Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotatedPDBFileInputTest	49	82	20	0.00%	Show methods

Class AnnotatedPDBFileInputTest

Class AnnotatedPDBFileInputTest	Line # 49	Total Statements 82	Complexity 20	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5252	2.02	1.01	0.0 0.00%
setup() : void   setup() : void	6969	7.07	1.01	0.0 0.00%
checkNoDuplicates() : void   checkNoDuplicates() : void	8787	5.05	3.03	0.0 0.00%
checkPDBannotationSource() : void   checkPDBannotationSource() : void	106106	6.06	2.02	0.0 0.00%
checkPDBSequenceFeatures() : void   checkPDBSequenceFeatures() : void	129129	21.021	1.01	0.0 0.00%
checkAnnotationWiring() : void   checkAnnotationWiring() : void	166166	11.011	3.03	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	197197	1.01	1.01	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	208208	2.02	2.02	0.0 0.00%
testJalviewProjectRelocationAnnotation() : void   testJalviewProjectRelocationAnnotation() : void	215215	27.027	6.06	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.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 java.io.File;
28		import java.util.List;
29
30		import org.junit.Assert;
31		import org.testng.annotations.AfterClass;
32		import org.testng.annotations.BeforeClass;
33		import org.testng.annotations.BeforeMethod;
34		import org.testng.annotations.Test;
35
36		import jalview.bin.Cache;
37		import jalview.datamodel.AlignmentAnnotation;
38		import jalview.datamodel.AlignmentI;
39		import jalview.datamodel.PDBEntry;
40		import jalview.datamodel.SequenceFeature;
41		import jalview.datamodel.SequenceI;
42		import jalview.datamodel.features.SequenceFeatures;
43		import jalview.gui.AlignFrame;
44		import jalview.gui.Desktop;
45		import jalview.gui.JvOptionPane;
46		import jalview.structure.StructureImportSettings;
47		import jalview.structure.StructureImportSettings.StructureParser;
48
		0% Uncovered Elements: 111 (111) Complexity: 20 Complexity Density: 0.24
49		public class AnnotatedPDBFileInputTest
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		AlignmentI al;
60
61		String pdbId;
62
63		/**
64		* Ensure 'process secondary structure from PDB and add annotations' are set
65		* in preferences, and load PDB example file 1gaq
66		*
67		* @throws Exception
68		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
69	0	@BeforeMethod(alwaysRun = true)...
70		public void setup() throws Exception
71		{
72	0	Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
73		Boolean.TRUE.toString());
74	0	Cache.applicationProperties.setProperty("ADD_SS_ANN",
75		Boolean.TRUE.toString());
76	0	FileLoader loader = new FileLoader(false);
77	0	AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
78		DataSourceType.FILE);
79	0	al = af.getViewport().getAlignment();
80	0	pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
81		.get(0).getId();
82	0	StructureImportSettings.setDefaultStructureFileFormat("PDB");
83		// StructureImportSettings
84		// .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
85		}
86
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6 4-
87	0	@Test(groups = { "Functional" })...
88		public void checkNoDuplicates()
89		{
90		// not strictly a requirement, but strange things may happen if multiple
91		// instances of the same annotation are placed in the alignment annotation
92		// vector
93	0	assertNotNull(al.getAlignmentAnnotation());
94		// verify that all sequence annotation is doubly referenced
95	0	AlignmentAnnotation[] avec = al.getAlignmentAnnotation();
96	0	for (int p = 0; p < avec.length; p++)
97		{
98	0	for (int q = p + 1; q < avec.length; q++)
99		{
100	0	assertTrue("Found a duplicate annotation row " + avec[p].label,
101		avec[p] != avec[q]);
102		}
103		}
104		}
105
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33 4-
106	0	@Test(groups = { "Functional" }, enabled = false)...
107		public void checkPDBannotationSource()
108		{
109	0	Assert.fail(
110		"This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
111	0	for (SequenceI asq : al.getSequences())
112		{
113	0	for (AlignmentAnnotation aa : asq.getAnnotation())
114		{
115
116	0	System.out.println("CalcId: " + aa.getCalcId());
117	0	if (StructureImportSettings.getDefaultPDBFileParser()
118		.equals(StructureParser.JALVIEW_PARSER))
119		{
120	0	assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
121		}
122		}
123		}
124		}
125
126		/**
127		* Check sequence features have been added
128		*/
		0% Uncovered Elements: 21 (21) Complexity: 1 Complexity Density: 0.05 4-
129	0	@Test(groups = { "Functional" })...
