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;
44 import java.awt.EventQueue;
45 import java.awt.event.MouseEvent;
46 import java.lang.reflect.InvocationTargetException;
48 import javax.swing.JLabel;
50 import org.testng.annotations.AfterMethod;
51 import org.testng.annotations.BeforeClass;
52 import org.testng.annotations.Test;
54 import junit.extensions.PA;
56 public class SeqPanelTest
60 @BeforeClass(alwaysRun = true)
61 public void setUpJvOptionPane()
63 System.out.println("BH testing");
64 Jalview.setSynchronous(true);
65 JvOptionPane.setInteractiveMode(false);
66 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
68 @Test(groups = "Functional")
69 public void testSetStatusReturnsNearestResiduePosition()
71 SequenceI seq1 = new Sequence("Seq1", "AACDE");
72 SequenceI seq2 = new Sequence("Seq2", "AA--E");
73 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
74 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
76 AlignmentI visAl = alignFrame.getViewport().getAlignment();
78 // Test either side of gap
80 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
81 visAl.getSequenceAt(1), 1, 1), 2);
82 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
83 "Sequence 2 ID: Seq2 Residue: ALA (2)");
85 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
86 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
91 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
92 visAl.getSequenceAt(1), 2, 1), 3);
93 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
94 "Sequence 2 ID: Seq2");
96 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
97 visAl.getSequenceAt(1), 3, 1), 3);
98 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
99 "Sequence 2 ID: Seq2");
102 @Test(groups = "Functional")
103 public void testAmbiguousAminoAcidGetsStatusMessage()
105 SequenceI seq1 = new Sequence("Seq1", "ABCDE");
106 SequenceI seq2 = new Sequence("Seq2", "AB--E");
107 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
108 AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
110 AlignmentI visAl = alignFrame.getViewport().getAlignment();
113 alignFrame.alignPanel.getSeqPanel().setStatusMessage(
114 visAl.getSequenceAt(1), 1, 1), 2);
115 assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
116 "Sequence 2 ID: Seq2 Residue: B (2)");
119 @Test(groups = "Functional")
120 public void testGetEditStatusMessage()
122 assertNull(SeqPanel.getEditStatusMessage(null));
124 EditCommand edit = new EditCommand(); // empty
125 assertNull(SeqPanel.getEditStatusMessage(edit));
127 SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
130 edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-'));
131 String expected = MessageManager.formatMessage("label.insert_gap", "1");
132 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
134 // 3 more gaps makes +4
135 edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 3, '-'));
136 expected = MessageManager.formatMessage("label.insert_gaps", "4");
137 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
139 // 2 deletes makes + 2
140 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'));
141 expected = MessageManager.formatMessage("label.insert_gaps", "2");
142 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
144 // 2 more deletes makes 0 - no text
145 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'));
146 assertNull(SeqPanel.getEditStatusMessage(edit));
148 // 1 more delete makes 1 delete
149 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'));
150 expected = MessageManager.formatMessage("label.delete_gap", "1");
151 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
153 // 1 more delete makes 2 deletes
154 edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'));
155 expected = MessageManager.formatMessage("label.delete_gaps", "2");
156 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
160 * Tests that simulate 'locked editing', where an inserted gap is balanced by
161 * a gap deletion in the selection group, and vice versa
163 @Test(groups = "Functional")
164 public void testGetEditStatusMessage_lockedEditing()
166 EditCommand edit = new EditCommand(); // empty
167 SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
169 // 1 gap inserted, balanced by 1 delete
170 Edit e1 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-');
172 Edit e2 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 1, '-');
173 e2.setSystemGenerated(true);
175 String expected = MessageManager.formatMessage("label.insert_gap", "1");
176 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
178 // 2 more gaps makes +3
179 Edit e3 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-');
181 Edit e4 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 2, '-');
182 e4.setSystemGenerated(true);
184 expected = MessageManager.formatMessage("label.insert_gaps", "3");
