Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SeqCanvasTest	43	162	7	0.8757396387.6%	Show methods

Class SeqCanvasTest

Class SeqCanvasTest	Line # 43	Total Statements 162	Complexity 7	TOTAL Coverage 0.8757396387.6%
testCalculateWrappedGeometry_noAnnotations() : void   testCalculateWrappedGeometry_noAnnotations() : void	5151	80.080	1.01	1.0 1.0100%
testCalculateWrappedGeometry_withAnnotations() : void   testCalculateWrappedGeometry_withAnnotations() : void	224224	46.046	1.01	1.0 1.0100%
testCalculateWrappedGeometry_fromScrolled() : void   testCalculateWrappedGeometry_fromScrolled() : void	323323	20.020	1.01	0.0 0.00%
setUp() : void   setUp() : void	353353	6.06	3.03	1.0 1.0100%
testClear_HighlightAndSelection() : void   testClear_HighlightAndSelection() : void	376376	10.010	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.47928995	jalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_noAnnotationsjalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_noAnnotations	1PASS
	0.2781065	jalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_withAnnotationsjalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_withAnnotations	1PASS
	0.06508876	jalview.gui.SeqCanvasTest.testClear_HighlightAndSelectionjalview.gui.SeqCanvasTest.testClear_HighlightAndSelection	1PASS

 

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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.gui;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotNull;
26		import static org.testng.Assert.assertNull;
27		import static org.testng.Assert.assertTrue;
28
29		import java.awt.Font;
30		import java.awt.FontMetrics;
31
32		import org.testng.annotations.BeforeMethod;
33		import org.testng.annotations.Test;
34
35		import jalview.bin.Cache;
36		import jalview.datamodel.AlignmentI;
37		import jalview.datamodel.SearchResults;
38		import jalview.datamodel.SearchResultsI;
39		import jalview.io.DataSourceType;
40		import jalview.io.FileLoader;
41		import junit.extensions.PA;
42
		87.6% Uncovered Elements: 21 (169) Complexity: 7 Complexity Density: 0.04
43		public class SeqCanvasTest
44		{
45		private AlignFrame af;
46
47		/**
48		* Test the method that computes wrapped width in residues, height of wrapped
49		* widths in pixels, and the number of widths visible
50		*/
		100% Uncovered Elements: 0 (80) Complexity: 1 Complexity Density: 0.01 1PASS
51	1	@Test(groups = "Functional")...
52		public void testCalculateWrappedGeometry_noAnnotations()
53		{
54	1	AlignViewport av = af.getViewport();
55	1	AlignmentI al = av.getAlignment();
56	1	assertEquals(al.getWidth(), 157);
57	1	assertEquals(al.getHeight(), 15);
58	1	av.getRanges().setStartEndSeq(0, 14);
59
60	1	SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
61
62	1	av.setWrapAlignment(true);
63	1	av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
64	1	int charHeight = av.getCharHeight();
65	1	int charWidth = av.getCharWidth();
66	1	assertEquals(charHeight, 17);
67	1	assertEquals(charWidth, 12);
68
69		/*
70		* first with scales above, left, right
71		*/
72	1	av.setShowAnnotation(false);
73	1	av.setScaleAboveWrapped(true);
74	1	av.setScaleLeftWrapped(true);
75	1	av.setScaleRightWrapped(true);
76	1	FontMetrics fm = testee.getFontMetrics(av.getFont());
77	1	int labelWidth = fm.stringWidth("000") + charWidth;
78		// some leeway for different OS rendering of text
79	1	assertTrue(labelWidth >= 36 && labelWidth <= 39);
80
81		/*
82		* width 400 pixels leaves (400 - 2*labelWidth) for residue columns
83		* take the whole multiple of character widths
84		*/
85	1	int canvasWidth = 400;
86	1	int canvasHeight = 300;
87	1	int residueColumns = (canvasWidth - 2 * labelWidth) / charWidth;
88	1	int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
89		canvasHeight);
90	1	assertEquals(wrappedWidth, residueColumns);
91	1	assertEquals(PA.getValue(testee, "labelWidthWest"), labelWidth);
92	1	assertEquals(PA.getValue(testee, "labelWidthEast"), labelWidth);
93	1	assertEquals(PA.getValue(testee, "wrappedSpaceAboveAlignment"),
94		2 * charHeight);
95	1	int repeatingHeight = (int) PA.getValue(testee,
96		"wrappedRepeatHeightPx");
97	1	assertEquals(repeatingHeight, charHeight * (2 + al.getHeight()));
98	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
99
100		/*
101		* repeat height is 17 * (2 + 15) = 289
102		* make canvas height 2 * 289 + 3 * charHeight so just enough to
103		* draw 2 widths and the first sequence of a third
104		*/
105	1	canvasHeight = charHeight * (17 * 2 + 3);
106	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
107	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
108
109		/*
110		* reduce canvas height by 1 pixel
111		* - should not be enough height to draw 3 widths
112		*/
113	1	canvasHeight -= 1;
114	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
115	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 2);
116
117		/*
118		* turn off scale above - can now fit in 2 and a bit widths
119		*/
120	1	av.setScaleAboveWrapped(false);
121	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
