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 jalview.api.AlignViewportI;
28 import jalview.bin.Cache;
29 import jalview.bin.Jalview;
30 import jalview.commands.EditCommand;
31 import jalview.commands.EditCommand.Action;
32 import jalview.commands.EditCommand.Edit;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentAnnotation;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.Sequence;
37 import jalview.datamodel.SequenceI;
38 import jalview.gui.SeqPanel.MousePos;
39 import jalview.io.DataSourceType;
40 import jalview.io.FileLoader;
41 import jalview.util.MessageManager;
43 import java.awt.event.InputEvent;import java.awt.EventQueue;
44 import java.awt.event.MouseEvent;
45 import java.lang.reflect.InvocationTargetException;
47 import javax.swing.JLabel;
49 import org.testng.annotations.AfterMethod;
50 import org.testng.annotations.BeforeClass;
51 import org.testng.annotations.Test;
53 import junit.extensions.PA;
55 public class SeqPanelTest
59 @BeforeClass(alwaysRun = true)
60 public void setUpJvOptionPane()
62 JvOptionPane.setInteractiveMode(false);
63 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
65 @Test(groups = "Functional")
66 public void testSetStatusReturnsNearestResiduePosition()
68 SequenceI seq1 = new Sequence("Seq1", "AACDE");
69 SequenceI seq2 = new Sequence("Seq2", "AA--E");
70 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
71 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
73 AlignmentI visAl = alignFrame.getViewport().getAlignment();
75 // Test either side of gap
77 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
78 visAl.getSequenceAt(1), 1, 1), 2);
79 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
80 "Sequence 2 ID: Seq2 Residue: ALA (2)");
82 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
83 visAl.getSequenceAt(1), 4, 1), 3);
84 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
85 "Sequence 2 ID: Seq2 Residue: GLU (3)");
86 // no status message at a gap, returns next residue position to the right
88 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
89 visAl.getSequenceAt(1), 2, 1), 3);
90 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
91 "Sequence 2 ID: Seq2");
93 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
94 visAl.getSequenceAt(1), 3, 1), 3);
95 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
96 "Sequence 2 ID: Seq2");
99 @Test(groups = "Functional")
100 public void testAmbiguousAminoAcidGetsStatusMessage()
102 SequenceI seq1 = new Sequence("Seq1", "ABCDE");
103 SequenceI seq2 = new Sequence("Seq2", "AB--E");
104 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
105 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
107 AlignmentI visAl = alignFrame.getViewport().getAlignment();
110 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
111 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, x, y,
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, x, y,
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, 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, 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, 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, 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, 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, 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, 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, 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, 0, 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, 0, 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, 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, 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, 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, x, y,
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, 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, 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, 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, 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, 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, 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, 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, 0,
548 pos = testee.findMousePosition(evt);
549 assertEquals(pos.seqIndex, alignmentHeight - 1);
550 assertEquals(pos.annotationIndex, -1);
552 AlignmentAnnotation[] annotationRows = av.getAlignment().getAlignmentAnnotation();
553 for (int n = 0; n < annotationRows.length; n++)
556 * cursor at the top of the n'th annotation
559 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
561 pos = testee.findMousePosition(evt);
562 assertEquals(pos.seqIndex, alignmentHeight - 1);
563 assertEquals(pos.annotationIndex, n); // over n'th annotation
566 * cursor at the bottom of the n'th annotation
568 y += annotationRows[n].height - 1;
569 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
571 pos = testee.findMousePosition(evt);
572 assertEquals(pos.seqIndex, alignmentHeight - 1);
573 assertEquals(pos.annotationIndex, n);
577 * cursor in gap between wrapped widths
580 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
582 pos = testee.findMousePosition(evt);
583 assertEquals(pos.seqIndex, -1);
584 assertEquals(pos.annotationIndex, -1);
587 * cursor at bottom of gap between wrapped widths
590 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
592 pos = testee.findMousePosition(evt);
593 assertEquals(pos.seqIndex, -1);
594 assertEquals(pos.annotationIndex, -1);
597 * cursor at top of scale, second wrapped width
600 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
602 pos = testee.findMousePosition(evt);
603 assertEquals(pos.seqIndex, -1);
604 assertEquals(pos.annotationIndex, -1);
607 * cursor at bottom of scale, second wrapped width
610 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
612 pos = testee.findMousePosition(evt);
613 assertEquals(pos.seqIndex, -1);
614 assertEquals(pos.annotationIndex, -1);
617 * cursor at top of first sequence, second wrapped width
620 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
622 pos = testee.findMousePosition(evt);
623 assertEquals(pos.seqIndex, 0);
624 assertEquals(pos.annotationIndex, -1);
627 @Test(groups = "Functional")
628 public void testFindMousePosition_wrapped_noAnnotations()
630 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false");
631 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
632 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
633 "examples/uniref50.fa", DataSourceType.FILE);
634 AlignViewportI av = alignFrame.getViewport();
635 av.setScaleAboveWrapped(false);
636 av.setScaleLeftWrapped(false);
