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AnnotationLabels | 81 | 578 | 244 |
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 java.awt.Canvas; | |
24 | import java.awt.Color; | |
25 | import java.awt.Cursor; | |
26 | import java.awt.Dimension; | |
27 | import java.awt.Font; | |
28 | import java.awt.FontMetrics; | |
29 | import java.awt.Graphics; | |
30 | import java.awt.Graphics2D; | |
31 | import java.awt.RenderingHints; | |
32 | import java.awt.Toolkit; | |
33 | import java.awt.datatransfer.StringSelection; | |
34 | import java.awt.event.ActionEvent; | |
35 | import java.awt.event.ActionListener; | |
36 | import java.awt.event.MouseEvent; | |
37 | import java.awt.event.MouseListener; | |
38 | import java.awt.event.MouseMotionListener; | |
39 | import java.awt.geom.AffineTransform; | |
40 | import java.util.Arrays; | |
41 | import java.util.Collections; | |
42 | import java.util.Iterator; | |
43 | import java.util.List; | |
44 | import java.util.Locale; | |
45 | ||
46 | import javax.swing.JCheckBoxMenuItem; | |
47 | import javax.swing.JMenuItem; | |
48 | import javax.swing.JPanel; | |
49 | import javax.swing.JPopupMenu; | |
50 | import javax.swing.SwingUtilities; | |
51 | import javax.swing.ToolTipManager; | |
52 | ||
53 | import jalview.analysis.AlignSeq; | |
54 | import jalview.analysis.AlignmentUtils; | |
55 | import jalview.api.AlignCalcWorkerI; | |
56 | import jalview.bin.Cache; | |
57 | import jalview.bin.Jalview; | |
58 | import jalview.datamodel.Alignment; | |
59 | import jalview.datamodel.AlignmentAnnotation; | |
60 | import jalview.datamodel.Annotation; | |
61 | import jalview.datamodel.ContactMatrixI; | |
62 | import jalview.datamodel.GroupSet; | |
63 | import jalview.datamodel.HiddenColumns; | |
64 | import jalview.datamodel.Sequence; | |
65 | import jalview.datamodel.SequenceGroup; | |
66 | import jalview.datamodel.SequenceI; | |
67 | import jalview.io.FileFormat; | |
68 | import jalview.io.FormatAdapter; | |
69 | import jalview.util.Comparison; | |
70 | import jalview.util.Constants; | |
71 | import jalview.util.MessageManager; | |
72 | import jalview.util.ParseHtmlBodyAndLinks; | |
73 | import jalview.util.Platform; | |
74 | import jalview.workers.SecondaryStructureConsensusThread; | |
75 | ||
76 | /** | |
77 | * The panel that holds the labels for alignment annotations, providing | |
78 | * tooltips, context menus, drag to reorder rows, and drag to adjust panel | |
79 | * height | |
80 | */ | |
81 | public class AnnotationLabels extends JPanel | |
82 | implements MouseListener, MouseMotionListener, ActionListener | |
83 | { | |
84 | private static final String HTML_END_TAG = "</html>"; | |
85 | ||
86 | private static final String HTML_START_TAG = "<html>"; | |
87 | ||
88 | /** | |
89 | * width in pixels within which height adjuster arrows are shown and active | |
90 | */ | |
91 | private static final int HEIGHT_ADJUSTER_WIDTH = 50; | |
92 | ||
93 | /** | |
94 | * height in pixels for allowing height adjuster to be active | |
95 | */ | |
96 | public static int HEIGHT_ADJUSTER_HEIGHT = 10; | |
97 | ||
98 | private static final Font font = new Font("Arial", Font.PLAIN, 11); | |
99 | ||
100 | private static final String TOGGLE_LABELSCALE = MessageManager | |
101 | .getString("label.scale_label_to_column"); | |
102 | ||
103 | private static final String ADDNEW = MessageManager | |
104 | .getString("label.add_new_row"); | |
105 | ||
106 | private static final String EDITNAME = MessageManager | |
107 | .getString("label.edit_label_description"); | |
108 | ||
109 | private static final String HIDE = MessageManager | |
110 | .getString("label.hide_row"); | |
111 | ||
112 | private static final String DELETE = MessageManager | |
113 | .getString("label.delete_row"); | |
114 | ||
115 | private static final String SHOWALL = MessageManager | |
116 | .getString("label.show_all_hidden_rows"); | |
117 | ||
118 | private static final String OUTPUT_TEXT = MessageManager | |
119 | .getString("label.export_annotation"); | |
120 | ||
121 | private static final String COPYCONS_SEQ = MessageManager | |
122 | .getString("label.copy_consensus_sequence"); | |
123 | ||
124 | private static final String ADJUST_ANNOTATION_LABELS_WIDTH_PREF = "ADJUST_ANNOTATION_LABELS_WIDTH"; | |
125 | ||
126 | private final boolean debugRedraw = false; | |
127 | ||
128 | private AlignmentPanel ap; | |
129 | ||
130 | AlignViewport av; | |
131 | ||
132 | private MouseEvent dragEvent; | |
133 | ||
134 | private int oldY; | |
135 | ||
136 | private int selectedRow; | |
137 | ||
138 | private int scrollOffset = 0; | |
139 | ||
140 | private boolean hasHiddenRows; | |
141 | ||
142 | private boolean resizePanel = false; | |
143 | ||
144 | private int annotationIdWidth = -1; | |
145 | ||
146 | public static final String RESIZE_MARGINS_MARK_PREF = "RESIZE_MARGINS_MARK"; | |
147 | ||
148 | /** | |
149 | * Creates a new AnnotationLabels object | |
150 | * | |
151 | * @param ap | |
152 | */ | |
153 | 478 | public AnnotationLabels(AlignmentPanel ap) |
154 | { | |
155 | 478 | this.ap = ap; |
156 | 478 | av = ap.av; |
157 | 478 | ToolTipManager.sharedInstance().registerComponent(this); |
158 | ||
159 | 478 | addMouseListener(this); |
160 | 478 | addMouseMotionListener(this); |
161 | 478 | addMouseWheelListener(ap.getAnnotationPanel()); |
162 | } | |
163 | ||
164 | 604 | public AnnotationLabels(AlignViewport av) |
165 | { | |
166 | 604 | this.av = av; |
167 | } | |
168 | ||
169 | /** | |
170 | * DOCUMENT ME! | |
171 | * | |
172 | * @param y | |
173 | * DOCUMENT ME! | |
174 | */ | |
175 | 905 | public void setScrollOffset(int y) |
176 | { | |
177 | 905 | scrollOffset = y; |
178 | 905 | repaint(); |
179 | } | |
180 | ||
181 | /** | |
182 | * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at | |
183 | * y | |
184 | * | |
185 | * @param y | |
186 | * coordinate position to search for a row | |
187 | */ | |
188 | 0 | void getSelectedRow(int y) |
189 | { | |
190 | 0 | int height = 0; |
191 | 0 | AlignmentAnnotation[] aa = ap.av.getAlignment() |
192 | .getAlignmentAnnotation(); | |
193 | 0 | selectedRow = -2; |
194 | 0 | if (aa != null) |
195 | { | |
196 | 0 | for (int i = 0; i < aa.length; i++) |
197 | { | |
198 | 0 | selectedRow = -1; |
199 | 0 | if (!aa[i].visible) |
200 | { | |
201 | 0 | continue; |
202 | } | |
203 | ||
204 | 0 | height += aa[i].height; |
205 | ||
206 | 0 | if (y < height) |
207 | { | |
208 | 0 | selectedRow = i; |
209 | ||
210 | 0 | break; |
211 | } | |
212 | } | |
213 | } | |
214 | } | |
215 | ||
216 | /** | |
217 | * DOCUMENT ME! | |
218 | * | |
219 | * @param evt | |
220 | * DOCUMENT ME! | |
221 | */ | |
222 | 0 | @Override |
223 | public void actionPerformed(ActionEvent evt) | |
224 | { | |
225 | 0 | AlignmentAnnotation[] aa = ap.av.getAlignment() |
226 | .getAlignmentAnnotation(); | |
227 | ||
228 | 0 | String action = evt.getActionCommand(); |
229 | 0 | if (ADDNEW.equals(action)) |
230 | { | |
231 | /* | |
232 | * non-returning dialog | |
233 | */ | |
234 | 0 | AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, |
235 | null, new Annotation[ap.av.getAlignment().getWidth()]); | |
236 | 0 | editLabelDescription(newAnnotation, true); |
237 | } | |
