Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
FeatureSettings | 121 | 570 | 173 | ||
FeatureSettings.FeatureTableModel | 1660 | 21 | 15 | ||
FeatureSettings.ColorRenderer | 1749 | 20 | 6 | ||
FeatureSettings.FilterRenderer | 1804 | 18 | 6 | ||
FeatureSettings.ColorEditor | 1879 | 53 | 12 | ||
FeatureSettings.FilterEditor | 2048 | 36 | 8 | ||
FeatureIcon | 2171 | 26 | 7 |
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.BorderLayout; | |
24 | import java.awt.Color; | |
25 | import java.awt.Component; | |
26 | import java.awt.Dimension; | |
27 | import java.awt.FlowLayout; | |
28 | import java.awt.Font; | |
29 | import java.awt.Graphics; | |
30 | import java.awt.GridLayout; | |
31 | import java.awt.Point; | |
32 | import java.awt.Rectangle; | |
33 | import java.awt.event.ActionEvent; | |
34 | import java.awt.event.ActionListener; | |
35 | import java.awt.event.ItemEvent; | |
36 | import java.awt.event.ItemListener; | |
37 | import java.awt.event.MouseAdapter; | |
38 | import java.awt.event.MouseEvent; | |
39 | import java.awt.event.MouseMotionAdapter; | |
40 | import java.beans.PropertyChangeEvent; | |
41 | import java.beans.PropertyChangeListener; | |
42 | import java.io.File; | |
43 | import java.io.FileInputStream; | |
44 | import java.io.FileOutputStream; | |
45 | import java.io.InputStreamReader; | |
46 | import java.io.OutputStreamWriter; | |
47 | import java.io.PrintWriter; | |
48 | import java.io.Reader; | |
49 | import java.util.Arrays; | |
50 | import java.util.Comparator; | |
51 | import java.util.HashMap; | |
52 | import java.util.HashSet; | |
53 | import java.util.Hashtable; | |
54 | import java.util.Iterator; | |
55 | import java.util.List; | |
56 | import java.util.Locale; | |
57 | import java.util.Map; | |
58 | import java.util.Set; | |
59 | ||
60 | import javax.help.HelpSetException; | |
61 | import javax.swing.AbstractCellEditor; | |
62 | import javax.swing.BorderFactory; | |
63 | import javax.swing.Icon; | |
64 | import javax.swing.JButton; | |
65 | import javax.swing.JCheckBox; | |
66 | import javax.swing.JInternalFrame; | |
67 | import javax.swing.JLabel; | |
68 | import javax.swing.JLayeredPane; | |
69 | import javax.swing.JMenuItem; | |
70 | import javax.swing.JPanel; | |
71 | import javax.swing.JPopupMenu; | |
72 | import javax.swing.JScrollPane; | |
73 | import javax.swing.JSlider; | |
74 | import javax.swing.JTable; | |
75 | import javax.swing.ListSelectionModel; | |
76 | import javax.swing.SwingConstants; | |
77 | import javax.swing.ToolTipManager; | |
78 | import javax.swing.border.Border; | |
79 | import javax.swing.event.ChangeEvent; | |
80 | import javax.swing.event.ChangeListener; | |
81 | import javax.swing.table.AbstractTableModel; | |
82 | import javax.swing.table.JTableHeader; | |
83 | import javax.swing.table.TableCellEditor; | |
84 | import javax.swing.table.TableCellRenderer; | |
85 | import javax.swing.table.TableColumn; | |
86 | import javax.xml.bind.JAXBContext; | |
87 | import javax.xml.bind.JAXBElement; | |
88 | import javax.xml.bind.Marshaller; | |
89 | import javax.xml.stream.XMLInputFactory; | |
90 | import javax.xml.stream.XMLStreamReader; | |
91 | ||
92 | import jalview.api.AlignViewControllerGuiI; | |
93 | import jalview.api.AlignViewportI; | |
94 | import jalview.api.FeatureColourI; | |
95 | import jalview.api.FeatureSettingsControllerI; | |
96 | import jalview.api.SplitContainerI; | |
97 | import jalview.api.ViewStyleI; | |
98 | import jalview.controller.FeatureSettingsControllerGuiI; | |
99 | import jalview.datamodel.AlignmentI; | |
100 | import jalview.datamodel.SequenceI; | |
101 | import jalview.datamodel.features.FeatureMatcher; | |
102 | import jalview.datamodel.features.FeatureMatcherI; | |
103 | import jalview.datamodel.features.FeatureMatcherSet; | |
104 | import jalview.datamodel.features.FeatureMatcherSetI; | |
105 | import jalview.gui.Help.HelpId; | |
106 | import jalview.gui.JalviewColourChooser.ColourChooserListener; | |
107 | import jalview.io.DataSourceType; | |
108 | import jalview.io.FileParse; | |
109 | import jalview.io.JalviewFileChooser; | |
110 | import jalview.io.JalviewFileView; | |
111 | import jalview.schemes.FeatureColour; | |
112 | import jalview.util.MessageManager; | |
113 | import jalview.util.Platform; | |
114 | import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; | |
115 | import jalview.viewmodel.styles.ViewStyle; | |
116 | import jalview.xml.binding.jalview.JalviewUserColours; | |
117 | import jalview.xml.binding.jalview.JalviewUserColours.Colour; | |
118 | import jalview.xml.binding.jalview.JalviewUserColours.Filter; | |
119 | import jalview.xml.binding.jalview.ObjectFactory; | |
120 | ||
121 | public class FeatureSettings extends JPanel | |
122 | implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI | |
123 | { | |
124 | private static final String SEQUENCE_FEATURE_COLOURS = MessageManager | |
125 | .getString("label.sequence_feature_colours"); | |
126 | ||
127 | /* | |
128 | * column indices of fields in Feature Settings table | |
129 | */ | |
130 | static final int TYPE_COLUMN = 0; | |
131 | ||
132 | static final int COLOUR_COLUMN = 1; | |
133 | ||
134 | static final int FILTER_COLUMN = 2; | |
135 | ||
136 | static final int SHOW_COLUMN = 3; | |
137 | ||
138 | private static final int COLUMN_COUNT = 4; | |
139 | ||
140 | private static final int MIN_WIDTH = 400; | |
141 | ||
142 | private static final int MIN_HEIGHT = 400; | |
143 | ||
144 | private final static String BASE_TOOLTIP = MessageManager | |
145 | .getString("label.click_to_edit"); | |
146 | ||
147 | final FeatureRenderer fr; | |
148 | ||
149 | public final AlignFrame af; | |
150 | ||
151 | /* | |
152 | * 'original' fields hold settings to restore on Cancel | |
153 | */ | |
154 | Object[][] originalData; | |
155 | ||
156 | private float originalTransparency; | |
157 | ||
158 | private ViewStyleI originalViewStyle; | |
159 | ||
160 | private Map<String, FeatureMatcherSetI> originalFilters; | |
161 | ||
162 | final JInternalFrame frame; | |
163 | ||
164 | JScrollPane scrollPane = new JScrollPane(); | |
165 | ||
166 | JTable table; | |
167 | ||
168 | JPanel groupPanel; | |
169 | ||
170 | JSlider transparency = new JSlider(); | |
171 | ||
172 | private JCheckBox showComplementOnTop; | |
173 | ||
174 | private JCheckBox showComplement; | |
175 | ||
176 | /* | |
177 | * when true, constructor is still executing - so ignore UI events | |
178 | */ | |
179 | protected volatile boolean inConstruction = true; | |
180 | ||
181 | int selectedRow = -1; | |
182 | ||
183 | boolean resettingTable = false; | |
184 | ||
185 | /* | |
186 | * true when Feature Settings are updating from feature renderer | |
187 | */ | |
188 | private boolean handlingUpdate = false; | |
189 | ||
190 | /* | |
191 | * a change listener to ensure the dialog is updated if | |
192 | * FeatureRenderer discovers new features | |
193 | */ | |
194 | private PropertyChangeListener change; | |
195 | ||
196 | /* | |
197 | * holds {featureCount, totalExtent} for each feature type | |
198 | */ | |
199 | Map<String, float[]> typeWidth = null; | |
200 | ||
201 | 1 | private void storeOriginalSettings() |
202 | { | |
203 | // save transparency for restore on Cancel | |
204 | 1 | originalTransparency = fr.getTransparency(); |
205 | ||
206 | 1 | updateTransparencySliderFromFR(); |
207 | ||
208 | 1 | originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy |
209 | 1 | originalViewStyle = new ViewStyle(af.viewport.getViewStyle()); |
210 | } | |
211 | ||
212 | 1 | private void updateTransparencySliderFromFR() |
213 | { | |
214 | 1 | boolean incon = inConstruction; |
215 | 1 | inConstruction = true; |
216 | ||
217 | 1 | int transparencyAsPercent = (int) (fr.getTransparency() * 100); |
218 | 1 | transparency.setValue(100 - transparencyAsPercent); |
219 | 1 | inConstruction = incon; |
220 | } | |
221 | ||
222 | /** | |
223 | * Constructor | |
224 | * | |
225 | * @param af | |
226 | */ | |
227 | 1 | public FeatureSettings(AlignFrame alignFrame) |
228 | { | |
229 | 1 | this.af = alignFrame; |
230 | 1 | fr = af.getFeatureRenderer(); |
231 | ||
232 | 1 | storeOriginalSettings(); |
233 | ||
234 | 1 | try |
235 | { | |
236 | 1 | jbInit(); |
237 | } catch (Exception ex) | |
238 | { | |
239 | 0 | ex.printStackTrace(); |
240 | } | |
241 | ||
242 | 1 | table = new JTable() |
243 | { | |
244 | 0 | @Override |
245 | public String getToolTipText(MouseEvent e) | |
246 | { | |
247 | 0 | String tip = null; |
248 | 0 | int column = table.columnAtPoint(e.getPoint()); |
249 | 0 | int row = table.rowAtPoint(e.getPoint()); |
250 | ||
251 | 0 | switch (column) |
252 | { | |
253 | 0 | case TYPE_COLUMN: |
254 | 0 | tip = JvSwingUtils.wrapTooltip(true, MessageManager |
255 | .getString("label.feature_settings_click_drag")); | |
256 | 0 | break; |
257 | 0 | case COLOUR_COLUMN: |
258 | 0 | FeatureColourI colour = (FeatureColourI) table.getValueAt(row, |
259 | column); | |
260 | 0 | tip = getColorTooltip(colour, true); |
261 | 0 | break; |
262 | 0 | case FILTER_COLUMN: |
263 | 0 | FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, |
264 | column); | |
265 | 0 | tip = o.isEmpty() |
266 | ? MessageManager | |
267 | .getString("label.configure_feature_tooltip") | |
268 | : o.toString(); | |
269 | 0 | break; |
270 | 0 | default: |
271 | 0 | break; |
272 | } | |
273 | ||
274 | 0 | return tip; |
275 | } | |
276 | ||
277 | /** | |
278 | * Position the tooltip near the bottom edge of, and half way across, the | |
279 | * current cell | |
280 | */ | |
281 | 0 | @Override |
282 | public Point getToolTipLocation(MouseEvent e) | |
283 | { | |
