Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationLabelsTest2	45	68	16	0.8850574588.5%	Show methods

Class AnnotationLabelsTest2

Class AnnotationLabelsTest2	Line # 45	Total Statements 68	Complexity 16	TOTAL Coverage 0.8850574588.5%
setUpBeforeClass() : void   setUpBeforeClass() : void	4949	6.06	2.02	0.75 0.7575%
tearDown() : void   tearDown() : void	6565	2.02	2.02	0.75 0.7575%
setUp() : void   setUp() : void	7676	2.02	1.01	1.0 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	8585	2.02	1.01	1.0 1.0100%
testIdWidthChanges(String,boolean,int,int,int,String,String,boolean,TFType,ViewerType,int,int) : void   testIdWidthChanges(String,boolean,int,int,int,String,String,boolean,TFType,ViewerType,int,int) : void	9191	26.026	4.04	0.9285714 0.928571492.9%
testIdWidthNoChanges(String,boolean,int,int,int,String,String,boolean,TFType,ViewerType,int,int) : void   testIdWidthNoChanges(String,boolean,int,int,int,String,String,boolean,TFType,ViewerType,int,int) : void	162162	25.025	2.02	0.96 0.9696%
openFilesWithIdWidthChanges() : Object[][]   openFilesWithIdWidthChanges() : Object[][]	222222	5.05	4.04	0.6363636 0.636363663.6%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.29885057	jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges	1PASS
	0.28735632	jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges	1PASS
	0.28735632	jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges	1PASS
	0.25287357	jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges	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.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertTrue;
26
27		import java.io.File;
28
29		import org.testng.annotations.AfterMethod;
30		import org.testng.annotations.BeforeClass;
31		import org.testng.annotations.BeforeMethod;
32		import org.testng.annotations.DataProvider;
33		import org.testng.annotations.Test;
34
35		import jalview.bin.Cache;
36		import jalview.bin.Jalview;
37		import jalview.datamodel.AlignmentI;
38		import jalview.datamodel.SequenceI;
39		import jalview.gui.StructureViewer.ViewerType;
40		import jalview.io.DataSourceType;
41		import jalview.io.FileLoader;
42		import jalview.structure.StructureImportSettings.TFType;
43		import jalview.util.Platform;
44
		88.5% Uncovered Elements: 10 (87) Complexity: 16 Complexity Density: 0.24
45		public class AnnotationLabelsTest2
46		{
47		private static double scaling;
48
		75% Uncovered Elements: 2 (8) Complexity: 2 Complexity Density: 0.33
49	1	@BeforeClass(alwaysRun = true)...
50		public static void setUpBeforeClass() throws Exception
51		{
52	1	if (Desktop.instance != null)
53	0	Desktop.instance.closeAll_actionPerformed(null);
54
55	1	setUpJvOptionPane();
56		/*
57		* use read-only test properties file
58		*/
59	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
60	1	Jalview.main(new String[] { "--nonews", "--nosplash", });
61
62	1	scaling = JvSwingUtilsTest.getScaling(Desktop.instance);
63		}
64
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 1
65	4	@AfterMethod(alwaysRun = true)...
66		public void tearDown()
67		{
68	4	if (Desktop.instance != null)
69	4	Desktop.instance.closeAll_actionPerformed(null);
70		}
71
72		/**
73		* configure (read-only) properties for test to ensure Consensus is computed
74		* for colour Above PID testing
75		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
76	4	@BeforeMethod(alwaysRun = true)...
77		public void setUp()
78		{
79	4	Cache.loadProperties("test/jalview/io/testProps.jvprops");
80	4	Cache.applicationProperties.setProperty("SHOW_IDENTITY",
81		Boolean.TRUE.toString());
82
83		}
84
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
85	1	public static void setUpJvOptionPane()...
86		{
87	1	JvOptionPane.setInteractiveMode(false);
88	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
89		}
90
		92.9% Uncovered Elements: 2 (28) Complexity: 4 Complexity Density: 0.15 1PASS
91	2	@Test(...
92		groups =
93		{ "Functional", "testTask1" },
94		dataProvider = "openFilesWithIdWidthChanges")
95		public void testIdWidthChanges(String alignmentFilename, boolean wrap,
96		int idWidth1min, int idWidth1max, int manualWidth,
97		String structureFilename, String paeFilename,
98		boolean secondaryStructureView, TFType temperatureFactorType,
99		ViewerType viewerType, int idWidth2min, int idWidth2max)
100		{
101	2	AlignFrame af = new FileLoader()
102		.LoadFileWaitTillLoaded(alignmentFilename, DataSourceType.FILE);
103
104	2	try
105		{
106	2	Thread.sleep(200); // to allow alignment annotations to open
107		} catch (InterruptedException e)
108		{
109		// TODO Auto-generated catch block
110	0	e.printStackTrace();
111		}
112	2	AlignViewport av = af.getCurrentView();
113
114	2	int idWidth = 0;
115
116	2	idWidth = av.getIdWidth();
117	2	assertTrue(idWidth > idWidth1min,
118		"idWidth (" + idWidth + ") is not greater than " + idWidth1min);
119	2	assertTrue(idWidth < idWidth1max, "idWidth (" + idWidth
120		+ ") is not narrower than " + idWidth1max);
121
122		// set wrap
123	2	if (wrap)
124		{
125	1	af.setWrapFormat(true, false);
126	1	idWidth = av.getIdWidth();
127	1	assertTrue(idWidth > idWidth1min, "After wrap idWidth (" + idWidth
128		+ ") is not greater than " + idWidth1min);
129	1	assertTrue(idWidth < idWidth1max, "After wrap idWidth (" + idWidth
130		+ ") is not narrower than" + idWidth1max);
131		}
132
133	2	AlignmentI al = av.getAlignment();
134	2	SequenceI s = al.getSequenceAt(0);
135	2	AlignmentPanel ap = af.alignPanel;
136
137	2	File structureFile = new File(structureFilename);
138	2	File paeFile = new File(paeFilename);
139
140	2	StructureViewer sv = StructureChooser.openStructureFileForSequence(null,
141		null, ap, s, false, structureFile.getAbsolutePath(),
142		temperatureFactorType, paeFile.getAbsolutePath(), true,
143		secondaryStructureView, false, viewerType);
144		// give time for annotations to open
145	2	try
146		{
147	2	Thread.sleep(200); // to allow alignment annotations to open
148		} catch (InterruptedException e)
149		{
150		// TODO Auto-generated catch block
151	0	e.printStackTrace();
152		}
153
154		// idWidth = ap.getIdPanel().getWidth();
155	2	idWidth = av.getIdWidth();
156	2	assertTrue(idWidth >= idWidth2min,
157		"idWidth (" + idWidth + ") is not greater than " + idWidth2min);
158	2	assertTrue(idWidth <= idWidth2max, "idWidth (" + idWidth
159		+ ") is not narrower than " + idWidth2max);
160		}
161
		96% Uncovered Elements: 1 (25) Complexity: 2 Complexity Density: 0.08 1PASS
162	2	@Test(...
