Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JmolViewerTest	50	58	19	0.9367088793.7%	Show methods

Class JmolViewerTest

Class JmolViewerTest	Line # 50	Total Statements 58	Complexity 19	TOTAL Coverage 0.9367088793.7%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5353	2.02	1.01	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	6363	1.01	1.01	1.0 1.0100%
tearDownAfterClass() : void   tearDownAfterClass() : void	7575	2.02	2.02	0.75 0.7575%
testSingleSeqViewJMol() : void   testSingleSeqViewJMol() : void	8282	19.019	7.07	0.8518519 0.851851985.2%
testAddStrToSingleSeqViewJMol() : void   testAddStrToSingleSeqViewJMol() : void	132132	34.034	8.08	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.51898736	jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol	1PASS
	0.30379745	jalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMol	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.ext.jmol;
22
23		import static org.junit.Assert.assertNotNull;
24		import static org.testng.Assert.assertEquals;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import java.lang.reflect.InvocationTargetException;
28
29		import org.testng.annotations.AfterClass;
30		import org.testng.annotations.BeforeClass;
31		import org.testng.annotations.Test;
32
33		import jalview.api.structures.JalviewStructureDisplayI;
34		import jalview.bin.Cache;
35		import jalview.bin.Jalview;
36		import jalview.datamodel.PDBEntry;
37		import jalview.datamodel.SearchResultsI;
38		import jalview.datamodel.SequenceI;
39		import jalview.gui.AlignFrame;
40		import jalview.gui.Desktop;
41		import jalview.gui.JvOptionPane;
42		import jalview.gui.Preferences;
43		import jalview.gui.StructureViewer;
44		import jalview.gui.StructureViewer.ViewerType;
45		import jalview.io.DataSourceType;
46		import jalview.io.FileFormat;
47		import jalview.io.FileLoader;
48
49		@Test(singleThreaded = true)
		93.7% Uncovered Elements: 5 (79) Complexity: 19 Complexity Density: 0.33
50		public class JmolViewerTest
51		{
52
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
53	1	@BeforeClass(alwaysRun = true)...
54		public void setUpJvOptionPane()
55		{
56	1	JvOptionPane.setInteractiveMode(false);
57	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
58		}
59
60		/**
61		* @throws java.lang.Exception
62		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
63	1	@BeforeClass(alwaysRun = true)...
64		public static void setUpBeforeClass() throws Exception
65		{
66	1	Jalview.main(
67		new String[]
68		{ "--noquestionnaire", "--nonews", "--props",
69		"test/jalview/ext/rbvi/chimera/testProps.jvprops" });
70		}
71
72		/**
73		* @throws java.lang.Exception
74		*/
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 1
75	1	@AfterClass(alwaysRun = true)...
76		public static void tearDownAfterClass() throws Exception
77		{
78	1	if (Desktop.instance != null)
79	1	Desktop.instance.closeAll_actionPerformed(null);
80		}
81
		85.2% Uncovered Elements: 4 (27) Complexity: 7 Complexity Density: 0.37 1PASS
82	1	@Test(groups = { "Functional" })...
83		public void testSingleSeqViewJMol()
84		{
85	1	Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
86		ViewerType.JMOL.name());
87	1	String inFile = "examples/1gaq.txt";
88	1	AlignFrame af = new jalview.io.FileLoader()
89		.LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
90	1	assertTrue("Didn't read input file " + inFile, af != null);
91	1	for (SequenceI sq : af.getViewport().getAlignment().getSequences())
92		{
93	1	SequenceI dsq = sq.getDatasetSequence();
94	1	while (dsq.getDatasetSequence() != null)
95		{
96	0	dsq = dsq.getDatasetSequence();
97		}
98	1	if (dsq.getAllPDBEntries() != null
99		&& dsq.getAllPDBEntries().size() > 0)
100		{
101	1	for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
102		{
103	1	final StructureViewer structureViewer = new StructureViewer(
104		af.getViewport().getStructureSelectionManager());
105	1	structureViewer.setViewerType(ViewerType.JMOL);
106	1	JalviewStructureDisplayI jmolViewer = structureViewer
107		.viewStructures(dsq.getAllPDBEntries().elementAt(q),
108		new SequenceI[]
109		{ sq }, af.getCurrentView().getAlignPanel());
110		/*
111		* Wait for viewer load thread to complete
112		*/
113	1	try
114		{
115	2	while (!jmolViewer.getBinding().isFinishedInit())
116		{
117	1	Thread.sleep(500);
118		}
119		} catch (InterruptedException e)
120		{
121		}
122
123	1	jmolViewer.closeViewer(true);
124		// todo: break here means only once through this loop?
