2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertNull;
25 import static org.testng.Assert.assertTrue;
27 import java.awt.EventQueue;
28 import java.awt.FontMetrics;
29 import java.awt.event.MouseEvent;
30 import java.lang.reflect.InvocationTargetException;
32 import javax.swing.JLabel;
34 import org.testng.annotations.AfterMethod;
35 import org.testng.annotations.BeforeClass;
36 import org.testng.annotations.Test;
37 import jalview.api.AlignViewportI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.EditCommand;
41 import jalview.commands.EditCommand.Action;
42 import jalview.commands.EditCommand.Edit;
43 import jalview.datamodel.Alignment;
44 import jalview.datamodel.AlignmentAnnotation;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.SearchResults;
47 import jalview.datamodel.SearchResultsI;
48 import jalview.datamodel.Sequence;
49 import jalview.datamodel.SequenceI;
50 import jalview.gui.SeqPanel.MousePos;
51 import jalview.io.DataSourceType;
52 import jalview.io.FileLoader;
53 import jalview.util.MessageManager;
54 import jalview.viewmodel.ViewportRanges;
57 import junit.extensions.PA;
59 public class SeqPanelTest
63 @BeforeClass(alwaysRun = true)
64 public void setUpJvOptionPane()
66 JvOptionPane.setInteractiveMode(false);
67 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
70 @Test(groups = "Functional")
71 public void testSetStatusReturnsNearestResiduePosition()
73 SequenceI seq1 = new Sequence("Seq1", "AACDE");
74 SequenceI seq2 = new Sequence("Seq2", "AA--E");
75 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
76 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
78 AlignmentI visAl = alignFrame.getViewport().getAlignment();
80 // Test either side of gap
81 assertEquals(alignFrame.alignPanel.getSeqPanel()
82 .setStatusMessage(visAl.getSequenceAt(1), 1, 1), 2);
83 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
84 "Sequence 2 ID: Seq2 Residue: ALA (2)");
85 assertEquals(alignFrame.alignPanel.getSeqPanel()
86 .setStatusMessage(visAl.getSequenceAt(1), 4, 1), 3);
87 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
88 "Sequence 2 ID: Seq2 Residue: GLU (3)");
89 // no status message at a gap, returns next residue position to the right
90 assertEquals(alignFrame.alignPanel.getSeqPanel()
91 .setStatusMessage(visAl.getSequenceAt(1), 2, 1), 3);
92 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
93 "Sequence 2 ID: Seq2");
94 assertEquals(alignFrame.alignPanel.getSeqPanel()
95 .setStatusMessage(visAl.getSequenceAt(1), 3, 1), 3);
96 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
97 "Sequence 2 ID: Seq2");
100 @Test(groups = "Functional")
101 public void testAmbiguousAminoAcidGetsStatusMessage()
103 SequenceI seq1 = new Sequence("Seq1", "ABCDE");
104 SequenceI seq2 = new Sequence("Seq2", "AB--E");
105 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
106 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
108 AlignmentI visAl = alignFrame.getViewport().getAlignment();
110 assertEquals(alignFrame.alignPanel.getSeqPanel()
111 .setStatusMessage(visAl.getSequenceAt(1), 1, 1), 2);
112 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
113 "Sequence 2 ID: Seq2 Residue: B (2)");
116 @Test(groups = "Functional")
117 public void testGetEditStatusMessage()
119 assertNull(SeqPanel.getEditStatusMessage(null));
121 EditCommand edit = new EditCommand(); // empty
122 assertNull(SeqPanel.getEditStatusMessage(edit));
124 SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
127 edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-'));
128 String expected = MessageManager.formatMessage("label.insert_gap", "1");
129 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
131 // 3 more gaps makes +4
132 edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 3, '-'));
133 expected = MessageManager.formatMessage("label.insert_gaps", "4");
134 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
136 // 2 deletes makes + 2
137 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'));
138 expected = MessageManager.formatMessage("label.insert_gaps", "2");
139 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
141 // 2 more deletes makes 0 - no text
142 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'));
143 assertNull(SeqPanel.getEditStatusMessage(edit));
