Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DisorderAnnotExportImport	55	45	12	0.00%	Show methods

Class DisorderAnnotExportImport

Class DisorderAnnotExportImport	Line # 55	Total Statements 45	Complexity 12	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5858	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	7575	13.013	3.03	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	105105	4.04	2.02	0.0 0.00%
testDisorderAnnotExport() : void   testDisorderAnnotExport() : void	119119	14.014	4.04	0.0 0.00%
checkAnnotationFileIO(String,AlignmentI) : void   checkAnnotationFileIO(String,AlignmentI) : void	153153	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
25		import static org.testng.AssertJUnit.assertNotNull;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.bin.Cache;
29		import jalview.bin.Console;
30		import jalview.datamodel.AlignmentAnnotation;
31		import jalview.datamodel.AlignmentI;
32		import jalview.gui.JvOptionPane;
33		import jalview.io.AnnotationFile;
34		import jalview.io.DataSourceType;
35		import jalview.io.FileFormat;
36		import jalview.io.FormatAdapter;
37		import jalview.io.StockholmFileTest;
38		import jalview.ws.jws2.AADisorderClient;
39		import jalview.ws.jws2.Jws2Discoverer;
40		import jalview.ws.jws2.jabaws2.Jws2Instance;
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.Test;
49
50		/*
51		* All methods in this class are set to the Network group because setUpBeforeClass will fail
52		* if there is no network.
53		*/
54		@Test(singleThreaded = true)
		0% Uncovered Elements: 60 (60) Complexity: 12 Complexity Density: 0.27
55		public class DisorderAnnotExportImport
56		{
57
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
58	0	@BeforeClass(alwaysRun = true)...
59		public void setUpJvOptionPane()
60		{
61	0	JvOptionPane.setInteractiveMode(false);
62	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
63		}
64
65		public static String testseqs = "examples/uniref50.fa";
66
67		public static Jws2Discoverer disc;
68
69		public static List<Jws2Instance> iupreds;
70
71		jalview.ws.jws2.AADisorderClient disorderClient;
72
73		public static jalview.gui.AlignFrame af = null;
74
		0% Uncovered Elements: 17 (17) Complexity: 3 Complexity Density: 0.23
75	0	@BeforeClass(alwaysRun = true)...
76		public static void setUpBeforeClass() throws Exception
77		{
78	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
79	0	Console.initLogger();
80	0	disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
81
82	0	while (disc.isRunning())
83		{
84		// don't get services until discoverer has finished
85	0	Thread.sleep(100);
86		}
87
88	0	iupreds = new ArrayList<Jws2Instance>();
89	0	for (Jws2Instance svc : disc.getServices())
90		{
91	0	if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
92		.contains("iupredws"))
93		{
94	0	iupreds.add(svc);
95		}
96		}
97	0	assertTrue("Couldn't discover any IUPred services to use to test.",
98		iupreds.size() > 0);
99	0	jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
100	0	af = fl.LoadFileWaitTillLoaded(testseqs,
101		jalview.io.DataSourceType.FILE);
102	0	assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
103		}
104
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
105	0	@AfterClass(alwaysRun = true)...
106		public static void tearDownAfterClass() throws Exception
107		{
108	0	if (af != null)
109		{
110	0	af.setVisible(false);
111	0	af.dispose();
112	0	af = null;
113		}
114		}
115
116		/**
117		* test for patches to JAL-1294
118		*/
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.29 4-
119	0	@Test(groups = { "External", "Network" })...
120		public void testDisorderAnnotExport()
121		{
122	0	disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
123	0	af.getViewport().getCalcManager().startWorker(disorderClient);
124	0	do
125		{
126	0	try
127		{
128	0	Thread.sleep(50);
129		} catch (InterruptedException x)
130		{
131		}
132	0	;
133	0	} while (af.getViewport().getCalcManager().isWorking());
134	0	AlignmentI orig_alig = af.getViewport().getAlignment();
135		// NOTE: Consensus annotation row cannot be exported and reimported
136		// faithfully - so we remove them
137	0	List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
138	0	for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
139		{
140	0	if (aa.autoCalculated)
141		{
142	0	toremove.add(aa);
143		}
144		}
145	0	for (AlignmentAnnotation aa : toremove)
146		{
147	0	orig_alig.deleteAnnotation(aa);
148		}
149	0	checkAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
150
151		}
152
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.17
153	0	static void checkAnnotationFileIO(String testname, AlignmentI al)...
154		{
155	0	try
156		{
157	0	String aligfileout = FileFormat.Pfam.getWriter(al)
158		.print(al.getSequencesArray(), true);
159	0	String anfileout = new AnnotationFile()
160		.printAnnotationsForAlignment(al);
161	0	assertTrue("Test " + testname
162		+ "\nAlignment annotation file was not regenerated. Null string",
163		anfileout != null);
164	0	assertTrue("Test " + testname
165		+ "\nAlignment annotation file was not regenerated. Empty string",
166		anfileout.length() > "JALVIEW_ANNOTATION".length());
167
168	0	System.out.println(
169		"Output annotation file:\n" + anfileout + "\n<<EOF\n");
170
171	0	AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
172		DataSourceType.PASTE, FileFormat.Pfam);
173	0	assertTrue("Test " + testname
174		+ "\nregenerated annotation file did not annotate alignment.",
175		new AnnotationFile().readAnnotationFile(al_new, anfileout,
176		DataSourceType.PASTE));
177
178		// test for consistency in io
179	0	StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
180		false);
181	0	return;
182		} catch (Exception e)
183		{
184	0	e.printStackTrace();
185		}
186	0	Assert.fail("Test " + testname
187		+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
188		}
189
190		}