Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentPanelTest	45	92	9	0.881188188.1%	Show methods

Class AlignmentPanelTest

Class AlignmentPanelTest	Line # 45	Total Statements 92	Complexity 9	TOTAL Coverage 0.881188188.1%
run() : void   run() : void	6464	1.01	1.01	1.0 1.0100%
setUp() : void   setUp() : void	4949	7.07	3.03	0.8888889 0.888888988.9%
testSetScrollValues() : void   testSetScrollValues() : void	8787	25.025	1.01	1.0 1.0100%
testUpdateLayout_endRes() : void   testUpdateLayout_endRes() : void	148148	8.08	1.01	1.0 1.0100%
testCalculateIdWidth_noArgs() : void   testCalculateIdWidth_noArgs() : void	174174	16.016	1.01	1.0 1.0100%
testCalculateIdWidth_withMaxWidth() : void   testCalculateIdWidth_withMaxWidth() : void	205205	25.025	1.01	1.0 1.0100%
testGetVisibleWidth() : void   testGetVisibleWidth() : void	256256	10.010	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.25742576	jalview.gui.AlignmentPanelTest.testCalculateIdWidth_withMaxWidthjalview.gui.AlignmentPanelTest.testCalculateIdWidth_withMaxWidth	1PASS
	0.25742576	jalview.gui.AlignmentPanelTest.testSetScrollValuesjalview.gui.AlignmentPanelTest.testSetScrollValues	1PASS
	0.16831683	jalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgsjalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgs	1PASS
	0.089108914	jalview.gui.AlignmentPanelTest.testUpdateLayout_endResjalview.gui.AlignmentPanelTest.testUpdateLayout_endRes	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.assertNotEquals;
25
26		import java.awt.Dimension;
27		import java.awt.Font;
28		import java.awt.FontMetrics;
29		import java.lang.reflect.InvocationTargetException;
30
31		import javax.swing.SwingUtilities;
32
33		import org.testng.annotations.BeforeMethod;
34		import org.testng.annotations.Test;
35
36		import jalview.api.AlignViewportI;
37		import jalview.bin.Cache;
38		import jalview.bin.Jalview;
39		import jalview.datamodel.AlignmentAnnotation;
40		import jalview.datamodel.SequenceI;
41		import jalview.io.DataSourceType;
42		import jalview.io.FileLoader;
43		import jalview.viewmodel.ViewportRanges;
44
		88.1% Uncovered Elements: 12 (101) Complexity: 9 Complexity Density: 0.1
45		public class AlignmentPanelTest
46		{
47		AlignFrame af;
48
		88.9% Uncovered Elements: 1 (9) Complexity: 3 Complexity Density: 0.43
49	4	@BeforeMethod(alwaysRun = true)...
50		public void setUp() throws InvocationTargetException, InterruptedException
51		{
52	4	Jalview.main(new String[] { "-nonews", "-props",
53		"test/jalview/testProps.jvprops" });
54
55	4	Cache.applicationProperties.setProperty("SHOW_IDENTITY",
56		Boolean.TRUE.toString());
57	4	af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
58		DataSourceType.FILE);
59
60		/*
61		* ensure the panel has been repainted and so ViewportRanges set
62		*/
63	4	SwingUtilities.invokeAndWait(new Runnable() {
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
64	4	@Override...
65		public void run() {
66	4	af.repaint();
67		}});
68
69		/*
70		* wait for Consensus thread to complete
71		*/
72	4	do
73		{
74	4	try
75		{
76	4	Thread.sleep(50);
77		} catch (InterruptedException x)
78		{
79		}
80	4	} while (af.getViewport().getCalcManager().isWorking());
81		}
82
83		/**
84		* Test side effect that end residue is set correctly by setScrollValues, with
85		* or without hidden columns
86		*/
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
87	1	@Test(groups = "Functional")...