284 | 0 | Point point = e.getPoint(); |
285 | 0 | int column = table.columnAtPoint(point); |
286 | 0 | int row = table.rowAtPoint(point); |
287 | 0 | Rectangle r = getCellRect(row, column, false); |
288 | 0 | Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3); |
289 | 0 | return loc; |
290 | } | |
291 | }; | |
292 | 1 | JTableHeader tableHeader = table.getTableHeader(); |
293 | 1 | tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12)); |
294 | 1 | tableHeader.setReorderingAllowed(false); |
295 | 1 | table.setFont(new Font("Verdana", Font.PLAIN, 12)); |
296 | 1 | ToolTipManager.sharedInstance().registerComponent(table); |
297 | 1 | table.setDefaultEditor(FeatureColour.class, new ColorEditor()); |
298 | 1 | table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); |
299 | ||
300 | 1 | table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor()); |
301 | 1 | table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer()); |
302 | ||
303 | 1 | TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75, |
304 | new ColorRenderer(), new ColorEditor()); | |
305 | 1 | table.addColumn(colourColumn); |
306 | ||
307 | 1 | TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75, |
308 | new FilterRenderer(), new FilterEditor()); | |
309 | 1 | table.addColumn(filterColumn); |
310 | ||
311 | 1 | table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); |
312 | ||
313 | 1 | table.addMouseListener(new MouseAdapter() |
314 | { | |
315 | 0 | @Override |
316 | public void mousePressed(MouseEvent evt) | |
317 | { | |
318 | 0 | Point pt = evt.getPoint(); |
319 | 0 | selectedRow = table.rowAtPoint(pt); |
320 | 0 | String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); |
321 | 0 | if (evt.isPopupTrigger()) |
322 | { | |
323 | 0 | Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); |
324 | 0 | showPopupMenu(selectedRow, type, colour, evt.getPoint()); |
325 | } | |
326 | 0 | else if (evt.getClickCount() == 2 |
327 | && table.columnAtPoint(pt) == TYPE_COLUMN) | |
328 | { | |
329 | 0 | boolean invertSelection = evt.isAltDown(); |
330 | 0 | boolean toggleSelection = Platform.isControlDown(evt); |
331 | 0 | boolean extendSelection = evt.isShiftDown(); |
332 | 0 | fr.ap.alignFrame.avc.markColumnsContainingFeatures( |
333 | invertSelection, extendSelection, toggleSelection, type); | |
334 | 0 | fr.ap.av.sendSelection(); |
335 | } | |
336 | } | |
337 | ||
338 | // isPopupTrigger fires on mouseReleased on Windows | |
339 | 0 | @Override |
340 | public void mouseReleased(MouseEvent evt) | |
341 | { | |
342 | 0 | selectedRow = table.rowAtPoint(evt.getPoint()); |
343 | 0 | if (evt.isPopupTrigger()) |
344 | { | |
345 | 0 | String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); |
346 | 0 | Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); |
347 | 0 | showPopupMenu(selectedRow, type, colour, evt.getPoint()); |
348 | } | |
349 | } | |
350 | }); | |
351 | ||
352 | 1 | table.addMouseMotionListener(new MouseMotionAdapter() |
353 | { | |
354 | 0 | @Override |
355 | public void mouseDragged(MouseEvent evt) | |
356 | { | |
357 | 0 | int newRow = table.rowAtPoint(evt.getPoint()); |
358 | 0 | if (newRow != selectedRow && selectedRow != -1 && newRow != -1) |
359 | { | |
360 | /* | |
361 | * reposition 'selectedRow' to 'newRow' (the dragged to location) | |
362 | * this could be more than one row away for a very fast drag action | |
363 | * so just swap it with adjacent rows until we get it there | |
364 | */ | |
365 | 0 | Object[][] data = ((FeatureTableModel) table.getModel()) |
366 | .getData(); | |
367 | 0 | int direction = newRow < selectedRow ? -1 : 1; |
368 | 0 | for (int i = selectedRow; i != newRow; i += direction) |
369 | { | |
370 | 0 | Object[] temp = data[i]; |
371 | 0 | data[i] = data[i + direction]; |
372 | 0 | data[i + direction] = temp; |
373 | } | |
374 | 0 | updateFeatureRenderer(data); |
375 | 0 | table.repaint(); |
376 | 0 | selectedRow = newRow; |
377 | } | |
378 | } | |
379 | }); | |
380 | // table.setToolTipText(JvSwingUtils.wrapTooltip(true, | |
381 | // MessageManager.getString("label.feature_settings_click_drag"))); | |
382 | 1 | scrollPane.setViewportView(table); |
383 | ||
384 | 1 | if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) |
385 | { | |
386 | 1 | fr.findAllFeatures(true); // display everything! |
387 | } | |
388 | ||
389 | 1 | discoverAllFeatureData(); |
390 | 1 | final FeatureSettings fs = this; |
391 | 1 | fr.addPropertyChangeListener(change = new PropertyChangeListener() |
392 | { | |
393 | 0 | @Override |
394 | public void propertyChange(PropertyChangeEvent evt) | |
395 | { | |
396 | 0 | if (!fs.resettingTable && !fs.handlingUpdate) |
397 | { | |
398 | 0 | fs.handlingUpdate = true; |
399 | 0 | fs.resetTable(null); |
400 | // new groups may be added with new sequence feature types only | |
401 | 0 | fs.handlingUpdate = false; |
402 | } | |
403 | } | |
404 | ||
405 | }); | |
406 | ||
407 | 1 | SplitContainerI splitframe = af.getSplitViewContainer(); |
408 | 1 | if (splitframe != null) |
409 | { | |
410 | 0 | frame = null; // keeps eclipse happy |
411 | 0 | splitframe.addFeatureSettingsUI(this); |
412 | } | |
413 | else | |
414 | { | |
415 | 1 | frame = new JInternalFrame(); |
416 | 1 | frame.setContentPane(this); |
417 | 1 | frame.setFrameIcon(null); |
418 | 1 | Rectangle bounds = af.getFeatureSettingsGeometry(); |
419 | 1 | String title; |
420 | 1 | if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels( |
421 | af.alignPanel.av.getSequenceSetId()).length > 1) | |
422 | { | |
423 | 0 | title = MessageManager.formatMessage( |
424 | "label.sequence_feature_settings_for_view", | |
425 | af.alignPanel.getViewName()); | |
426 | } | |
427 | else | |
428 | { | |
429 | 1 | title = MessageManager.getString("label.sequence_feature_settings"); |
430 | } | |
431 | 1 | if (bounds == null) |
432 | { | |
433 | 1 | if (Platform.isAMacAndNotJS()) |
434 | { | |
435 | 0 | Desktop.addInternalFrame(frame, title, 600, 480); |
436 | } | |
437 | else | |
438 | { | |
439 | 1 | Desktop.addInternalFrame(frame, title, 600, 450); |
440 | } | |
441 | } | |
442 | else | |
443 | { | |
444 | 0 | Desktop.addInternalFrame(frame, title, false, bounds.width, |
445 | bounds.height); | |
446 | 0 | frame.setBounds(bounds); |
447 | 0 | frame.setVisible(true); |
448 | } | |
449 | 1 | frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); |
450 | ||
451 | 1 | frame.addInternalFrameListener( |
452 | new javax.swing.event.InternalFrameAdapter() | |
453 | { | |
454 | 1 | @Override |
455 | public void internalFrameClosed( | |
456 | javax.swing.event.InternalFrameEvent evt) | |
457 | { | |
458 | 1 | featureSettings_isClosed(); |
459 | }; | |
460 | }); | |
461 | 1 | frame.setLayer(JLayeredPane.PALETTE_LAYER); |
462 | } | |
463 | 1 | inConstruction = false; |
464 | } | |
465 | ||
466 | /** | |
467 | * Sets the state of buttons to show complement features from viewport | |
468 | * settings | |
469 | */ | |
470 | 1 | private void updateComplementButtons() |
471 | { | |
472 | 1 | showComplement.setSelected(af.getViewport().isShowComplementFeatures()); |
473 | 1 | showComplementOnTop |
474 | .setSelected(af.getViewport().isShowComplementFeaturesOnTop()); | |
475 | } | |
476 | ||
477 | 0 | @Override |
478 | public AlignViewControllerGuiI getAlignframe() | |
479 | { | |
480 | 0 | return af; |
481 | } | |
482 | ||
483 | 1 | @Override |
484 | public void featureSettings_isClosed() | |
485 | { | |
486 | 1 | fr.removePropertyChangeListener(change); |
487 | 1 | change = null; |
488 | } | |
489 | ||
490 | /** | |
491 | * Constructs and shows a popup menu of possible actions on the selected row | |
492 | * and feature type | |
493 | * | |
494 | * @param rowSelected | |
495 | * @param type | |
496 | * @param typeCol | |
497 | * @param pt | |
498 | */ | |
499 | 0 | protected void showPopupMenu(final int rowSelected, final String type, |
500 | final Object typeCol, final Point pt) | |
501 | { | |
502 | 0 | JPopupMenu men = new JPopupMenu(MessageManager |
503 | .formatMessage("label.settings_for_param", new String[] | |
504 | { type })); | |
505 | ||
506 | 0 | JMenuItem scr = new JMenuItem( |
507 | MessageManager.getString("label.sort_by_score")); | |
508 | 0 | men.add(scr); |
509 | 0 | scr.addActionListener(new ActionListener() |
510 | { | |
511 | 0 | @Override |
512 | public void actionPerformed(ActionEvent e) | |
513 | { | |
514 | 0 | sortByScore(Arrays.asList(new String[] { type })); |
515 | } | |
516 | }); | |
517 | 0 | JMenuItem dens = new JMenuItem( |
518 | MessageManager.getString("label.sort_by_density")); | |
519 | 0 | dens.addActionListener(new ActionListener() |
520 | { | |
521 | 0 | @Override |
522 | public void actionPerformed(ActionEvent e) | |
523 | { | |
524 | 0 | sortByDensity(Arrays.asList(new String[] { type })); |
525 | } | |
526 | }); | |
527 | 0 | men.add(dens); |
528 | ||
529 | 0 | JMenuItem selCols = new JMenuItem( |
530 | MessageManager.getString("label.select_columns_containing")); | |
531 | 0 | selCols.addActionListener(new ActionListener() |
532 | { | |
533 | 0 | @Override |
534 | public void actionPerformed(ActionEvent arg0) | |
535 | { | |
536 | 0 | fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, |
537 | false, type); | |
538 | 0 | fr.ap.av.sendSelection(); |
539 | } | |
540 | }); | |
541 | 0 | JMenuItem clearCols = new JMenuItem(MessageManager |
542 | .getString("label.select_columns_not_containing")); | |
543 | 0 | clearCols.addActionListener(new ActionListener() |
544 | { | |
545 | 0 | @Override |
546 | public void actionPerformed(ActionEvent arg0) | |
547 | { | |
548 | 0 | fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, |
