Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentPanelTest	50	140	15	0.5350318653.5%	Show methods

Class AlignmentPanelTest

Class AlignmentPanelTest	Line # 50	Total Statements 140	Complexity 15	TOTAL Coverage 0.5350318653.5%
run() : void   run() : void	7171	1.01	1.01	1.0 1.0100%
setUp() : void   setUp() : void	5454	7.07	3.03	1.0 1.0100%
testSetScrollValues() : void   testSetScrollValues() : void	9696	25.025	1.01	1.0 1.0100%
testUpdateLayout_endRes() : void   testUpdateLayout_endRes() : void	159159	8.08	1.01	1.0 1.0100%
testCalculateIdWidth_noArgs() : void   testCalculateIdWidth_noArgs() : void	185185	16.016	1.01	1.0 1.0100%
testCalculateIdWidth_withMaxWidth() : void   testCalculateIdWidth_withMaxWidth() : void	217217	26.026	1.01	0.0 0.00%
computeExpectedWidth(double) : int   computeExpectedWidth(double) : int	275275	1.01	3.03	0.0 0.00%
testGetVisibleWidth() : void   testGetVisibleWidth() : void	281281	14.014	1.01	0.0 0.00%
testresetIdWidth() : void   testresetIdWidth() : void	321321	24.024	1.01	0.0 0.00%
testSetOverviewTitle() : void   testSetOverviewTitle() : void	368368	7.07	1.01	1.0 1.0100%
testSetOverviewTitle_automaticOverview() : void   testSetOverviewTitle_automaticOverview() : void	386386	11.011	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.1656051	jalview.gui.AlignmentPanelTest.testSetScrollValuesjalview.gui.AlignmentPanelTest.testSetScrollValues	1PASS
	0.10828026	jalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgsjalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgs	1PASS
	0.07643312	jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview	1PASS
	0.05732484	jalview.gui.AlignmentPanelTest.testUpdateLayout_endResjalview.gui.AlignmentPanelTest.testUpdateLayout_endRes	1PASS
	0.050955415	jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle	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		import static org.testng.Assert.assertNotNull;
26		import static org.testng.Assert.assertTrue;
27
28		import java.awt.Container;
29		import java.awt.Dimension;
30		import java.awt.Font;
31		import java.awt.FontMetrics;
32		import java.awt.event.MouseEvent;
33		import java.lang.reflect.InvocationTargetException;
34
35		import javax.swing.SwingUtilities;
36
37		import org.testng.annotations.BeforeMethod;
38		import org.testng.annotations.Test;
39
40		import jalview.api.AlignViewportI;
41		import jalview.bin.Cache;
42		import jalview.bin.Jalview;
43		import jalview.datamodel.AlignmentAnnotation;
44		import jalview.datamodel.SequenceI;
45		import jalview.io.DataSourceType;
46		import jalview.io.FileLoader;
47		import jalview.util.Platform;
48		import jalview.viewmodel.ViewportRanges;
49
		53.5% Uncovered Elements: 73 (157) Complexity: 15 Complexity Density: 0.11
50		public class AlignmentPanelTest
51		{
52		AlignFrame af;
53
		100% Uncovered Elements: 0 (9) Complexity: 3 Complexity Density: 0.43
54	5	@BeforeMethod(alwaysRun = true)...
55		public void setUp() throws InvocationTargetException, InterruptedException
56		{
57	5	Jalview.main(
58		new String[]
59		{ "--nonews", "--props", "test/jalview/testProps.jvprops" });
60
61	5	Cache.applicationProperties.setProperty("SHOW_IDENTITY",
62		Boolean.TRUE.toString());
63	5	af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
64		DataSourceType.FILE);
65
66		/*
67		* ensure the panel has been repainted and so ViewportRanges set
68		*/
69	5	SwingUtilities.invokeAndWait(new Runnable()
70		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
71	5	@Override...
72		public void run()
73		{
74	5	af.repaint();
75		}
76		});
77
78		/*
79		* wait for Consensus thread to complete
80		*/
81	5	do
82		{
83	7	try
84		{
85	7	Thread.sleep(50);
86		} catch (InterruptedException x)
87		{
88		}
89	7	} while (af.getViewport().getCalcManager().isWorking());
90		}
91
92		/**
93		* Test side effect that end residue is set correctly by setScrollValues, with
94		* or without hidden columns
95		*/
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
96	1	@Test(groups = "Functional")...
