Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AAConAnnotAndSettingsIO	49	51	13	0.00%	Show methods

Class AAConAnnotAndSettingsIO

Class AAConAnnotAndSettingsIO	Line # 49	Total Statements 51	Complexity 13	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5252	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	6969	12.012	4.04	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	103103	4.04	2.02	0.0 0.00%
getAaconArray() : Object[][]   getAaconArray() : Object[][]	114114	5.05	1.01	0.0 0.00%
testAAConAnnotAndRecovery(ServiceWithParameters) : void   testAAConAnnotAndRecovery(ServiceWithParameters) : void	130130	10.010	1.01	0.0 0.00%
testAAConClient(AlignFrame,ServiceWithParameters) : void   testAAConClient(AlignFrame,ServiceWithParameters) : void	160160	18.018	4.04	0.0 0.00%

 

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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.ws.jabaws;
22
23		import static org.testng.AssertJUnit.assertNotNull;
24		import static org.testng.AssertJUnit.assertTrue;
25
26		import jalview.bin.Cache;
27		import jalview.datamodel.AlignmentAnnotation;
28		import jalview.datamodel.AlignmentI;
29		import jalview.gui.AlignFrame;
30		import jalview.gui.JvOptionPane;
31		import jalview.ws.api.ServiceWithParameters;
32		import jalview.ws.jws2.Jws2Discoverer;
33		import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
34		import jalview.ws.slivkaws.SlivkaWSDiscoverer;
35
36		import java.util.ArrayList;
37		import java.util.List;
38
39		import org.testng.annotations.AfterClass;
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.DataProvider;
42		import org.testng.annotations.Test;
43
44		/*
45		* All methods in this class are set to the Network group because setUpBeforeClass will fail
46		* if there is no network.
47		*/
48		@Test(singleThreaded = true)
		0% Uncovered Elements: 69 (69) Complexity: 13 Complexity Density: 0.25
49		public class AAConAnnotAndSettingsIO
50		{
51
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
52	0	@BeforeClass(alwaysRun = true)...
53		public void setUpJvOptionPane()
54		{
55	0	JvOptionPane.setInteractiveMode(false);
56	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57		}
58
59		public static String testseqs = "examples/uniref50.fa";
60
61		public static Jws2Discoverer disc;
62
63		public static List<ServiceWithParameters[]> aacon;
64
65		jalview.ws.jws2.SeqAnnotationServiceCalcWorker aaconClient;
66
67		public static jalview.gui.AlignFrame af = null;
68
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.33
69	0	@BeforeClass(alwaysRun = true)...
70		public static void setUpBeforeClass() throws Exception
71		{
72	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
73	0	disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
74
75	0	while (disc.isRunning())
76		{
77		// don't get services until discoverer has finished
78	0	Thread.sleep(100);
79		}
80
81
82	0	aacon = new ArrayList<>();
83	0	for (ServiceWithParameters svc : disc.getServices())
84		{
85	0	if (svc.getNameURI().toLowerCase().contains("aacon"))
86		{
87	0	aacon.add(new ServiceWithParameters[] { svc });
88		}
89		}
90
91	0	for (ServiceWithParameters svc : SlivkaWSDiscoverer.getInstance()
92		.getServices())
93		{
94	0	if (svc.getNameURI().toLowerCase().contains("aacon"))
95		{
96	0	aacon.add(new ServiceWithParameters[] { svc });
97		}
98		}
99	0	assertTrue("Couldn't discover any AACon services to use to test.",
100		aacon.size() > 0);
101		}
102
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
103	0	@AfterClass(alwaysRun = true)...
104		public static void tearDownAfterClass() throws Exception
105		{
106	0	if (af != null)
107		{
108	0	af.setVisible(false);
109	0	af.dispose();
110	0	af = null;
111		}
112		}
113
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
114	0	@DataProvider(name = "aacons")...
115		public Object[][] getAaconArray()
116		{
117
118	0	Object[][] rtn = new Object[aacon.size()][1];
119	0	int i = 0;
120	0	for (ServiceWithParameters[] aa : aacon)
121		{
122	0	rtn[i++] = aa;
123		}
124	0	return rtn;
125		}
126		/**
127		* Run AACon on an alignment with defaults and verify Just Shenkin annotation
128		* appears
129		*/
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 4-
130	0	@Test(groups = { "External", "Network" }, dataProvider = "aacons")...
131		public void testAAConAnnotAndRecovery(ServiceWithParameters service)
132		{
133	0	jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
134	0	AlignFrame _af = fl.LoadFileWaitTillLoaded(testseqs,
135		jalview.io.DataSourceType.FILE);
136	0	assertNotNull("Couldn't load test data ('" + testseqs + "')", _af);
137	0	af = _af;
138	0	try
139		{
140	0	testAAConClient(_af, service);
141		} finally
142		{
143	0	af = null;
144	0	_af.setVisible(false);
145	0	_af.dispose();
146	0	_af = null;
147
148		}
149		}
150
151		/**
152		* triggers the given aacon worker on the alignment, waits for 5s and gives up
153		* or verifies SHENKIN annotation is produced.
154		*
155		* @param af
156		* - test data in an alignment frame
157		* @param aacon
158		* - the service to test
159		*/
		0% Uncovered Elements: 22 (22) Complexity: 4 Complexity Density: 0.22
160	0	static void testAAConClient(AlignFrame af, ServiceWithParameters aacon)...
161		{
162	0	SeqAnnotationServiceCalcWorker aaconClient = new SeqAnnotationServiceCalcWorker(
163		aacon, af, null,
164		null);
165	0	long current = System.currentTimeMillis(), limit = 15;
166	0	af.getViewport().getCalcManager().startWorker(aaconClient);
167	0	do
168		{
169	0	try
170		{
171	0	Thread.sleep(50);
172		} catch (InterruptedException x)
173		{
174		}
175	0	;
176	0	assertTrue(
177		"Waited " + limit + "s for " + aacon.getHostURL()
178		+ " - giving up.",
179		(System.currentTimeMillis() - current) < limit * 1000);
180	0	} while (af.getViewport().getCalcManager().isWorking());
181	0	AlignmentI orig_alig = af.getViewport().getAlignment();
182	0	boolean foundShenkin = false;
183	0	Iterable<AlignmentAnnotation> _aa=orig_alig
184		.findAnnotation(aacon.getAlignAnalysisUI().getCalcId());
185	0	assertTrue("No annotation from service",
186		_aa != null && _aa.iterator().hasNext());
187
188	0	for (AlignmentAnnotation aa : _aa)
189		{
190	0	assertTrue("AACon annotation not marked as autocalculated!",
191		aa.autoCalculated);
192	0	if ("shenkin".equals(aa.label.toLowerCase()))
193		{
194	0	foundShenkin = true;
195	0	break;
196		}
197		}
198	0	assertTrue("Failed to locate 'SHENKIN' annotation row.", foundShenkin);
199		}
200		}