238 | 0 | else if (EDITNAME.equals(action)) |
239 | { | |
240 | /* | |
241 | * non-returning dialog | |
242 | */ | |
243 | 0 | editLabelDescription(aa[selectedRow], false); |
244 | } | |
245 | 0 | else if (HIDE.equals(action)) |
246 | { | |
247 | 0 | aa[selectedRow].visible = false; |
248 | } | |
249 | 0 | else if (DELETE.equals(action)) |
250 | { | |
251 | 0 | ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); |
252 | 0 | ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); |
253 | ||
254 | 0 | List<AlignCalcWorkerI> workers = ap.av.getCalcManager() |
255 | .getRegisteredWorkersOfClass( | |
256 | SecondaryStructureConsensusThread.class); | |
257 | 0 | if (!workers.isEmpty()) |
258 | { | |
259 | ||
260 | 0 | ap.alignFrame.getViewport().getCalcManager() |
261 | .startWorker(workers.remove(0)); | |
262 | ||
263 | } | |
264 | } | |
265 | 0 | else if (SHOWALL.equals(action)) |
266 | { | |
267 | 0 | for (int i = 0; i < aa.length; i++) |
268 | { | |
269 | 0 | if (!aa[i].visible && aa[i].annotations != null) |
270 | { | |
271 | 0 | aa[i].visible = true; |
272 | } | |
273 | } | |
274 | } | |
275 | 0 | else if (OUTPUT_TEXT.equals(action)) |
276 | { | |
277 | 0 | new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); |
278 | } | |
279 | 0 | else if (COPYCONS_SEQ.equals(action)) |
280 | { | |
281 | 0 | SequenceI cons = null; |
282 | 0 | if (aa[selectedRow].groupRef != null) |
283 | { | |
284 | 0 | cons = aa[selectedRow].groupRef.getConsensusSeq(); |
285 | } | |
286 | else | |
287 | { | |
288 | 0 | cons = av.getConsensusSeq(); |
289 | } | |
290 | 0 | if (cons != null) |
291 | { | |
292 | 0 | copy_annotseqtoclipboard(cons); |
293 | } | |
294 | } | |
295 | 0 | else if (TOGGLE_LABELSCALE.equals(action)) |
296 | { | |
297 | 0 | aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; |
298 | } | |
299 | ||
300 | 0 | ap.refresh(true); |
301 | } | |
302 | ||
303 | /** | |
304 | * Shows a dialog where the annotation name and description may be edited. If | |
305 | * parameter addNew is true, then on confirmation, a new AlignmentAnnotation | |
306 | * is added, else an existing annotation is updated. | |
307 | * | |
308 | * @param annotation | |
309 | * @param addNew | |
310 | */ | |
311 | 0 | void editLabelDescription(AlignmentAnnotation annotation, boolean addNew) |
312 | { | |
313 | 0 | String name = MessageManager.getString("label.annotation_name"); |
314 | 0 | String description = MessageManager |
315 | .getString("label.annotation_description"); | |
316 | 0 | String title = MessageManager |
317 | .getString("label.edit_annotation_name_description"); | |
318 | 0 | EditNameDialog dialog = new EditNameDialog(annotation.label, |
319 | annotation.description, name, description); | |
320 | ||
321 | 0 | dialog.showDialog(ap.alignFrame, title, () -> { |
322 | 0 | annotation.label = dialog.getName(); |
323 | 0 | String text = dialog.getDescription(); |
324 | 0 | if (text != null && text.length() == 0) |
325 | { | |
326 | 0 | text = null; |
327 | } | |
328 | 0 | annotation.description = text; |
329 | 0 | if (addNew) |
330 | { | |
331 | 0 | ap.av.getAlignment().addAnnotation(annotation); |
332 | 0 | ap.av.getAlignment().setAnnotationIndex(annotation, 0); |
333 | } | |
334 | 0 | ap.refresh(true); |
335 | }); | |
336 | } | |
337 | ||
338 | 0 | @Override |
339 | public void mousePressed(MouseEvent evt) | |
340 | { | |
341 | 0 | getSelectedRow(evt.getY() - getScrollOffset()); |
342 | 0 | oldY = evt.getY(); |
343 | 0 | if (evt.isPopupTrigger()) |
344 | { | |
345 | 0 | showPopupMenu(evt); |
346 | } | |
347 | } | |
348 | ||
349 | /** | |
350 | * Build and show the Pop-up menu at the right-click mouse position | |
351 | * | |
352 | * @param evt | |
353 | */ | |
354 | 0 | void showPopupMenu(MouseEvent evt) |
355 | { | |
356 | 0 | evt.consume(); |
357 | 0 | final AlignmentAnnotation[] aa = ap.av.getAlignment() |
358 | .getAlignmentAnnotation(); | |
359 | ||
360 | 0 | JPopupMenu pop = new JPopupMenu( |
361 | MessageManager.getString("label.annotations")); | |
362 | 0 | JMenuItem item = new JMenuItem(ADDNEW); |
363 | 0 | item.addActionListener(this); |
364 | 0 | pop.add(item); |
365 | 0 | if (selectedRow < 0) |
366 | { | |
367 | 0 | if (hasHiddenRows) |
368 | { // let the user make everything visible again | |
369 | 0 | item = new JMenuItem(SHOWALL); |
370 | 0 | item.addActionListener(this); |
371 | 0 | pop.add(item); |
372 | } | |
373 | 0 | pop.show(this, evt.getX(), evt.getY()); |
374 | 0 | return; |
375 | } | |
376 | 0 | item = new JMenuItem(EDITNAME); |
377 | 0 | item.addActionListener(this); |
378 | 0 | pop.add(item); |
379 | 0 | item = new JMenuItem(HIDE); |
380 | 0 | item.addActionListener(this); |
381 | 0 | pop.add(item); |
382 | // JAL-1264 hide all sequence-specific annotations of this type | |
383 | 0 | if (selectedRow < aa.length) |
384 | { | |
385 | 0 | if (aa[selectedRow].sequenceRef != null) |
386 | { | |
387 | 0 | final String label = aa[selectedRow].label; |
388 | 0 | JMenuItem hideType = new JMenuItem(); |
389 | 0 | String text = MessageManager.getString("label.hide_all") + " " |
390 | + label; | |
391 | 0 | hideType.setText(text); |
392 | 0 | hideType.addActionListener(new ActionListener() |
393 | { | |
394 | 0 | @Override |
395 | public void actionPerformed(ActionEvent e) | |
396 | { | |
397 | 0 | AlignmentUtils.showOrHideSequenceAnnotations( |
398 | ap.av.getAlignment(), Collections.singleton(label), | |
399 | null, false, false); | |
400 | 0 | ap.refresh(true); |
401 | } | |
402 | }); | |
403 | 0 | pop.add(hideType); |
404 | } | |
405 | } | |
406 | 0 | item = new JMenuItem(DELETE); |
407 | 0 | item.addActionListener(this); |
408 | 0 | pop.add(item); |
409 | 0 | if (hasHiddenRows) |
410 | { | |
411 | 0 | item = new JMenuItem(SHOWALL); |
412 | 0 | item.addActionListener(this); |
413 | 0 | pop.add(item); |
414 | } | |
415 | 0 | item = new JMenuItem(OUTPUT_TEXT); |
416 | 0 | item.addActionListener(this); |
417 | 0 | pop.add(item); |
418 | // TODO: annotation object should be typed for autocalculated/derived | |
419 | // property methods | |
420 | 0 | if (selectedRow < aa.length) |
421 | { | |
422 | 0 | final String label = aa[selectedRow].label; |
423 | 0 | if (!aa[selectedRow].autoCalculated) |
424 | { | |
425 | 0 | if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) |
426 | { | |
427 | // display formatting settings for this row. | |
428 | 0 | pop.addSeparator(); |
429 | // av and sequencegroup need to implement same interface for | |
430 | 0 | item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, |
431 | aa[selectedRow].scaleColLabel); | |
432 | 0 | item.addActionListener(this); |
433 | 0 | pop.add(item); |
434 | } | |
435 | } | |
436 | 0 | else if (label.indexOf("Consensus") > -1) |
437 | { | |
438 | 0 | addConsensusMenuOptions(ap, aa[selectedRow], pop); |
439 | ||
440 | 0 | final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); |
441 | 0 | consclipbrd.addActionListener(this); |
442 | 0 | pop.add(consclipbrd); |
443 | } | |
444 | ||
445 | 0 | addColourOrFilterByOptions(ap, aa[selectedRow], pop); |
446 | ||
447 | 0 | if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP) |
448 | { | |
449 | 0 | addContactMatrixOptions(ap, aa[selectedRow], pop); |
450 | // Set/adjust threshold for grouping ? | |