549 | false, type); | |
550 | 0 | fr.ap.av.sendSelection(); |
551 | } | |
552 | }); | |
553 | 0 | JMenuItem hideCols = new JMenuItem( |
554 | MessageManager.getString("label.hide_columns_containing")); | |
555 | 0 | hideCols.addActionListener(new ActionListener() |
556 | { | |
557 | 0 | @Override |
558 | public void actionPerformed(ActionEvent arg0) | |
559 | { | |
560 | 0 | fr.ap.alignFrame.hideFeatureColumns(type, true); |
561 | 0 | fr.ap.av.sendSelection(); |
562 | } | |
563 | }); | |
564 | 0 | JMenuItem hideOtherCols = new JMenuItem( |
565 | MessageManager.getString("label.hide_columns_not_containing")); | |
566 | 0 | hideOtherCols.addActionListener(new ActionListener() |
567 | { | |
568 | 0 | @Override |
569 | public void actionPerformed(ActionEvent arg0) | |
570 | { | |
571 | 0 | fr.ap.alignFrame.hideFeatureColumns(type, false); |
572 | 0 | fr.ap.av.sendSelection(); |
573 | } | |
574 | }); | |
575 | 0 | men.add(selCols); |
576 | 0 | men.add(clearCols); |
577 | 0 | men.add(hideCols); |
578 | 0 | men.add(hideOtherCols); |
579 | 0 | men.show(table, pt.x, pt.y); |
580 | } | |
581 | ||
582 | /** | |
583 | * Sort the sequences in the alignment by the number of features for the given | |
584 | * feature types (or all features if null) | |
585 | * | |
586 | * @param featureTypes | |
587 | */ | |
588 | 0 | protected void sortByDensity(List<String> featureTypes) |
589 | { | |
590 | 0 | af.avc.sortAlignmentByFeatureDensity(featureTypes); |
591 | } | |
592 | ||
593 | /** | |
594 | * Sort the sequences in the alignment by average score for the given feature | |
595 | * types (or all features if null) | |
596 | * | |
597 | * @param featureTypes | |
598 | */ | |
599 | 0 | protected void sortByScore(List<String> featureTypes) |
600 | { | |
601 | 0 | af.avc.sortAlignmentByFeatureScore(featureTypes); |
602 | } | |
603 | ||
604 | /** | |
605 | * Returns true if at least one feature type is visible. Else shows a warning | |
606 | * dialog and returns false. | |
607 | * | |
608 | * @param title | |
609 | * @return | |
610 | */ | |
611 | 0 | private boolean canSortBy(String title) |
612 | { | |
613 | 0 | if (fr.getDisplayedFeatureTypes().isEmpty()) |
614 | { | |
615 | 0 | JvOptionPane.showMessageDialog(this, |
616 | MessageManager.getString("label.no_features_to_sort_by"), | |
617 | title, JvOptionPane.OK_OPTION); | |
618 | 0 | return false; |
619 | } | |
620 | 0 | return true; |
621 | } | |
622 | ||
623 | 1 | @Override |
624 | synchronized public void discoverAllFeatureData() | |
625 | { | |
626 | 1 | Set<String> allGroups = new HashSet<>(); |
627 | 1 | AlignmentI alignment = af.getViewport().getAlignment(); |
628 | ||
629 | 2 | for (int i = 0; i < alignment.getHeight(); i++) |
630 | { | |
631 | 1 | SequenceI seq = alignment.getSequenceAt(i); |
632 | 1 | for (String group : seq.getFeatures().getFeatureGroups(true)) |
633 | { | |
634 | 1 | if (group != null && !allGroups.contains(group)) |
635 | { | |
636 | 1 | allGroups.add(group); |
637 | 1 | checkGroupState(group); |
638 | } | |
639 | } | |
640 | } | |
641 | ||
642 | 1 | resetTable(null); |
643 | ||
644 | 1 | validate(); |
645 | } | |
646 | ||
647 | /** | |
648 | * Synchronise gui group list and check visibility of group | |
649 | * | |
650 | * @param group | |
651 | * @return true if group is visible | |
652 | */ | |
653 | 3 | private boolean checkGroupState(String group) |
654 | { | |
655 | 3 | boolean visible = fr.checkGroupVisibility(group, true); |
656 | ||
657 | 3 | for (int g = 0; g < groupPanel.getComponentCount(); g++) |
658 | { | |
659 | 2 | if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) |
660 | { | |
661 | 2 | ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); |
662 | 2 | return visible; |
663 | } | |
664 | } | |
665 | ||
666 | 1 | final String grp = group; |
667 | 1 | final JCheckBox check = new JCheckBox(group, visible); |
668 | 1 | check.setFont(new Font("Serif", Font.BOLD, 12)); |
669 | 1 | check.setToolTipText(group); |
670 | 1 | check.addItemListener(new ItemListener() |
671 | { | |
672 | 0 | @Override |
673 | public void itemStateChanged(ItemEvent evt) | |
674 | { | |
675 | 0 | fr.setGroupVisibility(check.getText(), check.isSelected()); |
676 | 0 | resetTable(new String[] { grp }); |
677 | 0 | refreshDisplay(); |
678 | } | |
679 | }); | |
680 | 1 | groupPanel.add(check); |
681 | 1 | return visible; |
682 | } | |
683 | ||
684 | 2 | synchronized void resetTable(String[] groupChanged) |
685 | { | |
686 | 2 | if (resettingTable) |
687 | { | |
688 | 0 | return; |
689 | } | |
690 | 2 | resettingTable = true; |
691 | 2 | typeWidth = new Hashtable<>(); |
692 | // TODO: change avWidth calculation to 'per-sequence' average and use long | |
693 | // rather than float | |
694 | ||
695 | 2 | Set<String> displayableTypes = new HashSet<>(); |
696 | 2 | Set<String> foundGroups = new HashSet<>(); |
697 | ||
698 | /* | |
699 | * determine which feature types may be visible depending on | |
700 | * which groups are selected, and recompute average width data | |
701 | */ | |
702 | 4 | for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) |
703 | { | |
704 | ||
705 | 2 | SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); |
706 | ||
707 | /* | |
708 | * get the sequence's groups for positional features | |
709 | * and keep track of which groups are visible | |
710 | */ | |
711 | 2 | Set<String> groups = seq.getFeatures().getFeatureGroups(true); |
712 | 2 | Set<String> visibleGroups = new HashSet<>(); |
713 | 2 | for (String group : groups) |
714 | { | |
715 | 2 | if (group == null || checkGroupState(group)) |
716 | { | |
717 | 2 | visibleGroups.add(group); |
718 | } | |
719 | } | |
720 | 2 | foundGroups.addAll(groups); |
721 | ||
722 | /* | |
723 | * get distinct feature types for visible groups | |
724 | * record distinct visible types, and their count and total length | |
725 | */ | |
726 | 2 | Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true, |
727 | visibleGroups.toArray(new String[visibleGroups.size()])); | |
728 | 2 | for (String type : types) |
729 | { | |
730 | 10 | displayableTypes.add(type); |
731 | 10 | float[] avWidth = typeWidth.get(type); |
732 | 10 | if (avWidth == null) |
733 | { | |
734 | 10 | avWidth = new float[2]; |
735 | 10 | typeWidth.put(type, avWidth); |
736 | } | |
737 | // todo this could include features with a non-visible group | |
738 | // - do we greatly care? | |
739 | // todo should we include non-displayable features here, and only | |
740 | // update when features are added? | |
741 | 10 | avWidth[0] += seq.getFeatures().getFeatureCount(true, type); |
742 | 10 | avWidth[1] += seq.getFeatures().getTotalFeatureLength(type); |
743 | } | |
744 | } | |
745 | ||
746 | 2 | Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; |
747 | 2 | int dataIndex = 0; |
748 | ||
749 | 2 | if (fr.hasRenderOrder()) |
750 | { | |
751 | 2 | if (!handlingUpdate) |
752 | { | |
753 | 2 | fr.findAllFeatures(groupChanged != null); // prod to update |
754 | // colourschemes. but don't | |
755 | // affect display | |
756 | // First add the checks in the previous render order, | |
757 | // in case the window has been closed and reopened | |
758 | } | |
759 | 2 | List<String> frl = fr.getRenderOrder(); |
760 | 12 | for (int ro = frl.size() - 1; ro > -1; ro--) |
761 | { | |
762 | 10 | String type = frl.get(ro); |
763 | ||
764 | 10 | if (!displayableTypes.contains(type)) |
765 | { | |
766 | 0 | continue; |
767 | } | |
768 | ||
769 | 10 | data[dataIndex][TYPE_COLUMN] = type; |
770 | 10 | data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); |
771 | 10 | FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); |
772 | 10 | data[dataIndex][FILTER_COLUMN] = featureFilter == null |
773 | ? new FeatureMatcherSet() | |
774 | : featureFilter; | |
775 | 10 | data[dataIndex][SHOW_COLUMN] = Boolean.valueOf( |
776 | af.getViewport().getFeaturesDisplayed().isVisible(type)); | |
777 | 10 | dataIndex++; |
778 | 10 | displayableTypes.remove(type); |
779 | } | |
780 | } | |
781 | ||
782 | /* | |
783 | * process any extra features belonging only to | |
784 | * a group which was just selected | |
785 | */ | |
786 | 2 | while (!displayableTypes.isEmpty()) |
787 | { | |
788 | 0 | String type = displayableTypes.iterator().next(); |
789 | 0 | data[dataIndex][TYPE_COLUMN] = type; |
790 | ||
791 | 0 | data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); |
792 | 0 | if (data[dataIndex][COLOUR_COLUMN] == null) |
793 | { | |
794 | // "Colour has been updated in another view!!" | |
795 | 0 | fr.clearRenderOrder(); |
796 | 0 | return; |
797 | } | |
798 | 0 | FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); |
799 | 0 | data[dataIndex][FILTER_COLUMN] = featureFilter == null |
800 | ? new FeatureMatcherSet() | |
801 | : featureFilter; | |
802 | 0 | data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true); |
803 | 0 | dataIndex++; |
804 | 0 | displayableTypes.remove(type); |
805 | } | |
806 | ||
807 | 2 | if (originalData == null) |
808 | { | |
809 | 1 | originalData = new Object[data.length][COLUMN_COUNT]; |
810 | 6 | for (int i = 0; i < data.length; i++) |
811 | { | |
812 | 5 | System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); |
813 | } | |
814 | } | |
815 | else | |
816 | { | |
817 | 1 | updateOriginalData(data); |
818 | } | |
819 | ||
820 | 2 | table.setModel(new FeatureTableModel(data)); |
821 | 2 | table.getColumnModel().getColumn(0).setPreferredWidth(200); |
822 | ||
823 | 2 | groupPanel.setLayout( |
824 | new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); | |
825 | 2 | pruneGroups(foundGroups); |
826 | 2 | groupPanel.validate(); |
827 | ||