130		public void checkPDBSequenceFeatures()
131		{
132		/*
133		* 1GAQ/A
134		*/
135	0	List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
136	0	SequenceFeatures.sortFeatures(sf, true);
137	0	assertEquals(296, sf.size());
138	0	assertEquals("RESNUM", sf.get(0).getType());
139	0	assertEquals("GLU: 19 1gaqA", sf.get(0).getDescription());
140	0	assertEquals("RESNUM", sf.get(295).getType());
141	0	assertEquals("TYR: 314 1gaqA", sf.get(295).getDescription());
142
143		/*
144		* 1GAQ/B
145		*/
146	0	sf = al.getSequenceAt(1).getSequenceFeatures();
147	0	SequenceFeatures.sortFeatures(sf, true);
148	0	assertEquals(98, sf.size());
149	0	assertEquals("RESNUM", sf.get(0).getType());
150	0	assertEquals("ALA: 1 1gaqB", sf.get(0).getDescription());
151	0	assertEquals("RESNUM", sf.get(97).getType());
152	0	assertEquals("ALA: 98 1gaqB", sf.get(97).getDescription());
153
154		/*
155		* 1GAQ/C
156		*/
157	0	sf = al.getSequenceAt(2).getSequenceFeatures();
158	0	SequenceFeatures.sortFeatures(sf, true);
159	0	assertEquals(296, sf.size());
160	0	assertEquals("RESNUM", sf.get(0).getType());
161	0	assertEquals("GLU: 19 1gaqC", sf.get(0).getDescription());
162	0	assertEquals("RESNUM", sf.get(295).getType());
163	0	assertEquals("TYR: 314 1gaqC", sf.get(295).getDescription());
164		}
165
		0% Uncovered Elements: 15 (15) Complexity: 3 Complexity Density: 0.27 4-
166	0	@Test(groups = { "Functional" })...
167		public void checkAnnotationWiring()
168		{
169	0	assertTrue(al.getAlignmentAnnotation() != null);
170		// verify that all sequence annotation is doubly referenced
171	0	for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
172		{
173	0	if (aa.sequenceRef != null)
174		{
175	0	assertTrue(al.getSequences().contains(aa.sequenceRef));
176	0	assertNotNull(aa.sequenceRef.getAnnotation());
177	0	boolean found = false;
178	0	for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
179		{
180	0	if (sqan == aa)
181		{
182	0	found = true;
183	0	break;
184		}
185		}
186	0	assertTrue("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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
197	0	@BeforeClass(alwaysRun = true)...
198		public static void setUpBeforeClass() throws Exception
199		{
200	0	jalview.bin.Jalview
201		.main(new String[]
202		{ "--props", "test/jalview/io/testProps.jvprops" });
203		}
204
205		/**
206		* @throws java.lang.Exception
207		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
208	0	@AfterClass(alwaysRun = true)...
209		public static void tearDownAfterClass() throws Exception
210		{
211	0	if (Desktop.instance != null)
212	0	Desktop.instance.closeAll_actionPerformed(null);
213		}
214
		0% Uncovered Elements: 35 (35) Complexity: 6 Complexity Density: 0.22 4-
215	0	@Test(groups = { "Functional" })...
216		public void testJalviewProjectRelocationAnnotation() throws Exception
217		{
218
219	0	String inFile = "examples/1gaq.txt";
220	0	String tfile = File.createTempFile("JalviewTest", ".jvp")
221		.getAbsolutePath();
222	0	AlignFrame af = new jalview.io.FileLoader()
223		.LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
224	0	assertTrue("Didn't read input file " + inFile, af != null);
225	0	af.saveAlignment(tfile, FileFormat.Jalview);
226	0	assertTrue("Failed to store as a project.",
227		af.isSaveAlignmentSuccessful());
228	0	af.closeMenuItem_actionPerformed(true);
229	0	af = null;
230	0	af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
231		DataSourceType.FILE);
232	0	assertTrue("Failed to import new project", af != null);
233	0	for (SequenceI asq : af.getViewport().getAlignment().getSequences())
234		{
235	0	SequenceI sq = asq;
236	0	while (sq.getDatasetSequence() != null)
237		{
238	0	sq = sq.getDatasetSequence();
239		}
240	0	assertNotNull(sq.getAllPDBEntries());
241	0	assertEquals("Expected only one PDB ID", 1,
242		sq.getAllPDBEntries().size());
243	0	for (PDBEntry pdbentry : sq.getAllPDBEntries())
244		{
245	0	System.err.println(
246		"PDB Entry " + pdbentry.getId() + " " + pdbentry.getFile());
247	0	boolean exists = false, found = false;
248	0	for (AlignmentAnnotation ana : sq.getAnnotation())
249		{
250	0	System.err.println("CalcId " + ana.getCalcId());
251	0	if (ana.getCalcId() != null
252		&& mc_view.PDBfile.isCalcIdHandled(ana.getCalcId()))
253		{
254	0	exists = true;
255	0	if (mc_view.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
256		{
257	0	found = true;
258		}
259		}
260		}
261	0	if (exists)
262		{
263	0	assertTrue(
264		"Couldn't find any annotation for " + pdbentry.getId()
265		+ " (file handle " + pdbentry.getFile() + ")",
266		found);
267		}
268		}
269		}
270		}
271		}