451 | // colour alignment by this [type] | |
452 | // select/hide columns by this row | |
453 | ||
454 | } | |
455 | } | |
456 | ||
457 | 0 | pop.show(this, evt.getX(), evt.getY()); |
458 | } | |
459 | ||
460 | 0 | static void addColourOrFilterByOptions(final AlignmentPanel ap, |
461 | final AlignmentAnnotation alignmentAnnotation, | |
462 | final JPopupMenu pop) | |
463 | { | |
464 | 0 | JMenuItem item; |
465 | 0 | item = new JMenuItem( |
466 | MessageManager.getString("label.colour_by_annotation")); | |
467 | 0 | item.addActionListener(new ActionListener() |
468 | { | |
469 | ||
470 | 0 | @Override |
471 | public void actionPerformed(ActionEvent e) | |
472 | { | |
473 | 0 | AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, |
474 | false); | |
475 | }; | |
476 | }); | |
477 | 0 | pop.add(item); |
478 | 0 | if (alignmentAnnotation.sequenceRef != null) |
479 | { | |
480 | 0 | item = new JMenuItem( |
481 | MessageManager.getString("label.colour_by_annotation") + " (" | |
482 | + MessageManager.getString("label.per_seq") + ")"); | |
483 | 0 | item.addActionListener(new ActionListener() |
484 | { | |
485 | 0 | @Override |
486 | public void actionPerformed(ActionEvent e) | |
487 | { | |
488 | 0 | AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, |
489 | true); | |
490 | }; | |
491 | }); | |
492 | 0 | pop.add(item); |
493 | } | |
494 | 0 | item = new JMenuItem( |
495 | MessageManager.getString("action.select_by_annotation")); | |
496 | 0 | item.addActionListener(new ActionListener() |
497 | { | |
498 | ||
499 | 0 | @Override |
500 | public void actionPerformed(ActionEvent e) | |
501 | { | |
502 | 0 | AnnotationColumnChooser.displayFor(ap.av, ap, alignmentAnnotation); |
503 | }; | |
504 | }); | |
505 | 0 | pop.add(item); |
506 | } | |
507 | ||
508 | 0 | static void addContactMatrixOptions(final AlignmentPanel ap, |
509 | final AlignmentAnnotation alignmentAnnotation, | |
510 | final JPopupMenu pop) | |
511 | { | |
512 | ||
513 | 0 | final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation); |
514 | 0 | JMenuItem item; |
515 | 0 | if (cm != null) |
516 | { | |
517 | 0 | pop.addSeparator(); |
518 | ||
519 | 0 | if (cm.hasGroups()) |
520 | { | |
521 | 0 | JCheckBoxMenuItem chitem = new JCheckBoxMenuItem( |
522 | MessageManager.getString("action.show_groups_on_matrix")); | |
523 | 0 | chitem.setToolTipText(MessageManager |
524 | .getString("action.show_groups_on_matrix_tooltip")); | |
525 | 0 | boolean showGroups = alignmentAnnotation |
526 | .isShowGroupsForContactMatrix(); | |
527 | 0 | final AlignmentAnnotation sel_row = alignmentAnnotation; |
528 | 0 | chitem.setState(showGroups); |
529 | 0 | chitem.addActionListener(new ActionListener() |
530 | { | |
531 | ||
532 | 0 | @Override |
533 | public void actionPerformed(ActionEvent e) | |
534 | { | |
535 | 0 | sel_row.setShowGroupsForContactMatrix(chitem.getState()); |
536 | // so any annotation colour changes are propagated - though they | |
537 | // probably won't be unless the annotation row colours are removed | |
538 | // too! | |
539 | 0 | ap.alignmentChanged(); |
540 | } | |
541 | }); | |
542 | 0 | pop.add(chitem); |
543 | } | |
544 | 0 | if (cm.hasTree()) |
545 | { | |
546 | 0 | item = new JMenuItem( |
547 | MessageManager.getString("action.show_tree_for_matrix")); | |
548 | 0 | item.setToolTipText(MessageManager |
549 | .getString("action.show_tree_for_matrix_tooltip")); | |
550 | 0 | item.addActionListener(new ActionListener() |
551 | { | |
552 | ||
553 | 0 | @Override |
554 | public void actionPerformed(ActionEvent e) | |
555 | { | |
556 | ||
557 | 0 | ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); |
558 | ||
559 | } | |
560 | }); | |
561 | 0 | pop.add(item); |
562 | } | |
563 | else | |
564 | { | |
565 | 0 | item = new JMenuItem( |
566 | MessageManager.getString("action.cluster_matrix")); | |
567 | 0 | item.setToolTipText( |
568 | MessageManager.getString("action.cluster_matrix_tooltip")); | |
569 | 0 | item.addActionListener(new ActionListener() |
570 | { | |
571 | 0 | @Override |
572 | public void actionPerformed(ActionEvent e) | |
573 | { | |
574 | 0 | new Thread(new Runnable() |
575 | { | |
576 | 0 | @Override |
577 | public void run() | |
578 | { | |
579 | 0 | final long progBar; |
580 | 0 | ap.alignFrame.setProgressBar( |
581 | MessageManager.formatMessage( | |
582 | "action.clustering_matrix_for", | |
583 | cm.getAnnotDescr(), 5f), | |
584 | progBar = System.currentTimeMillis()); | |
585 | 0 | cm.setGroupSet(GroupSet.makeGroups(cm, true)); |
586 | 0 | cm.randomlyReColourGroups(); |
587 | 0 | cm.transferGroupColorsTo(alignmentAnnotation); |
588 | 0 | ap.alignmentChanged(); |
589 | 0 | ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); |
590 | 0 | ap.alignFrame.setProgressBar(null, progBar); |
591 | } | |
592 | }).start(); | |
593 | } | |
594 | }); | |
595 | 0 | pop.add(item); |
596 | } | |
597 | } | |
598 | } | |
599 | ||
600 | /** | |
601 | * A helper method that adds menu options for calculation and visualisation of | |
602 | * group and/or alignment consensus annotation to a popup menu. This is | |
603 | * designed to be reusable for either unwrapped mode (popup menu is shown on | |
604 | * component AnnotationLabels), or wrapped mode (popup menu is shown on | |
605 | * IdPanel when the mouse is over an annotation label). | |
606 | * | |
607 | * @param ap | |
608 | * @param ann | |
609 | * @param pop | |
610 | */ | |
611 | 0 | static void addConsensusMenuOptions(AlignmentPanel ap, |
612 | AlignmentAnnotation ann, JPopupMenu pop) | |
613 | { | |
614 | 0 | pop.addSeparator(); |
615 | ||
616 | 0 | final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( |
617 | MessageManager.getString("label.ignore_gaps_consensus"), | |
618 | 0 | (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus() |
619 | : ap.av.isIgnoreGapsConsensus()); | |
620 | 0 | final AlignmentAnnotation aaa = ann; |
621 | 0 | cbmi.addActionListener(new ActionListener() |
622 | { | |
623 | 0 | @Override |
624 | public void actionPerformed(ActionEvent e) | |
625 | { | |
626 | 0 | if (aaa.groupRef != null) |
627 | { | |
628 | 0 | aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); |
629 | 0 | ap.getAnnotationPanel() |
630 | .paint(ap.getAnnotationPanel().getGraphics()); | |
631 | } | |
632 | else | |
633 | { | |
634 | 0 | ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); |
635 | } | |
636 | 0 | ap.alignmentChanged(); |
637 | } | |
638 | }); | |
639 | 0 | pop.add(cbmi); |
640 | ||
641 | 0 | if (aaa.groupRef != null) |
642 | { | |
643 | /* | |
644 | * group consensus options | |
645 | */ | |
646 | 0 | final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( |
647 | MessageManager.getString("label.show_group_histogram"), | |
648 | ann.groupRef.isShowConsensusHistogram()); | |
649 | 0 | chist.addActionListener(new ActionListener() |
650 | { | |
651 | 0 | @Override |
652 | public void actionPerformed(ActionEvent e) | |
653 | { | |
654 | 0 | aaa.groupRef.setShowConsensusHistogram(chist.getState()); |
655 | 0 | ap.repaint(); |
656 | } | |
657 | }); | |
658 | 0 | pop.add(chist); |
659 | 0 | final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( |
660 | MessageManager.getString("label.show_group_logo"), | |
