Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBSequenceFetcherTest	43	43	10	0.00%	Show methods
PDBSequenceFetcherTest.TestRetrieveObject	113	3	1	0.00%	Show methods

Class PDBSequenceFetcherTest

Class PDBSequenceFetcherTest	Line # 43	Total Statements 43	Complexity 10	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	2.02	1.01	0.0 0.00%
setUp() : void   setUp() : void	5555	4.04	1.01	0.0 0.00%
testRnaSeqRetrieve() : void   testRnaSeqRetrieve() : void	7676	9.09	1.01	0.0 0.00%
testPdbSeqRetrieve() : void   testPdbSeqRetrieve() : void	9696	3.03	1.01	0.0 0.00%
testmmCifSeqRetrieve() : void   testmmCifSeqRetrieve() : void	106106	2.02	1.01	0.0 0.00%
testRetrieveProteinSeqFromPDB() : void   testRetrieveProteinSeqFromPDB() : void	132132	23.023	5.05	0.0 0.00%

 

Class PDBSequenceFetcherTest.TestRetrieveObject

Class PDBSequenceFetcherTest.TestRetrieveObject	Line # 113	Total Statements 3	Complexity 1	TOTAL Coverage 0.00%
TestRetrieveObject(String,int)   TestRetrieveObject(String,int)	119119	3.03	1.01	0.0 0.00%

 

Contributing tests

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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;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.AssertJUnit.assertTrue;
25
26		import jalview.bin.Cache;
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.SequenceFeature;
29		import jalview.datamodel.SequenceI;
30		import jalview.gui.JvOptionPane;
31		import jalview.structure.StructureImportSettings;
32		import jalview.structure.StructureImportSettings.StructureParser;
33		import jalview.ws.seqfetcher.DbSourceProxy;
34
35		import java.util.Arrays;
36		import java.util.List;
37
38		import org.testng.Assert;
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.BeforeMethod;
41		import org.testng.annotations.Test;
42
		0% Uncovered Elements: 57 (57) Complexity: 10 Complexity Density: 0.23
43		public class PDBSequenceFetcherTest
44		{
45
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
46	0	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	0	JvOptionPane.setInteractiveMode(false);
50	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51		}
52
53		SequenceFetcher sf;
54
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
55	0	@BeforeMethod(alwaysRun = true)...
56		public void setUp() throws Exception
57		{
58	0	Cache.loadProperties("test/jalview/io/testProps.jvprops");
59		// ensure 'add annotation from structure' is selected
60	0	Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
61		Boolean.TRUE.toString());
62	0	Cache.applicationProperties.setProperty("ADD_SS_ANN",
63		Boolean.TRUE.toString());
64
65	0	sf = new SequenceFetcher();
66		}
67
68		/**
69		* Test that RNA structure can be added by a call to the RNAML service.
70		*
71		* Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
72		* not always reliable.
73		*
74		* @throws Exception
75		*/
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11 4-
76	0	@Test(groups = { "Network" }, enabled = true)...
77		public void testRnaSeqRetrieve() throws Exception
78		{
79	0	Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
80	0	List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
81	0	AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
82	0	assertTrue(response != null);
83	0	assertTrue(response.getHeight() == 1);
84	0	for (SequenceI sq : response.getSequences())
85		{
86	0	assertTrue("No annotation transfered to sequence.",
87		sq.getAnnotation().length > 0);
88	0	assertTrue("No PDBEntry on sequence.",
89		sq.getAllPDBEntries().size() > 0);
90	0	assertTrue(
91		"No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
92		sq.getRNA() != null);
93		}
94		}
95
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33 4-
96	0	@Test(groups = { "Network" }, enabled = true)...
97		public void testPdbSeqRetrieve() throws Exception
98		{
99	0	StructureImportSettings.setDefaultStructureFileFormat("PDB");
100	0	StructureImportSettings
101		.setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
102
103	0	testRetrieveProteinSeqFromPDB();
104		}
105
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 4-
106	0	@Test(groups = { "Network" }, enabled = true)...
107		public void testmmCifSeqRetrieve() throws Exception
108		{
109	0	StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
110	0	testRetrieveProteinSeqFromPDB();
111		}
112
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.33
113		private class TestRetrieveObject
114		{
115		String id;
116
117		int expectedHeight;
118
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
119	0	public TestRetrieveObject(String id, int expectedHeight)...
120		{
121	0	super();
122	0	this.id = id;
123	0	this.expectedHeight = expectedHeight;
124		}
125
126		}
127
128		private List<TestRetrieveObject> toRetrieve = Arrays.asList(
129		new TestRetrieveObject("1QIP", 4),
130		new TestRetrieveObject("4IM2", 1));
131
		0% Uncovered Elements: 31 (31) Complexity: 5 Complexity Density: 0.22
132	0	private void testRetrieveProteinSeqFromPDB() throws Exception...
133		{
134	0	List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
135	0	StringBuilder errors = new StringBuilder();
136	0	for (TestRetrieveObject str : toRetrieve)
137		{
138	0	AlignmentI response = sps.get(0).getSequenceRecords(str.id);
139	0	assertTrue("No aligment for " + str.id, response != null);
140	0	assertEquals(response.getHeight(), str.expectedHeight,
141		"Number of chains for " + str.id);
142	0	for (SequenceI sq : response.getSequences())
143		{
144	0	assertTrue("No annotation transfered to sequence " + sq.getName(),
145		sq.getAnnotation().length > 0);
146	0	assertTrue("No PDBEntry on sequence " + sq.getName(),
147		sq.getAllPDBEntries().size() > 0);
148		// FIXME: should test that all residues extracted as sequences from
149		// chains in structure have a mapping to data in the structure
150	0	List<SequenceFeature> prev = null;
151	0	int lastp = -1;
152	0	for (int col = 1; col <= sq.getLength(); col++)
153		{
154	0	List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
155	0	if (sf.size() != 1)
156		{
157	0	errors.append(str.id + ": "
158		+ "Expected one feature at column (position): "
159		+ (col - 1) + " (" + sq.findPosition(col - 1) + ")"
160		+ ": saw " + sf.size());
161	0	errors.append("\n");
162	0	if (prev != null)
163		{
164	0	errors.append("Last Feature was at position " + lastp + ": "
165		+ prev.get(0).toString());
166	0	errors.append("\n");
167		}
168		}
169		else
170		{
171	0	prev = sf;
172	0	lastp = sq.findPosition(col - 1);
173		}
174		}
175		}
176		}
177	0	if (errors.length() > 0)
178		{
179	0	Assert.fail(errors.toString());
180		}
181		}
182		}