
39		import jalview.gui.Desktop;
40		import jalview.gui.JvOptionPane;
41		import jalview.gui.StructureViewerBase;
42
43		@Test
		0% Uncovered Elements: 62 (62) Complexity: 13 Complexity Density: 0.28
44		public class CommandsTest2
45		{
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
46	0	@BeforeClass(alwaysRun = true)...
47		public static void setUpBeforeClass() throws Exception
48		{
49	0	Cache.loadProperties("test/jalview/bin/commandsTest.jvprops");
50	0	Date oneHourFromNow = new Date(
51		System.currentTimeMillis() + 3600 * 1000);
52	0	Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
53	0	if (Desktop.instance != null)
54	0	Desktop.instance.closeAll_actionPerformed(null);
55
56		}
57
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
58	0	@AfterClass(alwaysRun = true)...
59		public static void resetProps()
60		{
61	0	Cache.loadProperties("test/jalview/testProps.jvprops");
62		}
63
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
64	0	@BeforeClass(alwaysRun = true)...
65		public void setUpJvOptionPane()
66		{
67	0	JvOptionPane.setInteractiveMode(false);
68	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
69		}
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	@AfterMethod(alwaysRun = true)...
72		public void tearDown()
73		{
74	0	Desktop.closeDesktop();
75		}
76
		0% Uncovered Elements: 44 (44) Complexity: 7 Complexity Density: 0.19 4-
77	0	@Test(...
78		groups =
79		{ "Functional", "testTask1" },
80		dataProvider = "structureOpeningArgsParams",
81		singleThreaded = true)
82		public void structureOpeningArgsTest(String cmdLine, int seqNum,
83		int annNum, int viewerNum)
84		{
85	0	String[] args = cmdLine.split("\\s+");
86
87	0	CommandsTest.callJalviewMain(args);
88	0	while (Desktop.instance != null
89		&& Desktop.instance.operationsAreInProgress())
90		{
91	0	try
92		{
93		// sleep for slow build server to open annotations and viewer windows
94	0	Thread.sleep(viewerNum * 50);
95		} catch (InterruptedException e)
96		{
97	0	e.printStackTrace();
98		}
99		}
100	0	;
101
102	0	AlignFrame[] afs = Desktop.getDesktopAlignFrames();
103	0	Assert.assertNotNull(afs);
104	0	Assert.assertTrue(afs.length > 0);
105
106	0	AlignFrame af = afs[0];
107	0	Assert.assertNotNull(af);
108
109	0	AlignmentPanel ap = af.alignPanel;
110	0	Assert.assertNotNull(ap);
111
112	0	AlignmentI al = ap.getAlignment();
113	0	Assert.assertNotNull(al);
114
115	0	List<SequenceI> seqs = al.getSequences();
116	0	Assert.assertNotNull(seqs);
117
118	0	Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
119
120	0	AlignViewportI av = ap.getAlignViewport();
121	0	Assert.assertNotNull(av);
122
123	0	AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
124	0	int visibleAnn = 0;
125	0	int dcount = 0;
126	0	for (AlignmentAnnotation aa : aas)
127		{
128	0	if (aa.visible)
129	0	visibleAnn++;
130		}
131
132	0	Assert.assertEquals(visibleAnn, annNum,
133		"Wrong number of visible annotations");
134
135	0	if (viewerNum > -1)
136		{
137	0	List<StructureViewerBase> openViewers = Desktop.instance
138		.getStructureViewers(ap, null);
139	0	Assert.assertNotNull(openViewers);
140	0	int count = 0;
141	0	for (StructureViewerBase svb : openViewers)
142		{
143	0	if (svb.isVisible())
144	0	count++;
145		}
146	0	Assert.assertEquals(count, viewerNum,
147		"Wrong number of structure viewers opened");
148		}
149		}
150
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	@DataProvider(name = "structureOpeningArgsParams")...
152		public Object[][] structureOpeningArgsParams()
153		{
154		/*
155		String cmdLine,
156		int seqNum,
157		int annNum,
158		int structureViewerNum,
159		*/
160	0	return new Object[][] {
161		//
162		/*
163		*/
164		{ "--gui --nonews --nosplash --debug "
165		+ "--append=examples/uniref50.fa "
166		+ "--colour=gecos-flower "
167		+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
168		+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
169		+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
170		15, 7, 1 },
171		{ "--gui --nonews --nosplash --debug "
172		+ "--append=examples/uniref50.fa "
173		+ "--colour=gecos-flower "
174		+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
175		+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
176		+ "--props=test/jalview/bin/commandsTest2.jvprops2 ",
177		15, 4, 1 },
178		{ "--gui --nonews --nosplash --debug "
179		+ "--append=examples/uniref50.fa "
180		+ "--colour=gecos-flower "
181		+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
182		+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
183		+ "--noshowssannotations "
184		+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
185		15, 4, 1 },
186		{ "--gui --nonews --nosplash --debug "
187		+ "--append=examples/uniref50.fa "
188		+ "--colour=gecos-flower "
189		+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
190		+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
191		+ "--noshowannotations "
192		+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
193		15, 3, 1 },
194		{ "--gui --nonews --nosplash --debug "
195		+ "--append=examples/uniref50.fa "
196		+ "--colour=gecos-flower "
197		+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
198		+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
199		+ "--noshowannotations " + "--noshowssannotations "
200		+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
201		15, 0, 1 },
202		{ "--gui --nonews --nosplash --debug "
203		+ "--append=examples/uniref50.fa "
204		+ "--colour=gecos-flower "
205		+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
206		+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
207		+ "--noshowannotations " + "--noshowssannotations "
208		+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
209		15, 0, 1 },
210		{ "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
211		16, 19, 3 },
212		{ "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
213		16, 0, 2 },
214		{ "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
215		+ "--allstructures "
216		+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
217		+ "--structureviewer=none "
218		+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
219		+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
220		16, 10, 0 },
221		{ "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
222		+ "--allstructures "
223		+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
224		+ "--noallstructures " + "--structureviewer=none "
225		+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
226		+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
227		16, 10, 2 },
228		/*
229		*/
230		//
231		};
232		}
233		}