828 | 2 | updateFeatureRenderer(data, groupChanged != null); |
829 | 2 | resettingTable = false; |
830 | } | |
831 | ||
832 | /** | |
833 | * Updates 'originalData' (used for restore on Cancel) if we detect that | |
834 | * changes have been made outwith this dialog | |
835 | * <ul> | |
836 | * <li>a new feature type added (and made visible)</li> | |
837 | * <li>a feature colour changed (in the Amend Features dialog)</li> | |
838 | * </ul> | |
839 | * | |
840 | * @param foundData | |
841 | */ | |
842 | 1 | protected void updateOriginalData(Object[][] foundData) |
843 | { | |
844 | // todo LinkedHashMap instead of Object[][] would be nice | |
845 | ||
846 | 1 | Object[][] currentData = ((FeatureTableModel) table.getModel()) |
847 | .getData(); | |
848 | 1 | for (Object[] row : foundData) |
849 | { | |
850 | 5 | String type = (String) row[TYPE_COLUMN]; |
851 | 5 | boolean found = false; |
852 | 5 | for (Object[] current : currentData) |
853 | { | |
854 | 15 | if (type.equals(current[TYPE_COLUMN])) |
855 | { | |
856 | 5 | found = true; |
857 | /* | |
858 | * currently dependent on object equality here; | |
859 | * really need an equals method on FeatureColour | |
860 | */ | |
861 | 5 | if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN])) |
862 | { | |
863 | /* | |
864 | * feature colour has changed externally - update originalData | |
865 | */ | |
866 | 5 | for (Object[] original : originalData) |
867 | { | |
868 | 15 | if (type.equals(original[TYPE_COLUMN])) |
869 | { | |
870 | 5 | original[COLOUR_COLUMN] = row[COLOUR_COLUMN]; |
871 | 5 | break; |
872 | } | |
873 | } | |
874 | } | |
875 | 5 | break; |
876 | } | |
877 | } | |
878 | 5 | if (!found) |
879 | { | |
880 | /* | |
881 | * new feature detected - add to original data (on top) | |
882 | */ | |
883 | 0 | Object[][] newData = new Object[originalData.length |
884 | + 1][COLUMN_COUNT]; | |
885 | 0 | for (int i = 0; i < originalData.length; i++) |
886 | { | |
887 | 0 | System.arraycopy(originalData[i], 0, newData[i + 1], 0, |
888 | COLUMN_COUNT); | |
889 | } | |
890 | 0 | newData[0] = row; |
891 | 0 | originalData = newData; |
892 | } | |
893 | } | |
894 | } | |
895 | ||
896 | /** | |
897 | * Remove from the groups panel any checkboxes for groups that are not in the | |
898 | * foundGroups set. This enables removing a group from the display when the | |
899 | * last feature in that group is deleted. | |
900 | * | |
901 | * @param foundGroups | |
902 | */ | |
903 | 2 | protected void pruneGroups(Set<String> foundGroups) |
904 | { | |
905 | 4 | for (int g = 0; g < groupPanel.getComponentCount(); g++) |
906 | { | |
907 | 2 | JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); |
908 | 2 | if (!foundGroups.contains(checkbox.getText())) |
909 | { | |
910 | 0 | groupPanel.remove(checkbox); |
911 | } | |
912 | } | |
913 | } | |
914 | ||
915 | /** | |
916 | * reorder data based on the featureRenderers global priority list. | |
917 | * | |
918 | * @param data | |
919 | */ | |
920 | 1 | private void ensureOrder(Object[][] data) |
921 | { | |
922 | 1 | boolean sort = false; |
923 | 1 | float[] order = new float[data.length]; |
924 | 6 | for (int i = 0; i < order.length; i++) |
925 | { | |
926 | 5 | order[i] = fr.getOrder(data[i][0].toString()); |
927 | 5 | if (order[i] < 0) |
928 | { | |
929 | 0 | order[i] = fr.setOrder(data[i][0].toString(), i / order.length); |
930 | } | |
931 | 5 | if (i > 1) |
932 | { | |
933 | 3 | sort = sort || order[i - 1] > order[i]; |
934 | } | |
935 | } | |
936 | 1 | if (sort) |
937 | { | |
938 | 0 | jalview.util.QuickSort.sort(order, data); |
939 | } | |
940 | } | |
941 | ||
942 | /** | |
943 | * Offers a file chooser dialog, and then loads the feature colours and | |
944 | * filters from file in XML format and unmarshals to Jalview feature settings | |
945 | */ | |
946 | 0 | void load() |
947 | { | |
948 | 0 | JalviewFileChooser chooser = new JalviewFileChooser("fc", |
949 | SEQUENCE_FEATURE_COLOURS); | |
950 | 0 | chooser.setFileView(new JalviewFileView()); |
951 | 0 | chooser.setDialogTitle( |
952 | MessageManager.getString("label.load_feature_colours")); | |
953 | 0 | chooser.setToolTipText(MessageManager.getString("action.load")); |
954 | 0 | chooser.setResponseHandler(0, () -> { |
955 | 0 | File file = chooser.getSelectedFile(); |
956 | 0 | load(file); |
957 | }); | |
958 | 0 | chooser.showOpenDialog(this); |
959 | } | |
960 | ||
961 | 0 | public static boolean loadFeatureSettingsFile(FeatureRenderer fr, |
962 | File file) throws Exception | |
963 | { | |
964 | 0 | InputStreamReader in = new InputStreamReader(new FileInputStream(file), |
965 | "UTF-8"); | |
966 | 0 | return loadFeatureSettingsFile(fr, in); |
967 | } | |
968 | ||
969 | 1 | public static void loadFeatureSettingsFile( |
970 | FeatureRenderer featureRenderer, Object fileObject, | |
971 | DataSourceType sourceType) throws Exception | |
972 | { | |
973 | 1 | FileParse fp = new FileParse(fileObject, sourceType); |
974 | 1 | loadFeatureSettingsFile(featureRenderer, fp.getReader()); |
975 | } | |
976 | ||
977 | 1 | private static boolean loadFeatureSettingsFile(FeatureRenderer fr, |
978 | Reader in) throws Exception | |
979 | { | |
980 | 1 | JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.jalview"); |
981 | 1 | javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); |
982 | 1 | XMLStreamReader streamReader = XMLInputFactory.newInstance() |
983 | .createXMLStreamReader(in); | |
984 | 1 | JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader, |
985 | JalviewUserColours.class); | |
986 | 1 | JalviewUserColours jucs = jbe.getValue(); |
987 | ||
988 | // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); | |
989 | ||
990 | /* | |
991 | * load feature colours | |
992 | */ | |
993 | 6 | for (int i = jucs.getColour().size() - 1; i >= 0; i--) |
994 | { | |
995 | 5 | Colour newcol = jucs.getColour().get(i); |
996 | 5 | FeatureColourI colour = jalview.project.Jalview2XML |
997 | .parseColour(newcol); | |
998 | 5 | fr.setColour(newcol.getName(), colour); |
999 | 5 | fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); |
1000 | } | |
1001 | ||
1002 | /* | |
1003 | * load feature filters; loaded filters will replace any that are | |
1004 | * currently defined, other defined filters are left unchanged | |
1005 | */ | |
1006 | 4 | for (int i = 0; i < jucs.getFilter().size(); i++) |
1007 | { | |
1008 | 3 | Filter filterModel = jucs.getFilter().get(i); |
1009 | 3 | String featureType = filterModel.getFeatureType(); |
1010 | 3 | FeatureMatcherSetI filter = jalview.project.Jalview2XML |
1011 | .parseFilter(featureType, filterModel.getMatcherSet()); | |
1012 | 3 | if (!filter.isEmpty()) |
1013 | { | |
1014 | 3 | fr.setFeatureFilter(featureType, filter); |
1015 | } | |
1016 | } | |
1017 | 1 | return true; |
1018 | } | |
1019 | ||
1020 | /** | |
1021 | * Loads feature colours and filters from XML stored in the given file | |
1022 | * | |
1023 | * @param file | |
1024 | */ | |
1025 | 1 | void load(File file) |
1026 | { | |
1027 | 1 | load(file, DataSourceType.FILE); |
1028 | } | |
1029 | ||
1030 | /** | |
1031 | * Loads feature colours and filters from XML at a specified source | |
1032 | * | |
1033 | * @param file | |
1034 | * - string or file or other object that allows FileParse to be | |
1035 | * created | |
1036 | */ | |
1037 | 1 | void load(Object file, DataSourceType sourceType) |
1038 | { | |
1039 | 1 | try |
1040 | { | |
1041 | 1 | loadFeatureSettingsFile(fr, file, sourceType); |
1042 | /* | |
1043 | * update feature settings table | |
1044 | */ | |
1045 | 1 | if (table != null) |
1046 | { | |
1047 | 1 | resetTable(null); |
1048 | 1 | Object[][] data = ((FeatureTableModel) table.getModel()).getData(); |
1049 | 1 | ensureOrder(data); |
1050 | 1 | updateFeatureRenderer(data, false); |
1051 | 1 | table.repaint(); |
1052 | } | |
1053 | } catch (Exception ex) | |
1054 | { | |
1055 | 0 | jalview.bin.Console |
1056 | .outPrintln("Error loading User Colour File\n" + ex); | |
1057 | } | |
1058 | } | |
1059 | ||
1060 | /** | |
1061 | * Offers a file chooser dialog, and then saves the current feature colours | |
1062 | * and any filters to the selected file in XML format | |
1063 | */ | |
1064 | 0 | void save() |
1065 | { | |
1066 | 0 | JalviewFileChooser chooser = new JalviewFileChooser("fc", |
1067 | SEQUENCE_FEATURE_COLOURS); | |
1068 | 0 | chooser.setFileView(new JalviewFileView()); |
1069 | 0 | chooser.setDialogTitle( |
1070 | MessageManager.getString("label.save_feature_colours")); | |
1071 | 0 | chooser.setToolTipText(MessageManager.getString("action.save")); |
1072 | 0 | int option = chooser.showSaveDialog(this); |
1073 | 0 | if (option == JalviewFileChooser.APPROVE_OPTION) |
1074 | { | |
1075 | 0 | File file = chooser.getSelectedFile(); |
1076 | 0 | save(file); |
1077 | } | |
1078 | } | |
1079 | ||
1080 | /** | |
1081 | * Saves feature colours and filters to the given file | |
1082 | * | |
1083 | * @param file | |
1084 | */ | |
1085 | 1 | void save(File file) |
1086 | { | |
1087 | 1 | JalviewUserColours ucs = new JalviewUserColours(); |
1088 | 1 | ucs.setSchemeName("Sequence Features"); |
1089 | 1 | try |
1090 | { | |
1091 | 1 | PrintWriter out = new PrintWriter( |
1092 | new OutputStreamWriter(new FileOutputStream(file), "UTF-8")); | |
1093 | ||
1094 | /* | |
1095 | * sort feature types by colour order, from 0 (highest) | |
1096 | * to 1 (lowest) | |
1097 | */ | |
1098 | 1 | Set<String> fr_colours = fr.getAllFeatureColours(); |
1099 | 1 | String[] sortedTypes = fr_colours |
1100 | .toArray(new String[fr_colours.size()]); | |
1101 | 1 | Arrays.sort(sortedTypes, new Comparator<String>() |
1102 | { | |
1103 | 4 | @Override |
