Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
AnnotationColumnChooser | 55 | 223 | 75 | ||
AnnotationColumnChooser.FurtherActionPanel | 606 | 15 | 5 | ||
AnnotationColumnChooser.StructureFilterPanel | 657 | 58 | 18 | ||
AnnotationColumnChooser.SearchPanel | 794 | 31 | 10 |
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.appletgui; | |
22 | ||
23 | import java.awt.BorderLayout; | |
24 | import java.awt.CardLayout; | |
25 | import java.awt.Checkbox; | |
26 | import java.awt.Choice; | |
27 | import java.awt.Color; | |
28 | import java.awt.Dimension; | |
29 | import java.awt.Frame; | |
30 | import java.awt.Panel; | |
31 | import java.awt.TextField; | |
32 | import java.awt.event.ActionEvent; | |
33 | import java.awt.event.ActionListener; | |
34 | import java.awt.event.AdjustmentEvent; | |
35 | import java.awt.event.AdjustmentListener; | |
36 | import java.awt.event.ItemEvent; | |
37 | import java.awt.event.ItemListener; | |
38 | import java.awt.event.MouseAdapter; | |
39 | import java.awt.event.MouseEvent; | |
40 | import java.awt.event.MouseListener; | |
41 | import java.awt.event.TextEvent; | |
42 | import java.awt.event.TextListener; | |
43 | import java.util.Vector; | |
44 | ||
45 | import jalview.datamodel.AlignmentAnnotation; | |
46 | import jalview.datamodel.HiddenColumns; | |
47 | import jalview.schemes.AnnotationColourGradient; | |
48 | import jalview.util.MessageManager; | |
49 | import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; | |
50 | ||
51 | //import javax.swing.JPanel; | |
52 | ||
53 | //import net.miginfocom.swing.MigLayout; | |
54 | ||
55 | public class AnnotationColumnChooser extends AnnotationRowFilter implements | |
56 | ActionListener, AdjustmentListener, ItemListener, MouseListener | |
57 | { | |
58 | ||
59 | private Choice annotations = new Choice(); | |
60 | ||
61 | private Panel actionPanel = new Panel(); | |
62 | ||
63 | private TitledPanel thresholdPanel = new TitledPanel(); | |
64 | ||
65 | private Panel switchableViewsPanel = new Panel(new CardLayout()); | |
66 | ||
67 | private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel | |
68 | .getLayout()); | |
69 | ||
70 | private Panel noGraphFilterView = new Panel(); | |
71 | ||
72 | private Panel graphFilterView = new Panel(); | |
73 | ||
74 | private Panel annotationComboBoxPanel = new Panel(); | |
75 | ||
76 | private BorderLayout borderLayout1 = new BorderLayout(); | |
77 | ||
78 | private BorderLayout gBorderLayout = new BorderLayout(); | |
79 | ||
80 | private BorderLayout ngBorderLayout = new BorderLayout(); | |
81 | ||
82 | private Choice threshold = new Choice(); | |
83 | ||
84 | private StructureFilterPanel gStructureFilterPanel; | |
85 | ||
86 | private StructureFilterPanel ngStructureFilterPanel; | |
87 | ||
88 | private StructureFilterPanel currentStructureFilterPanel; | |
89 | ||
90 | private SearchPanel currentSearchPanel; | |
91 | ||
92 | private SearchPanel gSearchPanel; | |
93 | ||
94 | private SearchPanel ngSearchPanel; | |
95 | ||
96 | private FurtherActionPanel currentFurtherActionPanel; | |
97 | ||
98 | private FurtherActionPanel gFurtherActionPanel; | |
99 | ||
100 | private FurtherActionPanel ngFurtherActionPanel; | |
101 | ||
102 | public static final int ACTION_OPTION_SELECT = 1; | |
103 | ||
104 | public static int ACTION_OPTION_HIDE = 2; | |
105 | ||
106 | public static String NO_GRAPH_VIEW = "0"; | |
107 | ||