122	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
123
124		/*
125		* reduce height to enough for 2 widths and not quite a third
126		* i.e. two repeating heights + spacer + sequence - 1 pixel
127		*/
128	1	canvasHeight = charHeight * (16 * 2 + 2) - 1;
129	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
130	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 2);
131
132		/*
133		* make canvas width enough for scales and 20 residues
134		*/
135	1	canvasWidth = 2 * labelWidth + 20 * charWidth;
136	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
137		canvasHeight);
138	1	assertEquals(wrappedWidth, 20);
139
140		/*
141		* reduce width by 1 pixel - rounds down to 19 residues
142		*/
143	1	canvasWidth -= 1;
144	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
145		canvasHeight);
146	1	assertEquals(wrappedWidth, 19);
147
148		/*
149		* turn off West scale - adds labelWidth (39) to available for residues
150		* which with the 11 remainder makes 50 which is 4 more charWidths rem 2
151		*/
152	1	av.setScaleLeftWrapped(false);
153	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
154		canvasHeight);
155		// some leeway for different OS rendering of text
156	1	assertTrue(wrappedWidth >= 22 && wrappedWidth <= 23);
157	1	int difference = wrappedWidth - 23;
158
159		/*
160		* add 10 pixels to width to fit in another whole residue column
161		*/
162	1	canvasWidth += 9;
163	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
164		canvasHeight);
165	1	assertEquals(wrappedWidth, 23);
166	1	canvasWidth += 1;
167	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
168		canvasHeight);
169	1	assertEquals(wrappedWidth, 24 + difference);
170
171		/*
172		* turn off East scale to gain 39 more pixels (3 columns remainder 3)
173		*/
174	1	av.setScaleRightWrapped(false);
175	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
176		canvasHeight);
177	1	assertEquals(wrappedWidth, 27 + difference);
178
179		/*
180		* add 9 pixels to width to gain a residue column
181		*/
182	1	canvasWidth += 8;
183	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
184		canvasHeight);
185	1	assertEquals(wrappedWidth, 27); // 8px not enough
186	1	canvasWidth += 1;
187	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
188		canvasHeight);
189	1	assertEquals(wrappedWidth, 28 + difference); // 9px is enough
190
191		/*
192		* now West but not East scale - lose 39 pixels or 4 columns
193		*/
194	1	av.setScaleLeftWrapped(true);
195	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
196		canvasHeight);
197	1	assertEquals(wrappedWidth, 24);
198
199		/*
200		* adding 3 pixels to width regains one column
201		*/
202	1	canvasWidth += 2;
203	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
204		canvasHeight);
205	1	assertEquals(wrappedWidth, 24); // 2px not enough
206	1	canvasWidth += 1;
207	1	wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
208		canvasHeight);
209	1	assertEquals(wrappedWidth, 25 + difference); // 3px is enough
210
211		/*
212		* turn off scales left and right, make width exactly 157 columns
213		*/
214	1	av.setScaleLeftWrapped(false);
215	1	canvasWidth = al.getWidth() * charWidth;
216	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
217	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
218		}
219
220		/**
221		* Test the method that computes wrapped width in residues, height of wrapped
222		* widths in pixels, and the number of widths visible
223		*/
		100% Uncovered Elements: 0 (46) Complexity: 1 Complexity Density: 0.02 1PASS
224	1	@Test(groups = "Functional")...
225		public void testCalculateWrappedGeometry_withAnnotations()
226		{
227	1	AlignViewport av = af.getViewport();
228	1	AlignmentI al = av.getAlignment();
229	1	assertEquals(al.getWidth(), 157);
230	1	assertEquals(al.getHeight(), 15);
231
232	1	av.setWrapAlignment(true);
233	1	av.getRanges().setStartEndSeq(0, 14);
234	1	av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
235	1	int charHeight = av.getCharHeight();
236	1	int charWidth = av.getCharWidth();
237	1	assertEquals(charHeight, 17);
238	1	assertEquals(charWidth, 12);
239
240	1	SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
241
242		/*
243		* first with scales above, left, right
244		*/
245	1	av.setShowAnnotation(true);
246	1	av.setScaleAboveWrapped(true);
247	1	av.setScaleLeftWrapped(true);
248	1	av.setScaleRightWrapped(true);
249	1	FontMetrics fm = testee.getFontMetrics(av.getFont());
250	1	int labelWidth = fm.stringWidth("000") + charWidth;
251		// some leeway for different OS rendering of text
252	1	assertTrue(labelWidth >= 36 && labelWidth <= 39);
253	1	int annotationHeight = testee.getAnnotationHeight();
254
255		/*
256		* width 400 pixels leaves (400 - 2*labelWidth) for residue columns
257		* take the whole multiple of character widths
258		*/
259	1	int canvasWidth = 400;
260	1	int canvasHeight = 300;
261	1	int residueColumns = (canvasWidth - 2 * labelWidth) / charWidth;
262	1	int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
263		canvasHeight);
264	1	assertEquals(wrappedWidth, residueColumns);
265	1	assertEquals(PA.getValue(testee, "labelWidthWest"), labelWidth);