88		public void testSetScrollValues()
89		{
90	1	ViewportRanges ranges = af.getViewport().getRanges();
91	1	af.alignPanel.setScrollValues(0, 0);
92
93	1	int oldres = ranges.getEndRes();
94	1	af.alignPanel.setScrollValues(-1, 5);
95
96		// setting -ve x value does not change residue
97	1	assertEquals(ranges.getEndRes(), oldres);
98
99	1	af.alignPanel.setScrollValues(0, 5);
100
101		// setting 0 as x value does not change residue
102	1	assertEquals(ranges.getEndRes(), oldres);
103
104	1	af.alignPanel.setScrollValues(5, 5);
105		// setting x value to 5 extends endRes by 5 residues
106	1	assertEquals(ranges.getEndRes(), oldres + 5);
107
108		// scroll to position after hidden columns sets endres to oldres (width) +
109		// position
110	1	int scrollpos = 60;
111	1	af.getViewport().hideColumns(30, 50);
112	1	af.alignPanel.setScrollValues(scrollpos, 5);
113	1	assertEquals(ranges.getEndRes(), oldres + scrollpos);
114
115		// scroll to position within hidden columns, still sets endres to oldres +
116		// position
117		// not sure if this is actually correct behaviour but this is what Jalview
118		// currently does
119	1	scrollpos = 40;
120	1	af.getViewport().showAllHiddenColumns();
121	1	af.getViewport().hideColumns(30, 50);
122	1	af.alignPanel.setScrollValues(scrollpos, 5);
123	1	assertEquals(ranges.getEndRes(), oldres + scrollpos);
124
125		// scroll to position within <width> distance of the end of the alignment
126		// endRes should be set to width of alignment - 1
127	1	scrollpos = 130;
128	1	af.getViewport().showAllHiddenColumns();
129	1	af.alignPanel.setScrollValues(scrollpos, 5);
130	1	assertEquals(ranges.getEndRes(), af.getViewport()
131		.getAlignment().getWidth() - 1);
132
133		// now hide some columns, and scroll to position within <width>
134		// distance of the end of the alignment
135		// endRes should be set to width of alignment - 1 - the number of hidden
136		// columns
137	1	af.getViewport().hideColumns(30, 50);
138	1	af.alignPanel.setScrollValues(scrollpos, 5);
139	1	assertEquals(ranges.getEndRes(), af.getViewport()
140		.getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
141		// columns
142		}
143
144		/**
145		* Test that update layout reverts to original (unwrapped) values for endRes
146		* when switching from wrapped back to unwrapped mode (JAL-2739)
147		*/
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
148	1	@Test(groups = "Functional")...
149		public void testUpdateLayout_endRes()
150		{
151		// get details of original alignment dimensions
152	1	ViewportRanges ranges = af.getViewport().getRanges();
153	1	int endres = ranges.getEndRes();
154
155		// wrap
156	1	af.alignPanel.getAlignViewport().setWrapAlignment(true);
157	1	af.alignPanel.updateLayout();
158
159		// endRes has changed
160	1	assertNotEquals(ranges.getEndRes(), endres);
161
162		// unwrap
163	1	af.alignPanel.getAlignViewport().setWrapAlignment(false);
164	1	af.alignPanel.updateLayout();
165
166		// endRes back to original value
167	1	assertEquals(ranges.getEndRes(), endres);
168		}
169
170		/**
171		* Test the variant of calculateIdWidth that only recomputes the width if it is
172		* not already saved in the viewport (initial value is -1)
173		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
174	1	@Test(groups = "Functional")...
175		public void testCalculateIdWidth_noArgs()
176		{
177	1	AlignViewportI av = af.alignPanel.getAlignViewport();
178	1	av.setShowJVSuffix(true);
179	1	av.setFont(new Font("Courier", Font.PLAIN, 15), true);
180
181	1	av.setIdWidth(0);
182	1	Dimension d = af.alignPanel.calculateIdWidth();
183	1	assertEquals(d.width, 0);
184	1	assertEquals(d.height, 0);
185
186	1	av.setIdWidth(99);
187	1	d = af.alignPanel.calculateIdWidth();
188	1	assertEquals(d.width, 99);
189	1	assertEquals(d.height, 0);
190
191		/*
192		* note 4 pixels padding are added to the longest sequence name width
193		*/
194	1	av.setIdWidth(-1); // force recalculation
195	1	d = af.alignPanel.calculateIdWidth();
196	1	assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
197	1	assertEquals(d.height, 12);
198	1	assertEquals(d.width, av.getIdWidth());
199		}
200
201		/**
202		* Test the variant of calculateIdWidth that computes the longest of any
203		* sequence name or annotation label width
204		*/
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
205	1	@Test(groups = "Functional")...