108 | public static String GRAPH_VIEW = "1"; | |
109 | ||
110 | private int actionOption = ACTION_OPTION_SELECT; | |
111 | ||
112 | private HiddenColumns oldHiddenColumns; | |
113 | ||
114 | 0 | public AnnotationColumnChooser() |
115 | { | |
116 | 0 | try |
117 | { | |
118 | 0 | jbInit(); |
119 | } catch (Exception ex) | |
120 | { | |
121 | 0 | ex.printStackTrace(); |
122 | } | |
123 | } | |
124 | ||
125 | 0 | public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap) |
126 | { | |
127 | 0 | super(av, ap); |
128 | 0 | frame = new Frame(); |
129 | 0 | frame.add(this); |
130 | 0 | jalview.bin.JalviewLite.addFrame(frame, |
131 | MessageManager.getString("label.select_by_annotation"), 520, | |
132 | 215); | |
133 | ||
134 | 0 | slider.addAdjustmentListener(this); |
135 | 0 | slider.addMouseListener(this); |
136 | ||
137 | 0 | AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); |
138 | 0 | if (anns == null) |
139 | { | |
140 | 0 | return; |
141 | } | |
142 | 0 | setOldHiddenColumns(av.getAlignment().getHiddenColumns()); |
143 | 0 | adjusting = true; |
144 | 0 | Vector<String> list = new Vector<>(); |
145 | 0 | int index = 1; |
146 | 0 | for (int i = 0; i < anns.length; i++) |
147 | { | |
148 | 0 | String label = anns[i].label; |
149 | 0 | if (anns[i].sequenceRef != null) |
150 | { | |
151 | 0 | label = label + "_" + anns[i].sequenceRef.getName(); |
152 | } | |
153 | 0 | if (!list.contains(label)) |
154 | { | |
155 | 0 | list.addElement(label); |
156 | } | |
157 | else | |
158 | { | |
159 | 0 | list.addElement(label + "_" + (index++)); |
160 | } | |
161 | } | |
162 | ||
163 | 0 | for (int i = 0; i < list.size(); i++) |
164 | { | |
165 | 0 | annotations.addItem(list.elementAt(i).toString()); |
166 | } | |
167 | ||
168 | 0 | populateThresholdComboBox(threshold); |
169 | 0 | AnnotationColumnChooser lastChooser = av |
170 | .getAnnotationColumnSelectionState(); | |
171 | // restore Object state from the previous session if one exists | |
172 | 0 | if (lastChooser != null) |
173 | { | |
174 | 0 | currentSearchPanel = lastChooser.getCurrentSearchPanel(); |
175 | 0 | currentStructureFilterPanel = lastChooser |
176 | .getCurrentStructureFilterPanel(); | |
177 | 0 | annotations.select(lastChooser.getAnnotations().getSelectedIndex()); |
178 | 0 | threshold.select(lastChooser.getThreshold().getSelectedIndex()); |
179 | 0 | actionOption = lastChooser.getActionOption(); |
180 | 0 | percentThreshold.setState(lastChooser.percentThreshold.getState()); |
181 | } | |
182 | ||
183 | 0 | try |
184 | { | |
185 | 0 | jbInit(); |
186 | } catch (Exception ex) | |
187 | { | |
188 | } | |
189 | 0 | adjusting = false; |
190 | ||
191 | 0 | updateView(); |
192 | 0 | frame.invalidate(); |
193 | 0 | frame.pack(); |
194 | } | |
195 | ||
196 | 0 | private void jbInit() throws Exception |
197 | { | |
198 | 0 | ok.setLabel(MessageManager.getString("action.ok")); |
199 | ||
200 | 0 | cancel.setLabel(MessageManager.getString("action.cancel")); |
201 | ||
202 | 0 | thresholdValue.setEnabled(false); |
203 | 0 | thresholdValue.setColumns(7); |
204 | 0 | thresholdValue.setCaretPosition(0); |
205 | ||
206 | 0 | ok.addActionListener(this); |
207 | 0 | cancel.addActionListener(this); |
208 | 0 | annotations.addItemListener(this); |
209 | 0 | thresholdValue.addActionListener(this); |
210 | 0 | threshold.addItemListener(this); |
211 | ||
212 | 0 | slider.setBackground(Color.white); |