145 // 1 more delete makes 1 delete
146 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'));
147 expected = MessageManager.formatMessage("label.delete_gap", "1");
148 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
150 // 1 more delete makes 2 deletes
151 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'));
152 expected = MessageManager.formatMessage("label.delete_gaps", "2");
153 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
157 * Tests that simulate 'locked editing', where an inserted gap is balanced by
158 * a gap deletion in the selection group, and vice versa
160 @Test(groups = "Functional")
161 public void testGetEditStatusMessage_lockedEditing()
163 EditCommand edit = new EditCommand(); // empty
164 SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
166 // 1 gap inserted, balanced by 1 delete
167 Edit e1 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-');
169 Edit e2 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 1, '-');
170 e2.setSystemGenerated(true);
172 String expected = MessageManager.formatMessage("label.insert_gap", "1");
173 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
175 // 2 more gaps makes +3
176 Edit e3 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-');
178 Edit e4 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 2, '-');
179 e4.setSystemGenerated(true);
181 expected = MessageManager.formatMessage("label.insert_gaps", "3");
182 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
184 // 2 deletes makes + 1
185 Edit e5 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
187 Edit e6 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-');
188 e6.setSystemGenerated(true);
190 expected = MessageManager.formatMessage("label.insert_gap", "1");
191 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
193 // 1 more delete makes 0 - no text
194 Edit e7 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
196 Edit e8 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-');
197 e8.setSystemGenerated(true);
199 expected = MessageManager.formatMessage("label.insert_gaps", "2");
200 assertNull(SeqPanel.getEditStatusMessage(edit));
202 // 1 more delete makes 1 delete
203 Edit e9 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
205 Edit e10 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-');
206 e10.setSystemGenerated(true);
208 expected = MessageManager.formatMessage("label.delete_gap", "1");
209 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
211 // 2 more deletes makes 3 deletes
212 Edit e11 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
214 Edit e12 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-');
215 e12.setSystemGenerated(true);
217 expected = MessageManager.formatMessage("label.delete_gaps", "3");
218 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
221 public void testFindMousePosition_unwrapped()
223 String seqData = ">Seq1\nAACDE\n>Seq2\nAA--E\n";
224 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(seqData,
225 DataSourceType.PASTE);
226 AlignViewportI av = alignFrame.getViewport();
227 av.setShowAnnotation(true);
228 av.setWrapAlignment(false);
229 final int charHeight = av.getCharHeight();
230 final int charWidth = av.getCharWidth();
232 assertTrue(charHeight > 0);
233 assertTrue(charWidth > 0);
234 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
236 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
241 * mouse at top left of unwrapped panel
243 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
244 x, y, 0, 0, 0, false, 0);
245 MousePos pos = testee.findMousePosition(evt);
246 assertEquals(pos.column, 0);
247 assertEquals(pos.seqIndex, 0);
248 assertEquals(pos.annotationIndex, -1);
251 @AfterMethod(alwaysRun = true)
252 public void tearDown()
254 Desktop.instance.closeAll_actionPerformed(null);
257 @Test(groups = "Functional")
258 public void testFindMousePosition_wrapped_annotations()
260 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
261 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
262 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
263 "examples/uniref50.fa", DataSourceType.FILE);
264 AlignViewportI av = alignFrame.getViewport();
265 av.setScaleAboveWrapped(false);
266 av.setScaleLeftWrapped(false);