185 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
187 // 2 deletes makes + 1
188 Edit e5 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
190 Edit e6 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-');
191 e6.setSystemGenerated(true);
193 expected = MessageManager.formatMessage("label.insert_gap", "1");
194 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
196 // 1 more delete makes 0 - no text
197 Edit e7 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
199 Edit e8 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-');
200 e8.setSystemGenerated(true);
202 expected = MessageManager.formatMessage("label.insert_gaps", "2");
203 assertNull(SeqPanel.getEditStatusMessage(edit));
205 // 1 more delete makes 1 delete
206 Edit e9 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
208 Edit e10 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-');
209 e10.setSystemGenerated(true);
211 expected = MessageManager.formatMessage("label.delete_gap", "1");
212 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
214 // 2 more deletes makes 3 deletes
215 Edit e11 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
217 Edit e12 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-');
218 e12.setSystemGenerated(true);
220 expected = MessageManager.formatMessage("label.delete_gaps", "3");
221 assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
224 public void testFindMousePosition_unwrapped()
226 String seqData = ">Seq1\nAACDE\n>Seq2\nAA--E\n";
227 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(seqData,
228 DataSourceType.PASTE);
229 AlignViewportI av = alignFrame.getViewport();
230 av.setShowAnnotation(true);
231 av.setWrapAlignment(false);
232 final int charHeight = av.getCharHeight();
233 final int charWidth = av.getCharWidth();
235 assertTrue(charHeight > 0);
236 assertTrue(charWidth > 0);
237 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
239 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
244 * mouse at top left of unwrapped panel
246 MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
248 MousePos pos = testee.findMousePosition(evt);
249 assertEquals(pos.column, 0);
250 assertEquals(pos.seqIndex, 0);
251 assertEquals(pos.annotationIndex, -1);
254 @AfterMethod(alwaysRun = true)
255 public void tearDown()
257 Desktop.getInstance().closeAll_actionPerformed(null);
260 @Test(groups = "Functional")
261 public void testFindMousePosition_wrapped_annotations()
263 Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "true");
264 Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
265 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
266 "examples/uniref50.fa", DataSourceType.FILE);
267 AlignViewportI av = alignFrame.getViewport();
268 av.setScaleAboveWrapped(false);
269 av.setScaleLeftWrapped(false);
270 av.setScaleRightWrapped(false);
272 alignFrame.alignPanel.updateLayout();
274 final int charHeight = av.getCharHeight();
275 final int charWidth = av.getCharWidth();
276 final int alignmentHeight = av.getAlignment().getHeight();
279 assertTrue(charHeight > 0);
280 assertTrue(charWidth > 0);
281 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
283 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
288 * mouse at top left of wrapped panel; there is a gap of charHeight
289 * above the alignment
291 MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
293 MousePos pos = testee.findMousePosition(evt);
294 assertEquals(pos.column, 0);
295 assertEquals(pos.seqIndex, -1); // above sequences
296 assertEquals(pos.annotationIndex, -1);
299 * cursor at bottom of gap above
302 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
304 pos = testee.findMousePosition(evt);
305 assertEquals(pos.seqIndex, -1);
306 assertEquals(pos.annotationIndex, -1);
309 * cursor over top of first sequence
312 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
314 pos = testee.findMousePosition(evt);
315 assertEquals(pos.seqIndex, 0);
316 assertEquals(pos.annotationIndex, -1);
319 * cursor at bottom of first sequence
321 y = 2 * charHeight - 1;
322 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
324 pos = testee.findMousePosition(evt);
325 assertEquals(pos.seqIndex, 0);
326 assertEquals(pos.annotationIndex, -1);
329 * cursor at top of second sequence
332 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
334 pos = testee.findMousePosition(evt);
335 assertEquals(pos.seqIndex, 1);
336 assertEquals(pos.annotationIndex, -1);
339 * cursor at bottom of second sequence
341 y = 3 * charHeight - 1;
342 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
344 pos = testee.findMousePosition(evt);
345 assertEquals(pos.seqIndex, 1);
346 assertEquals(pos.annotationIndex, -1);
349 * cursor at bottom of last sequence
351 y = charHeight * (1 + alignmentHeight) - 1;
352 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
