1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.gui

File AlignmentPanelTest.java

 

Code metrics

10
139
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401
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16
0.12
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1.6

Classes

Class
Line #
Actions
AlignmentPanelTest 50 139 16
0.522012652.2%
 

Contributing tests

This file is covered by 5 tests. .

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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.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   
 
50    public class AlignmentPanelTest
51    {
52    AlignFrame af;
53   
 
54  5 toggle @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    {
 
71  5 toggle @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  5 try
84    {
85  5 Thread.sleep(50);
86    } catch (InterruptedException x)
87    {
88    }
89  5 } 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    */
 
96  1 toggle @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    */
 
159  1 toggle @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    */
 
185  1 toggle @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    */
 
217  0 toggle @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   
 
275  0 toggle @Test(groups = { "Functional", "Not-bamboo" })
276    public void testGetVisibleWidth()
277    {
278  0 double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
279    /*
280    * width for onscreen rendering is IDPanel width
281    */
282  0 int w = af.alignPanel.getVisibleIdWidth(true);
283  0 assertEquals(w, af.alignPanel.getIdPanel().getWidth());
284   
285    // different scaling (1.0, 2.0) gives different results
286  0 int expectedWidth = scaling == 1.0 ? 112 : Platform.isMac() ? 115 : 107;
287  0 assertEquals(w, expectedWidth);
288   
289    /*
290    * width for offscreen rendering is the same
291    * if no fixed id width is specified in preferences
292    */
293  0 Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.FALSE.toString());
294  0 Cache.removeProperty("FIGURE_FIXEDIDWIDTH");
295  0 assertEquals(w, af.alignPanel.getVisibleIdWidth(false));
296   
297    /*
298    * preference for fixed id width - note 4 pixels padding is added
299    */
300  0 Cache.setProperty("FIGURE_FIXEDIDWIDTH", "120");
301  0 assertEquals(124, af.alignPanel.getVisibleIdWidth(false));
302   
303    /*
304    * preference for auto id width overrides fixed width
305    */
306  0 Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
307  0 w = af.alignPanel.getVisibleIdWidth(false);
308    // allow some leeway for different OS renderings
309  0 assertTrue(w > 105 && w < 120);
310    // different scaling (1.0, 2.0) gives different results
311  0 assertEquals(w, expectedWidth);
312    }
313   
 
314  0 toggle @Test(groups = { "Functional", "Not-bamboo" })
315    public void testresetIdWidth()
316    {
317  0 double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
318    /*
319    * width for onscreen rendering is IDPanel width
320    */
321  0 int w = af.alignPanel.getVisibleIdWidth(true);
322  0 int actual = af.alignPanel.getIdPanel().getWidth();
323  0 assertEquals(w, actual);
324    // allow some leeway for different OS renderings
325  0 assertTrue(w > 105 && w < 120);
326    // different scaling (1.0, 2.0) gives different results
327  0 int expectedWidth = scaling == 1.0 ? 112 : Platform.isMac() ? 115 : 107;
328  0 assertEquals(w, expectedWidth);
329   
330    // manually adjust
331  0 af.viewport.setIdWidth(200);
332    // fake mouse drag sets manuallyAdjusted to true (0,0 not moving mouse)
333  0 MouseEvent drag = new MouseEvent(af.alignPanel,
334    MouseEvent.MOUSE_DRAGGED, System.currentTimeMillis(), 0, 0, 0,
335    MouseEvent.BUTTON1, false);
336  0 af.alignPanel.idwidthAdjuster.mouseDragged(drag);
337  0 af.alignPanel.paintComponent(af.alignPanel.getGraphics());
338  0 w = af.alignPanel.calculateIdWidth().width;
339  0 assertTrue(
340    af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
341  0 actual = af.alignPanel.getIdPanel().getWidth();
342  0 assertEquals(w, actual);
343   
344  0 af.viewport.setIdWidth(-1);
345  0 af.alignPanel.calculateIdWidth();
346  0 af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
347  0 w = af.alignPanel.calculateIdWidth().width;
348  0 af.alignPanel.paintComponent(af.alignPanel.getGraphics());
349   
350  0 actual = af.alignPanel.getIdPanel().getWidth();
351  0 assertEquals(w, actual);
352   
353    // setting a negative IdWidth and then running calculateIdWidth resets width
354    // to optimal id width
355    // allow some leeway for different OS renderings
356  0 assertTrue(w > 105 && w < 120);
357    // different scaling (1.0, 2.0) gives different results
358  0 assertEquals(w, expectedWidth);
359    }
360   
 
361  1 toggle @Test(groups = "Functional")
362    public void testSetOverviewTitle()
363    {
364  1 OverviewPanel ov1 = this.af.openOverviewPanel(true);
365  1 String alignFrameTitle = af.getTitle();
366  1 assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
367   
368    /*
369    * on New View, existing overview should get " Original" added to title
370    * and new view's overview should get " View 1" added
371    */
372  1 af.newView_actionPerformed(null);
373  1 assertEquals(ov1.getTitle(),
374    "Overview " + alignFrameTitle + " Original");
375  1 OverviewPanel ov2 = this.af.openOverviewPanel(true);
376  1 assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
377    }
378   
 
379  1 toggle @Test(groups = "Functional")
380    public void testSetOverviewTitle_automaticOverview()
381    {
382  1 Cache.setProperty("SHOW_OVERVIEW", "true");
383  1 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
384    "examples/uniref50.fa", DataSourceType.FILE);
385  1 OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel();
386  1 assertNotNull(ov1);
387  1 String alignFrameTitle = alignFrame.getTitle();
388  1 assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
389   
390    /*
391    * on New View, existing overview should get " Original" added to title
392    * and new view's automatic overview should have " View 1" added
393    */
394  1 alignFrame.newView_actionPerformed(null);
395  1 assertEquals(ov1.getTitle(),
396    "Overview " + alignFrameTitle + " Original");
397  1 OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel();
398  1 assertNotNull(ov2);
399  1 assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
400    }
401    }