213 | 0 | slider.setEnabled(false); |
214 | 0 | slider.setPreferredSize(new Dimension(100, 32)); |
215 | ||
216 | 0 | thresholdPanel.setBackground(Color.white); |
217 | // thresholdPanel.setFont(JvSwingUtils.getLabelFont()); | |
218 | // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]")); | |
219 | ||
220 | 0 | percentThreshold.setLabel("As percentage"); |
221 | 0 | percentThreshold.addItemListener(this); |
222 | ||
223 | 0 | actionPanel.setBackground(Color.white); |
224 | // actionPanel.setFont(JvSwingUtils.getLabelFont()); | |
225 | ||
226 | 0 | graphFilterView.setLayout(gBorderLayout); |
227 | 0 | graphFilterView.setBackground(Color.white); |
228 | ||
229 | 0 | noGraphFilterView.setLayout(ngBorderLayout); |
230 | 0 | noGraphFilterView.setBackground(Color.white); |
231 | ||
232 | 0 | annotationComboBoxPanel.setBackground(Color.white); |
233 | // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont()); | |
234 | ||
235 | 0 | gSearchPanel = new SearchPanel(this); |
236 | 0 | ngSearchPanel = new SearchPanel(this); |
237 | 0 | gFurtherActionPanel = new FurtherActionPanel(this); |
238 | 0 | ngFurtherActionPanel = new FurtherActionPanel(this); |
239 | 0 | gStructureFilterPanel = new StructureFilterPanel(this); |
240 | 0 | ngStructureFilterPanel = new StructureFilterPanel(this); |
241 | ||
242 | 0 | thresholdPanel.setTitle("Threshold Filter"); |
243 | 0 | thresholdPanel.add(getThreshold()); |
244 | 0 | thresholdPanel.add(slider); |
245 | 0 | thresholdPanel.add(thresholdValue); |
246 | 0 | thresholdPanel.add(percentThreshold); |
247 | ||
248 | 0 | actionPanel.add(ok); |
249 | 0 | actionPanel.add(cancel); |
250 | ||
251 | 0 | Panel staticPanel = new Panel(); |
252 | 0 | staticPanel.setLayout(new BorderLayout()); |
253 | 0 | staticPanel.setBackground(Color.white); |
254 | ||
255 | 0 | staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH); |
256 | 0 | staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH); |
257 | ||
258 | 0 | graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH); |
259 | 0 | graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER); |
260 | 0 | graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH); |
261 | ||
262 | 0 | noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START); |
263 | 0 | noGraphFilterView.add(ngStructureFilterPanel, |
264 | java.awt.BorderLayout.CENTER); | |
265 | 0 | noGraphFilterView.add(ngFurtherActionPanel, |
266 | java.awt.BorderLayout.CENTER); | |
267 | ||
268 | 0 | annotationComboBoxPanel.add(getAnnotations()); |
269 | 0 | switchableViewsPanel.add(noGraphFilterView, |
270 | AnnotationColumnChooser.NO_GRAPH_VIEW); | |
271 | 0 | switchableViewsPanel.add(graphFilterView, |
272 | AnnotationColumnChooser.GRAPH_VIEW); | |
273 | ||
274 | 0 | this.setLayout(borderLayout1); |
275 | 0 | this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START); |
276 | 0 | this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER); |
277 | 0 | this.add(actionPanel, java.awt.BorderLayout.SOUTH); |
278 | ||
279 | 0 | selectedAnnotationChanged(); |
280 | 0 | this.validate(); |
281 | } | |
282 | ||
283 | 0 | @Override |
284 | @SuppressWarnings("unchecked") | |
285 | public void reset() | |
286 | { | |
287 | 0 | if (this.getOldHiddenColumns() != null) |
288 | { | |
289 | 0 | av.getColumnSelection().clear(); |
290 | ||
291 | 0 | if (av.getAnnotationColumnSelectionState() != null) |
