Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AnnotatedPDBFileInputTest	48	81	19	17	0.842592684.3%	Show methods

Class AnnotatedPDBFileInputTest

Class AnnotatedPDBFileInputTest	Line # 48	Total Statements 81	Complexity 19	Uncovered Elements 17	TOTAL Coverage 0.842592684.3%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5151	2.02	1.01	0.00	1.0 1.0100%
setup() : void   setup() : void	6868	7.07	1.01	0.00	1.0 1.0100%
checkNoDuplicates() : void   checkNoDuplicates() : void	8686	5.05	3.03	0.00	1.0 1.0100%
checkPDBannotationSource() : void   checkPDBannotationSource() : void	105105	6.06	2.02	8.08	0.0 0.00%
checkPDBSequenceFeatures() : void   checkPDBSequenceFeatures() : void	128128	21.021	1.01	0.00	1.0 1.0100%
checkAnnotationWiring() : void   checkAnnotationWiring() : void	165165	11.011	3.03	0.00	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	197197	1.01	1.01	0.00	1.0 1.0100%
tearDownAfterClass() : void   tearDownAfterClass() : void	207207	1.01	1.01	0.00	1.0 1.0100%
testJalviewProjectRelocationAnnotation() : void   testJalviewProjectRelocationAnnotation() : void	214214	27.027	6.06	8.08	0.7714286 0.771428677.1%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.25925925	jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation	1PASS
	0.2037037	jalview.io.AnnotatedPDBFileInputTest.checkPDBSequenceFeaturesjalview.io.AnnotatedPDBFileInputTest.checkPDBSequenceFeatures	1PASS
	0.14814815	jalview.io.AnnotatedPDBFileInputTest.checkAnnotationWiringjalview.io.AnnotatedPDBFileInputTest.checkAnnotationWiring	1PASS
	0.09259259	jalview.io.AnnotatedPDBFileInputTest.checkNoDuplicatesjalview.io.AnnotatedPDBFileInputTest.checkNoDuplicates	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.io;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.bin.Cache;
28		import jalview.datamodel.AlignmentAnnotation;
29		import jalview.datamodel.AlignmentI;
30		import jalview.datamodel.PDBEntry;
31		import jalview.datamodel.SequenceFeature;
32		import jalview.datamodel.SequenceI;
33		import jalview.datamodel.features.SequenceFeatures;
34		import jalview.gui.AlignFrame;
35		import jalview.gui.JvOptionPane;
36		import jalview.structure.StructureImportSettings;
37		import jalview.structure.StructureImportSettings.StructureParser;
38
39		import java.io.File;
40		import java.util.List;
41
42		import org.junit.Assert;
43		import org.testng.annotations.AfterClass;
44		import org.testng.annotations.BeforeClass;
45		import org.testng.annotations.BeforeMethod;
46		import org.testng.annotations.Test;
47
		84.3% Uncovered Elements: 17 (108) Complexity: 19 Complexity Density: 0.23
48		public class AnnotatedPDBFileInputTest
49		{
50
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
51	1	@BeforeClass(alwaysRun = true)...
52		public void setUpJvOptionPane()
53		{
54	1	JvOptionPane.setInteractiveMode(false);
55	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56		}
57
58		AlignmentI al;
59
60		String pdbId;
61
62		/**
63		* Ensure 'process secondary structure from PDB and add annotations' are set
64		* in preferences, and load PDB example file 1gaq
65		*
66		* @throws Exception
67		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
68	4	@BeforeMethod(alwaysRun = true)...
69		public void setup() throws Exception
70		{
71	4	Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
72		Boolean.TRUE.toString());
73	4	Cache.applicationProperties.setProperty("ADD_SS_ANN",
74		Boolean.TRUE.toString());
75	4	FileLoader loader = new FileLoader(false);
76	4	AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
77		DataSourceType.FILE);
78	4	al = af.getViewport().getAlignment();
79	4	pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
80		.get(0).getId();
81	4	StructureImportSettings.setDefaultStructureFileFormat("PDB");
82		// StructureImportSettings
83		// .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
84		}
85
		100% Uncovered Elements: 0 (9) Complexity: 3 Complexity Density: 0.6 1PASS
86	1	@Test(groups = { "Functional" })...
87		public void checkNoDuplicates()
88		{
89		// not strictly a requirement, but strange things may happen if multiple
90		// instances of the same annotation are placed in the alignment annotation
91		// vector
92	1	assertNotNull(al.getAlignmentAnnotation());
93		// verify that all sequence annotation is doubly referenced
94	1	AlignmentAnnotation[] avec = al.getAlignmentAnnotation();
95	11	for (int p = 0; p < avec.length; p++)
96		{
97	55	for (int q = p + 1; q < avec.length; q++)
98		{
99	45	assertTrue("Found a duplicate annotation row " + avec[p].label,
100		avec[p] != avec[q]);
101		}
102		}
103		}
104
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33 1PASS
105	0	@Test(groups = { "Functional" }, enabled = false)...
106		public void checkPDBannotationSource()
107		{
108	0	Assert.fail(
109		"This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
110	0	for (SequenceI asq : al.getSequences())
111		{
112	0	for (AlignmentAnnotation aa : asq.getAnnotation())
113		{
114
115	0	System.out.println("CalcId: " + aa.getCalcId());
116	0	if (StructureImportSettings.getDefaultPDBFileParser()
117		.equals(StructureParser.JALVIEW_PARSER))
118		{
119	0	assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
120		}
121		}
122		}
123		}
124
125		/**
126		* Check sequence features have been added
127		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
128	1	@Test(groups = { "Functional" })...