163		groups =
164		{ "Functional", "testTask1" },
165		dataProvider = "openFilesWithIdWidthChanges")
166		public void testIdWidthNoChanges(String alignmentFilename, boolean wrap,
167		int idWidth1min, int idWidth1max, int manualWidth,
168		String structureFilename, String paeFilename,
169		boolean secondaryStructureView, TFType temperatureFactorType,
170		ViewerType viewerType, int idWidth2min, int idWidth2max)
171		{
172	2	AlignFrame af = new FileLoader()
173		.LoadFileWaitTillLoaded(alignmentFilename, DataSourceType.FILE);
174	2	try
175		{
176	2	Thread.sleep(200); // to allow alignment annotations to open
177		} catch (InterruptedException e)
178		{
179		// TODO Auto-generated catch block
180	0	e.printStackTrace();
181		}
182	2	AlignViewport av = af.getCurrentView();
183
184	2	int idWidth = 0;
185	2	idWidth = av.getIdWidth();
186	2	assertTrue(idWidth > idWidth1min,
187		"idWidth (" + idWidth + ") is not greater than " + idWidth1min);
188	2	assertTrue(idWidth < idWidth1max,
189		"idWidth (" + idWidth + ") is not narrower than" + idWidth1max);
190
191	2	AlignmentI al = av.getAlignment();
192	2	SequenceI s = al.getSequenceAt(0);
193	2	AlignmentPanel ap = af.alignPanel;
194
195		// set width manually
196	2	av.setIdWidth(manualWidth);
197	2	ap.validateAnnotationDimensions(false);
198	2	ap.paintAlignment(true, false);
199	2	ap.getIdPanel().getIdCanvas().setManuallyAdjusted(true);
200
201	2	idWidth = av.getIdWidth();
202	2	assertEquals(idWidth, manualWidth,
203		"idWidth is not set to the manually set width " + manualWidth);
204
205	2	File structureFile = new File(structureFilename);
206	2	File paeFile = new File(paeFilename);
207
208	2	StructureViewer sv = StructureChooser.openStructureFileForSequence(null,
209		null, ap, s, false, structureFile.getAbsolutePath(),
210		temperatureFactorType, paeFile.getAbsolutePath(), false,
211		secondaryStructureView, false, viewerType);
212
213	2	idWidth = ap.getIdPanel().getWidth();// av.getIdWidth();
214	2	idWidth = av.getIdWidth();
215	2	assertEquals(idWidth, manualWidth,
216		"idWidth is not set to the manually set width " + manualWidth
217		+ " after adding structure annotations");
218	2	assertFalse(idWidth > idWidth2min,
219		"idWidth (" + idWidth + ") is greater than " + idWidth2min);
220		}
221
		63.6% Uncovered Elements: 4 (11) Complexity: 4 Complexity Density: 0.8
222	2	@DataProvider(name = "openFilesWithIdWidthChanges")...
223		public Object[][] openFilesWithIdWidthChanges()
224		{
225		/*
226		String alignmentFilename,
227		boolean wrap,
228		int idWidth1min,
229		int idWidth1max,
230		int manualWidth, // ignored by testIdWidthChanges()
231		String structureFilename,
232		String paeFilename,
233		boolean secondaryStructureView,
234		TFType temperatureFactorType,
235		ViewerType viewerType,
236		int idWidth2min,
237		int idWidth2max,
238		*/
239	2	int idWidth2min = scaling == 1.0 ? 114 : 108;
240	2	int idWidth2max = scaling == 1.0 ? 117 : 114; // was 130
241	2	if (Platform.isMac())
242		{
243	0	idWidth2max = 122;
244		}
245
246	2	return new Object[][] {
247		//
248		/*
249		*/
250		{ "./test/files/annotation_label_width/sample.a2m", false, 50, 70,
251		100,
252		"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
253		"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json",
254		true, TFType.PLDDT, null, idWidth2min, idWidth2max },
255		{ "./test/files/annotation_label_width/sample.a2m", true, 50, 70,
256		100,
257		"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
258		"./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json",
259		true, TFType.PLDDT, null, idWidth2min, idWidth2max },
260		/*
261		*/
262		};
263		}
264
265		}