1104 | public int compare(String type1, String type2) | |
1105 | { | |
1106 | 4 | return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); |
1107 | } | |
1108 | }); | |
1109 | ||
1110 | /* | |
1111 | * save feature colours | |
1112 | */ | |
1113 | 1 | for (String featureType : sortedTypes) |
1114 | { | |
1115 | 5 | FeatureColourI fcol = fr.getFeatureStyle(featureType); |
1116 | 5 | Colour col = jalview.project.Jalview2XML.marshalColour(featureType, |
1117 | fcol); | |
1118 | 5 | ucs.getColour().add(col); |
1119 | } | |
1120 | ||
1121 | /* | |
1122 | * save any feature filters | |
1123 | */ | |
1124 | 1 | for (String featureType : sortedTypes) |
1125 | { | |
1126 | 5 | FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); |
1127 | 5 | if (filter != null && !filter.isEmpty()) |
1128 | { | |
1129 | 3 | Iterator<FeatureMatcherI> iterator = filter.getMatchers() |
1130 | .iterator(); | |
1131 | 3 | FeatureMatcherI firstMatcher = iterator.next(); |
1132 | 3 | jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML |
1133 | .marshalFilter(firstMatcher, iterator, filter.isAnded()); | |
1134 | 3 | Filter filterModel = new Filter(); |
1135 | 3 | filterModel.setFeatureType(featureType); |
1136 | 3 | filterModel.setMatcherSet(ms); |
1137 | 3 | ucs.getFilter().add(filterModel); |
1138 | } | |
1139 | } | |
1140 | 1 | JAXBContext jaxbContext = JAXBContext |
1141 | .newInstance(JalviewUserColours.class); | |
1142 | 1 | Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); |
1143 | 1 | jaxbMarshaller.marshal( |
1144 | new ObjectFactory().createJalviewUserColours(ucs), out); | |
1145 | ||
1146 | // jaxbMarshaller.marshal(object, pout); | |
1147 | // marshaller.marshal(object); | |
1148 | 1 | out.flush(); |
1149 | ||
1150 | // ucs.marshal(out); | |
1151 | 1 | out.close(); |
1152 | } catch (Exception ex) | |
1153 | { | |
1154 | 0 | ex.printStackTrace(); |
1155 | } | |
1156 | } | |
1157 | ||
1158 | 0 | public void invertSelection() |
1159 | { | |
1160 | 0 | Object[][] data = ((FeatureTableModel) table.getModel()).getData(); |
1161 | 0 | for (int i = 0; i < data.length; i++) |
1162 | { | |
1163 | 0 | data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; |
1164 | } | |
1165 | 0 | updateFeatureRenderer(data, true); |
1166 | 0 | table.repaint(); |
1167 | } | |
1168 | ||
1169 | 0 | public void orderByAvWidth() |
1170 | { | |
1171 | 0 | if (table == null || table.getModel() == null) |
1172 | { | |
1173 | 0 | return; |
1174 | } | |
1175 | 0 | Object[][] data = ((FeatureTableModel) table.getModel()).getData(); |
1176 | 0 | float[] width = new float[data.length]; |
1177 | 0 | float[] awidth; |
1178 | 0 | float max = 0; |
1179 | ||
1180 | 0 | for (int i = 0; i < data.length; i++) |
1181 | { | |
1182 | 0 | awidth = typeWidth.get(data[i][TYPE_COLUMN]); |
1183 | 0 | if (awidth[0] > 0) |
1184 | { | |
1185 | 0 | width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better |
1186 | // weight - but have to make per | |
1187 | // sequence, too (awidth[2]) | |
1188 | // if (width[i]==1) // hack to distinguish single width sequences. | |
1189 | } | |
1190 | else | |
1191 | { | |
1192 | 0 | width[i] = 0; |
1193 | } | |
1194 | 0 | if (max < width[i]) |
1195 | { | |
1196 | 0 | max = width[i]; |
1197 | } | |
1198 | } | |
1199 | 0 | boolean sort = false; |
1200 | 0 | for (int i = 0; i < width.length; i++) |
1201 | { | |
1202 | // awidth = (float[]) typeWidth.get(data[i][0]); | |
1203 | 0 | if (width[i] == 0) |
1204 | { | |
1205 | 0 | width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString()); |
1206 | 0 | if (width[i] < 0) |
1207 | { | |
1208 | 0 | width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(), |
1209 | i / data.length); | |
1210 | } | |
1211 | } | |
1212 | else | |
1213 | { | |
1214 | 0 | width[i] /= max; // normalize |
1215 | 0 | fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for |
1216 | // later | |
1217 | } | |
1218 | 0 | if (i > 0) |
1219 | { | |
1220 | 0 | sort = sort || width[i - 1] > width[i]; |
1221 | } | |
1222 | } | |
1223 | 0 | if (sort) |
1224 | { | |
1225 | 0 | jalview.util.QuickSort.sort(width, data); |
1226 | // update global priority order | |
1227 | } | |
1228 | ||
1229 | 0 | updateFeatureRenderer(data, false); |
1230 | 0 | table.repaint(); |
1231 | } | |
1232 | ||
1233 | /** | |
1234 | * close ourselves but leave any existing UI handlers (e.g a CDS/Protein | |
1235 | * tabbed feature settings dialog) intact | |
1236 | */ | |
1237 | 0 | public void closeOldSettings() |
1238 | { | |
1239 | 0 | closeDialog(false); |
1240 | } | |
1241 | ||
1242 | /** | |
1243 | * close the feature settings dialog (and any containing frame) | |
1244 | */ | |
1245 | 0 | public void close() |
1246 | { | |
1247 | 0 | closeDialog(true); |
1248 | } | |
1249 | ||
1250 | 0 | private void closeDialog(boolean closeContainingFrame) |
1251 | { | |
1252 | 0 | try |
1253 | { | |
1254 | 0 | if (frame != null) |
1255 | { | |
1256 | 0 | af.setFeatureSettingsGeometry(frame.getBounds()); |
1257 | 0 | frame.setClosed(true); |
1258 | } | |
1259 | else | |
1260 | { | |
1261 | 0 | SplitContainerI sc = af.getSplitViewContainer(); |
1262 | 0 | sc.closeFeatureSettings(this, closeContainingFrame); |
1263 | 0 | af.featureSettings = null; |
1264 | } | |
1265 | } catch (Exception exe) | |
1266 | { | |
1267 | } | |
1268 | ||
1269 | } | |
1270 | ||
1271 | 0 | public void updateFeatureRenderer(Object[][] data) |
1272 | { | |
1273 | 0 | updateFeatureRenderer(data, true); |
1274 | } | |
1275 | ||
1276 | /** | |
1277 | * Update the priority order of features; only repaint if this changed the | |
1278 | * order of visible features | |
1279 | * | |
1280 | * @param data | |
1281 | * @param visibleNew | |
1282 | */ | |
1283 | 3 | void updateFeatureRenderer(Object[][] data, boolean visibleNew) |
1284 | { | |
1285 | 3 | FeatureSettingsBean[] rowData = getTableAsBeans(data); |
1286 | ||
1287 | 3 | if (fr.setFeaturePriority(rowData, visibleNew)) |
1288 | { | |
1289 | 0 | refreshDisplay(); |
1290 | } | |
1291 | } | |
1292 | ||
1293 | /** | |
1294 | * Converts table data into an array of data beans | |
1295 | */ | |
1296 | 3 | private FeatureSettingsBean[] getTableAsBeans(Object[][] data) |
1297 | { | |
1298 | 3 | FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; |
1299 | 18 | for (int i = 0; i < data.length; i++) |
1300 | { | |
1301 | 15 | String type = (String) data[i][TYPE_COLUMN]; |
1302 | 15 | FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; |
1303 | 15 | FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN]; |
1304 | 15 | Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; |
1305 | 15 | rowData[i] = new FeatureSettingsBean(type, colour, theFilter, |
1306 | isShown); | |
1307 | } | |
1308 | 3 | return rowData; |
1309 | } | |
1310 | ||
1311 | 1 | private void jbInit() throws Exception |
1312 | { | |
1313 | 1 | this.setLayout(new BorderLayout()); |
1314 | ||
1315 | 1 | final boolean hasComplement = af.getViewport() |
1316 | .getCodingComplement() != null; | |
1317 | ||
1318 | 1 | JPanel settingsPane = new JPanel(); |
1319 | 1 | settingsPane.setLayout(new BorderLayout()); |
1320 | ||
1321 | 1 | JPanel bigPanel = new JPanel(); |
1322 | 1 | bigPanel.setLayout(new BorderLayout()); |
1323 | ||
1324 | 1 | groupPanel = new JPanel(); |
1325 | 1 | bigPanel.add(groupPanel, BorderLayout.NORTH); |
1326 | ||
1327 | 1 | JButton invert = new JButton( |
1328 | MessageManager.getString("label.invert_selection")); | |
1329 | 1 | invert.setFont(JvSwingUtils.getLabelFont()); |
1330 | 1 | invert.addActionListener(new ActionListener() |
1331 | { | |
1332 | 0 | @Override |
1333 | public void actionPerformed(ActionEvent e) | |
1334 | { | |
1335 | 0 | invertSelection(); |
1336 | } | |
1337 | }); | |
1338 | ||
1339 | 1 | JButton optimizeOrder = new JButton( |
1340 | MessageManager.getString("label.optimise_order")); | |
1341 | 1 | optimizeOrder.setFont(JvSwingUtils.getLabelFont()); |
1342 | 1 | optimizeOrder.addActionListener(new ActionListener() |
1343 | { | |
1344 | 0 | @Override |
1345 | public void actionPerformed(ActionEvent e) | |
1346 | { | |
1347 | 0 | orderByAvWidth(); |
1348 | } | |
1349 | }); | |
1350 | ||
1351 | 1 | final String byScoreLabel = MessageManager |
1352 | .getString("label.seq_sort_by_score"); | |
1353 | 1 | JButton sortByScore = new JButton(byScoreLabel); |
1354 | 1 | sortByScore.setFont(JvSwingUtils.getLabelFont()); |
1355 | 1 | sortByScore.addActionListener(new ActionListener() |
1356 | { | |
1357 | 0 | @Override |
1358 | public void actionPerformed(ActionEvent e) | |
1359 | { | |
1360 | 0 | if (canSortBy(byScoreLabel)) |
1361 | { | |
1362 | 0 | sortByScore(null); |
1363 | } | |
1364 | } | |
1365 | }); | |
1366 | 1 | final String byDensityLabel = MessageManager |
1367 | .getString("label.sequence_sort_by_density"); | |
1368 | 1 | JButton sortByDens = new JButton(byDensityLabel); |
1369 | 1 | sortByDens.setFont(JvSwingUtils.getLabelFont()); |
1370 | 1 | sortByDens.addActionListener(new ActionListener() |
1371 | { | |
1372 | 0 | @Override |
1373 | public void actionPerformed(ActionEvent e) | |
1374 | { | |
1375 | 0 | if (canSortBy(byDensityLabel)) |
1376 | { | |
1377 | 0 | sortByDensity(null); |
1378 | } | |
1379 | } | |
1380 | }); | |
1381 | ||
1382 | 1 | JButton help = new JButton(MessageManager.getString("action.help")); |
1383 | 1 | help.setFont(JvSwingUtils.getLabelFont()); |
1384 | 1 | help.addActionListener(new ActionListener() |
1385 | { | |
1386 | 0 | @Override |
1387 | public void actionPerformed(ActionEvent e) | |
1388 | { | |
1389 | 0 | try |
1390 | { | |
1391 | 0 | Help.showHelpWindow(HelpId.SequenceFeatureSettings); |
1392 | } catch (HelpSetException e1) | |
