Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
PDBfileTest	47	121	10	2	0.984848598.5%	Show methods

Class PDBfileTest

Class PDBfileTest	Line # 47	Total Statements 121	Complexity 10	Uncovered Elements 2	TOTAL Coverage 0.984848598.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	0.00	1.0 1.0100%
testIsRna() : void   testIsRna() : void	5757	8.08	1.01	0.00	1.0 1.0100%
testParse() : void   testParse() : void	7979	52.052	1.01	0.00	1.0 1.0100%
testParse_withAnnotations_noSS() : void   testParse_withAnnotations_noSS() : void	158158	24.024	1.01	0.00	1.0 1.0100%
testParse_withJmol_noAnnotations() : void   testParse_withJmol_noAnnotations() : void	216216	5.05	1.01	0.00	1.0 1.0100%
testParse_withJmolAddAlignmentAnnotations() : void   testParse_withJmolAddAlignmentAnnotations() : void	245245	21.021	2.02	0.00	1.0 1.0100%
testParse_withAnnotate3D() : void   testParse_withAnnotate3D() : void	302302	1.01	1.01	1.01	0.0 0.00%
getAlignmentAnnotations(PDBfile) : AlignmentAnnotation[]   getAlignmentAnnotations(PDBfile) : AlignmentAnnotation[]	317317	3.03	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	324324	5.05	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.4318182	mc_view.PDBfileTest.testParsemc_view.PDBfileTest.testParse	1PASS
	0.21969697	mc_view.PDBfileTest.testParse_withAnnotations_noSSmc_view.PDBfileTest.testParse_withAnnotations_noSS	1PASS
	0.21212122	mc_view.PDBfileTest.testParse_withJmolAddAlignmentAnnotationsmc_view.PDBfileTest.testParse_withJmolAddAlignmentAnnotations	1PASS
	0.07575758	mc_view.PDBfileTest.testParse_withJmol_noAnnotationsmc_view.PDBfileTest.testParse_withJmol_noAnnotations	1PASS
	0.06818182	mc_view.PDBfileTest.testIsRnamc_view.PDBfileTest.testIsRna	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 mc_view;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertNull;
26		import static org.testng.AssertJUnit.assertSame;
27		import static org.testng.AssertJUnit.assertTrue;
28
29		import jalview.bin.Cache;
30		import jalview.datamodel.Alignment;
31		import jalview.datamodel.AlignmentAnnotation;
32		import jalview.datamodel.AlignmentI;
33		import jalview.datamodel.PDBEntry;
34		import jalview.datamodel.Sequence;
35		import jalview.datamodel.SequenceI;
36		import jalview.gui.JvOptionPane;
37		import jalview.io.DataSourceType;
38		import jalview.structure.StructureImportSettings;
39
40		import java.io.IOException;
41		import java.util.List;
42
43		import org.testng.annotations.BeforeClass;
44		import org.testng.annotations.BeforeMethod;
45		import org.testng.annotations.Test;
46
		98.5% Uncovered Elements: 2 (132) Complexity: 10 Complexity Density: 0.08
47		public class PDBfileTest
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	1	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	1	JvOptionPane.setInteractiveMode(false);
54	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
57	1	@Test(groups = { "Functional" })...
58		public void testIsRna()
59		{
60	1	SequenceI seq = new Sequence("Seq1", "CGAU");
61	1	assertTrue(PDBfile.isRNA(seq));
62
63	1	seq.setSequence("CGAu");
64	1	assertFalse(PDBfile.isRNA(seq));
65
66	1	seq.setSequence("CGAT");
67	1	assertFalse(PDBfile.isRNA(seq));
68
69	1	seq.setSequence("GRSWYFLAVM");
70	1	assertFalse(PDBfile.isRNA(seq));
71		}
72
73		/**
74		* Test the 'high level' outputs of parsing. More detailed tests in
75		* PDBChainTest.
76		*
77		* @throws IOException
78		*/
		100% Uncovered Elements: 0 (52) Complexity: 1 Complexity Density: 0.02 1PASS
79	1	@Test(groups = { "Functional" })...
