Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
Jalview2xmlBase	36	16	10	7	0.740740774.1%	Show methods

Class Jalview2xmlBase

Class Jalview2xmlBase	Line # 36	Total Statements 16	Complexity 10	Uncovered Elements 7	TOTAL Coverage 0.740740774.1%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	2.02	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	4949	4.04	1.01	0.00	1.0 1.0100%
tearDownAfterClass() : void   tearDownAfterClass() : void	7070	1.01	1.01	0.00	1.0 1.0100%
clearDesktop() : void   clearDesktop() : void	7676	2.02	4.04	2.02	0.5 0.550%
countDsAnn(jalview.viewmodel.AlignmentViewport) : int   countDsAnn(jalview.viewmodel.AlignmentViewport) : int	8686	7.07	3.03	2.02	0.8181818 0.818181881.8%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.37037036	jalview.io.Jalview2xmlTests.testRNAStructureRecoveryjalview.io.Jalview2xmlTests.testRNAStructureRecovery	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.io;
22
23		import jalview.bin.Cache;
24		import jalview.bin.Jalview;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.SequenceI;
27		import jalview.gui.Desktop;
28		import jalview.gui.JvOptionPane;
29
30		import java.util.Date;
31
32		import org.testng.annotations.AfterClass;
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.BeforeTest;
35
		74.1% Uncovered Elements: 7 (27) Complexity: 10 Complexity Density: 0.62
36		public class Jalview2xmlBase
37		{
38
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
39	0	@BeforeClass(alwaysRun = true)...
40		public void setUpJvOptionPane()
41		{
42	0	JvOptionPane.setInteractiveMode(false);
43	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
44		}
45
46		/**
47		* @throws java.lang.Exception
48		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
49	2	@BeforeClass(alwaysRun = true)...
50		public static void setUpBeforeClass() throws Exception
51		{
52		/*
53		* use read-only test properties file
54		*/
55	2	Cache.loadProperties("test/jalview/io/testProps.jvprops");
56
57		/*
58		* set news feed last read to a future time to ensure no
59		* 'unread' news item is displayed
60		*/
61	2	Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000);
62	2	Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
63
64	2	Jalview.main(new String[] {});
65		}
66
67		/**
68		* @throws java.lang.Exception
69		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
70	2	@AfterClass(alwaysRun = true)...
71		public static void tearDownAfterClass() throws Exception
72		{
73	2	jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
74		}
75
		50% Uncovered Elements: 2 (4) Complexity: 4 Complexity Density: 2
76	1	@BeforeTest(alwaysRun = true)...
77		public static void clearDesktop()
78		{
79	1	if (Desktop.instance != null && Desktop.getFrames() != null
80		&& Desktop.getFrames().length > 0)
81		{
82	0	Desktop.instance.closeAll_actionPerformed(null);
83		}
84		}
85
		81.8% Uncovered Elements: 2 (11) Complexity: 3 Complexity Density: 0.43
86	2	public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)...
87		{
88	2	int numdsann = 0;
89	2	for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
90		{
91	122	if (sq.getAnnotation() != null)
92		{
93	122	for (AlignmentAnnotation dssa : sq.getAnnotation())
94		{
95	122	if (dssa.isValidStruc())
96		{
97	122	numdsann++;
98		}
99		}
100		}
101		}
102	2	return numdsann;
103		}
104
105		}