267 av.setScaleRightWrapped(false);
269 alignFrame.alignPanel.updateLayout();
271 final int charHeight = av.getCharHeight();
272 final int charWidth = av.getCharWidth();
273 final int alignmentHeight = av.getAlignment().getHeight();
276 assertTrue(charHeight > 0);
277 assertTrue(charWidth > 0);
278 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
280 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
285 * mouse at top left of wrapped panel; there is a gap of charHeight
286 * above the alignment
288 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
289 x, y, 0, 0, 0, false, 0);
290 MousePos pos = testee.findMousePosition(evt);
291 assertEquals(pos.column, 0);
292 assertEquals(pos.seqIndex, -1); // above sequences
293 assertEquals(pos.annotationIndex, -1);
296 * cursor at bottom of gap above
299 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
301 pos = testee.findMousePosition(evt);
302 assertEquals(pos.seqIndex, -1);
303 assertEquals(pos.annotationIndex, -1);
306 * cursor over top of first sequence
309 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
311 pos = testee.findMousePosition(evt);
312 assertEquals(pos.seqIndex, 0);
313 assertEquals(pos.annotationIndex, -1);
316 * cursor at bottom of first sequence
318 y = 2 * charHeight - 1;
319 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
321 pos = testee.findMousePosition(evt);
322 assertEquals(pos.seqIndex, 0);
323 assertEquals(pos.annotationIndex, -1);
326 * cursor at top of second sequence
329 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
331 pos = testee.findMousePosition(evt);
332 assertEquals(pos.seqIndex, 1);
333 assertEquals(pos.annotationIndex, -1);
336 * cursor at bottom of second sequence
338 y = 3 * charHeight - 1;
339 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
341 pos = testee.findMousePosition(evt);
342 assertEquals(pos.seqIndex, 1);
343 assertEquals(pos.annotationIndex, -1);
346 * cursor at bottom of last sequence
348 y = charHeight * (1 + alignmentHeight) - 1;
349 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
351 pos = testee.findMousePosition(evt);
352 assertEquals(pos.seqIndex, alignmentHeight - 1);
353 assertEquals(pos.annotationIndex, -1);
356 * cursor below sequences, in 3-pixel gap above annotations
357 * method reports index of nearest sequence above
360 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
362 pos = testee.findMousePosition(evt);
363 assertEquals(pos.seqIndex, alignmentHeight - 1);
364 assertEquals(pos.annotationIndex, -1);
367 * cursor still in the gap above annotations, now at the bottom of it
369 y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
370 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
372 pos = testee.findMousePosition(evt);
373 assertEquals(pos.seqIndex, alignmentHeight - 1);
374 assertEquals(pos.annotationIndex, -1);
376 AlignmentAnnotation[] annotationRows = av.getAlignment()
377 .getAlignmentAnnotation();
378 for (int n = 0; n < annotationRows.length; n++)
381 * cursor at the top of the n'th annotation
384 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
386 pos = testee.findMousePosition(evt);
387 assertEquals(pos.seqIndex, alignmentHeight - 1);
388 assertEquals(pos.annotationIndex, n); // over n'th annotation
391 * cursor at the bottom of the n'th annotation
393 y += annotationRows[n].height - 1;
394 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
396 pos = testee.findMousePosition(evt);
397 assertEquals(pos.seqIndex, alignmentHeight - 1);
398 assertEquals(pos.annotationIndex, n);
402 * cursor in gap between wrapped widths
405 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
407 pos = testee.findMousePosition(evt);
408 assertEquals(pos.seqIndex, -1);
409 assertEquals(pos.annotationIndex, -1);
412 * cursor at bottom of gap between wrapped widths
415 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
417 pos = testee.findMousePosition(evt);
418 assertEquals(pos.seqIndex, -1);
419 assertEquals(pos.annotationIndex, -1);
422 * cursor at top of first sequence, second wrapped width
425 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
427 pos = testee.findMousePosition(evt);
428 assertEquals(pos.seqIndex, 0);
429 assertEquals(pos.annotationIndex, -1);
432 @Test(groups = "Functional")
