Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DisorderAnnotExportImport	56	54	14	0.00%	Show methods

Class DisorderAnnotExportImport

Class DisorderAnnotExportImport	Line # 56	Total Statements 54	Complexity 14	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5959	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	7676	17.017	4.04	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	111111	4.04	2.02	0.0 0.00%
getIuPreds() : ServiceWithParameters[][]   getIuPreds() : ServiceWithParameters[][]	122122	5.05	1.01	0.0 0.00%
testDisorderAnnotExport(ServiceWithParameters) : void   testDisorderAnnotExport(ServiceWithParameters) : void	139139	14.014	4.04	0.0 0.00%
checkAnnotationFileIO(String,AlignmentI) : void   checkAnnotationFileIO(String,AlignmentI) : void	174174	12.012	2.02	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 java.util.Locale;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.bin.Cache;
28		import jalview.bin.Console;
29		import jalview.datamodel.AlignmentAnnotation;
30		import jalview.datamodel.AlignmentI;
31		import jalview.gui.JvOptionPane;
32		import jalview.io.AnnotationFile;
33		import jalview.io.DataSourceType;
34		import jalview.io.FileFormat;
35		import jalview.io.FormatAdapter;
36		import jalview.io.StockholmFileTest;
37		import jalview.ws.api.ServiceWithParameters;
38		import jalview.ws.jws2.Jws2Discoverer;
39		import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
40		import jalview.ws.slivkaws.SlivkaWSDiscoverer;
41
42		import java.util.ArrayList;
43		import java.util.List;
44
45		import org.testng.Assert;
46		import org.testng.annotations.AfterClass;
47		import org.testng.annotations.BeforeClass;
48		import org.testng.annotations.DataProvider;
49		import org.testng.annotations.Test;
50
51		/*
52		* All methods in this class are set to the Network group because setUpBeforeClass will fail
53		* if there is no network.
54		*/
55		@Test(singleThreaded = true)
		0% Uncovered Elements: 72 (72) Complexity: 14 Complexity Density: 0.26
56		public class DisorderAnnotExportImport
57		{
58
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
59	0	@BeforeClass(alwaysRun = true)...
60		public void setUpJvOptionPane()
61		{
62	0	JvOptionPane.setInteractiveMode(false);
63	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64		}
65
66		public static String testseqs = "examples/uniref50.fa";
67
68		public static Jws2Discoverer disc;
69
70		public static List<ServiceWithParameters> iupreds;
71
72		jalview.ws.jws2.SeqAnnotationServiceCalcWorker disorderClient;
73
74		public static jalview.gui.AlignFrame af = null;
75
		0% Uncovered Elements: 23 (23) Complexity: 4 Complexity Density: 0.24
76	0	@BeforeClass(alwaysRun = true)...
77		public static void setUpBeforeClass() throws Exception
78		{
79	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
80	0	Console.initLogger();
81	0	disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
82
83	0	while (disc.isRunning())
84		{
85		// don't get services until discoverer has finished
86	0	Thread.sleep(100);
87		}
88
89	0	SlivkaWSDiscoverer disc2 = SlivkaWSDiscoverer.getInstance();
90	0	disc2.startDiscoverer();
91	0	while (disc2.isRunning())
92		{
93	0	Thread.sleep(100);
94		}
95	0	iupreds = new ArrayList<>();
96	0	for (ServiceWithParameters svc : disc2.getServices())
97		{
98	0	if (svc.getNameURI().toLowerCase().contains("iupred"))
99		{
100	0	iupreds.add(svc);
101		}
102		}
103	0	assertTrue("Couldn't discover any IUPred services to use to test.",
104		iupreds.size() > 0);
105	0	jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
106	0	af = fl.LoadFileWaitTillLoaded(testseqs,
107		jalview.io.DataSourceType.FILE);
108	0	assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
109		}
110
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
111	0	@AfterClass(alwaysRun = true)...
112		public static void tearDownAfterClass() throws Exception
113		{
114	0	if (af != null)
115		{
116	0	af.setVisible(false);
117	0	af.dispose();
118	0	af = null;
119		}
120		}
121
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
122	0	@DataProvider(name="getIuPreds",parallel = false)...
123		public static ServiceWithParameters[][] getIuPreds()
124		{
125	0	ServiceWithParameters[][] services = new ServiceWithParameters[iupreds
126		.size()][1];
127
128	0	int i = 0;
129	0	for (ServiceWithParameters iupred : iupreds)
130		{
131	0	services[i++][0] = iupred;
132		}
133	0	return services;
134		}
135
136		/**
137		* test for patches to JAL-1294
138		*/
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.29 4-
139	0	@Test(groups = { "External", "Network" },dataProvider = "getIuPreds")...
140		public void testDisorderAnnotExport(ServiceWithParameters iuPred)
141		{
142	0	disorderClient = new SeqAnnotationServiceCalcWorker(iuPred, af, null,
143		null);
144	0	af.getViewport().getCalcManager().startWorker(disorderClient);
145	0	do
146		{
147	0	try
148		{
149	0	Thread.sleep(50);
150		} catch (InterruptedException x)
151		{
152		}
153	0	;
154	0	} while (af.getViewport().getCalcManager().isWorking());
155	0	AlignmentI orig_alig = af.getViewport().getAlignment();
156		// NOTE: Consensus annotation row cannot be exported and reimported
157		// faithfully - so we remove them
158	0	List<AlignmentAnnotation> toremove = new ArrayList<>();
159	0	for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
160		{
161	0	if (aa.autoCalculated)
162		{
163	0	toremove.add(aa);
164		}
165		}
166	0	for (AlignmentAnnotation aa : toremove)
167		{
168	0	orig_alig.deleteAnnotation(aa);
169		}
170	0	checkAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
171
172		}
173
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.17
174	0	static void checkAnnotationFileIO(String testname, AlignmentI al)...
175		{
176	0	try
177		{
178	0	String aligfileout = FileFormat.Pfam.getWriter(al)
179		.print(al.getSequencesArray(), true);
180	0	String anfileout = new AnnotationFile()
181		.printAnnotationsForAlignment(al);
182	0	assertTrue("Test " + testname
183		+ "\nAlignment annotation file was not regenerated. Null string",
184		anfileout != null);
185	0	assertTrue("Test " + testname
186		+ "\nAlignment annotation file was not regenerated. Empty string",
187		anfileout.length() > "JALVIEW_ANNOTATION".length());
188
189	0	System.out.println(
190		"Output annotation file:\n" + anfileout + "\n<<EOF\n");
191
192	0	AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
193		DataSourceType.PASTE, FileFormat.Pfam);
194	0	assertTrue("Test " + testname
195		+ "\nregenerated annotation file did not annotate alignment.",
196		new AnnotationFile().readAnnotationFile(al_new, anfileout,
197		DataSourceType.PASTE));
198
199		// test for consistency in io
200	0	StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
201		false);
202	0	return;
203		} catch (Exception e)
204		{
205	0	e.printStackTrace();
206		}
207	0	Assert.fail("Test " + testname
208		+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
209		}
210
211		}