292 | { | |
293 | 0 | HiddenColumns oldHidden = av.getAnnotationColumnSelectionState() |
294 | .getOldHiddenColumns(); | |
295 | 0 | av.getAlignment().setHiddenColumns(oldHidden); |
296 | } | |
297 | 0 | av.sendSelection(); |
298 | 0 | ap.paintAlignment(true, true); |
299 | } | |
300 | ||
301 | } | |
302 | ||
303 | 0 | @Override |
304 | public void adjustmentValueChanged(AdjustmentEvent evt) | |
305 | { | |
306 | 0 | if (!adjusting) |
307 | { | |
308 | 0 | setThresholdValueText(); |
309 | 0 | valueChanged(!sliderDragging); |
310 | } | |
311 | } | |
312 | ||
313 | 0 | protected void addSliderMouseListeners() |
314 | { | |
315 | ||
316 | 0 | slider.addMouseListener(new MouseAdapter() |
317 | { | |
318 | 0 | @Override |
319 | public void mousePressed(MouseEvent e) | |
320 | { | |
321 | 0 | sliderDragging = true; |
322 | 0 | super.mousePressed(e); |
323 | } | |
324 | ||
325 | 0 | @Override |
326 | public void mouseDragged(MouseEvent e) | |
327 | { | |
328 | 0 | sliderDragging = true; |
329 | 0 | super.mouseDragged(e); |
330 | } | |
331 | ||
332 | 0 | @Override |
333 | public void mouseReleased(MouseEvent evt) | |
334 | { | |
335 | 0 | if (sliderDragging) |
336 | { | |
337 | 0 | sliderDragging = false; |
338 | 0 | valueChanged(true); |
339 | } | |
340 | 0 | ap.paintAlignment(true, true); |
341 | } | |
342 | }); | |
343 | } | |
344 | ||
345 | 0 | @Override |
346 | public void valueChanged(boolean updateAllAnnotation) | |
347 | { | |
348 | 0 | if (slider.isEnabled()) |
349 | { | |
350 | 0 | getCurrentAnnotation().threshold.value = slider.getValue() / 1000f; |
351 | 0 | updateView(); // this also calls paintAlignment(true,true) |
352 | } | |
353 | } | |
354 | ||
355 | 0 | public Choice getThreshold() |
356 | { | |
357 | 0 | return threshold; |
358 | } | |
359 | ||
360 | 0 | public void setThreshold(Choice threshold) |
361 | { | |
362 | 0 | this.threshold = threshold; |
363 | } | |
364 | ||
365 | 0 | public Choice getAnnotations() |
366 | { | |
367 | 0 | return annotations; |
368 | } | |
369 | ||
370 | 0 | public void setAnnotations(Choice annotations) |
371 | { | |
372 | 0 | this.annotations = annotations; |
373 | } | |
374 | ||
375 | 0 | @Override |
376 | public void updateView() | |
377 | { | |
378 | // Check if combobox is still adjusting | |
379 | 0 | if (adjusting) |
380 | { | |
381 | 0 | return; |
382 | } | |
383 | ||
384 | 0 | AnnotationFilterParameter filterParams = new AnnotationFilterParameter(); |
385 | 0 | setCurrentAnnotation(av.getAlignment() |
386 | .getAlignmentAnnotation()[getAnnotations().getSelectedIndex()]); | |
387 | ||
388 | 0 | int selectedThresholdItem = getSelectedThresholdItem( |
389 | getThreshold().getSelectedIndex()); | |
390 | ||
391 | 0 | slider.setEnabled(true); |
392 | 0 | thresholdValue.setEnabled(true); |
393 | 0 | percentThreshold.setEnabled(true); |
394 | ||
395 | 0 | if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD) |
396 | { | |
397 | 0 | slider.setEnabled(false); |
398 | 0 | thresholdValue.setEnabled(false); |
399 | 0 | thresholdValue.setText(""); |
400 | 0 | percentThreshold.setEnabled(false); |
401 | // build filter params | |
402 | } | |
403 | 0 | else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD) |
404 | { | |
405 | 0 | if (getCurrentAnnotation().threshold == null) |
406 | { | |
407 | 0 | getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine( |
408 | (getCurrentAnnotation().graphMax | |