433 public void testFindMousePosition_wrapped_scaleAbove()
435 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
436 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
437 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
438 "examples/uniref50.fa", DataSourceType.FILE);
439 AlignViewportI av = alignFrame.getViewport();
440 av.setScaleAboveWrapped(true);
441 av.setScaleLeftWrapped(false);
442 av.setScaleRightWrapped(false);
443 alignFrame.alignPanel.updateLayout();
445 final int charHeight = av.getCharHeight();
446 final int charWidth = av.getCharWidth();
447 final int alignmentHeight = av.getAlignment().getHeight();
450 assertTrue(charHeight > 0);
451 assertTrue(charWidth > 0);
452 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
454 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
459 * mouse at top left of wrapped panel; there is a gap of charHeight
460 * above the alignment
462 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
463 x, y, 0, 0, 0, false, 0);
464 MousePos pos = testee.findMousePosition(evt);
465 assertEquals(pos.column, 0);
466 assertEquals(pos.seqIndex, -1); // above sequences
467 assertEquals(pos.annotationIndex, -1);
470 * cursor at bottom of gap above
471 * two charHeights including scale panel
473 y = 2 * charHeight - 1;
474 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
476 pos = testee.findMousePosition(evt);
477 assertEquals(pos.seqIndex, -1);
478 assertEquals(pos.annotationIndex, -1);
481 * cursor over top of first sequence
484 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
486 pos = testee.findMousePosition(evt);
487 assertEquals(pos.seqIndex, 0);
488 assertEquals(pos.annotationIndex, -1);
491 * cursor at bottom of first sequence
494 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
496 pos = testee.findMousePosition(evt);
497 assertEquals(pos.seqIndex, 0);
498 assertEquals(pos.annotationIndex, -1);
501 * cursor at top of second sequence
504 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
506 pos = testee.findMousePosition(evt);
507 assertEquals(pos.seqIndex, 1);
508 assertEquals(pos.annotationIndex, -1);
511 * cursor at bottom of second sequence
514 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
516 pos = testee.findMousePosition(evt);
517 assertEquals(pos.seqIndex, 1);
518 assertEquals(pos.annotationIndex, -1);
521 * cursor at bottom of last sequence
522 * (scale + gap + sequences)
524 y = charHeight * (2 + alignmentHeight) - 1;
525 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
527 pos = testee.findMousePosition(evt);
528 assertEquals(pos.seqIndex, alignmentHeight - 1);
529 assertEquals(pos.annotationIndex, -1);
532 * cursor below sequences, in 3-pixel gap above annotations
535 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
537 pos = testee.findMousePosition(evt);
538 assertEquals(pos.seqIndex, alignmentHeight - 1);
539 assertEquals(pos.annotationIndex, -1);
542 * cursor still in the gap above annotations, now at the bottom of it
543 * method reports index of nearest sequence above
545 y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
546 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
548 pos = testee.findMousePosition(evt);
549 assertEquals(pos.seqIndex, alignmentHeight - 1);
550 assertEquals(pos.annotationIndex, -1);
552 AlignmentAnnotation[] annotationRows = av.getAlignment()
553 .getAlignmentAnnotation();
554 for (int n = 0; n < annotationRows.length; n++)
557 * cursor at the top of the n'th annotation
560 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
562 pos = testee.findMousePosition(evt);
563 assertEquals(pos.seqIndex, alignmentHeight - 1);
564 assertEquals(pos.annotationIndex, n); // over n'th annotation
567 * cursor at the bottom of the n'th annotation
569 y += annotationRows[n].height - 1;
570 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
572 pos = testee.findMousePosition(evt);
573 SeqCanvas sc = testee.seqCanvas;
574 assertEquals(pos.seqIndex, alignmentHeight - 1,
575 String.format("%s n=%d y=%d %d, %d, %d, %d",
576 annotationRows[n].label, n, y, sc.getWidth(),
577 sc.getHeight(), sc.wrappedRepeatHeightPx,
578 sc.wrappedSpaceAboveAlignment));
579 assertEquals(pos.annotationIndex, n);
583 * cursor in gap between wrapped widths
