Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HMMERTest	29	36	6	0.00%	Show methods

Class HMMERTest

Class HMMERTest	Line # 29	Total Statements 36	Complexity 6	TOTAL Coverage 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	3333	2.02	1.01	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	4848	1.01	1.01	0.0 0.00%
testHMMBuildThenHMMAlign() : void   testHMMBuildThenHMMAlign() : void	6060	4.04	1.01	0.0 0.00%
testHMMBuild() : void   testHMMBuild() : void	7878	13.013	1.01	0.0 0.00%
testHMMAlign() : void   testHMMAlign() : void	103103	16.016	2.02	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.hmmer;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertFalse;
5		import static org.testng.Assert.assertNotNull;
6		import static org.testng.Assert.assertTrue;
7		import static org.testng.Assert.fail;
8
9		import jalview.bin.Jalview;
10		import jalview.datamodel.AlignmentI;
11		import jalview.datamodel.HiddenMarkovModel;
12		import jalview.datamodel.SequenceI;
13		import jalview.gui.AlignFrame;
14		import jalview.gui.Desktop;
15		import jalview.io.HMMFile;
16		import jalview.util.MessageManager;
17		import jalview.ws.params.ArgumentI;
18		import jalview.ws.params.simple.Option;
19
20		import java.io.IOException;
21		import java.net.MalformedURLException;
22		import java.util.ArrayList;
23		import java.util.List;
24
25		import org.testng.annotations.AfterClass;
26		import org.testng.annotations.BeforeClass;
27		import org.testng.annotations.Test;
28
		0% Uncovered Elements: 43 (43) Complexity: 6 Complexity Density: 0.17
29		public class HMMERTest {
30
31		AlignFrame frame;
32
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
33	0	@BeforeClass(alwaysRun = true)...
34		public void setUpBeforeClass() throws Exception
35		{
36		/*
37		* NB: check HMMER_PATH in testProps.jvprops is valid for
38		* the machine on which this runs
39		*/
40	0	Jalview.main(
41		new String[]
42		{ "-noquestionnaire", "-nonews", "-props",
43		"test/jalview/hmmer/testProps.jvprops", "-open",
44		"examples/uniref50.fa" });
45	0	frame = Desktop.getDesktopAlignFrames()[0];
46		}
47
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
48	0	@AfterClass(alwaysRun = true)...
49		public static void tearDownAfterClass() throws Exception
50		{
51	0	Desktop.getInstance().closeAll_actionPerformed(null);
52		}
53
54		/**
55		* Test with a dependency on locally installed hmmbuild binaries
56		*
57		* @throws MalformedURLException
58		* @throws IOException
59		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
60	0	@Test(groups = "External")...
61		public void testHMMBuildThenHMMAlign()
62		throws MalformedURLException, IOException
63		{
64		/*
65		* run hmmbuild
66		*/
67	0	testHMMBuild();
68	0	List<SequenceI> hmms = frame.getViewport().getAlignment()
69		.getHmmSequences();
70	0	assertFalse(hmms.isEmpty());
71
72		/*
73		* now run hmmalign - by default with respect to the added HMM profile
74		*/
75	0	testHMMAlign();
76		}
77
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08 4-
78	0	public void testHMMBuild()...
79		{
80		/*
81		* set up argument to run hmmbuild for the alignment
82		*/
83	0	ArrayList<ArgumentI> params = new ArrayList<>();
84	0	String argName = MessageManager.getString("label.hmmbuild_for");
85	0	String argValue = MessageManager.getString("label.alignment");
86	0	params.add(
87		new Option(argName, null, false, null, argValue, null, null));
88
89	0	HMMBuild builder = new HMMBuild(frame, params);
90	0	builder.run();
91
92	0	SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
93	0	HiddenMarkovModel hmm = seq.getHMM();
94	0	assertNotNull(hmm);
95
96	0	assertEquals(hmm.getLength(), 148);
97	0	assertEquals(hmm.getAlphabetType(), "amino");
98	0	assertEquals(hmm.getName(), "Alignment_HMM");
99	0	assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
100		"0.648193");
101		}
102
		0% Uncovered Elements: 18 (18) Complexity: 2 Complexity Density: 0.12 4-
103	0	public void testHMMAlign()...
104		{
105	0	HmmerCommand thread = new HMMAlign(frame,
106		new ArrayList<ArgumentI>());
107	0	thread.run();
108
109	0	AlignFrame[] alignFrames = Desktop.getDesktopAlignFrames();
110	0	if (alignFrames == null)
111		{
112	0	fail("No align frame loaded");
113		}
114
115		/*
116		* now have the original align frame, and another for realigned sequences
117		*/
118	0	assertEquals(alignFrames.length, 2);
119	0	AlignmentI original = alignFrames[0].getViewport().getAlignment();
120	0	assertNotNull(original);
121	0	AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
122	0	assertNotNull(realigned);
123	0	assertFalse(original.getHmmSequences().isEmpty());
124	0	assertFalse(realigned.getHmmSequences().isEmpty());
125
126	0	SequenceI ferCapan = original.findName("FER_CAPAN");
127	0	assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
128
129	0	SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
130	0	assertTrue(ferCapanRealigned.getSequenceAsString()
131		.startsWith("-------m-A----SVSAT"));
132		}
133		}
134