661 | ann.groupRef.isShowSequenceLogo()); | |
662 | 0 | cprofl.addActionListener(new ActionListener() |
663 | { | |
664 | 0 | @Override |
665 | public void actionPerformed(ActionEvent e) | |
666 | { | |
667 | 0 | aaa.groupRef.setshowSequenceLogo(cprofl.getState()); |
668 | 0 | ap.repaint(); |
669 | } | |
670 | }); | |
671 | 0 | pop.add(cprofl); |
672 | 0 | final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( |
673 | MessageManager.getString("label.normalise_group_logo"), | |
674 | ann.groupRef.isNormaliseSequenceLogo()); | |
675 | 0 | cproflnorm.addActionListener(new ActionListener() |
676 | { | |
677 | 0 | @Override |
678 | public void actionPerformed(ActionEvent e) | |
679 | { | |
680 | 0 | aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); |
681 | // automatically enable logo display if we're clicked | |
682 | 0 | aaa.groupRef.setshowSequenceLogo(true); |
683 | 0 | ap.repaint(); |
684 | } | |
685 | }); | |
686 | 0 | pop.add(cproflnorm); |
687 | } | |
688 | else | |
689 | { | |
690 | /* | |
691 | * alignment consensus options | |
692 | */ | |
693 | 0 | final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( |
694 | MessageManager.getString("label.show_histogram"), | |
695 | ap.av.isShowConsensusHistogram()); | |
696 | 0 | chist.addActionListener(new ActionListener() |
697 | { | |
698 | 0 | @Override |
699 | public void actionPerformed(ActionEvent e) | |
700 | { | |
701 | 0 | ap.av.setShowConsensusHistogram(chist.getState()); |
702 | 0 | ap.alignFrame.setMenusForViewport(); |
703 | 0 | ap.repaint(); |
704 | } | |
705 | }); | |
706 | 0 | pop.add(chist); |
707 | 0 | final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( |
708 | MessageManager.getString("label.show_logo"), | |
709 | ap.av.isShowSequenceLogo()); | |
710 | 0 | cprof.addActionListener(new ActionListener() |
711 | { | |
712 | 0 | @Override |
713 | public void actionPerformed(ActionEvent e) | |
714 | { | |
715 | 0 | ap.av.setShowSequenceLogo(cprof.getState()); |
716 | 0 | ap.alignFrame.setMenusForViewport(); |
717 | 0 | ap.repaint(); |
718 | } | |
719 | }); | |
720 | 0 | pop.add(cprof); |
721 | 0 | final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( |
722 | MessageManager.getString("label.normalise_logo"), | |
723 | ap.av.isNormaliseSequenceLogo()); | |
724 | 0 | cprofnorm.addActionListener(new ActionListener() |
725 | { | |
726 | 0 | @Override |
727 | public void actionPerformed(ActionEvent e) | |
728 | { | |
729 | 0 | ap.av.setShowSequenceLogo(true); |
730 | 0 | ap.av.setNormaliseSequenceLogo(cprofnorm.getState()); |
731 | 0 | ap.alignFrame.setMenusForViewport(); |
732 | 0 | ap.repaint(); |
733 | } | |
734 | }); | |
735 | 0 | pop.add(cprofnorm); |
736 | } | |
737 | } | |
738 | ||
739 | /** | |
740 | * Reorders annotation rows after a drag of a label | |
741 | * | |
742 | * @param evt | |
743 | */ | |
744 | 0 | @Override |
745 | public void mouseReleased(MouseEvent evt) | |
746 | { | |
747 | 0 | if (evt.isPopupTrigger()) |
748 | { | |
749 | 0 | showPopupMenu(evt); |
750 | 0 | return; |
751 | } | |
752 | ||
753 | 0 | int start = selectedRow; |
754 | 0 | getSelectedRow(evt.getY() - getScrollOffset()); |
755 | 0 | int end = selectedRow; |
756 | ||
757 | /* | |
758 | * if dragging to resize instead, start == end | |
759 | */ | |
760 | 0 | if (start != end) |
761 | { | |
762 | // Swap these annotations | |
763 | 0 | AlignmentAnnotation startAA = ap.av.getAlignment() |
764 | .getAlignmentAnnotation()[start]; | |
765 | 0 | if (end == -1) |
766 | { | |
767 | 0 | end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; |
768 | } | |
769 | 0 | AlignmentAnnotation endAA = ap.av.getAlignment() |
770 | .getAlignmentAnnotation()[end]; | |
771 | ||
772 | 0 | ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; |
773 | 0 | ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; |
774 | } | |
775 | ||
776 | 0 | resizePanel = false; |
777 | 0 | dragEvent = null; |
778 | 0 | repaint(); |
779 | 0 | ap.getAnnotationPanel().repaint(); |
780 | } | |
781 | ||
782 | /** | |
783 | * Removes the height adjuster image on leaving the panel, unless currently | |
784 | * dragging it | |
785 | */ | |
786 | 0 | @Override |
787 | public void mouseExited(MouseEvent evt) | |
788 | { | |
789 | 0 | if (resizePanel && dragEvent == null) |
790 | { | |
791 | 0 | resizePanel = false; |
792 | 0 | repaint(); |
793 | } | |
794 | } | |
795 | ||
796 | /** | |
797 | * A mouse drag may be either an adjustment of the panel height (if flag | |
798 | * resizePanel is set on), or a reordering of the annotation rows. The former | |
799 | * is dealt with by this method, the latter in mouseReleased. | |
800 | * | |
801 | * @param evt | |
802 | */ | |
803 | 0 | @Override |
804 | public void mouseDragged(MouseEvent evt) | |
805 | { | |
806 | 0 | dragEvent = evt; |
807 | ||
808 | 0 | if (resizePanel) |
809 | { | |
810 | 0 | Dimension d = ap.annotationScroller.getPreferredSize(); |
811 | 0 | int dif = evt.getY() - oldY; |
812 | 0 | dif -= dif % ap.av.getCharHeight(); |
813 | ||
814 | // don't allow setting an annotation panel height larger than visible | |
815 | // (otherwise you can't get back) | |
816 | 0 | if (d.height - dif > ap.idPanelHolder.getHeight() |
817 | - ap.getIdSpaceFillerPanel1().getHeight()) | |
818 | { | |
819 | 0 | return; |
820 | } | |
821 | ||
822 | 0 | if ((d.height - dif) > 20) |
823 | { | |
824 | 0 | ap.annotationScroller |
825 | .setPreferredSize(new Dimension(d.width, d.height - dif)); | |
826 | 0 | d = ap.annotationSpaceFillerHolder.getPreferredSize(); |
827 | 0 | ap.annotationSpaceFillerHolder |
828 | .setPreferredSize(new Dimension(d.width, d.height - dif)); | |
829 | 0 | ap.paintAlignment(true, false); |
830 | } | |
831 | ||
832 | 0 | ap.addNotify(); |
833 | } | |
834 | else | |
835 | { | |
836 | 0 | repaint(); |
837 | } | |
838 | } | |
839 | ||
840 | /** | |
841 | * Updates the tooltip as the mouse moves over the labels | |
842 | * | |
843 | * @param evt | |
844 | */ | |
845 | 0 | @Override |
846 | public void mouseMoved(MouseEvent evt) | |
847 | { | |
848 | 0 | showOrHideAdjuster(evt); |
849 | ||
850 | 0 | getSelectedRow(evt.getY() - getScrollOffset()); |
851 | ||
852 | 0 | if (selectedRow > -1 && ap.av.getAlignment() |
853 | .getAlignmentAnnotation().length > selectedRow) | |
854 | { | |
855 | 0 | AlignmentAnnotation[] anns = ap.av.getAlignment() |
856 | .getAlignmentAnnotation(); | |
857 | 0 | AlignmentAnnotation aa = anns[selectedRow]; |
858 | ||
859 | 0 | String desc = getTooltip(aa); |
860 | 0 | this.setToolTipText(desc); |
861 | 0 | String msg = getStatusMessage(aa, anns); |
862 | 0 | ap.alignFrame.setStatus(msg); |
863 | } | |
864 | } | |
865 | ||
866 | /** | |
867 | * Constructs suitable text to show in the status bar when over an annotation | |
868 | * label, containing the associated sequence name (if any), and the annotation | |
869 | * labels (or all labels for a graph group annotation) | |
870 | * | |
871 | * @param aa | |
872 | * @param anns | |
873 | * @return | |
874 | */ | |
875 | 6 | static String getStatusMessage(AlignmentAnnotation aa, |
876 | AlignmentAnnotation[] anns) | |
877 | { | |
878 | 6 | if (aa == null) |
879 | { | |
880 | 1 | return null; |