586 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
588 pos = testee.findMousePosition(evt);
589 assertEquals(pos.seqIndex, -1);
590 assertEquals(pos.annotationIndex, -1);
593 * cursor at bottom of gap between wrapped widths
596 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
598 pos = testee.findMousePosition(evt);
599 assertEquals(pos.seqIndex, -1);
600 assertEquals(pos.annotationIndex, -1);
603 * cursor at top of scale, second wrapped width
606 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
608 pos = testee.findMousePosition(evt);
609 assertEquals(pos.seqIndex, -1);
610 assertEquals(pos.annotationIndex, -1);
613 * cursor at bottom of scale, second wrapped width
616 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
618 pos = testee.findMousePosition(evt);
619 assertEquals(pos.seqIndex, -1);
620 assertEquals(pos.annotationIndex, -1);
623 * cursor at top of first sequence, second wrapped width
626 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
628 pos = testee.findMousePosition(evt);
629 assertEquals(pos.seqIndex, 0);
630 assertEquals(pos.annotationIndex, -1);
633 @Test(groups = "Functional")
634 public void testFindMousePosition_wrapped_noAnnotations()
636 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
637 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
638 Cache.applicationProperties.setProperty("FONT_SIZE", "10");
639 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
640 "examples/uniref50.fa", DataSourceType.FILE);
641 AlignViewportI av = alignFrame.getViewport();
642 av.setScaleAboveWrapped(false);
643 av.setScaleLeftWrapped(false);
644 av.setScaleRightWrapped(false);
645 alignFrame.alignPanel.updateLayout();
647 final int charHeight = av.getCharHeight();
648 final int charWidth = av.getCharWidth();
649 final int alignmentHeight = av.getAlignment().getHeight();
652 assertTrue(charHeight > 0);
653 assertTrue(charWidth > 0);
654 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
656 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
661 * mouse at top left of wrapped panel; there is a gap of charHeight
662 * above the alignment
664 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
665 x, y, 0, 0, 0, false, 0);
666 MousePos pos = testee.findMousePosition(evt);
667 assertEquals(pos.column, 0);
668 assertEquals(pos.seqIndex, -1); // above sequences
669 assertEquals(pos.annotationIndex, -1);
672 * cursor over top of first sequence
675 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
677 pos = testee.findMousePosition(evt);
678 assertEquals(pos.seqIndex, 0);
679 assertEquals(pos.annotationIndex, -1);
682 * cursor at bottom of last sequence
684 y = charHeight * (1 + alignmentHeight) - 1;
685 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
687 pos = testee.findMousePosition(evt);
688 assertEquals(pos.seqIndex, alignmentHeight - 1);
689 assertEquals(pos.annotationIndex, -1);
692 * cursor below sequences, at top of charHeight gap between widths
695 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
697 pos = testee.findMousePosition(evt);
698 assertEquals(pos.seqIndex, -1);
699 assertEquals(pos.annotationIndex, -1);
702 * cursor below sequences, at top of charHeight gap between widths
705 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
707 pos = testee.findMousePosition(evt);
708 assertEquals(pos.seqIndex, -1);
709 assertEquals(pos.annotationIndex, -1);
712 * cursor at the top of the first sequence, second width
715 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
717 pos = testee.findMousePosition(evt);
718 assertEquals(pos.seqIndex, 0);
719 assertEquals(pos.annotationIndex, -1);
722 @Test(groups = "Functional")
723 public void testFindColumn_unwrapped()
725 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "false");
726 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
727 "examples/uniref50.fa", DataSourceType.FILE);
728 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
730 final int charWidth = alignFrame.getViewport().getCharWidth();
731 assertTrue(charWidth > 0); // sanity check
732 ViewportRanges ranges = alignFrame.getViewport().getRanges();
733 assertEquals(ranges.getStartRes(), 0);
736 * mouse at top left of unwrapped panel
738 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
739 x, 0, 0, 0, 0, false, 0);
