Classes

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

Class PDBfileTest

Class PDBfileTest	Line # 47	Total Statements 121	Complexity 10	TOTAL Coverage 0.984848598.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	1.0 1.0100%
testIsRna() : void   testIsRna() : void	5757	8.08	1.01	1.0 1.0100%
testParse() : void   testParse() : void	7979	52.052	1.01	1.0 1.0100%
testParse_withAnnotations_noSS() : void   testParse_withAnnotations_noSS() : void	160160	24.024	1.01	1.0 1.0100%
testParse_withJmol_noAnnotations() : void   testParse_withJmol_noAnnotations() : void	218218	5.05	1.01	1.0 1.0100%
testParse_withJmolAddAlignmentAnnotations() : void   testParse_withJmolAddAlignmentAnnotations() : void	247247	21.021	2.02	1.0 1.0100%
testParse_withAnnotate3D() : void   testParse_withAnnotate3D() : void	303303	1.01	1.01	0.0 0.00%
getAlignmentAnnotations(PDBfile) : AlignmentAnnotation[]   getAlignmentAnnotations(PDBfile) : AlignmentAnnotation[]	318318	3.03	1.01	1.0 1.0100%
setUp() : void   setUp() : void	325325	5.05	1.01	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 java.io.IOException;
30		import java.util.List;
31
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.Alignment;
38		import jalview.datamodel.AlignmentAnnotation;
39		import jalview.datamodel.AlignmentI;
40		import jalview.datamodel.PDBEntry;
41		import jalview.datamodel.Sequence;
42		import jalview.datamodel.SequenceI;
43		import jalview.gui.JvOptionPane;
44		import jalview.io.DataSourceType;
45		import jalview.structure.StructureImportSettings;
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(
106		chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
107	1	assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
108	1	assertEquals("3W5V|A", chainA.sequence.getName());
109	1	assertNull(chainA.sequence.getAnnotation());
110	1	assertEquals(1, seqA.getAllPDBEntries().size());
111	1	PDBEntry pdb = seqA.getAllPDBEntries().get(0);
112	1	assertEquals("A", pdb.getChainCode());
113	1	assertEquals("PDB", pdb.getType());
114	1	assertEquals("3W5V", pdb.getId());
115
116	1	PDBChain chainB = pf.getChains().get(1);
117	1	assertEquals(1, chainB.sequence.getStart());
118	1	assertEquals(96, chainB.sequence.getEnd());
119	1	assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK"));
120	1	assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT"));
121	1	assertEquals("3W5V|B", chainB.sequence.getName());
122
123	1	PDBChain chainC = pf.getChains().get(2);
124	1	assertEquals(18, chainC.sequence.getStart());
125	1	assertEquals(314, chainC.sequence.getEnd());
126	1	assertTrue(
127		chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
128	1	assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
129	1	assertEquals("3W5V|C", chainC.sequence.getName());
130
131	1	PDBChain chainD = pf.getChains().get(3);
132	1	assertEquals(1, chainD.sequence.getStart());
133	1	assertEquals(96, chainD.sequence.getEnd());
134	1	assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
135	1	assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
136	1	assertEquals("3W5V|D", chainD.sequence.getName());
137
138		/*
139		* verify PDB-related data in parsed sequences
140		*/
141	1	List<SequenceI> seqs = pf.getSeqs();
142	1	assertEquals(4, seqs.size());
143	1	assertEquals("3W5V|A", seqs.get(0).getName());
144	1	assertEquals("3W5V|B", seqs.get(1).getName());
145	1	assertEquals("3W5V|C", seqs.get(2).getName());
146	1	assertEquals("3W5V|D", seqs.get(3).getName());
147	1	assertEquals(1, seqs.get(0).getAllPDBEntries().size());
148	1	PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0);
149	1	assertEquals("A", pdbe.getChainCode());
150	1	assertEquals("3W5V", pdbe.getId());
151	1	assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
152		}
153
154		/**
155		* Test parsing, with annotations added to the alignment but no secondary
156		* structure prediction
157		*
158		* @throws IOException
159		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
160	1	@Test(groups = { "Functional" })...
161		public void testParse_withAnnotations_noSS() throws IOException
162		{
163	1	PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
164		DataSourceType.FILE);
165
166	1	AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
167	1	assertEquals(4, anns.length);
168
169		/*
170		* Inspect temp factor annotation for chain A
171		*/
172	1	AlignmentAnnotation chainAnnotation = anns[0];
173	1	assertEquals("Temperature Factor", chainAnnotation.label);
174		// PDBChain constructor changes PDB id to lower case (why?)
175	1	assertEquals("Temperature Factor for 3w5vA",
176		chainAnnotation.description);
177	1	assertSame(pf.getSeqs().get(0), chainAnnotation.sequenceRef);
178	1	assertEquals(AlignmentAnnotation.LINE_GRAPH, chainAnnotation.graph);
179	1	assertEquals(0f, chainAnnotation.graphMin, 0.001f);
180	1	assertEquals(40f, chainAnnotation.graphMax, 0.001f);
181	1	assertEquals(297, chainAnnotation.annotations.length);
182	1	assertEquals(40f, chainAnnotation.annotations[0].value, 0.001f);
183
184		/*
185		* Chain B temp factor
186		*/
187	1	chainAnnotation = anns[1];
188	1	assertEquals("Temperature Factor for 3w5vB",
189		chainAnnotation.description);
190	1	assertSame(pf.getSeqs().get(1), chainAnnotation.sequenceRef);
191	1	assertEquals(96, chainAnnotation.annotations.length);
