Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureChooserTest	46	63	9	0.905405490.5%	Show methods

Class StructureChooserTest

Class StructureChooserTest	Line # 46	Total Statements 63	Complexity 9	TOTAL Coverage 0.905405490.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5858	11.011	2.02	1.0 1.0100%
tearDown() : void   tearDown() : void	8080	1.01	1.01	1.0 1.0100%
buildQueryTest() : void   buildQueryTest() : void	8686	23.023	2.02	1.0 1.0100%
populateFilterComboBoxTest() : void   populateFilterComboBoxTest() : void	123123	12.012	1.01	1.0 1.0100%
fetchStructuresInfoTest() : void   fetchStructuresInfoTest() : void	145145	6.06	1.01	0.0 0.00%
sanitizeSeqNameTest() : void   sanitizeSeqNameTest() : void	158158	8.08	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.35135135	jalview.gui.StructureChooserTest.buildQueryTestjalview.gui.StructureChooserTest.buildQueryTest	1PASS
	0.17567568	jalview.gui.StructureChooserTest.populateFilterComboBoxTestjalview.gui.StructureChooserTest.populateFilterComboBoxTest	1PASS
	0.12162162	jalview.gui.StructureChooserTest.sanitizeSeqNameTestjalview.gui.StructureChooserTest.sanitizeSeqNameTest	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.gui;
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.datamodel.DBRefEntry;
28		import jalview.datamodel.DBRefSource;
29		import jalview.datamodel.PDBEntry;
30		import jalview.datamodel.Sequence;
31		import jalview.datamodel.SequenceI;
32		import jalview.fts.api.FTSData;
33		import jalview.jbgui.GStructureChooser.FilterOption;
34		import jalview.ws.params.InvalidArgumentException;
35
36		import java.util.Collection;
37		import java.util.Vector;
38
39		import org.testng.annotations.AfterMethod;
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.BeforeMethod;
42		import org.testng.annotations.Test;
43
44		import junit.extensions.PA;
45
		90.5% Uncovered Elements: 7 (74) Complexity: 9 Complexity Density: 0.14
46		public class StructureChooserTest
47		{
48
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
49	1	@BeforeClass(alwaysRun = true)...
50		public void setUpJvOptionPane()
51		{
52	1	JvOptionPane.setInteractiveMode(false);
53	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54		}
55
56		Sequence seq;
57
		100% Uncovered Elements: 0 (13) Complexity: 2 Complexity Density: 0.18
58	3	@BeforeMethod(alwaysRun = true)...
59		public void setUp() throws Exception
60		{
61	3	seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
62		26);
63	3	seq.createDatasetSequence();
64	15	for (int x = 1; x < 5; x++)
65		{
66	12	DBRefEntry dbRef = new DBRefEntry();
67	12	dbRef.setAccessionId("XYZ_" + x);
68	12	seq.addDBRef(dbRef);
69		}
70
71	3	PDBEntry dbRef = new PDBEntry();
72	3	dbRef.setId("1tim");
73
74	3	Vector<PDBEntry> pdbIds = new Vector<>();
75	3	pdbIds.add(dbRef);
76
77	3	seq.setPDBId(pdbIds);
78		}
79
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
80	3	@AfterMethod(alwaysRun = true)...
81		public void tearDown() throws Exception
82		{
83	3	seq = null;
84		}
85
		100% Uncovered Elements: 0 (25) Complexity: 2 Complexity Density: 0.09 1PASS
86	1	@Test(groups = { "Functional" })...
87		public void buildQueryTest()
88		{
89	1	String query = StructureChooser.buildQuery(seq);
90	1	assertEquals("pdb_id:1tim", query);
91	1	System.out.println("seq >>>> " + seq);
92	1	seq.getAllPDBEntries().clear();
93	1	query = StructureChooser.buildQuery(seq);
94	1	assertEquals(
95		"text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
96		query);
97	1	seq.setDBRefs(null);
98	1	query = StructureChooser.buildQuery(seq);
99	1	assertEquals("text:4kqy", query);
100
101	1	DBRefEntry uniprotDBRef = new DBRefEntry();
102	1	uniprotDBRef.setAccessionId("P12345");
103	1	uniprotDBRef.setSource(DBRefSource.UNIPROT);
104	1	seq.addDBRef(uniprotDBRef);
105
106	1	DBRefEntry pdbDBRef = new DBRefEntry();
107	1	pdbDBRef.setAccessionId("1XYZ");
108	1	pdbDBRef.setSource(DBRefSource.PDB);
109	1	seq.addDBRef(pdbDBRef);
110
111	5	for (int x = 1; x < 5; x++)
112		{
113	4	DBRefEntry dbRef = new DBRefEntry();
114	4	dbRef.setAccessionId("XYZ_" + x);
115	4	seq.addDBRef(dbRef);
116		}
117	1	query = StructureChooser.buildQuery(seq);
118	1	assertEquals(
119		"uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
120		query);
121		}
122
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
123	1	@Test(groups = { "Functional" })...
124		public void populateFilterComboBoxTest() throws InterruptedException
125		{
126	1	SequenceI[] selectedSeqs = new SequenceI[] { seq };
127	1	StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
128	1	sc.populateFilterComboBox(false, false);
129	1	int optionsSize = sc.getCmbFilterOption().getItemCount();
130	1	assertEquals(2, optionsSize); // if structures are not discovered then don't
131		// populate filter options
132
133	1	sc.populateFilterComboBox(true, false);
134	1	optionsSize = sc.getCmbFilterOption().getItemCount();
135	1	assertTrue(optionsSize > 3); // if structures are found, filter options
136		// should be populated
137
138	1	sc.populateFilterComboBox(true, true);
139	1	assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
140	1	FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
141		.getSelectedItem();
142	1	assertEquals("Cached Structures", filterOpt.getName());
143		}
144
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17 1PASS
145	0	@Test(groups = { "Network" })...
146		public void fetchStructuresInfoTest()
147		{
148	0	SequenceI[] selectedSeqs = new SequenceI[] { seq };
149	0	StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
150	0	sc.fetchStructuresMetaData();
151	0	Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
152		"discoveredStructuresSet");
153	0	assertNotNull(ss);
154	0	assertTrue(ss.size() > 0);
155
156		}
157
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
158	1	@Test(groups = { "Functional" })...
159		public void sanitizeSeqNameTest()
160		{
161	1	String name = "ab_cdEF|fwxyz012349";
162	1	assertEquals(name, StructureChooser.sanitizeSeqName(name));
163
164		// remove a [nn] substring
165	1	name = "abcde12[345]fg";
166	1	assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
167
168		// remove characters other than a-zA-Z0-9 | or _
169	1	name = "ab[cd],.\t£$*!- \\\"@:e";
170	1	assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
171
172	1	name = "abcde12[345a]fg";
173	1	assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
174		}
175		}