740 assertEquals(testee.findColumn(evt), 0);
743 * not quite one charWidth across
746 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
748 assertEquals(testee.findColumn(evt), 0);
751 * one charWidth across
754 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
756 assertEquals(testee.findColumn(evt), 1);
759 * two charWidths across
762 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
764 assertEquals(testee.findColumn(evt), 2);
767 * limited to last column of seqcanvas
770 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
772 SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
773 int w = seqCanvas.getWidth();
774 // limited to number of whole columns, base 0,
775 // and to end of visible range
776 int expected = w / charWidth;
777 expected = Math.min(expected, ranges.getEndRes());
778 assertEquals(testee.findColumn(evt), expected);
781 * hide columns 5-10 (base 1)
783 alignFrame.getViewport().hideColumns(4, 9);
784 x = 5 * charWidth + 2;
785 // x is in 6th visible column, absolute column 12, or 11 base 0
786 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
788 assertEquals(testee.findColumn(evt), 11);
791 @Test(groups = "Functional")
792 public void testFindColumn_wrapped()
794 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
795 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
796 "examples/uniref50.fa", DataSourceType.FILE);
797 AlignViewport av = alignFrame.getViewport();
798 av.setScaleAboveWrapped(false);
799 av.setScaleLeftWrapped(false);
800 av.setScaleRightWrapped(false);
801 alignFrame.alignPanel.updateLayout();
802 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
804 final int charWidth = av.getCharWidth();
805 assertTrue(charWidth > 0); // sanity check
806 assertEquals(av.getRanges().getStartRes(), 0);
809 * mouse at top left of wrapped panel, no West (left) scale
811 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
812 x, 0, 0, 0, 0, false, 0);
813 assertEquals(testee.findColumn(evt), 0);
816 * not quite one charWidth across
819 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
821 assertEquals(testee.findColumn(evt), 0);
824 * one charWidth across
827 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
829 assertEquals(testee.findColumn(evt), 1);
832 * x over scale left (before drawn columns) results in -1
834 av.setScaleLeftWrapped(true);
835 alignFrame.alignPanel.updateLayout();
836 SeqCanvas seqCanvas = testee.seqCanvas;
837 int labelWidth = (int) PA.getValue(seqCanvas, "labelWidthWest");
838 assertTrue(labelWidth > 0);
840 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
842 assertEquals(testee.findColumn(evt), -1);
845 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
847 assertEquals(testee.findColumn(evt), 0);
850 * x over right edge of last residue (including scale left)
852 int residuesWide = av.getRanges().getViewportWidth();
853 assertTrue(residuesWide > 0);
854 x = labelWidth + charWidth * residuesWide - 1;
855 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
857 assertEquals(testee.findColumn(evt), residuesWide - 1);
860 * x over scale right (beyond drawn columns) results in -1
862 av.setScaleRightWrapped(true);
863 alignFrame.alignPanel.updateLayout();
864 labelWidth = (int) PA.getValue(seqCanvas, "labelWidthEast");
865 assertTrue(labelWidth > 0);
866 int residuesWide2 = av.getRanges().getViewportWidth();
867 assertTrue(residuesWide2 > 0);
868 assertTrue(residuesWide2 < residuesWide); // available width reduced
869 x += 1; // just over left edge of scale right
870 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
872 assertEquals(testee.findColumn(evt), -1);
874 // todo add startRes offset, hidden columns
878 @BeforeClass(alwaysRun = true)
879 public static void setUpBeforeClass() throws Exception
882 * use read-only test properties file
884 Cache.loadProperties("test/jalview/io/testProps.jvprops");
885 Jalview.main(new String[] { "-nonews" });
889 * waits for Swing event dispatch queue to empty
891 synchronized void waitForSwing()
895 EventQueue.invokeAndWait(new Runnable()
902 } catch (InterruptedException | InvocationTargetException e)
908 @Test(groups = "Functional")
909 public void testFindMousePosition_wrapped_scales_longSequence()
911 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