206		public void testCalculateIdWidth_withMaxWidth()
207		{
208	1	AlignViewportI av = af.alignPanel.getAlignViewport();
209	1	av.setShowJVSuffix(true);
210	1	av.setFont(new Font("Courier", Font.PLAIN, 15), true);
211	1	av.setShowAnnotation(false);
212	1	av.setIdWidth(18);
213
214		/*
215		* note 4 pixels 'padding' are added to the longest seq name/annotation label
216		*/
217	1	Dimension d = af.alignPanel.calculateIdWidth(2000);
218	1	assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
219	1	assertEquals(d.height, 12); // fixed value (not used?)
220	1	assertEquals(av.getIdWidth(), 18); // not changed by this method
221
222		/*
223		* make the longest sequence name longer
224		*/
225	1	SequenceI seq = af.viewport.getAlignment()
226		.findSequenceMatch("Q93Z60_ARATH")[0];
227	1	seq.setName(seq.getName() + "MMMMM");
228	1	d = af.alignPanel.calculateIdWidth(2000);
229	1	assertEquals(d.width, 211); // 4 + pixel width of "Q93Z60_ARATHMMMMM/1-118"
230	1	assertEquals(d.height, 12);
231	1	assertEquals(av.getIdWidth(), 18); // unchanged
232
233		/*
234		* make the longest annotation name even longer
235		* note this is checked even if annotations are not shown
236		*/
237	1	AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[0];
238	1	aa.label = "THIS IS A VERY LONG LABEL INDEED";
239	1	FontMetrics fmfor = af.alignPanel
240		.getFontMetrics(af.alignPanel.getAlabels().getFont());
241		// Assumption ID_WIDTH_PADDING == 4
242	1	int expwidth = 4 + fmfor.stringWidth(aa.label);
243	1	d = af.alignPanel.calculateIdWidth(2000);
244	1	assertEquals(d.width, expwidth); // 228 == ID_WIDTH_PADDING + pixel width of "THIS IS A VERY LONG LABEL INDEED"
245	1	assertEquals(d.height, 12);
246
247		/*
248		* override with maxwidth
249		* note the 4 pixels padding is added to this value
250		*/
251	1	d = af.alignPanel.calculateIdWidth(213);
252	1	assertEquals(d.width, 217);
253	1	assertEquals(d.height, 12);
254		}
255
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 1PASS
256	0	@Test(groups = { "Functional", "Not-bamboo" })...
257		public void testGetVisibleWidth()
258		{
259		/*
260		* width for onscreen rendering is IDPanel width
261		*/
262	0	int w = af.alignPanel.getVisibleIdWidth(true);
263	0	assertEquals(w, af.alignPanel.getIdPanel().getWidth());
264	0	assertEquals(w, 115);
265
266		/*
267		* width for offscreen rendering is the same
268		* if no fixed id width is specified in preferences
269		*/
270	0	Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.FALSE.toString());
271	0	Cache.removeProperty("FIGURE_FIXEDIDWIDTH");
272	0	assertEquals(w, af.alignPanel.getVisibleIdWidth(false));
273
274		/*
275		* preference for fixed id width - note 4 pixels padding is added
276		*/
277	0	Cache.setProperty("FIGURE_FIXEDIDWIDTH", "120");
278	0	assertEquals(124, af.alignPanel.getVisibleIdWidth(false));
279
280		/*
281		* preference for auto id width overrides fixed width
282		*/
283	0	Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
284	0	assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
285		}
286		}