1393 | { | |
1394 | 0 | e1.printStackTrace(); |
1395 | } | |
1396 | } | |
1397 | }); | |
1398 | // Cancel for a SplitFrame should just revert changes to the currently | |
1399 | // displayed | |
1400 | // settings. May want to do this for either or both - so need a splitview | |
1401 | // feature settings cancel/OK. | |
1402 | 1 | JButton cancel = new JButton(MessageManager |
1403 | 1 | .getString(hasComplement ? "action.revert" : "action.cancel")); |
1404 | 1 | cancel.setToolTipText(MessageManager.getString(hasComplement |
1405 | ? "action.undo_changes_to_feature_settings" | |
1406 | : "action.undo_changes_to_feature_settings_and_close_the_dialog")); | |
1407 | 1 | cancel.setFont(JvSwingUtils.getLabelFont()); |
1408 | // TODO: disable cancel (and apply!) until current settings are different | |
1409 | 1 | cancel.addActionListener(new ActionListener() |
1410 | { | |
1411 | 0 | @Override |
1412 | public void actionPerformed(ActionEvent e) | |
1413 | { | |
1414 | 0 | revert(); |
1415 | 0 | refreshDisplay(); |
1416 | 0 | if (!hasComplement) |
1417 | { | |
1418 | 0 | close(); |
1419 | } | |
1420 | } | |
1421 | }); | |
1422 | // Cancel for the whole dialog should cancel both CDS and Protein. | |
1423 | // OK for an individual feature settings just applies changes, but dialog | |
1424 | // remains open | |
1425 | 1 | JButton ok = new JButton(MessageManager |
1426 | 1 | .getString(hasComplement ? "action.apply" : "action.ok")); |
1427 | 1 | ok.setFont(JvSwingUtils.getLabelFont()); |
1428 | 1 | ok.addActionListener(new ActionListener() |
1429 | { | |
1430 | 0 | @Override |
1431 | public void actionPerformed(ActionEvent e) | |
1432 | { | |
1433 | 0 | if (!hasComplement) |
1434 | { | |
1435 | 0 | close(); |
1436 | } | |
1437 | else | |
1438 | { | |
1439 | 0 | storeOriginalSettings(); |
1440 | } | |
1441 | } | |
1442 | }); | |
1443 | ||
1444 | 1 | JButton loadColours = new JButton( |
1445 | MessageManager.getString("label.load_colours")); | |
1446 | 1 | loadColours.setFont(JvSwingUtils.getLabelFont()); |
1447 | 1 | loadColours.setToolTipText( |
1448 | MessageManager.getString("label.load_colours_tooltip")); | |
1449 | 1 | loadColours.addActionListener(new ActionListener() |
1450 | { | |
1451 | 0 | @Override |
1452 | public void actionPerformed(ActionEvent e) | |
1453 | { | |
1454 | 0 | load(); |
1455 | } | |
1456 | }); | |
1457 | ||
1458 | 1 | JButton saveColours = new JButton( |
1459 | MessageManager.getString("label.save_colours")); | |
1460 | 1 | saveColours.setFont(JvSwingUtils.getLabelFont()); |
1461 | 1 | saveColours.setToolTipText( |
1462 | MessageManager.getString("label.save_colours_tooltip")); | |
1463 | 1 | saveColours.addActionListener(new ActionListener() |
1464 | { | |
1465 | 0 | @Override |
1466 | public void actionPerformed(ActionEvent e) | |
1467 | { | |
1468 | 0 | save(); |
1469 | } | |
1470 | }); | |
1471 | 1 | transparency.addChangeListener(new ChangeListener() |
1472 | { | |
1473 | 1 | @Override |
1474 | public void stateChanged(ChangeEvent evt) | |
1475 | { | |
1476 | 1 | if (!inConstruction) |
1477 | { | |
1478 | 0 | fr.setTransparency((100 - transparency.getValue()) / 100f); |
1479 | 0 | refreshDisplay(); |
1480 | } | |
1481 | } | |
1482 | }); | |
1483 | ||
1484 | 1 | transparency.setMaximum(70); |
1485 | 1 | transparency.setToolTipText( |
1486 | MessageManager.getString("label.transparency_tip")); | |
1487 | ||
1488 | 1 | boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); |
1489 | 1 | String text = MessageManager |
1490 | .formatMessage("label.show_linked_features", | |
1491 | 1 | nucleotide |
1492 | ? MessageManager.getString("label.protein") | |
1493 | .toLowerCase(Locale.ROOT) | |
1494 | : "CDS"); | |
1495 | 1 | showComplement = new JCheckBox(text); |
1496 | 1 | showComplement.addActionListener(new ActionListener() |
1497 | { | |
1498 | 0 | @Override |
1499 | public void actionPerformed(ActionEvent e) | |
1500 | { | |
1501 | 0 | af.getViewport() |
1502 | .setShowComplementFeatures(showComplement.isSelected()); | |
1503 | 0 | refreshDisplay(); |
1504 | } | |
1505 | }); | |
1506 | ||
1507 | 1 | showComplementOnTop = new JCheckBox( |
1508 | MessageManager.getString("label.on_top")); | |
1509 | 1 | showComplementOnTop.addActionListener(new ActionListener() |
1510 | { | |
1511 | 0 | @Override |
1512 | public void actionPerformed(ActionEvent e) | |
1513 | { | |
1514 | 0 | af.getViewport().setShowComplementFeaturesOnTop( |
1515 | showComplementOnTop.isSelected()); | |
1516 | 0 | refreshDisplay(); |
1517 | } | |
1518 | }); | |
1519 | ||
1520 | 1 | updateComplementButtons(); |
1521 | ||
1522 | 1 | JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); |
1523 | 1 | bigPanel.add(lowerPanel, BorderLayout.SOUTH); |
1524 | ||
1525 | 1 | JPanel transbuttons = new JPanel(new GridLayout(5, 1)); |
1526 | 1 | transbuttons.add(optimizeOrder); |
1527 | 1 | transbuttons.add(invert); |
1528 | 1 | transbuttons.add(sortByScore); |
1529 | 1 | transbuttons.add(sortByDens); |
1530 | 1 | transbuttons.add(help); |
1531 | ||
1532 | 1 | JPanel transPanelLeft = new JPanel( |
1533 | 1 | new GridLayout(hasComplement ? 4 : 2, 1)); |
1534 | 1 | transPanelLeft.add(new JLabel(" Colour transparency" + ":")); |
1535 | 1 | transPanelLeft.add(transparency); |
1536 | 1 | if (hasComplement) |
1537 | { | |
1538 | 0 | JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT)); |
1539 | 0 | cp.add(showComplement); |
1540 | 0 | cp.add(showComplementOnTop); |
1541 | 0 | transPanelLeft.add(cp); |
1542 | } | |
1543 | 1 | lowerPanel.add(transPanelLeft); |
1544 | 1 | lowerPanel.add(transbuttons); |
1545 | ||
1546 | 1 | JPanel buttonPanel = new JPanel(); |
1547 | 1 | buttonPanel.add(ok); |
1548 | 1 | buttonPanel.add(cancel); |
1549 | 1 | buttonPanel.add(loadColours); |
1550 | 1 | buttonPanel.add(saveColours); |
1551 | 1 | bigPanel.add(scrollPane, BorderLayout.CENTER); |
1552 | 1 | settingsPane.add(bigPanel, BorderLayout.CENTER); |
1553 | 1 | settingsPane.add(buttonPanel, BorderLayout.SOUTH); |
1554 | 1 | this.add(settingsPane); |
1555 | } | |
1556 | ||
1557 | /** | |
1558 | * Repaints alignment, structure and overview (if shown). If there is a | |
1559 | * complementary view which is showing this view's features, then also | |
1560 | * repaints that. | |
1561 | */ | |
1562 | 0 | void refreshDisplay() |
1563 | { | |
1564 | 0 | af.alignPanel.paintAlignment(true, true); |
1565 | 0 | AlignViewportI complement = af.getViewport().getCodingComplement(); |
1566 | 0 | if (complement != null && complement.isShowComplementFeatures()) |
1567 | { | |
1568 | 0 | AlignFrame af2 = Desktop.getAlignFrameFor(complement); |
1569 | 0 | af2.alignPanel.paintAlignment(true, true); |
1570 | } | |
1571 | } | |
1572 | ||
1573 | /** | |
1574 | * Answers a suitable tooltip to show on the colour cell of the table | |
1575 | * | |
1576 | * @param fcol | |
1577 | * @param withHint | |
1578 | * if true include 'click to edit' and similar text | |
1579 | * @return | |
1580 | */ | |
1581 | 9 | public static String getColorTooltip(FeatureColourI fcol, |
1582 | boolean withHint) | |
1583 | { | |
1584 | 9 | if (fcol == null) |
1585 | { | |
1586 | 1 | return null; |
1587 | } | |
1588 | 8 | if (fcol.isSimpleColour()) |
1589 | { | |
1590 | 2 | return withHint ? BASE_TOOLTIP : null; |
1591 | } | |
1592 | 6 | String description = fcol.getDescription(); |
1593 | 6 | description = description.replaceAll("<", "<"); |
1594 | 6 | description = description.replaceAll(">", ">"); |
1595 | 6 | StringBuilder tt = new StringBuilder(description); |
1596 | 6 | if (withHint) |
1597 | { | |
1598 | 3 | tt.append("<br>").append(BASE_TOOLTIP).append("</br>"); |
1599 | } | |
1600 | 6 | return JvSwingUtils.wrapTooltip(true, tt.toString()); |
1601 | } | |
1602 | ||
1603 | 0 | public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, |
1604 | int w, int h) | |
1605 | { | |
1606 | 0 | boolean thr = false; |
1607 | 0 | StringBuilder tx = new StringBuilder(); |
1608 | ||
1609 | 0 | if (gcol.isColourByAttribute()) |
1610 | { | |
1611 | 0 | tx.append(FeatureMatcher |
1612 | .toAttributeDisplayName(gcol.getAttributeName())); | |
1613 | } | |
1614 | 0 | else if (!gcol.isColourByLabel()) |
1615 | { | |
1616 | 0 | tx.append(MessageManager.getString("label.score")); |
1617 | } | |
1618 | 0 | tx.append(" "); |
1619 | 0 | if (gcol.isAboveThreshold()) |
1620 | { | |
1621 | 0 | thr = true; |
1622 | 0 | tx.append(">"); |
1623 | } | |
1624 | 0 | if (gcol.isBelowThreshold()) |
1625 | { | |
1626 | 0 | thr = true; |
1627 | 0 | tx.append("<"); |
1628 | } | |
1629 | 0 | if (gcol.isColourByLabel()) |
1630 | { | |
1631 | 0 | if (thr) |
1632 | { | |
1633 | 0 | tx.append(" "); |
1634 | } | |
1635 | 0 | if (!gcol.isColourByAttribute()) |
1636 | { | |
1637 | 0 | tx.append("Label"); |
1638 | } | |
1639 | 0 | comp.setIcon(null); |
1640 | } | |
1641 | else | |
1642 | { | |
1643 | 0 | Color newColor = gcol.getMaxColour(); |
1644 | 0 | comp.setBackground(newColor); |
1645 | // jalview.bin.Console.errPrintln("Width is " + w / 2); | |
1646 | 0 | Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); |
1647 | 0 | comp.setIcon(ficon); |
1648 | // tt+="RGB value: Max (" + newColor.getRed() + ", " | |
1649 | // + newColor.getGreen() + ", " + newColor.getBlue() | |
1650 | // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen() | |
1651 | // + ", " + minCol.getBlue() + ")"); | |
1652 | } | |
1653 | 0 | comp.setHorizontalAlignment(SwingConstants.CENTER); |
1654 | 0 | comp.setText(tx.toString()); |
1655 | } | |
1656 | ||
1657 | // /////////////////////////////////////////////////////////////////////// | |
1658 | // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html | |