912 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
913 Cache.applicationProperties.setProperty("FONT_SIZE", "14");
914 Cache.applicationProperties.setProperty("FONT_NAME", "SansSerif");
915 Cache.applicationProperties.setProperty("FONT_STYLE", "0");
916 // sequence of 50 bases, doubled 10 times, = 51200 bases
917 String dna = "ATGGCCATTGGGCCCAAATTTCCCAAAGGGTTTCCCTGAGGTCAGTCAGA";
918 for (int i = 0; i < 10; i++)
922 assertEquals(dna.length(), 51200);
923 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(dna,
924 DataSourceType.PASTE);
925 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
926 AlignViewport av = alignFrame.getViewport();
927 av.setScaleAboveWrapped(true);
928 av.setScaleLeftWrapped(true);
929 av.setScaleRightWrapped(true);
930 alignFrame.alignPanel.updateLayout();
935 } catch (InterruptedException e)
939 final int charHeight = av.getCharHeight();
940 final int charWidth = av.getCharWidth();
941 assertEquals(charHeight, 17);
942 assertEquals(charWidth, 12);
944 FontMetrics fm = testee.getFontMetrics(av.getFont());
945 int labelWidth = fm.stringWidth("00000") + charWidth;
946 assertEquals(labelWidth, 57); // 5 x 9 + charWidth
947 assertEquals(testee.seqCanvas.getLabelWidthWest(), labelWidth);
953 * mouse at top left of wrapped panel; there is a gap of 2 * charHeight
954 * above the alignment
956 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
957 x, y, 0, 0, 0, false, 0);
958 MousePos pos = testee.findMousePosition(evt);
959 assertEquals(pos.column, -1); // over scale left, not an alignment column
960 assertEquals(pos.seqIndex, -1); // above sequences
961 assertEquals(pos.annotationIndex, -1);
964 * cursor over scale above first sequence
968 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
970 pos = testee.findMousePosition(evt);
971 assertEquals(pos.seqIndex, -1);
972 assertEquals(pos.column, 0);
973 assertEquals(pos.annotationIndex, -1);
976 * cursor over scale left of first sequence
980 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
982 pos = testee.findMousePosition(evt);
983 assertEquals(pos.seqIndex, 0);
984 assertEquals(pos.column, -1);
985 assertEquals(pos.annotationIndex, -1);
988 * cursor over start of first sequence
991 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
993 pos = testee.findMousePosition(evt);
994 assertEquals(pos.seqIndex, 0);
995 assertEquals(pos.column, 0);
996 assertEquals(pos.annotationIndex, -1);
999 * move one character right, to bottom pixel of same row
1002 y += charHeight - 1;
1003 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
1005 pos = testee.findMousePosition(evt);
1006 assertEquals(pos.seqIndex, 0);
1007 assertEquals(pos.column, 1);
1010 * move down one pixel - now in the no man's land between rows
1013 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
1015 pos = testee.findMousePosition(evt);
1016 assertEquals(pos.seqIndex, -1);
1017 assertEquals(pos.column, 1);
1020 * move down two char heights less one pixel - still in the no man's land
1021 * (scale above + spacer line)
1023 y += (2 * charHeight - 1);
1024 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
1026 pos = testee.findMousePosition(evt);
1027 assertEquals(pos.seqIndex, -1);
1028 assertEquals(pos.column, 1);
1031 * move down one more pixel - now on the next row of the sequence
1034 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
1036 pos = testee.findMousePosition(evt);
1037 assertEquals(pos.seqIndex, 0);
1038 assertEquals(pos.column, 1 + av.getWrappedWidth());
1041 * scroll to near the end of the sequence
1043 SearchResultsI sr = new SearchResults();
1044 int scrollTo = dna.length() - 1000;
1045 sr.addResult(av.getAlignment().getSequenceAt(0), scrollTo, scrollTo);
1046 alignFrame.alignPanel.scrollToPosition(sr);
1049 * place the mouse on the first column of the 6th sequence, and
1050 * verify that (computed) findMousePosition matches (actual) ViewportRanges
1053 y = 17 * charHeight; // 17 = 6 times two header rows and 5 sequence rows
1054 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
1056 pos = testee.findMousePosition(evt);
1057 assertEquals(pos.seqIndex, 0);
1058 int expected = av.getRanges().getStartRes() + 5 * av.getWrappedWidth();
1059 assertEquals(pos.column, expected);