125	1	break;
126		}
127	1	break;
128		}
129		}
130		}
131
		100% Uncovered Elements: 0 (40) Complexity: 8 Complexity Density: 0.24 1PASS
132	1	@Test(groups = { "Functional" })...
133		public void testAddStrToSingleSeqViewJMol()
134		throws InvocationTargetException, InterruptedException
135		{
136	1	Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
137		ViewerType.JMOL.name());
138	1	String inFile = "examples/1gaq.txt";
139	1	AlignFrame af = new jalview.io.FileLoader(true)
140		.LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
141	1	assertTrue("Didn't read input file " + inFile, af != null);
142		// show a structure for 4th Sequence
143	1	SequenceI sq1 = af.getViewport().getAlignment().getSequences().get(0);
144	1	final StructureViewer structureViewer = new StructureViewer(
145		af.getViewport().getStructureSelectionManager());
146	1	structureViewer.setViewerType(ViewerType.JMOL);
147	1	JalviewStructureDisplayI jmolViewer = structureViewer.viewStructures(
148		sq1.getDatasetSequence().getAllPDBEntries().elementAt(0),
149		new SequenceI[]
150		{ sq1 }, af.getCurrentView().getAlignPanel());
151		/*
152		* Wait for viewer load thread to complete
153		*/
154	1	try
155		{
156	2	while (!jmolViewer.getBinding().isFinishedInit())
157		{
158	1	Thread.sleep(500);
159		}
160		} catch (InterruptedException e)
161		{
162		}
163
164	1	assertTrue(jmolViewer.isVisible());
165
166		// add another pdb file and add it to view
167	1	final String _inFile = "examples/3W5V.pdb";
168	1	inFile = _inFile;
169	1	FileLoader fl = new FileLoader();
170	1	fl.LoadFile(af.getCurrentView(), _inFile, DataSourceType.FILE,
171		FileFormat.PDB);
172	1	try
173		{
174	1	int time = 0;
175	1	do
176		{
177	5	Thread.sleep(50); // hope we can avoid race condition
178
179	5	} while (++time < 30
180		&& af.getViewport().getAlignment().getHeight() == 3);
181		} catch (Exception q)
182		{
183		}
184	1	;
185	1	assertTrue("Didn't paste additional structure" + inFile,
186		af.getViewport().getAlignment().getHeight() > 3);
187	1	SequenceI sq2 = af.getViewport().getAlignment().getSequenceAt(3);
188	1	PDBEntry pdbe = sq2.getDatasetSequence().getAllPDBEntries().get(0);
189	1	assertTrue(pdbe.getFile().contains(inFile));
190	1	structureViewer.viewStructures(pdbe, new SequenceI[] { sq2 },
191		af.alignPanel);
192		/*
193		* Wait for viewer load thread to complete
194		*/
195	1	try
196		{
197	4	while (structureViewer.isBusy())
198		{
199	3	Thread.sleep(500);
200		}
201		} catch (InterruptedException e)
202		{
203		}
204	1	assertEquals(jmolViewer.getBinding().getPdbCount(), 2);
205	1	String mouseOverTest = "[GLY]293:A.CA/2.1 #2164";
206	1	((JalviewJmolBinding) jmolViewer.getBinding()).mouseOverStructure(2164,
207		mouseOverTest);
208	1	SearchResultsI highlight = af.alignPanel.getSeqPanel()
209		.getLastSearchResults();
210	1	assertNotNull("Didn't find highlight from second structure mouseover",
211		highlight.getResults(sq2, sq2.getStart(), sq2.getEnd()));
212		}
213
214		}