881 | } | |
882 | ||
883 | 5 | StringBuilder msg = new StringBuilder(32); |
884 | 5 | if (aa.sequenceRef != null) |
885 | { | |
886 | 3 | msg.append(aa.sequenceRef.getName()).append(" : "); |
887 | } | |
888 | ||
889 | 5 | if (aa.graphGroup == -1) |
890 | { | |
891 | 2 | msg.append(aa.label); |
892 | 2 | if (aa.getNoOfSequencesIncluded() >= 0) |
893 | { | |
894 | 0 | msg.append(" ("); |
895 | 0 | msg.append(MessageManager.getString("label.sequence_count")); |
896 | 0 | msg.append(aa.getNoOfSequencesIncluded()); |
897 | 0 | msg.append(")"); |
898 | } | |
899 | } | |
900 | ||
901 | 3 | else if (anns != null) |
902 | { | |
903 | 3 | boolean first = true; |
904 | 9 | for (int i = anns.length - 1; i >= 0; i--) |
905 | { | |
906 | 6 | if (anns[i].graphGroup == aa.graphGroup) |
907 | { | |
908 | 5 | if (!first) |
909 | { | |
910 | 2 | msg.append(", "); |
911 | } | |
912 | 5 | msg.append(anns[i].label); |
913 | 5 | first = false; |
914 | } | |
915 | } | |
916 | } | |
917 | ||
918 | 5 | return msg.toString(); |
919 | } | |
920 | ||
921 | /** | |
922 | * Answers a tooltip, formatted as html, containing the annotation description | |
923 | * (prefixed by associated sequence id if applicable), and the annotation | |
924 | * (non-positional) score if it has one. Answers null if neither description | |
925 | * nor score is found. | |
926 | * | |
927 | * @param aa | |
928 | * @return | |
929 | */ | |
930 | 13 | static String getTooltip(AlignmentAnnotation aa) |
931 | { | |
932 | 13 | if (aa == null) |
933 | { | |
934 | 1 | return null; |
935 | } | |
936 | 12 | StringBuilder tooltip = new StringBuilder(); |
937 | 12 | if (aa.description != null && !aa.description.equals("New description")) |
938 | { | |
939 | // TODO: we could refactor and merge this code with the code in | |
940 | // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature | |
941 | // tooltips | |
942 | 10 | String desc = aa.getDescription(true).trim(); |
943 | 10 | if (aa.getNoOfSequencesIncluded() >= 0) |
944 | { | |
945 | 0 | desc += " (" + MessageManager.getString("label.sequence_count") |
946 | + aa.getNoOfSequencesIncluded() + ")"; | |
947 | } | |
948 | 10 | if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG)) |
949 | { | |
950 | 7 | tooltip.append(HTML_START_TAG); |
951 | 7 | desc = desc.replace("<", "<"); |
952 | } | |
953 | 3 | else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG)) |
954 | { | |
955 | 3 | desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); |
956 | } | |
957 | 10 | tooltip.append(desc); |
958 | } | |
959 | else | |
960 | { | |
961 | // begin the tooltip's html fragment | |
962 | 2 | tooltip.append(HTML_START_TAG); |
963 | } | |
964 | 12 | if (aa.hasScore()) |
965 | { | |
966 | 5 | if (tooltip.length() > HTML_START_TAG.length()) |
967 | { | |
968 | 3 | tooltip.append("<br/>"); |
969 | } | |
970 | // TODO: limit precision of score to avoid noise from imprecise | |
971 | // doubles | |
972 | // (64.7 becomes 64.7+/some tiny value). | |
973 | 5 | tooltip.append(" Score: ").append(String.valueOf(aa.score)); |
974 | } | |
975 | ||
976 | 12 | if (tooltip.length() > HTML_START_TAG.length()) |
977 | { | |
978 | 10 | return tooltip.append(HTML_END_TAG).toString(); |
979 | } | |
980 | ||
981 | /* | |
982 | * nothing in the tooltip (except "<html>") | |
983 | */ | |
984 | 2 | return null; |
985 | } | |
986 | ||
987 | /** | |
988 | * Shows the height adjuster image if the mouse moves into the top left | |
989 | * region, or hides it if the mouse leaves the regio | |
990 | * | |
991 | * @param evt | |
992 | */ | |
993 | 0 | protected void showOrHideAdjuster(MouseEvent evt) |
994 | { | |
995 | 0 | boolean was = resizePanel; |
996 | 0 | resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT |
997 | && evt.getX() < HEIGHT_ADJUSTER_WIDTH; | |
998 | ||
999 | 0 | if (resizePanel != was) |
1000 | { | |
1001 | 0 | setCursor(Cursor |
1002 | 0 | .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR |
1003 | : Cursor.DEFAULT_CURSOR)); | |
1004 | 0 | repaint(); |
1005 | } | |
1006 | } | |
1007 | ||
1008 | 0 | @Override |
1009 | public void mouseClicked(MouseEvent evt) | |
1010 | { | |
1011 | 0 | final AlignmentAnnotation[] aa = ap.av.getAlignment() |
1012 | .getAlignmentAnnotation(); | |
1013 | 0 | if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) |
1014 | { | |
1015 | 0 | if (selectedRow > -1 && selectedRow < aa.length) |
1016 | { | |
1017 | 0 | if (aa[selectedRow].groupRef != null) |
1018 | { | |
1019 | 0 | if (evt.getClickCount() >= 2) |
1020 | { | |
1021 | // todo: make the ap scroll to the selection - not necessary, first | |
1022 | // click highlights/scrolls, second selects | |
1023 | 0 | ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); |
1024 | // process modifiers | |
1025 | 0 | SequenceGroup sg = ap.av.getSelectionGroup(); |
1026 | 0 | if (sg == null || sg == aa[selectedRow].groupRef |
1027 | || !(Platform.isControlDown(evt) || evt.isShiftDown())) | |
1028 | { | |
1029 | 0 | if (Platform.isControlDown(evt) || evt.isShiftDown()) |
1030 | { | |
1031 | // clone a new selection group from the associated group | |
1032 | 0 | ap.av.setSelectionGroup( |
1033 | new SequenceGroup(aa[selectedRow].groupRef)); | |
1034 | } | |
1035 | else | |
1036 | { | |
1037 | // set selection to the associated group so it can be edited | |
1038 | 0 | ap.av.setSelectionGroup(aa[selectedRow].groupRef); |
1039 | } | |
1040 | } | |
1041 | else | |
1042 | { | |
1043 | // modify current selection with associated group | |
1044 | 0 | int remainToAdd = aa[selectedRow].groupRef.getSize(); |
1045 | 0 | for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) |
1046 | { | |
1047 | 0 | if (jalview.util.Platform.isControlDown(evt)) |
1048 | { | |
1049 | 0 | sg.addOrRemove(sgs, --remainToAdd == 0); |
1050 | } | |
1051 | else | |
1052 | { | |
1053 | // notionally, we should also add intermediate sequences from | |
1054 | // last added sequence ? | |
1055 | 0 | sg.addSequence(sgs, --remainToAdd == 0); |
1056 | } | |
1057 | } | |
1058 | } | |
1059 | ||
1060 | 0 | ap.paintAlignment(false, false); |
1061 | 0 | PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); |
1062 | 0 | ap.av.sendSelection(); |
1063 | } | |
1064 | else | |
1065 | { | |
1066 | 0 | ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( |
1067 | aa[selectedRow].groupRef.getSequences(null)); | |
1068 | } | |
1069 | 0 | return; |
1070 | } | |
1071 | 0 | else if (aa[selectedRow].sequenceRef != null) |
1072 | { | |
1073 | 0 | if (evt.getClickCount() == 1) |
1074 | { | |
1075 | 0 | ap.getSeqPanel().ap.getIdPanel() |
1076 | .highlightSearchResults(Arrays.asList(new SequenceI[] | |
1077 | { aa[selectedRow].sequenceRef })); | |
1078 | } | |
1079 | 0 | else if (evt.getClickCount() >= 2) |
1080 | { | |
1081 | 0 | ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); |
1082 | 0 | SequenceGroup sg = ap.av.getSelectionGroup(); |
1083 | 0 | if (sg != null) |
1084 | { | |
1085 | // we make a copy rather than edit the current selection if no | |
1086 | // modifiers pressed | |
1087 | // see Enhancement JAL-1557 | |
1088 | 0 | if (!(Platform.isControlDown(evt) || evt.isShiftDown())) |
1089 | { | |
1090 | 0 | sg = new SequenceGroup(sg); |
1091 | 0 | sg.clear(); |