80		public void testParse() throws IOException
81		{
82		/*
83		* Constructor with file path performs parse()
84		*/
85	1	PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
86		DataSourceType.FILE);
87
88	1	assertEquals("3W5V", pf.getId());
89		// verify no alignment annotations created
90	1	assertNull(getAlignmentAnnotations(pf));
91
92	1	assertEquals(4, pf.getChains().size());
93	1	assertEquals("A", pf.getChains().get(0).id);
94	1	assertEquals("B", pf.getChains().get(1).id);
95	1	assertEquals("C", pf.getChains().get(2).id);
96	1	assertEquals("D", pf.getChains().get(3).id);
97
98	1	PDBChain chainA = pf.getChains().get(0);
99	1	SequenceI seqA = pf.getSeqs().get(0);
100
101	1	assertEquals(0, chainA.seqstart); // not set
102	1	assertEquals(0, chainA.seqend); // not set
103	1	assertEquals(18, chainA.sequence.getStart());
104	1	assertEquals(314, chainA.sequence.getEnd());
105	1	assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
106	1	assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
107	1	assertEquals("3W5V|A", chainA.sequence.getName());
108	1	assertNull(chainA.sequence.getAnnotation());
109	1	assertEquals(1, seqA.getAllPDBEntries().size());
110	1	PDBEntry pdb = seqA.getAllPDBEntries().get(0);
111	1	assertEquals("A", pdb.getChainCode());
112	1	assertEquals("PDB", pdb.getType());
113	1	assertEquals("3W5V", pdb.getId());
114
115	1	PDBChain chainB = pf.getChains().get(1);
116	1	assertEquals(1, chainB.sequence.getStart());
117	1	assertEquals(96, chainB.sequence.getEnd());
118	1	assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK"));
119	1	assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT"));
120	1	assertEquals("3W5V|B", chainB.sequence.getName());
121
122	1	PDBChain chainC = pf.getChains().get(2);
123	1	assertEquals(18, chainC.sequence.getStart());
124	1	assertEquals(314, chainC.sequence.getEnd());
125	1	assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
126	1	assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
127	1	assertEquals("3W5V|C", chainC.sequence.getName());
128
129	1	PDBChain chainD = pf.getChains().get(3);
130	1	assertEquals(1, chainD.sequence.getStart());
131	1	assertEquals(96, chainD.sequence.getEnd());
132	1	assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
133	1	assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
134	1	assertEquals("3W5V|D", chainD.sequence.getName());
135
136		/*
137		* verify PDB-related data in parsed sequences
138		*/
139	1	List<SequenceI> seqs = pf.getSeqs();
140	1	assertEquals(4, seqs.size());
141	1	assertEquals("3W5V|A", seqs.get(0).getName());
142	1	assertEquals("3W5V|B", seqs.get(1).getName());
143	1	assertEquals("3W5V|C", seqs.get(2).getName());
144	1	assertEquals("3W5V|D", seqs.get(3).getName());
145	1	assertEquals(1, seqs.get(0).getAllPDBEntries().size());
146	1	PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0);
147	1	assertEquals("A", pdbe.getChainCode());
148	1	assertEquals("3W5V", pdbe.getId());
149	1	assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
150		}
151
152		/**
153		* Test parsing, with annotations added to the alignment but no secondary
154		* structure prediction
155		*
156		* @throws IOException
157		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
158	1	@Test(groups = { "Functional" })...
159		public void testParse_withAnnotations_noSS() throws IOException
160		{
161	1	PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
162		DataSourceType.FILE);
163
164	1	AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
165	1	assertEquals(4, anns.length);
166
167		/*
168		* Inspect temp factor annotation for chain A
169		*/
170	1	AlignmentAnnotation chainAnnotation = anns[0];
171	1	assertEquals("Temperature Factor", chainAnnotation.label);
172		// PDBChain constructor changes PDB id to lower case (why?)
173	1	assertEquals("Temperature Factor for 3w5vA",
174		chainAnnotation.description);
175	1	assertSame(pf.getSeqs().get(0), chainAnnotation.sequenceRef);
176	1	assertEquals(AlignmentAnnotation.LINE_GRAPH, chainAnnotation.graph);
177	1	assertEquals(0f, chainAnnotation.graphMin, 0.001f);
178	1	assertEquals(40f, chainAnnotation.graphMax, 0.001f);
179	1	assertEquals(297, chainAnnotation.annotations.length);
180	1	assertEquals(40f, chainAnnotation.annotations[0].value, 0.001f);
181
182		/*
183		* Chain B temp factor
184		*/
185	1	chainAnnotation = anns[1];
186	1	assertEquals("Temperature Factor for 3w5vB",
187		chainAnnotation.description);
188	1	assertSame(pf.getSeqs().get(1), chainAnnotation.sequenceRef);
189	1	assertEquals(96, chainAnnotation.annotations.length);
190
191		/*
192		* Chain C temp factor
193		*/
194	1	chainAnnotation = anns[2];
195	1	assertEquals("Temperature Factor for 3w5vC",
196		chainAnnotation.description);
197	1	assertSame(pf.getSeqs().get(2), chainAnnotation.sequenceRef);
198	1	assertEquals(297, chainAnnotation.annotations.length);
199
200		/*
201		* Chain D temp factor
202		*/
203	1	chainAnnotation = anns[3];
204	1	assertEquals("Temperature Factor for 3w5vD",
205		chainAnnotation.description);
206	1	assertSame(pf.getSeqs().get(3), chainAnnotation.sequenceRef);
207	1	assertEquals(96, chainAnnotation.annotations.length);
208		}
209
210		/**
211		* Test parsing including secondary structure annotation using JMol; this test
212		* for the case where flag to add annotations to alignment is set false
213		*
214		* @throws IOException
215		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
216	1	@Test(groups = { "Functional" })...