192
193		/*
194		* Chain C temp factor
195		*/
196	1	chainAnnotation = anns[2];
197	1	assertEquals("Temperature Factor for 3w5vC",
198		chainAnnotation.description);
199	1	assertSame(pf.getSeqs().get(2), chainAnnotation.sequenceRef);
200	1	assertEquals(297, chainAnnotation.annotations.length);
201
202		/*
203		* Chain D temp factor
204		*/
205	1	chainAnnotation = anns[3];
206	1	assertEquals("Temperature Factor for 3w5vD",
207		chainAnnotation.description);
208	1	assertSame(pf.getSeqs().get(3), chainAnnotation.sequenceRef);
209	1	assertEquals(96, chainAnnotation.annotations.length);
210		}
211
212		/**
213		* Test parsing including secondary structure annotation using JMol; this test
214		* for the case where flag to add annotations to alignment is set false
215		*
216		* @throws IOException
217		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
218	1	@Test(groups = { "Functional" })...
219		public void testParse_withJmol_noAnnotations() throws IOException
220		{
221	1	PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
222		DataSourceType.FILE);
223
224		/*
225		* alignment annotations _are_ created anyway (in
226		* AlignSeq.replaceMatchingSeqsWith())
227		*/
228	1	final AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
229	1	assertEquals(4, anns.length);
230
231		/*
232		* no sequence annotations created - tempFactor annotation is not added
233		* unless the flag to 'addAlignmentAnnotations' is set true
234		*/
235	1	for (PDBChain c : pf.getChains())
236		{
237	4	assertNull(c.sequence.getAnnotation());
238		}
239		}
240
241		/**
242		* Test parsing including secondary structure prediction and annotation using
243		* JMol
244		*
245		* @throws IOException
246		*/
		100% Uncovered Elements: 0 (23) Complexity: 2 Complexity Density: 0.1 1PASS
247	1	@Test(groups = { "Functional" })...
248		public void testParse_withJmolAddAlignmentAnnotations() throws IOException
249		{
250	1	PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
251		DataSourceType.FILE);
252
253		/*
254		* Alignment annotations for TempFactor, SecStruct, per sequence (chain)
255		*/
256	1	AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
257	1	assertEquals(8, anns.length);
258
259		/*
260		* other tests have detailed assertions for Temp Factor annotations
261		*/
262	1	assertEquals("Temperature Factor for 3w5vA", anns[1].description);
263	1	assertEquals("Temperature Factor for 3w5vB", anns[3].description);
264	1	assertEquals("Temperature Factor for 3w5vC", anns[5].description);
265	1	assertEquals("Temperature Factor for 3w5vD", anns[7].description);
266
267		/*
268		* PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
269		*/
270	1	assertEquals("Secondary Structure for 3w5vA", anns[0].description);
271	1	assertEquals("Secondary Structure for 3w5vB", anns[2].description);
272	1	assertEquals("Secondary Structure for 3w5vC", anns[4].description);
273	1	assertEquals("Secondary Structure for 3w5vD", anns[6].description);
274
275		/*
276		* Verify SS annotations are linked to respective sequences (chains)
277		*/
278	1	assertSame(pf.getSeqs().get(0), anns[0].sequenceRef);
279	1	assertSame(pf.getSeqs().get(1), anns[2].sequenceRef);
280	1	assertSame(pf.getSeqs().get(2), anns[4].sequenceRef);
281	1	assertSame(pf.getSeqs().get(3), anns[6].sequenceRef);
282
283		/*
284		* Verify a sample of SS predictions
285		*/
286	21	for (int i = 0; i < 20; i++)
287		{
288	20	assertNull(anns[0].annotations[i]);
289	20	assertNull(anns[0].annotations[20].displayCharacter);
290	20	assertEquals('E', anns[0].annotations[20].secondaryStructure);
291	20	assertEquals('E', anns[2].annotations[18].secondaryStructure);
292	20	assertEquals('H', anns[2].annotations[23].secondaryStructure);
293		}
294		}
295
296		/**
297		* Placeholder for a test of parsing RNA structure with secondary structure
298		* prediction using the Annotate3D service
299		*
300		* @throws IOException
301		*/
302
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
303	0	@Test(groups = { "Functional" }, enabled = false)...
304		public void testParse_withAnnotate3D() throws IOException
305		{
306		// TODO requires a mock for Annotate3D processing
307		// and/or run as an integration test
308	0	PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
309		DataSourceType.FILE);
310		}
311
312		/**
313		* Helper method to extract parsed annotations from the PDBfile
314		*
315		* @param pf
316		* @return
317		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
318	4	private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)...
319		{
320	4	AlignmentI al = new Alignment(pf.getSeqsAsArray());
321	4	pf.addAnnotations(al);
322	4	return al.getAlignmentAnnotation();
323		}
324
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
325	5	@BeforeMethod(alwaysRun = true)...
326		public void setUp()
327		{
328	5	Cache.loadProperties("test/jalview/io/testProps.jvprops");
329	5	Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
330		Boolean.TRUE.toString());
331	5	Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
332		Boolean.TRUE.toString());
333	5	Cache.applicationProperties.setProperty("ADD_SS_ANN",
334		Boolean.TRUE.toString());
335	5	StructureImportSettings.setDefaultStructureFileFormat("PDB");
336		}
337		}