1092 | 0 | sg.addSequence(aa[selectedRow].sequenceRef, false); |
1093 | } | |
1094 | else | |
1095 | { | |
1096 | 0 | if (Platform.isControlDown(evt)) |
1097 | { | |
1098 | 0 | sg.addOrRemove(aa[selectedRow].sequenceRef, true); |
1099 | } | |
1100 | else | |
1101 | { | |
1102 | // notionally, we should also add intermediate sequences from | |
1103 | // last added sequence ? | |
1104 | 0 | sg.addSequence(aa[selectedRow].sequenceRef, true); |
1105 | } | |
1106 | } | |
1107 | } | |
1108 | else | |
1109 | { | |
1110 | 0 | sg = new SequenceGroup(); |
1111 | 0 | sg.setStartRes(0); |
1112 | 0 | sg.setEndRes(ap.av.getAlignment().getWidth() - 1); |
1113 | 0 | sg.addSequence(aa[selectedRow].sequenceRef, false); |
1114 | } | |
1115 | 0 | ap.av.setSelectionGroup(sg); |
1116 | 0 | ap.paintAlignment(false, false); |
1117 | 0 | PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); |
1118 | 0 | ap.av.sendSelection(); |
1119 | } | |
1120 | ||
1121 | } | |
1122 | } | |
1123 | 0 | return; |
1124 | } | |
1125 | } | |
1126 | ||
1127 | /** | |
1128 | * do a single sequence copy to jalview and the system clipboard | |
1129 | * | |
1130 | * @param sq | |
1131 | * sequence to be copied to clipboard | |
1132 | */ | |
1133 | 0 | protected void copy_annotseqtoclipboard(SequenceI sq) |
1134 | { | |
1135 | 0 | SequenceI[] seqs = new SequenceI[] { sq }; |
1136 | 0 | String[] omitHidden = null; |
1137 | 0 | SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() }; |
1138 | 0 | if (dseqs[0] == null) |
1139 | { | |
1140 | 0 | dseqs[0] = new Sequence(sq); |
1141 | 0 | dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, |
1142 | sq.getSequenceAsString())); | |
1143 | ||
1144 | 0 | sq.setDatasetSequence(dseqs[0]); |
1145 | } | |
1146 | 0 | Alignment ds = new Alignment(dseqs); |
1147 | 0 | if (av.hasHiddenColumns()) |
1148 | { | |
1149 | 0 | Iterator<int[]> it = av.getAlignment().getHiddenColumns() |
1150 | .getVisContigsIterator(0, sq.getLength() + 1, false); | |
1151 | 0 | omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; |
1152 | } | |
1153 | ||
1154 | 0 | int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; |
1155 | 0 | if (av.hasHiddenColumns()) |
1156 | { | |
1157 | 0 | alignmentStartEnd = av.getAlignment().getHiddenColumns() |
1158 | .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); | |
1159 | } | |
1160 | ||
1161 | 0 | String output = new FormatAdapter().formatSequences(FileFormat.Fasta, |
1162 | seqs, omitHidden, alignmentStartEnd); | |
1163 | ||
1164 | 0 | Toolkit.getDefaultToolkit().getSystemClipboard() |
1165 | .setContents(new StringSelection(output), Desktop.instance); | |
1166 | ||
1167 | 0 | HiddenColumns hiddenColumns = null; |
1168 | ||
1169 | 0 | if (av.hasHiddenColumns()) |
1170 | { | |
1171 | 0 | hiddenColumns = new HiddenColumns( |
1172 | av.getAlignment().getHiddenColumns()); | |
1173 | } | |
1174 | ||
1175 | 0 | Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset |
1176 | // of a consensus | |
1177 | // sequence ? need to | |
1178 | // flag | |
1179 | // sequence as special. | |
1180 | hiddenColumns }; | |
1181 | } | |
1182 | ||
1183 | /** | |
1184 | * DOCUMENT ME! | |
1185 | * | |
1186 | * @param g1 | |
1187 | * DOCUMENT ME! | |
1188 | */ | |
1189 | 2162 | @Override |
1190 | public void paintComponent(Graphics g) | |
1191 | { | |
1192 | ||
1193 | 2162 | int width = getWidth(); |
1194 | 2162 | if (width == 0) |
1195 | { | |
1196 | 0 | width = ap.calculateIdWidth().width; |
1197 | } | |
1198 | ||
1199 | 2162 | Graphics2D g2 = (Graphics2D) g; |
1200 | 2162 | if (av.antiAlias) |
1201 | { | |
1202 | 765 | g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
1203 | RenderingHints.VALUE_ANTIALIAS_ON); | |
1204 | } | |
1205 | ||
1206 | 2162 | drawComponent(g2, true, width, true); |
1207 | } | |
1208 | ||
1209 | /** | |
1210 | * Draw the full set of annotation Labels for the alignment at the given | |
1211 | * cursor | |
1212 | * | |
1213 | * @param g | |
1214 | * Graphics2D instance (needed for font scaling) | |
1215 | * @param width | |
1216 | * Width for scaling labels | |
1217 | * | |
1218 | */ | |
1219 | 0 | public void drawComponent(Graphics g, int width) |
1220 | { | |
1221 | 0 | drawComponent(g, false, width, true); |
1222 | } | |
1223 | ||
1224 | /** | |
1225 | * Draw the full set of annotation Labels for the alignment at the given | |
1226 | * cursor | |
1227 | * | |
1228 | * @param g | |
1229 | * Graphics2D instance (needed for font scaling) | |
1230 | * @param clip | |
1231 | * - true indicates that only current visible area needs to be | |
1232 | * rendered | |
1233 | * @param width | |
1234 | * Width for scaling labels | |
1235 | */ | |
1236 | 2804 | public void drawComponent(Graphics g, boolean clip, int givenWidth, |
1237 | boolean forGUI) | |
1238 | { | |
1239 | 2804 | int width = givenWidth; |
1240 | 2804 | IdwidthAdjuster iwa = null; |
1241 | 2804 | if (ap != null) |
1242 | { | |
1243 | 2200 | iwa = ap.idwidthAdjuster; |
1244 | 2200 | if (Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true) |
1245 | || Jalview.isHeadlessMode()) | |
1246 | { | |
1247 | 2200 | Graphics2D g2d = (Graphics2D) g; |
1248 | 2200 | Graphics dummy = g2d.create(); |
1249 | 2200 | int newAnnotationIdWidth = drawLabels(dummy, clip, width, false, |
1250 | forGUI, null, false); | |
1251 | 2200 | dummy.dispose(); |
1252 | 2200 | Dimension d = ap.calculateDefaultAlignmentIdWidth(); |
1253 | 2200 | int alignmentIdWidth = d.width; |
1254 | 2200 | if (iwa != null && !iwa.manuallyAdjusted()) |
1255 | { | |
1256 | // If no manual adjustment to ID column with has been made then adjust | |
1257 | // width match widest of alignment or annotation id widths | |
1258 | 1055 | boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH", |
1259 | false); | |
1260 | 1055 | width = Math.max(alignmentIdWidth, newAnnotationIdWidth); |
1261 | 1055 | if (clip && width < givenWidth && !allowShrink) |
1262 | { | |
1263 | 0 | width = givenWidth; |
1264 | } | |
1265 | } | |
1266 | 1145 | else if (newAnnotationIdWidth != annotationIdWidth |
1267 | && newAnnotationIdWidth > givenWidth | |
1268 | && newAnnotationIdWidth > alignmentIdWidth) | |
1269 | { | |
1270 | // otherwise if the annotation id width has become larger than the | |
1271 | // current id width, increase | |
1272 | 12 | width = newAnnotationIdWidth; |
1273 | 12 | annotationIdWidth = newAnnotationIdWidth; |
1274 | } | |
1275 | // set the width if it's changed | |
1276 | 2200 | if (width != ap.av.getIdWidth()) |
1277 | { | |
1278 | 113 | iwa.setWidth(width); |
1279 | } | |
1280 | } | |
1281 | } | |
1282 | else | |
1283 | { | |
1284 | 604 | int newAnnotationIdWidth = drawLabels(g, clip, width, false, forGUI, |
1285 | null, false); | |
1286 | 604 | width = newAnnotationIdWidth < givenWidth ? givenWidth |
1287 | : Math.min(newAnnotationIdWidth, givenWidth); | |
1288 | } | |
1289 | 2804 | drawLabels(g, clip, width, true, forGUI, null, false); |
1290 | } | |
1291 | ||
1292 | /** | |
1293 | * Render the full set of annotation Labels for the alignment at the given | |
1294 | * cursor. If actuallyDraw is false or g is null then no actual drawing will | |
1295 | * occur, but the widest label width will be returned. If g is null then | |