97		public void testSetScrollValues()
98		{
99	1	ViewportRanges ranges = af.getViewport().getRanges();
100	1	af.alignPanel.setScrollValues(0, 0);
101
102	1	int oldres = ranges.getEndRes();
103	1	af.alignPanel.setScrollValues(-1, 5);
104
105		// setting -ve x value does not change residue
106	1	assertEquals(ranges.getEndRes(), oldres);
107
108	1	af.alignPanel.setScrollValues(0, 5);
109
110		// setting 0 as x value does not change residue
111	1	assertEquals(ranges.getEndRes(), oldres);
112
113	1	af.alignPanel.setScrollValues(5, 5);
114		// setting x value to 5 extends endRes by 5 residues
115	1	assertEquals(ranges.getEndRes(), oldres + 5);
116
117		// scroll to position after hidden columns sets endres to oldres (width) +
118		// position
119	1	int scrollpos = 60;
120	1	af.getViewport().hideColumns(30, 50);
121	1	af.alignPanel.setScrollValues(scrollpos, 5);
122	1	assertEquals(ranges.getEndRes(), oldres + scrollpos);
123
124		// scroll to position within hidden columns, still sets endres to oldres +
125		// position
126		// not sure if this is actually correct behaviour but this is what Jalview
127		// currently does
128	1	scrollpos = 40;
129	1	af.getViewport().showAllHiddenColumns();
130	1	af.getViewport().hideColumns(30, 50);
131	1	af.alignPanel.setScrollValues(scrollpos, 5);
132	1	assertEquals(ranges.getEndRes(), oldres + scrollpos);
133
134		// scroll to position within <width> distance of the end of the alignment
135		// endRes should be set to width of alignment - 1
136	1	scrollpos = 130;
137	1	af.getViewport().showAllHiddenColumns();
138	1	af.alignPanel.setScrollValues(scrollpos, 5);
139	1	assertEquals(ranges.getEndRes(),
140		af.getViewport().getAlignment().getWidth() - 1);
141
142		// now hide some columns, and scroll to position within <width>
143		// distance of the end of the alignment
144		// endRes should be set to width of alignment - 1 - the number of hidden
145		// columns
146	1	af.getViewport().hideColumns(30, 50);
147	1	af.alignPanel.setScrollValues(scrollpos, 5);
148	1	assertEquals(ranges.getEndRes(),
149		af.getViewport().getAlignment().getWidth() - 1 - 21); // 21 is the
150		// number of
151		// hidden
152		// columns
153		}
154
155		/**
156		* Test that update layout reverts to original (unwrapped) values for endRes
157		* when switching from wrapped back to unwrapped mode (JAL-2739)
158		*/
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
159	1	@Test(groups = "Functional")...
160		public void testUpdateLayout_endRes()
161		{
162		// get details of original alignment dimensions
163	1	ViewportRanges ranges = af.getViewport().getRanges();
164	1	int endres = ranges.getEndRes();
165
166		// wrap
167	1	af.alignPanel.getAlignViewport().setWrapAlignment(true);
168	1	af.alignPanel.updateLayout();
169
170		// endRes has changed
171	1	assertNotEquals(ranges.getEndRes(), endres);
172
173		// unwrap
174	1	af.alignPanel.getAlignViewport().setWrapAlignment(false);
175	1	af.alignPanel.updateLayout();
176
177		// endRes back to original value
178	1	assertEquals(ranges.getEndRes(), endres);
179		}
180
181		/**
182		* Test the variant of calculateIdWidth that only recomputes the width if it
183		* is not already saved in the viewport (initial value is -1)
184		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
185	1	@Test(groups = "Functional")...
186		public void testCalculateIdWidth_noArgs()
187		{
188	1	AlignViewportI av = af.alignPanel.getAlignViewport();
189	1	av.setShowJVSuffix(true);
190	1	av.setFont(new Font("Courier", Font.PLAIN, 15), true);
191
192	1	av.setIdWidth(0);
193	1	Dimension d = af.alignPanel.calculateIdWidth();
194	1	assertEquals(d.width, 0);
195	1	assertEquals(d.height, 0);
196
197	1	av.setIdWidth(99);
198	1	d = af.alignPanel.calculateIdWidth();
199	1	assertEquals(d.width, 99);
200	1	assertEquals(d.height, 0);
201
202		/*
203		* note 4 pixels padding are added to the longest sequence name width
204		*/
205	1	av.setIdWidth(-1); // force recalculation
206	1	d = af.alignPanel.calculateIdWidth();
207	1	assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
208	1	assertEquals(d.height, 12);
209	1	assertEquals(d.width, av.getIdWidth());
210		}
211
212		/**
213		* Test the variant of calculateIdWidth that computes the longest of any
214		* sequence name or annotation label width FIXME: JAL-4291: test needs
215		* updating for JAL-244 and JAL-4091
216		*/
		0% Uncovered Elements: 26 (26) Complexity: 1 Complexity Density: 0.04 1PASS
217	0	@Test(groups = "Functional", enabled = false)...
