Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JmolViewerTest	49	57	18	4	0.9473684494.7%	Show methods

Class JmolViewerTest

Class JmolViewerTest	Line # 49	Total Statements 57	Complexity 18	Uncovered Elements 4	TOTAL Coverage 0.9473684494.7%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5252	2.02	1.01	0.00	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	6262	1.01	1.01	0.00	1.0 1.0100%
tearDownAfterClass() : void   tearDownAfterClass() : void	7474	1.01	1.01	0.00	1.0 1.0100%
testSingleSeqViewJMol() : void   testSingleSeqViewJMol() : void	8080	19.019	7.07	4.04	0.8518519 0.851851985.2%
testAddStrToSingleSeqViewJMol() : void   testAddStrToSingleSeqViewJMol() : void	130130	34.034	8.08	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5394737	jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol	1PASS
	0.31578946	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 jalview.api.structures.JalviewStructureDisplayI;
28		import jalview.bin.Cache;
29		import jalview.bin.Jalview;
30		import jalview.datamodel.PDBEntry;
31		import jalview.datamodel.SearchResultsI;
32		import jalview.datamodel.SequenceI;
33		import jalview.gui.AlignFrame;
34		import jalview.gui.JvOptionPane;
35		import jalview.gui.Preferences;
36		import jalview.gui.StructureViewer;
37		import jalview.gui.StructureViewer.ViewerType;
38		import jalview.io.DataSourceType;
39		import jalview.io.FileFormat;
40		import jalview.io.FileLoader;
41
42		import java.lang.reflect.InvocationTargetException;
43
44		import org.testng.annotations.AfterClass;
45		import org.testng.annotations.BeforeClass;
46		import org.testng.annotations.Test;
47
48		@Test(singleThreaded = true)
		94.7% Uncovered Elements: 4 (76) Complexity: 18 Complexity Density: 0.32
49		public class JmolViewerTest
50		{
51
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
52	1	@BeforeClass(alwaysRun = true)...
53		public void setUpJvOptionPane()
54		{
55	1	JvOptionPane.setInteractiveMode(false);
56	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57		}
58
59		/**
60		* @throws java.lang.Exception
61		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
62	1	@BeforeClass(alwaysRun = true)...
63		public static void setUpBeforeClass() throws Exception
64		{
65	1	Jalview.main(
66		new String[]
67		{ "-noquestionnaire", "-nonews", "-props",
68		"test/jalview/ext/rbvi/chimera/testProps.jvprops" });
69		}
70
71		/**
72		* @throws java.lang.Exception
73		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
74	1	@AfterClass(alwaysRun = true)...
75		public static void tearDownAfterClass() throws Exception
76		{
77	1	jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
78		}
79
		85.2% Uncovered Elements: 4 (27) Complexity: 7 Complexity Density: 0.37 1PASS
80	1	@Test(groups = { "Functional" })...
81		public void testSingleSeqViewJMol()
82		{
83	1	Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
84		ViewerType.JMOL.name());
85	1	String inFile = "examples/1gaq.txt";
86	1	AlignFrame af = new jalview.io.FileLoader()
87		.LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
88	1	assertTrue("Didn't read input file " + inFile, af != null);
89	1	for (SequenceI sq : af.getViewport().getAlignment().getSequences())
90		{
91	1	SequenceI dsq = sq.getDatasetSequence();
92	1	while (dsq.getDatasetSequence() != null)
93		{
94	0	dsq = dsq.getDatasetSequence();
95		}
96	1	if (dsq.getAllPDBEntries() != null
97		&& dsq.getAllPDBEntries().size() > 0)
98		{
99	1	for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
100		{
101	1	final StructureViewer structureViewer = new StructureViewer(
102		af.getViewport().getStructureSelectionManager());
103	1	structureViewer.setViewerType(ViewerType.JMOL);
104	1	JalviewStructureDisplayI jmolViewer = structureViewer
105		.viewStructures(dsq.getAllPDBEntries().elementAt(q),
106		new SequenceI[]
107		{ sq }, af.getCurrentView().getAlignPanel());
108		/*
109		* Wait for viewer load thread to complete
110		*/
111	1	try
112		{
113	3	while (!jmolViewer.getBinding().isFinishedInit())
114		{
115	2	Thread.sleep(500);
116		}
117		} catch (InterruptedException e)
118		{
119		}
120
121	1	jmolViewer.closeViewer(true);
122		// todo: break here means only once through this loop?