354 pos = testee.findMousePosition(evt);
355 assertEquals(pos.seqIndex, alignmentHeight - 1);
356 assertEquals(pos.annotationIndex, -1);
359 * cursor below sequences, in 3-pixel gap above annotations
360 * method reports index of nearest sequence above
363 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
365 pos = testee.findMousePosition(evt);
366 assertEquals(pos.seqIndex, alignmentHeight - 1);
367 assertEquals(pos.annotationIndex, -1);
370 * cursor still in the gap above annotations, now at the bottom of it
372 y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
373 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
375 pos = testee.findMousePosition(evt);
376 assertEquals(pos.seqIndex, alignmentHeight - 1);
377 assertEquals(pos.annotationIndex, -1);
379 AlignmentAnnotation[] annotationRows = av.getAlignment()
380 .getAlignmentAnnotation();
381 for (int n = 0; n < annotationRows.length; n++)
384 * cursor at the top of the n'th annotation
387 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
389 pos = testee.findMousePosition(evt);
390 assertEquals(pos.seqIndex, alignmentHeight - 1);
391 assertEquals(pos.annotationIndex, n); // over n'th annotation
394 * cursor at the bottom of the n'th annotation
396 y += annotationRows[n].height - 1;
397 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
399 pos = testee.findMousePosition(evt);
400 assertEquals(pos.seqIndex, alignmentHeight - 1);
401 assertEquals(pos.annotationIndex, n);
405 * cursor in gap between wrapped widths
408 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
410 pos = testee.findMousePosition(evt);
411 assertEquals(pos.seqIndex, -1);
412 assertEquals(pos.annotationIndex, -1);
415 * cursor at bottom of gap between wrapped widths
418 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
420 pos = testee.findMousePosition(evt);
421 assertEquals(pos.seqIndex, -1);
422 assertEquals(pos.annotationIndex, -1);
425 * cursor at top of first sequence, second wrapped width
428 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
430 pos = testee.findMousePosition(evt);
431 assertEquals(pos.seqIndex, 0);
432 assertEquals(pos.annotationIndex, -1);
435 @Test(groups = "Functional")
436 public void testFindMousePosition_wrapped_scaleAbove()
438 Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "true");
439 Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
440 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
441 "examples/uniref50.fa", DataSourceType.FILE);
442 AlignViewportI av = alignFrame.getViewport();
443 av.setScaleAboveWrapped(true);
444 av.setScaleLeftWrapped(false);
445 av.setScaleRightWrapped(false);
446 alignFrame.alignPanel.updateLayout();
448 final int charHeight = av.getCharHeight();
449 final int charWidth = av.getCharWidth();
450 final int alignmentHeight = av.getAlignment().getHeight();
453 assertTrue(charHeight > 0);
454 assertTrue(charWidth > 0);
455 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
457 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
462 * mouse at top left of wrapped panel; there is a gap of charHeight
463 * above the alignment
465 MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
467 MousePos pos = testee.findMousePosition(evt);
468 assertEquals(pos.column, 0);
469 assertEquals(pos.seqIndex, -1); // above sequences
470 assertEquals(pos.annotationIndex, -1);
473 * cursor at bottom of gap above
474 * two charHeights including scale panel
476 y = 2 * charHeight - 1;
477 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
479 pos = testee.findMousePosition(evt);
480 assertEquals(pos.seqIndex, -1);
481 assertEquals(pos.annotationIndex, -1);
484 * cursor over top of first sequence
487 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
489 pos = testee.findMousePosition(evt);
490 assertEquals(pos.seqIndex, 0);
491 assertEquals(pos.annotationIndex, -1);
494 * cursor at bottom of first sequence
497 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
499 pos = testee.findMousePosition(evt);
500 assertEquals(pos.seqIndex, 0);
501 assertEquals(pos.annotationIndex, -1);
504 * cursor at top of second sequence
507 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
509 pos = testee.findMousePosition(evt);
510 assertEquals(pos.seqIndex, 1);
511 assertEquals(pos.annotationIndex, -1);
514 * cursor at bottom of second sequence
517 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
519 pos = testee.findMousePosition(evt);
520 assertEquals(pos.seqIndex, 1);
521 assertEquals(pos.annotationIndex, -1);
524 * cursor at bottom of last sequence
525 * (scale + gap + sequences)
527 y = charHeight * (2 + alignmentHeight) - 1;
528 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
530 pos = testee.findMousePosition(evt);
531 assertEquals(pos.seqIndex, alignmentHeight - 1);
