Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AssociatePDBFileTest	57	18	8	0.925925992.6%	Show methods

Class AssociatePDBFileTest

Class AssociatePDBFileTest	Line # 57	Total Statements 18	Complexity 8	TOTAL Coverage 0.925925992.6%
setUpBeforeClass() : void   setUpBeforeClass() : void	6161	3.03	1.01	1.0 1.0100%
tearDown() : void   tearDown() : void	7272	2.02	2.02	0.75 0.7575%
setUp() : void   setUp() : void	8383	6.06	3.03	0.875 0.87587.5%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	117117	2.02	1.01	1.0 1.0100%
testAssociatePDBFile() : void   testAssociatePDBFile() : void	123123	5.05	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.22222222	jalview.gui.AssociatePDBFileTest.testAssociatePDBFilejalview.gui.AssociatePDBFileTest.testAssociatePDBFile	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 java.awt.Color;
24		import java.io.File;
25		import java.util.Iterator;
26
27		import org.junit.Assert;
28		import org.testng.annotations.AfterMethod;
29		import org.testng.annotations.BeforeClass;
30		import org.testng.annotations.BeforeMethod;
31		import org.testng.annotations.Test;
32
33		import jalview.analysis.AlignmentAnnotationUtils;
34		import jalview.api.FeatureColourI;
35		import jalview.bin.Cache;
36		import jalview.bin.Jalview;
37		import jalview.datamodel.Alignment;
38		import jalview.datamodel.AlignmentI;
39		import jalview.datamodel.HiddenColumns;
40		import jalview.datamodel.PDBEntry;
41		import jalview.datamodel.Sequence;
42		import jalview.datamodel.SequenceFeature;
43		import jalview.datamodel.SequenceGroup;
44		import jalview.datamodel.SequenceI;
45		import jalview.io.DataSourceType;
46		import jalview.io.FileLoader;
47		import jalview.project.Jalview2xmlTests;
48		import jalview.renderer.ResidueShaderI;
49		import jalview.schemes.BuriedColourScheme;
50		import jalview.schemes.FeatureColour;
51		import jalview.schemes.HelixColourScheme;
52		import jalview.schemes.JalviewColourScheme;
53		import jalview.schemes.StrandColourScheme;
54		import jalview.schemes.TurnColourScheme;
55		import jalview.util.MessageManager;
56
		92.6% Uncovered Elements: 2 (27) Complexity: 8 Complexity Density: 0.44
57		public class AssociatePDBFileTest
58		{
59		AlignFrame af;
60
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
61	1	@BeforeClass(alwaysRun = true)...
62		public static void setUpBeforeClass() throws Exception
63		{
64	1	setUpJvOptionPane();
65		/*
66		* use read-only test properties file
67		*/
68	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
69	1	Jalview.main(new String[] { "--nonews" });
70		}
71
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 1
72	1	@AfterMethod(alwaysRun = true)...
73		public void tearDown()
74		{
75	1	if (Desktop.instance != null)
76	1	Desktop.instance.closeAll_actionPerformed(null);
77		}
78
79		/**
80		* configure (read-only) properties for test to ensure Consensus is computed
81		* for colour Above PID testing
82		*/
		87.5% Uncovered Elements: 1 (8) Complexity: 3 Complexity Density: 0.5
83	1	@BeforeMethod(alwaysRun = true)...
84		public void setUp()
85		{
86	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
87	1	Cache.applicationProperties.setProperty("SHOW_IDENTITY",
88		Boolean.TRUE.toString());
89	1	af = new FileLoader().LoadFileWaitTillLoaded(">1GAQ|A/19-314\n"
90		+ "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
91		+ "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
92		+ "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
93		+ "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
94		+ "DQWNVEVY\n" + ">1GAQ|B/1-98\n"
95		+ "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG\n"
96		+ "WVLTCHAYPTSDVVIETHKEEELTGA\n" + ">1GAQ|C/19-314\n"
97		+ "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
98		+ "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
99		+ "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
100		+ "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
101		+ "DQWNVEVY\n", DataSourceType.PASTE);
102
103		/*
104		* wait for Consensus thread to complete
105		*/
106	1	do
107		{
108	1	try
109		{
110	1	Thread.sleep(50);
111		} catch (InterruptedException x)
112		{
113		}
114	1	} while (af.getViewport().getCalcManager().isWorking());
115		}
116
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
117	1	public static void setUpJvOptionPane()...
118		{
119	1	JvOptionPane.setInteractiveMode(false);
120	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
121		}
122
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
123	1	@Test(groups = "Functional")...
124		public void testAssociatePDBFile()
125		{
126	1	String assoc_file = "examples/1gaq.txt";
127	1	for (SequenceI toassoc : af.getViewport().getAlignment().getSequences())
128		{
129	3	PDBEntry pe = new AssociatePdbFileWithSeq().associatePdbWithSeq(
130		assoc_file, DataSourceType.FILE, toassoc, false,
131		Desktop.instance);
132	3	Assert.assertNotNull(pe);
133	3	Assert.assertNotEquals(
134		toassoc.getDatasetSequence().getAnnotation().length, 0);
135		}
136		}
137		}