129		public void checkPDBSequenceFeatures()
130		{
131		/*
132		* 1GAQ/A
133		*/
134	1	List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
135	1	SequenceFeatures.sortFeatures(sf, true);
136	1	assertEquals(296, sf.size());
137	1	assertEquals("RESNUM", sf.get(0).getType());
138	1	assertEquals("GLU: 19 1gaqA", sf.get(0).getDescription());
139	1	assertEquals("RESNUM", sf.get(295).getType());
140	1	assertEquals("TYR: 314 1gaqA", sf.get(295).getDescription());
141
142		/*
143		* 1GAQ/B
144		*/
145	1	sf = al.getSequenceAt(1).getSequenceFeatures();
146	1	SequenceFeatures.sortFeatures(sf, true);
147	1	assertEquals(98, sf.size());
148	1	assertEquals("RESNUM", sf.get(0).getType());
149	1	assertEquals("ALA: 1 1gaqB", sf.get(0).getDescription());
150	1	assertEquals("RESNUM", sf.get(97).getType());
151	1	assertEquals("ALA: 98 1gaqB", sf.get(97).getDescription());
152
153		/*
154		* 1GAQ/C
155		*/
156	1	sf = al.getSequenceAt(2).getSequenceFeatures();
157	1	SequenceFeatures.sortFeatures(sf, true);
158	1	assertEquals(296, sf.size());
159	1	assertEquals("RESNUM", sf.get(0).getType());
160	1	assertEquals("GLU: 19 1gaqC", sf.get(0).getDescription());
161	1	assertEquals("RESNUM", sf.get(295).getType());
162	1	assertEquals("TYR: 314 1gaqC", sf.get(295).getDescription());
163		}
164
		100% Uncovered Elements: 0 (15) Complexity: 3 Complexity Density: 0.27 1PASS
165	1	@Test(groups = { "Functional" })...
166		public void checkAnnotationWiring()
167		{
168	1	assertTrue(al.getAlignmentAnnotation() != null);
169		// verify that all sequence annotation is doubly referenced
170	1	for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
171		{
172	10	if (aa.sequenceRef != null)
173		{
174	6	assertTrue(al.getSequences().contains(aa.sequenceRef));
175	6	assertNotNull(aa.sequenceRef.getAnnotation());
176	6	boolean found = false;
177	6	for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
178		{
179	9	if (sqan == aa)
180		{
181	6	found = true;
182	6	break;
183		}
184		}
185	6	assertTrue(
186		"Couldn't find sequence associated annotation "
187		+ aa.label
188		+ " on the sequence it is associated with.\nSequence associated editing will fail.",
189		found);
190		}
191		}
192		}
193
194		/**
195		* @throws java.lang.Exception
196		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
197	1	@BeforeClass(alwaysRun = true)...
198		public static void setUpBeforeClass() throws Exception
199		{
200	1	jalview.bin.Jalview.main(new String[] { "-props",
201		"test/jalview/io/testProps.jvprops" });
202		}
203
204		/**
205		* @throws java.lang.Exception
206		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
207	1	@AfterClass(alwaysRun = true)...
208		public static void tearDownAfterClass() throws Exception
209		{
210	1	jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
211
212		}
213
		77.1% Uncovered Elements: 8 (35) Complexity: 6 Complexity Density: 0.22 1PASS
214	1	@Test(groups = { "Functional" })...
215		public void testJalviewProjectRelocationAnnotation() throws Exception
216		{
217
218	1	String inFile = "examples/1gaq.txt";
219	1	String tfile = File.createTempFile("JalviewTest", ".jvp")
220		.getAbsolutePath();
221	1	AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
222		inFile, DataSourceType.FILE);
223	1	assertTrue("Didn't read input file " + inFile, af != null);
224	1	af.saveAlignment(tfile, FileFormat.Jalview);
225	1	assertTrue("Failed to store as a project.",
226		af.isSaveAlignmentSuccessful());
227	1	af.closeMenuItem_actionPerformed(true);
228	1	af = null;
229	1	af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
230		DataSourceType.FILE);
231	1	assertTrue("Failed to import new project", af != null);
232	1	for (SequenceI asq : af.getViewport().getAlignment().getSequences())
233		{
234	3	SequenceI sq = asq;
235	6	while (sq.getDatasetSequence() != null)
236		{
237	3	sq = sq.getDatasetSequence();
238		}
239	3	assertNotNull(sq.getAllPDBEntries());
240	3	assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
241		.size());
242	3	for (PDBEntry pdbentry : sq.getAllPDBEntries())
243		{
244	3	System.err.println("PDB Entry " + pdbentry.getId() + " "
245		+ pdbentry.getFile());
246	3	boolean exists = false, found = false;
247	3	for (AlignmentAnnotation ana : sq.getAnnotation())
248		{
249	6	System.err.println("CalcId " + ana.getCalcId());
250	6	if (ana.getCalcId() != null
251		&& mc_view.PDBfile.isCalcIdHandled(ana.getCalcId()))
252		{
253	0	exists = true;
254	0	if (mc_view.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
255		{
256	0	found = true;
257		}
258		}
259		}
260	3	if (exists)
261		{
262	0	assertTrue("Couldn't find any annotation for " + pdbentry.getId()
263		+ " (file handle " + pdbentry.getFile() + ")", found);
264		}
265		}
266		}
267		}
268		}