532 assertEquals(pos.annotationIndex, -1);
535 * cursor below sequences, in 3-pixel gap above annotations
538 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
540 pos = testee.findMousePosition(evt);
541 assertEquals(pos.seqIndex, alignmentHeight - 1);
542 assertEquals(pos.annotationIndex, -1);
545 * cursor still in the gap above annotations, now at the bottom of it
546 * method reports index of nearest sequence above
548 y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
549 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
551 pos = testee.findMousePosition(evt);
552 assertEquals(pos.seqIndex, alignmentHeight - 1);
553 assertEquals(pos.annotationIndex, -1);
555 AlignmentAnnotation[] annotationRows = av.getAlignment().getAlignmentAnnotation();
556 for (int n = 0; n < annotationRows.length; n++)
559 * cursor at the top of the n'th annotation
562 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
564 pos = testee.findMousePosition(evt);
565 assertEquals(pos.seqIndex, alignmentHeight - 1);
566 assertEquals(pos.annotationIndex, n); // over n'th annotation
569 * cursor at the bottom of the n'th annotation
571 y += annotationRows[n].height - 1;
572 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
574 pos = testee.findMousePosition(evt);
575 assertEquals(pos.seqIndex, alignmentHeight - 1);
576 assertEquals(pos.annotationIndex, n);
580 * cursor in gap between wrapped widths
583 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
585 pos = testee.findMousePosition(evt);
586 assertEquals(pos.seqIndex, -1);
587 assertEquals(pos.annotationIndex, -1);
590 * cursor at bottom of gap between wrapped widths
593 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
595 pos = testee.findMousePosition(evt);
596 assertEquals(pos.seqIndex, -1);
597 assertEquals(pos.annotationIndex, -1);
600 * cursor at top of scale, second wrapped width
603 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
605 pos = testee.findMousePosition(evt);
606 assertEquals(pos.seqIndex, -1);
607 assertEquals(pos.annotationIndex, -1);
610 * cursor at bottom of scale, second wrapped width
613 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
615 pos = testee.findMousePosition(evt);
616 assertEquals(pos.seqIndex, -1);
617 assertEquals(pos.annotationIndex, -1);
620 * cursor at top of first sequence, second wrapped width
623 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
625 pos = testee.findMousePosition(evt);
626 assertEquals(pos.seqIndex, 0);
627 assertEquals(pos.annotationIndex, -1);
630 @Test(groups = "Functional")
631 public void testFindMousePosition_wrapped_noAnnotations()
633 Cache.setPropertyNoSave("SHOW_ANNOTATIONS", "false");
634 Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
635 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
636 "examples/uniref50.fa", DataSourceType.FILE);
637 AlignViewportI av = alignFrame.getViewport();
638 av.setScaleAboveWrapped(false);
639 av.setScaleLeftWrapped(false);
640 av.setScaleRightWrapped(false);
641 alignFrame.alignPanel.updateLayout();
643 final int charHeight = av.getCharHeight();
644 final int charWidth = av.getCharWidth();
645 final int alignmentHeight = av.getAlignment().getHeight();
648 assertTrue(charHeight > 0);
649 assertTrue(charWidth > 0);
650 assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
652 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
657 * mouse at top left of wrapped panel; there is a gap of charHeight
658 * above the alignment
660 MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
662 MousePos pos = testee.findMousePosition(evt);
663 assertEquals(pos.column, 0);
664 assertEquals(pos.seqIndex, -1); // above sequences
665 assertEquals(pos.annotationIndex, -1);
668 * cursor over top of first sequence
671 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
673 pos = testee.findMousePosition(evt);
674 assertEquals(pos.seqIndex, 0);
675 assertEquals(pos.annotationIndex, -1);
678 * cursor at bottom of last sequence
680 y = charHeight * (1 + alignmentHeight) - 1;
681 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
683 pos = testee.findMousePosition(evt);
684 assertEquals(pos.seqIndex, alignmentHeight - 1);
685 assertEquals(pos.annotationIndex, -1);
688 * cursor below sequences, at top of charHeight gap between widths
691 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
693 pos = testee.findMousePosition(evt);
694 assertEquals(pos.seqIndex, -1);
695 assertEquals(pos.annotationIndex, -1);
698 * cursor below sequences, at top of charHeight gap between widths
701 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
703 pos = testee.findMousePosition(evt);
704 assertEquals(pos.seqIndex, -1);
705 assertEquals(pos.annotationIndex, -1);
708 * cursor at the top of the first sequence, second width
711 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