218		public void testCalculateIdWidth_withMaxWidth()
219		{
220	0	AlignViewportI av = af.alignPanel.getAlignViewport();
221	0	av.setShowJVSuffix(true);
222	0	av.setFont(new Font("Courier", Font.PLAIN, 15), true);
223	0	av.setShowAnnotation(false);
224	0	av.setIdWidth(18);
225
226	0	FontMetrics fmfor = new Container()
227		.getFontMetrics(new Font(af.viewport.font.getName(),
228		Font.ITALIC, af.viewport.font.getSize()));
229
230		/*
231		* note 4 pixels 'padding' are added to the longest seq name/annotation label
232		*/
233	0	Dimension d = af.alignPanel.calculateIdWidth(2000);
234		// Assumption ID_WIDTH_PADDING == 4
235	0	int expwidth = 3 + fmfor.stringWidth("Conservation");
236
237	0	assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
238	0	assertEquals(d.height, 12); // fixed value (not used?)
239	0	assertEquals(av.getIdWidth(), expwidth); // not changed by this method
240
241		/*
242		* make the longest sequence name longer
243		*/
244	0	SequenceI seq = af.viewport.getAlignment()
245		.findSequenceMatch("Q93Z60_ARATH")[0];
246	0	seq.setName(seq.getName() + "MMMMM");
247	0	d = af.alignPanel.calculateIdWidth(2000);
248	0	assertEquals(d.width, 211); // 4 + pixel width of "Q93Z60_ARATHMMMMM/1-118"
249	0	assertEquals(d.height, 12);
250	0	assertEquals(av.getIdWidth(), 18); // unchanged
251
252		/*
253		* make the longest annotation name even longer
254		* note this is checked even if annotations are not shown
255		*/
256	0	AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[0];
257	0	aa.label = "THIS IS A VERY LONG LABEL INDEED";
258	0	d = af.alignPanel.calculateIdWidth(2000);
259		// Assumption ID_WIDTH_PADDING == 3
260	0	expwidth = 3 + fmfor.stringWidth(aa.label);
261
262	0	assertEquals(d.width, expwidth); // 228 == ID_WIDTH_PADDING + pixel width of
263		// "THIS IS A VERY LONG LABEL INDEED"
264	0	assertEquals(d.height, 12);
265
266		/*
267		* override with maxwidth
268		* note the 4 pixels padding is added to this value
269		*/
270	0	d = af.alignPanel.calculateIdWidth(213);
271	0	assertEquals(d.width, 217);
272	0	assertEquals(d.height, 12);
273		}
274
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 3
275	0	private int computeExpectedWidth(double scaling)...
276		{
277	0	return Platform.isMac() ? 115 : scaling == 1.0 ? 112 : 107;
278		}
279
280
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07 1PASS
281	0	@Test(groups = { "Functional", "Not-bamboo" })...
282		public void testGetVisibleWidth()
283		{
284	0	double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
285		/*
286		* width for onscreen rendering is IDPanel width
287		*/
288	0	int w = af.alignPanel.getVisibleIdWidth(true);
289	0	assertEquals(w, af.alignPanel.getIdPanel().getWidth());
290
291		// different scaling (1.0, 2.0) gives different results
292	0	int expectedWidth = computeExpectedWidth(scaling);
293	0	assertEquals(w, expectedWidth);
294
295		/*
296		* width for offscreen rendering is the same
297		* if no fixed id width is specified in preferences
298		*/
299	0	Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.FALSE.toString());
300	0	Cache.removeProperty("FIGURE_FIXEDIDWIDTH");
301	0	assertEquals(w, af.alignPanel.getVisibleIdWidth(false));
302
303		/*
304		* preference for fixed id width - note 4 pixels padding is added
305		*/
306	0	Cache.setProperty("FIGURE_FIXEDIDWIDTH", "120");
307	0	assertEquals(124, af.alignPanel.getVisibleIdWidth(false));
308
309		/*
310		* preference for auto id width overrides fixed width
311		*/
312	0	Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
313	0	w = af.alignPanel.getVisibleIdWidth(false);
314		// allow some leeway for different OS renderings
315	0	assertTrue(w > 105 && w < 120);
316		// different scaling (1.0, 2.0) gives different results
317	0	assertEquals(w, expectedWidth);
318		}
319
320
		0% Uncovered Elements: 24 (24) Complexity: 1 Complexity Density: 0.04 1PASS
321	0	@Test(groups = { "Functional", "Not-bamboo" })...