637 av.setScaleRightWrapped(false);
638 alignFrame.alignPanel.updateLayout();
640 final int charHeight = av.getCharHeight();
641 final int charWidth = av.getCharWidth();
642 final int alignmentHeight = av.getAlignment().getHeight();
645 assertTrue(charHeight > 0);
646 assertTrue(charWidth > 0);
647 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
649 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
654 * mouse at top left of wrapped panel; there is a gap of charHeight
655 * above the alignment
657 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y,
659 MousePos pos = testee.findMousePosition(evt);
660 assertEquals(pos.column, 0);
661 assertEquals(pos.seqIndex, -1); // above sequences
662 assertEquals(pos.annotationIndex, -1);
665 * cursor over top of first sequence
668 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
670 pos = testee.findMousePosition(evt);
671 assertEquals(pos.seqIndex, 0);
672 assertEquals(pos.annotationIndex, -1);
675 * cursor at bottom of last sequence
677 y = charHeight * (1 + alignmentHeight) - 1;
678 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
680 pos = testee.findMousePosition(evt);
681 assertEquals(pos.seqIndex, alignmentHeight - 1);
682 assertEquals(pos.annotationIndex, -1);
685 * cursor below sequences, at top of charHeight gap between widths
688 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
690 pos = testee.findMousePosition(evt);
691 assertEquals(pos.seqIndex, -1);
692 assertEquals(pos.annotationIndex, -1);
695 * cursor below sequences, at top of charHeight gap between widths
698 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
700 pos = testee.findMousePosition(evt);
701 assertEquals(pos.seqIndex, -1);
702 assertEquals(pos.annotationIndex, -1);
705 * cursor at the top of the first sequence, second width
708 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
710 pos = testee.findMousePosition(evt);
711 assertEquals(pos.seqIndex, 0);
712 assertEquals(pos.annotationIndex, -1);
715 @Test(groups = "Functional")
716 public void testFindColumn_unwrapped()
718 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "false");
719 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
720 "examples/uniref50.fa", DataSourceType.FILE);
721 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
723 final int charWidth = alignFrame.getViewport().getCharWidth();
724 assertTrue(charWidth > 0); // sanity check
725 assertEquals(alignFrame.getViewport().getRanges().getStartRes(), 0);
728 * mouse at top left of unwrapped panel
730 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
732 assertEquals(testee.findColumn(evt), 0);
735 * not quite one charWidth across
738 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
740 assertEquals(testee.findColumn(evt), 0);
743 * one charWidth across
746 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
748 assertEquals(testee.findColumn(evt), 1);
751 * two charWidths across
754 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
756 assertEquals(testee.findColumn(evt), 2);
759 * limited to last column of seqcanvas
762 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
764 SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
765 int w = seqCanvas.getWidth();
766 // limited to number of whole columns, base 0
767 int expected = w / charWidth - 1;
768 assertEquals(testee.findColumn(evt), expected);
771 * hide columns 5-10 (base 1)
773 alignFrame.getViewport().hideColumns(4, 9);
774 x = 5 * charWidth + 2;
775 // x is in 6th visible column, absolute column 12, or 11 base 0
776 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
778 assertEquals(testee.findColumn(evt), 11);
781 @Test(groups = "Functional")
782 public void testFindColumn_wrapped()
784 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
785 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
786 "examples/uniref50.fa", DataSourceType.FILE);
787 AlignViewport av = alignFrame.getViewport();
788 av.setScaleAboveWrapped(false);
789 av.setScaleLeftWrapped(false);
790 av.setScaleRightWrapped(false);
791 alignFrame.alignPanel.updateLayout();
792 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
794 final int charWidth = av.getCharWidth();
795 assertTrue(charWidth > 0); // sanity check
796 assertEquals(av.getRanges().getStartRes(), 0);
799 * mouse at top left of wrapped panel, no West (left) scale
801 MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
803 assertEquals(testee.findColumn(evt), 0);
806 * not quite one charWidth across
809 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
811 assertEquals(testee.findColumn(evt), 0);
814 * one charWidth across
817 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
819 assertEquals(testee.findColumn(evt), 1);
822 * x over scale left (before drawn columns) results in -1
824 av.setScaleLeftWrapped(true);
825 alignFrame.alignPanel.updateLayout();
826 SeqCanvas seqCanvas = testee.seqCanvas;
827 int labelWidth = (int) PA.getValue(seqCanvas, "labelWidthWest");
828 assertTrue(labelWidth > 0);
830 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
832 assertEquals(testee.findColumn(evt), -1);
835 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
837 assertEquals(testee.findColumn(evt), 0);
840 * x over right edge of last residue (including scale left)
842 int residuesWide = av.getRanges().getViewportWidth();
843 assertTrue(residuesWide > 0);
844 x = labelWidth + charWidth * residuesWide - 1;
845 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
847 assertEquals(testee.findColumn(evt), residuesWide - 1);
850 * x over scale right (beyond drawn columns) results in -1
852 av.setScaleRightWrapped(true);
853 alignFrame.alignPanel.updateLayout();
854 labelWidth = (int) PA.getValue(seqCanvas, "labelWidthEast");
855 assertTrue(labelWidth > 0);
856 int residuesWide2 = av.getRanges().getViewportWidth();
857 assertTrue(residuesWide2 > 0);
858 assertTrue(residuesWide2 < residuesWide); // available width reduced
859 x += 1; // just over left edge of scale right
860 evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
862 assertEquals(testee.findColumn(evt), -1);
864 // todo add startRes offset, hidden columns
867 @BeforeClass(alwaysRun = true)
868 public static void setUpBeforeClass() throws Exception
871 * use read-only test properties file
873 Cache.loadProperties("test/jalview/io/testProps.jvprops");
874 Jalview.main(new String[] { "-nonews" });
878 * waits for Swing event dispatch queue to empty
880 synchronized void waitForSwing()
884 EventQueue.invokeAndWait(new Runnable()
891 } catch (InterruptedException | InvocationTargetException e)