713 pos = testee.findMousePosition(evt);
714 assertEquals(pos.seqIndex, 0);
715 assertEquals(pos.annotationIndex, -1);
718 @Test(groups = "Functional")
719 public void testFindColumn_unwrapped()
721 Cache.setPropertyNoSave("WRAP_ALIGNMENT", "false");
722 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
723 "examples/uniref50.fa", DataSourceType.FILE);
724 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
726 final int charWidth = alignFrame.getViewport().getCharWidth();
727 assertTrue(charWidth > 0); // sanity check
728 assertEquals(alignFrame.getViewport().getRanges().getStartRes(), 0);
730 * mouse at top left of unwrapped panel
732 MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
734 assertEquals(testee.findColumn(evt), 0);
737 * not quite one charWidth across
740 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
742 assertEquals(testee.findColumn(evt), 0);
745 * one charWidth across
748 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
750 assertEquals(testee.findColumn(evt), 1);
753 * two charWidths across
756 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
758 assertEquals(testee.findColumn(evt), 2);
761 * limited to last column of seqcanvas
764 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
766 SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
767 int w = seqCanvas.getWidth();
768 // limited to number of whole columns, base 0
770 int expected = w / charWidth;
772 alignFrame.getViewport().getRanges().getEndRes(),
774 int col = testee.findColumn(evt);
775 assertEquals(col, expected);
778 * hide columns 5-10 (base 1)
780 alignFrame.getViewport().hideColumns(4, 9);
781 x = 5 * charWidth + 2;
782 // x is in 6th visible column, absolute column 12, or 11 base 0
783 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
785 col = testee.findColumn(evt);
786 assertEquals(col, 11);
789 @Test(groups = "Functional")
790 public void testFindColumn_wrapped()
792 Cache.setPropertyNoSave("WRAP_ALIGNMENT", "true");
793 AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
794 "examples/uniref50.fa", DataSourceType.FILE);
795 AlignViewport av = alignFrame.getViewport();
796 av.setScaleAboveWrapped(false);
797 av.setScaleLeftWrapped(false);
798 av.setScaleRightWrapped(false);
799 alignFrame.alignPanel.updateLayout();
800 SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
802 final int charWidth = av.getCharWidth();
803 assertTrue(charWidth > 0); // sanity check
804 assertEquals(av.getRanges().getStartRes(), 0);
807 * mouse at top left of wrapped panel, no West (left) scale
809 MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
811 assertEquals(testee.findColumn(evt), 0);
814 * not quite one charWidth across
817 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0,
819 assertEquals(testee.findColumn(evt), 0);
822 * one charWidth across
825 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
827 assertEquals(testee.findColumn(evt), 1);
830 * x over scale left (before drawn columns) results in -1
832 av.setScaleLeftWrapped(true);
833 alignFrame.alignPanel.updateLayout();
834 SeqCanvas seqCanvas = testee.seqCanvas;
835 int labelWidth = (int) PA.getValue(seqCanvas, "labelWidthWest");
836 assertTrue(labelWidth > 0);
838 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
840 assertEquals(testee.findColumn(evt), -1);
843 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
845 assertEquals(testee.findColumn(evt), 0);
848 * x over right edge of last residue (including scale left)
850 int residuesWide = av.getRanges().getViewportWidth();
851 assertTrue(residuesWide > 0);
852 x = labelWidth + charWidth * residuesWide - 1;
853 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
855 assertEquals(testee.findColumn(evt), residuesWide - 1);
858 * x over scale right (beyond drawn columns) results in -1
860 av.setScaleRightWrapped(true);
861 alignFrame.alignPanel.updateLayout();
862 labelWidth = (int) PA.getValue(seqCanvas, "labelWidthEast");
863 assertTrue(labelWidth > 0);
864 int residuesWide2 = av.getRanges().getViewportWidth();
865 assertTrue(residuesWide2 > 0);
866 assertTrue(residuesWide2 < residuesWide); // available width reduced
867 x += 1; // just over left edge of scale right
868 evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, 0, 0, 0, 0,
870 assertEquals(testee.findColumn(evt), -1);
872 // todo add startRes offset, hidden columns
875 @BeforeClass(alwaysRun = true)
876 public static void setUpBeforeClass() throws Exception
879 * use read-only test properties file
881 Cache.loadProperties("test/jalview/io/testProps.jvprops");
882 Jalview.main(new String[] { "-nonews" });
886 * waits for Swing event dispatch queue to empty
888 synchronized void waitForSwing()
892 EventQueue.invokeAndWait(new Runnable()
899 } catch (InterruptedException | InvocationTargetException e)