217		public void testParse_withJmol_noAnnotations() throws IOException
218		{
219	1	PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
220		DataSourceType.FILE);
221
222		/*
223		* alignment annotations _are_ created anyway (in
224		* AlignSeq.replaceMatchingSeqsWith())
225		*/
226	1	final AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
227	1	assertEquals(4, anns.length);
228
229		/*
230		* no sequence annotations created - tempFactor annotation is not added
231		* unless the flag to 'addAlignmentAnnotations' is set true
232		*/
233	1	for (PDBChain c : pf.getChains())
234		{
235	4	assertNull(c.sequence.getAnnotation());
236		}
237		}
238
239		/**
240		* Test parsing including secondary structure prediction and annotation using
241		* JMol
242		*
243		* @throws IOException
244		*/
		100% Uncovered Elements: 0 (23) Complexity: 2 Complexity Density: 0.1 1PASS
245	1	@Test(groups = { "Functional" })...
246		public void testParse_withJmolAddAlignmentAnnotations()
247		throws IOException
248		{
249	1	PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
250		DataSourceType.FILE);
251
252		/*
253		* Alignment annotations for TempFactor, SecStruct, per sequence (chain)
254		*/
255	1	AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
256	1	assertEquals(8, anns.length);
257
258		/*
259		* other tests have detailed assertions for Temp Factor annotations
260		*/
261	1	assertEquals("Temperature Factor for 3w5vA", anns[1].description);
262	1	assertEquals("Temperature Factor for 3w5vB", anns[3].description);
263	1	assertEquals("Temperature Factor for 3w5vC", anns[5].description);
264	1	assertEquals("Temperature Factor for 3w5vD", anns[7].description);
265
266		/*
267		* PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
268		*/
269	1	assertEquals("Secondary Structure for 3w5vA", anns[0].description);
270	1	assertEquals("Secondary Structure for 3w5vB", anns[2].description);
271	1	assertEquals("Secondary Structure for 3w5vC", anns[4].description);
272	1	assertEquals("Secondary Structure for 3w5vD", anns[6].description);
273
274		/*
275		* Verify SS annotations are linked to respective sequences (chains)
276		*/
277	1	assertSame(pf.getSeqs().get(0), anns[0].sequenceRef);
278	1	assertSame(pf.getSeqs().get(1), anns[2].sequenceRef);
279	1	assertSame(pf.getSeqs().get(2), anns[4].sequenceRef);
280	1	assertSame(pf.getSeqs().get(3), anns[6].sequenceRef);
281
282		/*
283		* Verify a sample of SS predictions
284		*/
285	21	for (int i = 0; i < 20; i++)
286		{
287	20	assertNull(anns[0].annotations[i]);
288	20	assertEquals("E", anns[0].annotations[20].displayCharacter);
289	20	assertEquals('E', anns[0].annotations[20].secondaryStructure);
290	20	assertEquals("E", anns[2].annotations[18].displayCharacter);
291	20	assertEquals("H", anns[2].annotations[23].displayCharacter);
292		}
293		}
294
295		/**
296		* Placeholder for a test of parsing RNA structure with secondary structure
297		* prediction using the Annotate3D service
298		*
299		* @throws IOException
300		*/
301
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
302	0	@Test(groups = { "Functional" }, enabled = false)...
303		public void testParse_withAnnotate3D() throws IOException
304		{
305		// TODO requires a mock for Annotate3D processing
306		// and/or run as an integration test
307	0	PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
308		DataSourceType.FILE);
309		}
310
311		/**
312		* Helper method to extract parsed annotations from the PDBfile
313		*
314		* @param pf
315		* @return
316		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
317	4	private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)...
318		{
319	4	AlignmentI al = new Alignment(pf.getSeqsAsArray());
320	4	pf.addAnnotations(al);
321	4	return al.getAlignmentAnnotation();
322		}
323
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
324	5	@BeforeMethod(alwaysRun = true)...
325		public void setUp()
326		{
327	5	Cache.loadProperties("test/jalview/io/testProps.jvprops");
328	5	Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
329		Boolean.TRUE.toString());
330	5	Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
331		Boolean.TRUE.toString());
332	5	Cache.applicationProperties.setProperty("ADD_SS_ANN",
333		Boolean.TRUE.toString());
334	5	StructureImportSettings.setDefaultStructureFileFormat("PDB");
335		}
336		}