Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Jalview2xmlBase	36	17	11	0.00%	Show methods

Class Jalview2xmlBase

Class Jalview2xmlBase	Line # 36	Total Statements 17	Complexity 11	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3939	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	4949	4.04	1.01	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	7171	2.02	2.02	0.0 0.00%
clearDesktop() : void   clearDesktop() : void	7878	2.02	4.04	0.0 0.00%
countDsAnn(jalview.viewmodel.AlignmentViewport) : int   countDsAnn(jalview.viewmodel.AlignmentViewport) : int	8888	7.07	3.03	0.0 0.00%

 

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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.io;
22
23		import java.util.Date;
24
25		import org.testng.annotations.AfterClass;
26		import org.testng.annotations.BeforeClass;
27		import org.testng.annotations.BeforeTest;
28
29		import jalview.bin.Cache;
30		import jalview.bin.Jalview;
31		import jalview.datamodel.AlignmentAnnotation;
32		import jalview.datamodel.SequenceI;
33		import jalview.gui.Desktop;
34		import jalview.gui.JvOptionPane;
35
		0% Uncovered Elements: 30 (30) Complexity: 11 Complexity Density: 0.65
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		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
49	0	@BeforeClass(alwaysRun = true)...
50		public static void setUpBeforeClass() throws Exception
51		{
52		/*
53		* use read-only test properties file
54		*/
55	0	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	0	Date oneHourFromNow = new Date(
62		System.currentTimeMillis() + 3600 * 1000);
63	0	Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
64
65	0	Jalview.main(new String[] {});
66		}
67
68		/**
69		* @throws java.lang.Exception
70		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
71	0	@AfterClass(alwaysRun = true)...
72		public static void tearDownAfterClass() throws Exception
73		{
74	0	if (Desktop.instance != null)
75	0	Desktop.instance.closeAll_actionPerformed(null);
76		}
77
		0% Uncovered Elements: 4 (4) Complexity: 4 Complexity Density: 2
78	0	@BeforeTest(alwaysRun = true)...
79		public static void clearDesktop()
80		{
81	0	if (Desktop.instance != null && Desktop.getFrames() != null
82		&& Desktop.getFrames().length > 0)
83		{
84	0	Desktop.instance.closeAll_actionPerformed(null);
85		}
86		}
87
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
88	0	public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)...
89		{
90	0	int numdsann = 0;
91	0	for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
92		{
93	0	if (sq.getAnnotation() != null)
94		{
95	0	for (AlignmentAnnotation dssa : sq.getAnnotation())
96		{
97	0	if (dssa.isValidStruc())
98		{
99	0	numdsann++;
100		}
101		}
102		}
103		}
104	0	return numdsann;
105		}
106
107		}