266	1	assertEquals(PA.getValue(testee, "labelWidthEast"), labelWidth);
267	1	assertEquals(PA.getValue(testee, "wrappedSpaceAboveAlignment"),
268		2 * charHeight);
269	1	int repeatingHeight = (int) PA.getValue(testee,
270		"wrappedRepeatHeightPx");
271	1	assertEquals(repeatingHeight, charHeight * (2 + al.getHeight())
272		+ SeqCanvas.SEQS_ANNOTATION_GAP + annotationHeight);
273	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
274
275		/*
276		* repeat height is 17 * (2 + 15) = 289 + 3 + annotationHeight = 510
277		* make canvas height 2 of these plus 3 charHeights
278		* so just enough to draw 2 widths, gap + scale + the first sequence of a third
279		*/
280	1	canvasHeight = charHeight * (17 * 2 + 3)
281		+ 2 * (annotationHeight + SeqCanvas.SEQS_ANNOTATION_GAP);
282	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
283	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
284
285		/*
286		* reduce canvas height by 1 pixel - should not be enough height
287		* to draw 3 widths
288		*/
289	1	canvasHeight -= 1;
290	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
291	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 2);
292
293		/*
294		* turn off scale above - can now fit in 2 and a bit widths
295		*/
296	1	av.setScaleAboveWrapped(false);
297	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
298	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
299
300		/*
301		* reduce height to enough for 2 widths and not quite a third
302		* i.e. two repeating heights + spacer + sequence - 1 pixel
303		*/
304	1	canvasHeight = charHeight * (16 * 2 + 2)
305		+ 2 * (annotationHeight + SeqCanvas.SEQS_ANNOTATION_GAP) - 1;
306	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
307	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 2);
308
309		/*
310		* add 1 pixel to height - should now get 3 widths drawn
311		*/
312	1	canvasHeight += 1;
313	1	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
314	1	assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
315		}
316
317		/**
318		* Test simulates loading an unwrapped alignment, shrinking it vertically so
319		* not all sequences are visible, then changing to wrapped mode. The ranges
320		* endSeq should be unchanged, but the vertical repeat height should include
321		* all sequences.
322		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 1PASS
323	0	@Test(groups = "Functional_Failing")...
324		public void testCalculateWrappedGeometry_fromScrolled()
325		{
326	0	AlignViewport av = af.getViewport();
327	0	AlignmentI al = av.getAlignment();
328	0	assertEquals(al.getWidth(), 157);
329	0	assertEquals(al.getHeight(), 15);
330	0	av.getRanges().setStartEndSeq(0, 3);
331	0	av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
332	0	av.setWrapAlignment(true);
333	0	av.setShowAnnotation(false);
334	0	av.setScaleAboveWrapped(true);
335
336	0	SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
337
338	0	int charHeight = av.getCharHeight();
339	0	int charWidth = av.getCharWidth();
340	0	assertEquals(charHeight, 17);
341	0	assertEquals(charWidth, 12);
342
343	0	int canvasWidth = 400;
344	0	int canvasHeight = 300;
345	0	testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
346
347	0	assertEquals(av.getRanges().getEndSeq(), 3); // unchanged
348	0	int repeatingHeight = (int) PA.getValue(testee,
349		"wrappedRepeatHeightPx");
350	0	assertEquals(repeatingHeight, charHeight * (2 + al.getHeight()));
351		}
352
		100% Uncovered Elements: 0 (8) Complexity: 3 Complexity Density: 0.5
353	3	@BeforeMethod(alwaysRun = true)...
354		public void setUp()
355		{
356	3	Cache.loadProperties("test/jalview/io/testProps.jvprops");
357	3	Cache.applicationProperties.setProperty("SHOW_IDENTITY",
358		Boolean.TRUE.toString());
359	3	af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
360		DataSourceType.FILE);
361
362		/*
363		* wait for Consensus thread to complete
364		*/
365	3	do
366		{
367	7	try
368		{
369	7	Thread.sleep(50);
370		} catch (InterruptedException x)
371		{
372		}
373	7	} while (af.getViewport().getCalcManager().isWorking());
374		}
375
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
376	1	@Test(groups = "Functional")...
377		public void testClear_HighlightAndSelection()
378		{
379	1	AlignViewport av = af.getViewport();
380	1	SearchResultsI highlight = new SearchResults();
381	1	highlight.addResult(
382		av.getAlignment().getSequenceAt(1).getDatasetSequence(), 50,
383		80);
384	1	af.alignPanel.highlightSearchResults(highlight);
385	1	af.avc.markHighlightedColumns(false, false, false);
386	1	assertNotNull(av.getSearchResults(),
387		"No highlight was created on alignment");
388	1	assertFalse(av.getColumnSelection().isEmpty(),
389		"No selection was created from highlight");
390	1	af.deselectAllSequenceMenuItem_actionPerformed(null);
391	1	assertTrue(av.getColumnSelection().isEmpty(),
392		"No Selection should be present after deselecting all.");
393	1	assertNull(av.getSearchResults(),
394		"No higlighted search results should be present after deselecting all.");
395		}
396		}