322		public void testresetIdWidth()
323		{
324	0	double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
325		/*
326		* width for onscreen rendering is IDPanel width
327		*/
328	0	int w = af.alignPanel.getVisibleIdWidth(true);
329	0	int actual = af.alignPanel.getIdPanel().getWidth();
330	0	assertEquals(w, actual);
331		// allow some leeway for different OS renderings
332	0	assertTrue(w > 105 && w < 120);
333		// different scaling (1.0, 2.0) gives different results
334	0	int expectedWidth = computeExpectedWidth(scaling);
335	0	assertEquals(w, expectedWidth);
336
337		// manually adjust
338	0	af.viewport.setIdWidth(200);
339		// fake mouse drag sets manuallyAdjusted to true (0,0 not moving mouse)
340	0	MouseEvent drag = new MouseEvent(af.alignPanel,
341		MouseEvent.MOUSE_DRAGGED, System.currentTimeMillis(), 0, 0, 0,
342		MouseEvent.BUTTON1, false);
343	0	af.alignPanel.idwidthAdjuster.mouseDragged(drag);
344	0	af.alignPanel.paintComponent(af.alignPanel.getGraphics());
345	0	w = af.alignPanel.calculateIdWidth().width;
346	0	assertTrue(
347		af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
348	0	actual = af.alignPanel.getIdPanel().getWidth();
349	0	assertEquals(w, actual);
350
351	0	af.viewport.setIdWidth(-1);
352	0	af.alignPanel.calculateIdWidth();
353	0	af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
354	0	w = af.alignPanel.calculateIdWidth().width;
355	0	af.alignPanel.paintComponent(af.alignPanel.getGraphics());
356
357	0	actual = af.alignPanel.getIdPanel().getWidth();
358	0	assertEquals(w, actual);
359
360		// setting a negative IdWidth and then running calculateIdWidth resets width
361		// to optimal id width
362		// allow some leeway for different OS renderings
363	0	assertTrue(w > 105 && w < 120);
364		// different scaling (1.0, 2.0) gives different results
365	0	assertEquals(w, expectedWidth);
366		}
367
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
368	1	@Test(groups = "Functional")...
369		public void testSetOverviewTitle()
370		{
371	1	OverviewPanel ov1 = this.af.openOverviewPanel(true);
372	1	String alignFrameTitle = af.getTitle();
373	1	assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
374
375		/*
376		* on New View, existing overview should get " Original" added to title
377		* and new view's overview should get " View 1" added
378		*/
379	1	af.newView_actionPerformed(null);
380	1	assertEquals(ov1.getTitle(),
381		"Overview " + alignFrameTitle + " Original");
382	1	OverviewPanel ov2 = this.af.openOverviewPanel(true);
383	1	assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
384		}
385
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
386	1	@Test(groups = "Functional")...
387		public void testSetOverviewTitle_automaticOverview()
388		{
389	1	Cache.setProperty("SHOW_OVERVIEW", "true");
390	1	AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
391		"examples/uniref50.fa", DataSourceType.FILE);
392	1	OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel();
393	1	assertNotNull(ov1);
394	1	String alignFrameTitle = alignFrame.getTitle();
395	1	assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
396
397		/*
398		* on New View, existing overview should get " Original" added to title
399		* and new view's automatic overview should have " View 1" added
400		*/
401	1	alignFrame.newView_actionPerformed(null);
402	1	assertEquals(ov1.getTitle(),
403		"Overview " + alignFrameTitle + " Original");
404	1	OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel();
405	1	assertNotNull(ov2);
406	1	assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
407		}
408		}