1659 | // /////////////////////////////////////////////////////////////////////// | |
1660 | class FeatureTableModel extends AbstractTableModel | |
1661 | { | |
1662 | private String[] columnNames = { | |
1663 | MessageManager.getString("label.feature_type"), | |
1664 | MessageManager.getString("action.colour"), | |
1665 | MessageManager.getString("label.configuration"), | |
1666 | MessageManager.getString("label.show") }; | |
1667 | ||
1668 | private Object[][] data; | |
1669 | ||
1670 | 2 | FeatureTableModel(Object[][] data) |
1671 | { | |
1672 | 2 | this.data = data; |
1673 | } | |
1674 | ||
1675 | 2 | public Object[][] getData() |
1676 | { | |
1677 | 2 | return data; |
1678 | } | |
1679 | ||
1680 | 0 | public void setData(Object[][] data) |
1681 | { | |
1682 | 0 | this.data = data; |
1683 | } | |
1684 | ||
1685 | 10 | @Override |
1686 | public int getColumnCount() | |
1687 | { | |
1688 | 10 | return columnNames.length; |
1689 | } | |
1690 | ||
1691 | 0 | public Object[] getRow(int row) |
1692 | { | |
1693 | 0 | return data[row]; |
1694 | } | |
1695 | ||
1696 | 14 | @Override |
1697 | public int getRowCount() | |
1698 | { | |
1699 | 14 | return data.length; |
1700 | } | |
1701 | ||
1702 | 8 | @Override |
1703 | public String getColumnName(int col) | |
1704 | { | |
1705 | 8 | return columnNames[col]; |
1706 | } | |
1707 | ||
1708 | 0 | @Override |
1709 | public Object getValueAt(int row, int col) | |
1710 | { | |
1711 | 0 | return data[row][col]; |
1712 | } | |
1713 | ||
1714 | /** | |
1715 | * Answers the class of column c of the table | |
1716 | */ | |
1717 | 0 | @Override |
1718 | public Class<?> getColumnClass(int c) | |
1719 | { | |
1720 | 0 | switch (c) |
1721 | { | |
1722 | 0 | case TYPE_COLUMN: |
1723 | 0 | return String.class; |
1724 | 0 | case COLOUR_COLUMN: |
1725 | 0 | return FeatureColour.class; |
1726 | 0 | case FILTER_COLUMN: |
1727 | 0 | return FeatureMatcherSet.class; |
1728 | 0 | default: |
1729 | 0 | return Boolean.class; |
1730 | } | |
1731 | } | |
1732 | ||
1733 | 0 | @Override |
1734 | public boolean isCellEditable(int row, int col) | |
1735 | { | |
1736 | 0 | return col == 0 ? false : true; |
1737 | } | |
1738 | ||
1739 | 0 | @Override |
1740 | public void setValueAt(Object value, int row, int col) | |
1741 | { | |
1742 | 0 | data[row][col] = value; |
1743 | 0 | fireTableCellUpdated(row, col); |
1744 | 0 | updateFeatureRenderer(data); |
1745 | } | |
1746 | ||
1747 | } | |
1748 | ||
1749 | class ColorRenderer extends JLabel implements TableCellRenderer | |
1750 | { | |
1751 | Border unselectedBorder = null; | |
1752 | ||
1753 | Border selectedBorder = null; | |
1754 | ||
1755 | 2 | public ColorRenderer() |
1756 | { | |
1757 | 2 | setOpaque(true); // MUST do this for background to show up. |
1758 | 2 | setHorizontalTextPosition(SwingConstants.CENTER); |
1759 | 2 | setVerticalTextPosition(SwingConstants.CENTER); |
1760 | } | |
1761 | ||
1762 | 0 | @Override |
1763 | public Component getTableCellRendererComponent(JTable tbl, Object color, | |
1764 | boolean isSelected, boolean hasFocus, int row, int column) | |
1765 | { | |
1766 | 0 | FeatureColourI cellColour = (FeatureColourI) color; |
1767 | 0 | setOpaque(true); |
1768 | 0 | setBackground(tbl.getBackground()); |
1769 | 0 | if (!cellColour.isSimpleColour()) |
1770 | { | |
1771 | 0 | Rectangle cr = tbl.getCellRect(row, column, false); |
1772 | 0 | FeatureSettings.renderGraduatedColor(this, cellColour, |
1773 | (int) cr.getWidth(), (int) cr.getHeight()); | |
1774 | } | |
1775 | else | |
1776 | { | |
1777 | 0 | this.setText(""); |
1778 | 0 | this.setIcon(null); |
1779 | 0 | setBackground(cellColour.getColour()); |
1780 | } | |
1781 | 0 | if (isSelected) |
1782 | { | |
1783 | 0 | if (selectedBorder == null) |
1784 | { | |
1785 | 0 | selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1786 | tbl.getSelectionBackground()); | |
1787 | } | |
1788 | 0 | setBorder(selectedBorder); |
1789 | } | |
1790 | else | |
1791 | { | |
1792 | 0 | if (unselectedBorder == null) |
1793 | { | |
1794 | 0 | unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1795 | tbl.getBackground()); | |
1796 | } | |
1797 | 0 | setBorder(unselectedBorder); |
1798 | } | |
1799 | ||
1800 | 0 | return this; |
1801 | } | |
1802 | } | |
1803 | ||
1804 | class FilterRenderer extends JLabel implements TableCellRenderer | |
1805 | { | |
1806 | javax.swing.border.Border unselectedBorder = null; | |
1807 | ||
1808 | javax.swing.border.Border selectedBorder = null; | |
1809 | ||
1810 | 2 | public FilterRenderer() |
1811 | { | |
1812 | 2 | setOpaque(true); // MUST do this for background to show up. |
1813 | 2 | setHorizontalTextPosition(SwingConstants.CENTER); |
1814 | 2 | setVerticalTextPosition(SwingConstants.CENTER); |
1815 | } | |
1816 | ||
1817 | 0 | @Override |
1818 | public Component getTableCellRendererComponent(JTable tbl, | |
1819 | Object filter, boolean isSelected, boolean hasFocus, int row, | |
1820 | int column) | |
1821 | { | |
1822 | 0 | FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; |
1823 | 0 | setOpaque(true); |
1824 | 0 | setBackground(tbl.getBackground()); |
1825 | 0 | this.setIcon(null); |
1826 | ||
1827 | 0 | if (theFilter != null) |
1828 | { | |
1829 | 0 | String asText = theFilter.toString(); |
1830 | 0 | this.setText(asText); |
1831 | } | |
1832 | ||
1833 | 0 | if (isSelected) |
1834 | { | |
1835 | 0 | if (selectedBorder == null) |
1836 | { | |
1837 | 0 | selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1838 | tbl.getSelectionBackground()); | |
1839 | } | |
1840 | 0 | setBorder(selectedBorder); |
1841 | } | |
1842 | else | |
1843 | { | |
1844 | 0 | if (unselectedBorder == null) |
1845 | { | |
1846 | 0 | unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1847 | tbl.getBackground()); | |
1848 | } | |
1849 | 0 | setBorder(unselectedBorder); |
1850 | } | |
1851 | ||
1852 | 0 | return this; |
1853 | } | |
1854 | } | |
1855 | ||
1856 | /** | |
1857 | * update comp using rendering settings from gcol | |
1858 | * | |
1859 | * @param comp | |
1860 | * @param gcol | |
1861 | */ | |
1862 | 0 | public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol) |
1863 | { | |
1864 | 0 | int w = comp.getWidth(), h = comp.getHeight(); |
1865 | 0 | if (w < 20) |
1866 | { | |
1867 | 0 | w = (int) comp.getPreferredSize().getWidth(); |
1868 | 0 | h = (int) comp.getPreferredSize().getHeight(); |
1869 | 0 | if (w < 20) |
1870 | { | |
1871 | 0 | w = 80; |
1872 | 0 | h = 12; |
1873 | } | |
1874 | } | |
1875 | 0 | renderGraduatedColor(comp, gcol, w, h); |
1876 | } | |
1877 | ||
1878 | @SuppressWarnings("serial") | |
1879 | class ColorEditor extends AbstractCellEditor | |
1880 | implements TableCellEditor, ActionListener | |
1881 | { | |
1882 | FeatureColourI currentColor; | |
1883 | ||
1884 | FeatureTypeSettings chooser; | |
1885 | ||
1886 | String type; | |
1887 | ||
1888 | JButton button; | |
1889 | ||
1890 | protected static final String EDIT = "edit"; | |
1891 | ||
1892 | int rowSelected = 0; | |
1893 | ||
1894 | 2 | public ColorEditor() |
1895 | { | |
1896 | // Set up the editor (from the table's point of view), | |
1897 | // which is a button. | |
1898 | // This button brings up the color chooser dialog, | |
1899 | // which is the editor from the user's point of view. | |
1900 | 2 | button = new JButton(); |
1901 | 2 | button.setActionCommand(EDIT); |
1902 | 2 | button.addActionListener(this); |
1903 | 2 | button.setBorderPainted(false); |
1904 | } | |
1905 | ||
1906 | /** | |
1907 | * Handles events from the editor button, and from the colour/filters | |
1908 | * dialog's OK button | |
1909 | */ | |
1910 | 0 | @Override |
1911 | public void actionPerformed(ActionEvent e) | |
1912 | { | |
1913 | 0 | if (button == e.getSource()) |
1914 | { | |
1915 | 0 | if (currentColor.isSimpleColour()) |
1916 | { | |
1917 | /* | |
1918 | * simple colour chooser | |
1919 | */ | |
1920 | 0 | String ttl = MessageManager |
1921 | .formatMessage("label.select_colour_for", type); | |
1922 | 0 | Object last = (Boolean) table.getValueAt(selectedRow, |
1923 | SHOW_COLUMN); | |
1924 | 0 | table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); |
1925 | 0 | ColourChooserListener listener = new ColourChooserListener() |
1926 | { | |
1927 | 0 | @Override |
1928 | public void colourSelected(Color c) | |
1929 | { | |
1930 | 0 | currentColor = new FeatureColour(c); |
1931 | 0 | table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); |
1932 | 0 | table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); |
1933 | 0 | fireEditingStopped(); |
1934 | } | |
1935 | ||
1936 | 0 | @Override |
1937 | public void cancel() | |
1938 | { | |
1939 | 0 | table.setValueAt(last, selectedRow, SHOW_COLUMN); |
1940 | 0 | fireEditingStopped(); |
1941 | } | |
1942 | }; | |
1943 | 0 | JalviewColourChooser.showColourChooser(button, ttl, |
1944 | currentColor.getColour(), listener); | |
1945 | } | |
1946 | else | |
1947 | { | |
1948 | /* | |
1949 | * variable colour and filters dialog | |
1950 | */ | |
1951 | 0 | boolean last = (Boolean) table.getValueAt(selectedRow, |
1952 | SHOW_COLUMN); | |
1953 | 0 | table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); |
1954 | 0 | chooser = new FeatureTypeSettings(fr, type, last); |
1955 | 0 | if (!Platform.isJS()) |
1956 | /** | |
1957 | * Java only | |
1958 | * | |
1959 | * @j2sIgnore | |
1960 | */ | |
1961 | { | |
1962 | 0 | chooser.setRequestFocusEnabled(true); |
1963 | 0 | chooser.requestFocus(); |
1964 | } | |
1965 | 0 | chooser.addActionListener(this); |
1966 | 0 | fireEditingStopped(); |
1967 | } | |
1968 | } | |
1969 | else | |
1970 | { | |
1971 | /* | |