123	1	break;
124		}
125	1	break;
126		}
127		}
128		}
129
		100% Uncovered Elements: 0 (40) Complexity: 8 Complexity Density: 0.24 1PASS
130	1	@Test(groups = { "Functional" })...
131		public void testAddStrToSingleSeqViewJMol()
132		throws InvocationTargetException, InterruptedException
133		{
134	1	Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
135		ViewerType.JMOL.name());
136	1	String inFile = "examples/1gaq.txt";
137	1	AlignFrame af = new jalview.io.FileLoader(true)
138		.LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
139	1	assertTrue("Didn't read input file " + inFile, af != null);
140		// show a structure for 4th Sequence
141	1	SequenceI sq1 = af.getViewport().getAlignment().getSequences().get(0);
142	1	final StructureViewer structureViewer = new StructureViewer(
143		af.getViewport().getStructureSelectionManager());
144	1	structureViewer.setViewerType(ViewerType.JMOL);
145	1	JalviewStructureDisplayI jmolViewer = structureViewer.viewStructures(
146		sq1.getDatasetSequence().getAllPDBEntries().elementAt(0),
147		new SequenceI[]
148		{ sq1 }, af.getCurrentView().getAlignPanel());
149		/*
150		* Wait for viewer load thread to complete
151		*/
152	1	try
153		{
154	3	while (!jmolViewer.getBinding().isFinishedInit())
155		{
156	2	Thread.sleep(500);
157		}
158		} catch (InterruptedException e)
159		{
160		}
161
162	1	assertTrue(jmolViewer.isVisible());
163
164		// add another pdb file and add it to view
165	1	final String _inFile = "examples/3W5V.pdb";
166	1	inFile = _inFile;
167	1	FileLoader fl = new FileLoader();
168	1	fl.LoadFile(af.getCurrentView(), _inFile, DataSourceType.FILE,
169		FileFormat.PDB);
170	1	try
171		{
172	1	int time = 0;
173	1	do
174		{
175	4	Thread.sleep(50); // hope we can avoid race condition
176
177	4	} while (++time < 30
178		&& af.getViewport().getAlignment().getHeight() == 3);
179		} catch (Exception q)
180		{
181		}
182	1	;
183	1	assertTrue("Didn't paste additional structure" + inFile,
184		af.getViewport().getAlignment().getHeight() > 3);
185	1	SequenceI sq2 = af.getViewport().getAlignment().getSequenceAt(3);
186	1	PDBEntry pdbe = sq2.getDatasetSequence().getAllPDBEntries().get(0);
187	1	assertTrue(pdbe.getFile().contains(inFile));
188	1	structureViewer.viewStructures(pdbe, new SequenceI[] { sq2 },
189		af.alignPanel);
190		/*
191		* Wait for viewer load thread to complete
192		*/
193	1	try
194		{
195	3	while (structureViewer.isBusy())
196		{
197	2	Thread.sleep(500);
198		}
199		} catch (InterruptedException e)
200		{
201		}
202	1	assertEquals(jmolViewer.getBinding().getPdbCount(), 2);
203	1	String mouseOverTest = "[GLY]293:A.CA/2.1 #2164";
204	1	((JalviewJmolBinding) jmolViewer.getBinding()).mouseOverStructure(2164,
205		mouseOverTest);
206	1	SearchResultsI highlight = af.alignPanel.getSeqPanel()
207		.getLastSearchResults();
208	1	assertNotNull("Didn't find highlight from second structure mouseover",
209		highlight.getResults(sq2, sq2.getStart(), sq2.getEnd()));
210		}
211
212		}