1296 | * fmetrics must be supplied. | |
1297 | * | |
1298 | * @param g | |
1299 | * Graphics2D instance (used for rendering and font scaling if no | |
1300 | * fmetrics supplied) | |
1301 | * @param clip | |
1302 | * - true indicates that only current visible area needs to be | |
1303 | * rendered | |
1304 | * @param width | |
1305 | * Width for scaling labels | |
1306 | * @param actuallyDraw | |
1307 | * - when false, no graphics are rendered to g0 | |
1308 | * @param forGUI | |
1309 | * - when false, GUI relevant marks like indicators for dragging | |
1310 | * annotation panel height are not rendered | |
1311 | * @param fmetrics | |
1312 | * FontMetrics if Graphics object g is null | |
1313 | * @param includeHidden | |
1314 | * - when true returned width includes labels in hidden row width | |
1315 | * calculation | |
1316 | * @return the width of the annotation labels. | |
1317 | */ | |
1318 | 6008 | public int drawLabels(Graphics g0, boolean clip, int width, |
1319 | boolean actuallyDraw, boolean forGUI, FontMetrics fmetrics, | |
1320 | boolean includeHidden) | |
1321 | { | |
1322 | 6008 | if (clip) |
1323 | { | |
1324 | 4324 | clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS", |
1325 | true); | |
1326 | } | |
1327 | 6008 | Graphics g = null; |
1328 | // create a dummy Graphics object if not drawing and one is supplied | |
1329 | 6008 | if (g0 != null) |
1330 | { | |
1331 | 5932 | if (!actuallyDraw) |
1332 | { | |
1333 | 3128 | Graphics2D g2d = (Graphics2D) g0; |
1334 | 3128 | g = g2d.create(); |
1335 | } | |
1336 | else | |
1337 | { | |
1338 | 2804 | g = g0; |
1339 | } | |
1340 | } | |
1341 | 6008 | int actualWidth = 0; |
1342 | 6008 | if (g != null) |
1343 | { | |
1344 | 5932 | if (av.getFont().getSize() < 10) |
1345 | { | |
1346 | 0 | g.setFont(font); |
1347 | } | |
1348 | else | |
1349 | { | |
1350 | 5932 | g.setFont(av.getFont()); |
1351 | } | |
1352 | } | |
1353 | ||
1354 | 6008 | FontMetrics fm = fmetrics == null ? g.getFontMetrics(g.getFont()) |
1355 | : fmetrics; | |
1356 | 6008 | if (actuallyDraw) |
1357 | { | |
1358 | 2804 | g.setColor(Color.white); |
1359 | 2804 | g.fillRect(0, 0, getWidth(), getHeight()); |
1360 | ||
1361 | 2804 | if (!Cache.getDefault(RESIZE_MARGINS_MARK_PREF, false) |
1362 | && !av.getWrapAlignment() && forGUI) | |
1363 | { | |
1364 | 2162 | g.setColor(Color.LIGHT_GRAY); |
1365 | 2162 | g.drawLine(0, HEIGHT_ADJUSTER_HEIGHT / 4, HEIGHT_ADJUSTER_WIDTH / 4, |
1366 | HEIGHT_ADJUSTER_HEIGHT / 4); | |
1367 | 2162 | g.drawLine(0, 3 * HEIGHT_ADJUSTER_HEIGHT / 4, |
1368 | HEIGHT_ADJUSTER_WIDTH / 4, 3 * HEIGHT_ADJUSTER_HEIGHT / 4); | |
1369 | ||
1370 | } | |
1371 | } | |
1372 | ||
1373 | 6008 | if (actuallyDraw) |
1374 | { | |
1375 | 2804 | g.translate(0, getScrollOffset()); |
1376 | 2804 | g.setColor(Color.black); |
1377 | } | |
1378 | 6008 | SequenceI lastSeqRef = null; |
1379 | 6008 | String lastLabel = null; |
1380 | 6008 | String lastDescription = null; |
1381 | 6008 | AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); |
1382 | 6007 | boolean isShowStructureProvider = av.isShowStructureProvider(); |
1383 | 6007 | int fontHeight = g != null ? g.getFont().getSize() |
1384 | : fm.getFont().getSize(); | |
1385 | 6007 | int y = 0; |
1386 | 6007 | int x = 0; |
1387 | 6007 | int graphExtras = 0; |
1388 | 6007 | int offset = 0; |
1389 | 6007 | Font baseFont = g != null ? g.getFont() : fm.getFont(); |
1390 | 6007 | FontMetrics baseMetrics = fm; |
1391 | 6007 | int ofontH = fontHeight; |
1392 | 6007 | int sOffset = 0; |
1393 | 6007 | int visHeight = 0; |
1394 | 6007 | int[] visr = (ap != null && ap.getAnnotationPanel() != null) |
1395 | ? ap.getAnnotationPanel().getVisibleVRange() | |
1396 | : null; | |
1397 | 6007 | if (clip && visr != null) |
1398 | { | |
1399 | 4324 | sOffset = visr[0]; |
1400 | 4324 | visHeight = visr[1]; |
1401 | } | |
1402 | 6007 | boolean visible = true, before = false, after = false; |
1403 | 6007 | if (aa != null) |
1404 | { | |
1405 | 6007 | hasHiddenRows = false; |
1406 | 6007 | int olY = 0; |
1407 | 6007 | int nexAA = 0; |
1408 | 40075 | for (int i = 0; i < aa.length; i++) |
1409 | { | |
1410 | 34068 | visible = true; |
1411 | 34068 | if (!aa[i].visible && !includeHidden) |
1412 | { | |
1413 | 2382 | hasHiddenRows = true; |
1414 | 2382 | continue; |
1415 | } | |
1416 | 31686 | olY = y; |
1417 | // look ahead to next annotation | |
1418 | 31686 | for (nexAA = i + 1; nexAA < aa.length |
1419 | && (!aa[nexAA].visible && includeHidden); nexAA++) | |
1420 | 0 | ; |
1421 | 31686 | y += aa[i].height; |
1422 | 31686 | if (clip) |
1423 | { | |
1424 | 21580 | if (y < sOffset) |
1425 | { | |
1426 | 0 | if (!before) |
1427 | { | |
1428 | 0 | if (debugRedraw) |
1429 | { | |
1430 | 0 | jalview.bin.Console.outPrintln("before vis: " + i); |
1431 | } | |
1432 | 0 | before = true; |
1433 | } | |
1434 | // don't draw what isn't visible | |
1435 | 0 | continue; |
1436 | } | |
1437 | 21580 | if (olY > visHeight) |
1438 | { | |
1439 | ||
1440 | 1424 | if (!after) |
1441 | { | |
1442 | 654 | if (debugRedraw) |
1443 | { | |
1444 | 0 | jalview.bin.Console.outPrintln( |
1445 | "Scroll offset: " + sOffset + " after vis: " + i); | |
1446 | } | |
1447 | 654 | after = true; |
1448 | } | |
1449 | // don't draw what isn't visible | |
1450 | 1424 | continue; |
1451 | } | |
1452 | } | |
1453 | 30262 | if (actuallyDraw && g != null) |
1454 | { | |
1455 | 13865 | g.setColor(Color.black); |
1456 | } | |
1457 | 30262 | offset = -aa[i].height / 2; |
1458 | ||
1459 | 30262 | if (aa[i].hasText) |
1460 | { | |
1461 | 25580 | offset += fm.getHeight() / 2; |
1462 | 25580 | offset -= fm.getDescent(); |
1463 | } | |
1464 | else | |
1465 | { | |
1466 | 4682 | offset += fm.getDescent(); |
1467 | } | |
1468 | 30262 | String label = aa[i].label; |
1469 | 30262 | ParseHtmlBodyAndLinks phbDecription = new ParseHtmlBodyAndLinks( |
1470 | aa[i].description, true, "\n"); | |
1471 | 30262 | String description = phbDecription.getNonHtmlContent(); |
1472 | 30262 | boolean vertBar = false; |
1473 | 30262 | if (lastLabel != null && lastLabel.equals(label) && |
1474 | lastDescription != null && lastDescription.equals(description)) | |
1475 | { | |
1476 | //JAL-4427 | |
1477 | 0 | label = aa[i].label; // No change in label |
1478 | } | |
1479 | 30262 | else if (lastLabel != null && lastLabel.equals(label)) |
1480 | { | |
1481 | //JAL-4427 | |
1482 | 0 | if(!(lastDescription != null && lastDescription.equals(description)) |
1483 | && (aa[i].sequenceRef == lastSeqRef)) { | |
1484 | 0 | label = description; |
1485 | 0 | lastDescription = description; |
1486 | } | |
1487 | } | |
1488 | else | |
1489 | { | |
1490 | 30262 | if (nexAA < aa.length && label.equals(aa[nexAA].label)) // && |
1491 | // aa[nexY].sequenceRef==aa[i].sequenceRef) | |
1492 | { | |
1493 | 0 | lastLabel = label; |
1494 | // next label is the same as this label | |
1495 | //JAL-4427 | |
1496 | 0 | if(!(lastDescription != null && lastDescription.equals(description))) { |
1497 | 0 | if(aa[nexAA].sequenceRef == aa[i].sequenceRef) { |
1498 | 0 | label = description; |
1499 | } | |
1500 | 0 | lastDescription = description; |
1501 | } | |
1502 | } | |
1503 | else | |
1504 | { | |
1505 | 30262 | lastLabel = label; |