1972 | * after OK in variable colour dialog, any changes to colour | |
1973 | * (or filters!) are already set in FeatureRenderer, so just | |
1974 | * update table data without triggering updateFeatureRenderer | |
1975 | */ | |
1976 | 0 | currentColor = fr.getFeatureColours().get(type); |
1977 | 0 | FeatureMatcherSetI currentFilter = fr.getFeatureFilter(type); |
1978 | 0 | if (currentFilter == null) |
1979 | { | |
1980 | 0 | currentFilter = new FeatureMatcherSet(); |
1981 | } | |
1982 | 0 | Object[] data = ((FeatureTableModel) table.getModel()) |
1983 | .getData()[rowSelected]; | |
1984 | 0 | data[COLOUR_COLUMN] = currentColor; |
1985 | 0 | data[FILTER_COLUMN] = currentFilter; |
1986 | 0 | fireEditingStopped(); |
1987 | // SwingJS needs an explicit repaint() here, | |
1988 | // rather than relying upon no validation having | |
1989 | // occurred since the stopEditing call was made. | |
1990 | // Its laying out has not been stopped by the modal frame | |
1991 | 0 | table.validate(); |
1992 | 0 | table.repaint(); |
1993 | } | |
1994 | } | |
1995 | ||
1996 | /** | |
1997 | * Override allows access to this method from anonymous inner classes | |
1998 | */ | |
1999 | 0 | @Override |
2000 | protected void fireEditingStopped() | |
2001 | { | |
2002 | 0 | super.fireEditingStopped(); |
2003 | } | |
2004 | ||
2005 | // Implement the one CellEditor method that AbstractCellEditor doesn't. | |
2006 | 0 | @Override |
2007 | public Object getCellEditorValue() | |
2008 | { | |
2009 | 0 | return currentColor; |
2010 | } | |
2011 | ||
2012 | // Implement the one method defined by TableCellEditor. | |
2013 | 0 | @Override |
2014 | public Component getTableCellEditorComponent(JTable theTable, | |
2015 | Object value, boolean isSelected, int row, int column) | |
2016 | { | |
2017 | 0 | currentColor = (FeatureColourI) value; |
2018 | 0 | this.rowSelected = row; |
2019 | 0 | type = table.getValueAt(row, TYPE_COLUMN).toString(); |
2020 | 0 | button.setOpaque(true); |
2021 | 0 | button.setBackground(FeatureSettings.this.getBackground()); |
2022 | 0 | if (!currentColor.isSimpleColour()) |
2023 | { | |
2024 | 0 | JLabel btn = new JLabel(); |
2025 | 0 | btn.setSize(button.getSize()); |
2026 | 0 | FeatureSettings.renderGraduatedColor(btn, currentColor); |
2027 | 0 | button.setBackground(btn.getBackground()); |
2028 | 0 | button.setIcon(btn.getIcon()); |
2029 | 0 | button.setText(btn.getText()); |
2030 | } | |
2031 | else | |
2032 | { | |
2033 | 0 | button.setText(""); |
2034 | 0 | button.setIcon(null); |
2035 | 0 | button.setBackground(currentColor.getColour()); |
2036 | } | |
2037 | 0 | return button; |
2038 | } | |
2039 | } | |
2040 | ||
2041 | /** | |
2042 | * The cell editor for the Filter column. It displays the text of any filters | |
2043 | * for the feature type in that row (in full as a tooltip, possible | |
2044 | * abbreviated as display text). On click in the cell, opens the Feature | |
2045 | * Display Settings dialog at the Filters tab. | |
2046 | */ | |
2047 | @SuppressWarnings("serial") | |
2048 | class FilterEditor extends AbstractCellEditor | |
2049 | implements TableCellEditor, ActionListener | |
2050 | { | |
2051 | ||
2052 | FeatureMatcherSetI currentFilter; | |
2053 | ||
2054 | Point lastLocation; | |
2055 | ||
2056 | String type; | |
2057 | ||
2058 | JButton button; | |
2059 | ||
2060 | protected static final String EDIT = "edit"; | |
2061 | ||
2062 | int rowSelected = 0; | |
2063 | ||
2064 | 2 | public FilterEditor() |
2065 | { | |
2066 | 2 | button = new JButton(); |
2067 | 2 | button.setActionCommand(EDIT); |
2068 | 2 | button.addActionListener(this); |
2069 | 2 | button.setBorderPainted(false); |
2070 | } | |
2071 | ||
2072 | /** | |
2073 | * Handles events from the editor button | |
2074 | */ | |
2075 | 0 | @Override |
2076 | public void actionPerformed(ActionEvent e) | |
2077 | { | |
2078 | 0 | if (button == e.getSource()) |
2079 | { | |
2080 | 0 | boolean last = fr.getFeaturesDisplayed().isVisible(type); |
2081 | 0 | ((FeatureTableModel) table.getModel()).setValueAt(Boolean.TRUE, |
2082 | rowSelected, SHOW_COLUMN); | |
2083 | 0 | FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type, |
2084 | last); | |
2085 | 0 | chooser.addActionListener(this); |
2086 | 0 | chooser.setRequestFocusEnabled(true); |
2087 | 0 | chooser.requestFocus(); |
2088 | 0 | if (lastLocation != null) |
2089 | { | |
2090 | // todo open at its last position on screen | |
2091 | 0 | chooser.setBounds(lastLocation.x, lastLocation.y, |
2092 | chooser.getWidth(), chooser.getHeight()); | |
2093 | 0 | chooser.validate(); |
2094 | } | |
2095 | 0 | fireEditingStopped(); |
2096 | } | |
2097 | 0 | else if (e.getSource() instanceof Component) |
2098 | { | |
2099 | ||
2100 | /* | |
2101 | * after OK in variable colour dialog, any changes to filter | |
2102 | * (or colours!) are already set in FeatureRenderer, so just | |
2103 | * update table data without triggering updateFeatureRenderer | |
2104 | */ | |
2105 | 0 | FeatureColourI currentColor = fr.getFeatureColours().get(type); |
2106 | 0 | currentFilter = fr.getFeatureFilter(type); |
2107 | 0 | if (currentFilter == null) |
2108 | { | |
2109 | 0 | currentFilter = new FeatureMatcherSet(); |
2110 | } | |
2111 | ||
2112 | 0 | Object[] data = ((FeatureTableModel) table.getModel()) |
2113 | .getData()[rowSelected]; | |
2114 | 0 | data[COLOUR_COLUMN] = currentColor; |
2115 | 0 | data[FILTER_COLUMN] = currentFilter; |
2116 | 0 | data[SHOW_COLUMN] = fr.getFeaturesDisplayed().isVisible(type); |
2117 | ||
2118 | 0 | fireEditingStopped(); |
2119 | // SwingJS needs an explicit repaint() here, | |
2120 | // rather than relying upon no validation having | |
2121 | // occurred since the stopEditing call was made. | |
2122 | // Its laying out has not been stopped by the modal frame | |
2123 | 0 | table.validate(); |
2124 | 0 | table.repaint(); |
2125 | } | |
2126 | } | |
2127 | ||
2128 | 0 | @Override |
2129 | public Object getCellEditorValue() | |
2130 | { | |
2131 | 0 | return currentFilter; |
2132 | } | |
2133 | ||
2134 | 0 | @Override |
2135 | public Component getTableCellEditorComponent(JTable theTable, | |
2136 | Object value, boolean isSelected, int row, int column) | |
2137 | { | |
2138 | 0 | currentFilter = (FeatureMatcherSetI) value; |
2139 | 0 | this.rowSelected = row; |
2140 | 0 | type = table.getValueAt(row, TYPE_COLUMN).toString(); |
2141 | 0 | button.setOpaque(true); |
2142 | 0 | button.setBackground(FeatureSettings.this.getBackground()); |
2143 | 0 | button.setText(currentFilter.toString()); |
2144 | 0 | button.setIcon(null); |
2145 | 0 | return button; |
2146 | } | |
2147 | } | |
2148 | ||
2149 | 0 | public boolean isOpen() |
2150 | { | |
2151 | 0 | if (af.getSplitViewContainer() != null) |
2152 | { | |
2153 | 0 | return af.getSplitViewContainer().isFeatureSettingsOpen(); |
2154 | } | |
2155 | 0 | return frame != null && !frame.isClosed(); |
2156 | } | |
2157 | ||
2158 | 0 | @Override |
2159 | public void revert() | |
2160 | { | |
2161 | 0 | fr.setTransparency(originalTransparency); |
2162 | 0 | fr.setFeatureFilters(originalFilters); |
2163 | 0 | updateFeatureRenderer(originalData); |
2164 | 0 | af.getViewport().setViewStyle(originalViewStyle); |
2165 | 0 | updateTransparencySliderFromFR(); |
2166 | 0 | updateComplementButtons(); |
2167 | 0 | refreshDisplay(); |
2168 | } | |
2169 | } | |
2170 | ||
2171 | class FeatureIcon implements Icon | |
2172 | { | |
2173 | FeatureColourI gcol; | |
2174 | ||
2175 | Color backg; | |
2176 | ||
2177 | boolean midspace = false; | |
2178 | ||
2179 | int width = 50, height = 20; | |
2180 | ||
2181 | int s1, e1; // start and end of midpoint band for thresholded symbol | |
2182 | ||
2183 | Color mpcolour = Color.white; | |
2184 | ||
2185 | 0 | FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace) |
2186 | { | |
2187 | 0 | gcol = gfc; |
2188 | 0 | backg = bg; |
2189 | 0 | width = w; |
2190 | 0 | height = h; |
2191 | 0 | midspace = mspace; |
2192 | 0 | if (midspace) |
2193 | { | |
2194 | 0 | s1 = width / 3; |
2195 | 0 | e1 = s1 * 2; |
2196 | } | |
2197 | else | |
2198 | { | |
2199 | 0 | s1 = width / 2; |
2200 | 0 | e1 = s1; |
2201 | } | |
2202 | } | |
2203 | ||
2204 | 0 | @Override |
2205 | public int getIconWidth() | |
2206 | { | |
2207 | 0 | return width; |
2208 | } | |
2209 | ||
2210 | 0 | @Override |
2211 | public int getIconHeight() | |
2212 | { | |
2213 | 0 | return height; |
2214 | } | |
2215 | ||
2216 | 0 | @Override |
2217 | public void paintIcon(Component c, Graphics g, int x, int y) | |
2218 | { | |
2219 | ||
2220 | 0 | if (gcol.isColourByLabel()) |
2221 | { | |
2222 | 0 | g.setColor(backg); |
2223 | 0 | g.fillRect(0, 0, width, height); |
2224 | // need an icon here. | |
2225 | 0 | g.setColor(gcol.getMaxColour()); |
2226 | ||
2227 | 0 | g.setFont(new Font("Verdana", Font.PLAIN, 9)); |
2228 | ||
2229 | // g.setFont(g.getFont().deriveFont( | |
2230 | // AffineTransform.getScaleInstance( | |
2231 | // width/g.getFontMetrics().stringWidth("Label"), | |
2232 | // height/g.getFontMetrics().getHeight()))); | |
2233 | ||
2234 | 0 | g.drawString(MessageManager.getString("label.label"), 0, 0); |
2235 | ||
2236 | } | |
2237 | else | |
2238 | { | |
2239 | 0 | Color minCol = gcol.getMinColour(); |
2240 | 0 | g.setColor(minCol); |
2241 | 0 | g.fillRect(0, 0, s1, height); |
2242 | 0 | if (midspace) |
2243 | { | |
2244 | 0 | g.setColor(Color.white); |
2245 | 0 | g.fillRect(s1, 0, e1 - s1, height); |
2246 | } | |
2247 | 0 | g.setColor(gcol.getMaxColour()); |
2248 | // g.fillRect(0, e1, width - e1, height); // BH 2018 | |
2249 | 0 | g.fillRect(e1, 0, width - e1, height); |
2250 | } | |
2251 | } | |
2252 | } |