1506 | 30262 | lastDescription = description; |
1507 | } | |
1508 | } | |
1509 | 30262 | if (aa[i].sequenceRef != null) |
1510 | { | |
1511 | 4122 | if (aa[i].sequenceRef != lastSeqRef) |
1512 | { | |
1513 | 1294 | label = aa[i].sequenceRef.getName() + " " + label; |
1514 | // TODO record relationship between sequence and this annotation and | |
1515 | // display it here | |
1516 | } | |
1517 | else | |
1518 | { | |
1519 | 2828 | vertBar = true; |
1520 | } | |
1521 | } | |
1522 | ||
1523 | 30262 | if (isShowStructureProvider && aa[i].hasIcons |
1524 | && Constants.SECONDARY_STRUCTURE_LABELS.keySet() | |
1525 | .contains(aa[i].label)) | |
1526 | { | |
1527 | 0 | String ssSource = AlignmentUtils |
1528 | .extractSSSourceFromAnnotationDescription(aa[i]); | |
1529 | 0 | if (ssSource != null && ssSource.length() > 0) |
1530 | 0 | label += " (" + ssSource + ")"; |
1531 | } | |
1532 | ||
1533 | 30262 | int labelWidth = fm.stringWidth(label) + 3; |
1534 | 30262 | x = width - labelWidth; |
1535 | ||
1536 | 30262 | if (aa[i].graphGroup > -1) |
1537 | { | |
1538 | 0 | int groupSize = 0; |
1539 | // TODO: JAL-1291 revise rendering model so the graphGroup map is | |
1540 | // computed efficiently for all visible labels | |
1541 | 0 | for (int gg = 0; gg < aa.length; gg++) |
1542 | { | |
1543 | 0 | if (aa[gg].graphGroup == aa[i].graphGroup) |
1544 | { | |
1545 | 0 | groupSize++; |
1546 | } | |
1547 | } | |
1548 | 0 | if (groupSize * (fontHeight + 8) < aa[i].height) |
1549 | { | |
1550 | 0 | graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) |
1551 | / 2; | |
1552 | } | |
1553 | else | |
1554 | { | |
1555 | // scale font to fit | |
1556 | 0 | float h = aa[i].height / (float) groupSize, s; |
1557 | 0 | if (h < 9) |
1558 | { | |
1559 | 0 | visible = false; |
1560 | } | |
1561 | else | |
1562 | { | |
1563 | 0 | fontHeight = -8 + (int) h; |
1564 | 0 | s = ((float) fontHeight) / (float) ofontH; |
1565 | 0 | Font f = baseFont |
1566 | .deriveFont(AffineTransform.getScaleInstance(s, s)); | |
1567 | 0 | Canvas c = new Canvas(); |
1568 | 0 | fm = c.getFontMetrics(f); |
1569 | 0 | if (actuallyDraw && g != null) |
1570 | { | |
1571 | 0 | g.setFont(f); |
1572 | // fm = g.getFontMetrics(); | |
1573 | 0 | graphExtras = (aa[i].height |
1574 | - (groupSize * (fontHeight + 8))) / 2; | |
1575 | } | |
1576 | } | |
1577 | } | |
1578 | 0 | if (visible) |
1579 | { | |
1580 | 0 | for (int gg = 0; gg < aa.length; gg++) |
1581 | { | |
1582 | 0 | if (aa[gg].graphGroup == aa[i].graphGroup) |
1583 | { | |
1584 | 0 | labelWidth = fm.stringWidth(aa[gg].label) + 3; |
1585 | 0 | x = width - labelWidth; |
1586 | 0 | if (actuallyDraw && g != null) |
1587 | { | |
1588 | 0 | g.drawString(aa[gg].label, x, y - graphExtras); |
1589 | ||
1590 | 0 | if (aa[gg]._linecolour != null) |
1591 | { | |
1592 | ||
1593 | 0 | g.setColor(aa[gg]._linecolour); |
1594 | 0 | g.drawLine(x, y - graphExtras + 3, |
1595 | x + fm.stringWidth(aa[gg].label), | |
1596 | y - graphExtras + 3); | |
1597 | } | |
1598 | ||
1599 | 0 | g.setColor(Color.black); |
1600 | } | |
1601 | 0 | graphExtras += fontHeight + 8; |
1602 | } | |
1603 | } | |
1604 | } | |
1605 | 0 | if (actuallyDraw && g != null) |
1606 | { | |
1607 | 0 | g.setFont(baseFont); |
1608 | } | |
1609 | 0 | fm = baseMetrics; |
1610 | 0 | fontHeight = ofontH; |
1611 | } | |
1612 | else | |
1613 | { | |
1614 | 30262 | if (actuallyDraw && g != null) |
1615 | { | |
1616 | 13865 | if (vertBar) |
1617 | { | |
1618 | 1082 | g.drawLine(width - 3, y + offset - fontHeight, width - 3, |
1619 | (int) (y - 1.5 * aa[i].height - offset - fontHeight)); | |
1620 | // g.drawLine(20, y + offset, x - 20, y + offset); | |
1621 | ||
1622 | } | |
1623 | 13865 | if(label.contains("Secondary Structure Consensus")) { |
1624 | //label.replace("Secondary Structure Consensus", "Secondary Structure Consensus" + "\n"); | |
1625 | // Split the string into lines using the newline character | |
1626 | 0 | String[] lines = label.split("(?<=Secondary Structure Consensus)", 2); |
1627 | ||
1628 | // Set the starting y position | |
1629 | 0 | int lineHeight = g.getFontMetrics().getHeight(); |
1630 | 0 | labelWidth = Math.max(fm.stringWidth(lines[0]), fm.stringWidth(lines[1])) + 3; |
1631 | ||
1632 | 0 | x = width - labelWidth; |
1633 | 0 | for (int k = 0; k < lines.length; k++) { |
1634 | // Draw each line, offsetting the y position by lineHeight for each line | |
1635 | 0 | g.drawString(lines[k].trim(), x, y + offset +(k * lineHeight)); |
1636 | } | |
1637 | } | |
1638 | else { | |
1639 | ||
1640 | 13865 | if (aa[i].sequenceRef != null && (av.getSelectionGroup() != null) |
1641 | && (av.getSelectionGroup().getAnnotationsFromTree() != null) | |
1642 | && av.getSelectionGroup().getAnnotationsFromTree().contains(aa[i])) | |
1643 | { | |
1644 | 0 | g.setColor(Color.lightGray); |
1645 | 0 | g.fillRect(0, y + offset - (fontHeight), x + labelWidth - 3, fontHeight + 2); |
1646 | } | |
1647 | 13865 | else if (aa[i].sequenceRef != null && av.getAnnotationColour(aa[i]) != null) |
1648 | { | |
1649 | ||
1650 | //Highlight annotation labels with corresponding group colours | |
1651 | //(grouped by secondary structure similarity tree) | |
1652 | 1562 | g.setColor(av.getAnnotationColour(aa[i])); |
1653 | 1562 | g.fillRect(0, y + offset - (fontHeight), x + labelWidth - 3, fontHeight + 2); |
1654 | ||
1655 | } | |
1656 | else { | |
1657 | 12303 | g.setColor(Color.BLACK); |
1658 | 12303 | g.fillRect(x, y + offset - (fontHeight), labelWidth - 3, fontHeight + 2); |
1659 | } | |
1660 | 13865 | g.setColor(Color.BLACK); |
1661 | 13865 | g.drawString(label, x, y + offset); |
1662 | } | |
1663 | } | |
1664 | } | |
1665 | 30262 | lastSeqRef = aa[i].sequenceRef; |
1666 | ||
1667 | 30262 | if (labelWidth > actualWidth) |
1668 | { | |
1669 | 8211 | actualWidth = labelWidth; |
1670 | } | |
1671 | } | |
1672 | } | |
1673 | ||
1674 | 6007 | if (!resizePanel && dragEvent != null && aa != null && selectedRow > -1 |
1675 | && selectedRow < aa.length) | |
1676 | { | |
1677 | 0 | if (actuallyDraw && g != null) |
1678 | { | |
1679 | 0 | g.setColor(Color.lightGray); |
1680 | 0 | g.drawString( |
1681 | 0 | (aa[selectedRow].sequenceRef == null ? "" |
1682 | : aa[selectedRow].sequenceRef.getName()) | |
1683 | + aa[selectedRow].label, | |
1684 | dragEvent.getX(), dragEvent.getY() - getScrollOffset()); | |
1685 | } | |
1686 | } | |
1687 | ||
1688 | 6007 | if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) |
1689 | { | |
1690 | 0 | if (actuallyDraw && g != null) |
1691 | { | |
1692 | 0 | g.drawString(MessageManager.getString("label.right_click"), 2, 8); |
1693 | 0 | g.drawString(MessageManager.getString("label.to_add_annotation"), 2, |
1694 | 18); | |
1695 | } | |
1696 | } | |
1697 | ||
1698 | 6007 | return actualWidth; |
1699 | } | |
1700 | ||
1701 | 9438 | public int getScrollOffset() |
1702 | { | |
1703 | 9438 | return scrollOffset; |
1704 | } | |
1705 | ||
1706 | 0 | @Override |
1707 | public void mouseEntered(MouseEvent e) | |
1708 | { | |
1709 | } | |
1710 | ||
1711 | 38 | public void drawComponentNotGUI(Graphics idGraphics, int idWidth) |
1712 | { | |
1713 | 38 | drawComponent(idGraphics, false, idWidth, false); |
1714 | } | |
1715 | } |