409 | - getCurrentAnnotation().graphMin) / 2f, | |
410 | "Threshold", Color.black)); | |
411 | } | |
412 | ||
413 | 0 | adjusting = true; |
414 | // float range = getCurrentAnnotation().graphMax * 1000 | |
415 | // - getCurrentAnnotation().graphMin * 1000; | |
416 | ||
417 | 0 | slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000)); |
418 | 0 | slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000)); |
419 | 0 | slider.setValue( |
420 | (int) (getCurrentAnnotation().threshold.value * 1000)); | |
421 | 0 | setThresholdValueText(); |
422 | // slider.setMajorTickSpacing((int) (range / 10f)); | |
423 | 0 | slider.setEnabled(true); |
424 | 0 | thresholdValue.setEnabled(true); |
425 | 0 | percentThreshold.setEnabled(true); |
426 | 0 | adjusting = false; |
427 | ||
428 | // build filter params | |
429 | 0 | filterParams.setThresholdType( |
430 | AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); | |
431 | 0 | if (getCurrentAnnotation().isQuantitative()) |
432 | { | |
433 | 0 | filterParams |
434 | .setThresholdValue(getCurrentAnnotation().threshold.value); | |
435 | ||
436 | 0 | if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD) |
437 | { | |
438 | 0 | filterParams.setThresholdType( |
439 | AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD); | |
440 | } | |
441 | 0 | else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD) |
442 | { | |
443 | 0 | filterParams.setThresholdType( |
444 | AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD); | |
445 | } | |
446 | } | |
447 | } | |
448 | ||
449 | 0 | if (currentStructureFilterPanel != null) |
450 | { | |
451 | 0 | if (currentStructureFilterPanel.alphaHelix.getState()) |
452 | { | |
453 | 0 | filterParams.setFilterAlphaHelix(true); |
454 | } | |
455 | 0 | if (currentStructureFilterPanel.betaStrand.getState()) |
456 | { | |
457 | 0 | filterParams.setFilterBetaSheet(true); |
458 | } | |
459 | 0 | if (currentStructureFilterPanel.turn.getState()) |
460 | { | |
461 | 0 | filterParams.setFilterTurn(true); |
462 | } | |
463 | } | |
464 | ||
465 | 0 | if (currentSearchPanel != null) |
466 | { | |
467 | ||
468 | 0 | if (!currentSearchPanel.searchBox.getText().isEmpty()) |
469 | { | |
470 | 0 | currentSearchPanel.description.setEnabled(true); |
471 | 0 | currentSearchPanel.displayName.setEnabled(true); |
472 | 0 | filterParams.setRegexString(currentSearchPanel.searchBox.getText()); |
473 | 0 | if (currentSearchPanel.displayName.getState()) |
474 | { | |
475 | 0 | filterParams.addRegexSearchField( |
476 | AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING); | |
477 | } | |
478 | 0 | if (currentSearchPanel.description.getState()) |
479 | { | |
480 | 0 | filterParams.addRegexSearchField( |
481 | AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION); | |
482 | } | |
483 | } | |
484 | else | |
485 | { | |
486 | 0 | currentSearchPanel.description.setEnabled(false); |
487 | 0 | currentSearchPanel.displayName.setEnabled(false); |
488 | } | |
489 | } | |
490 | ||
491 | // show hidden columns here, before changing the column selection in | |
492 | // filterAnnotations, because showing hidden columns has the side effect of | |
493 | // adding them to the selection | |
494 | 0 | av.showAllHiddenColumns(); |
495 | 0 | av.getColumnSelection().filterAnnotations(getCurrentAnnotation(), |
496 | filterParams); | |
497 | ||
498 | 0 | if (getActionOption() == ACTION_OPTION_HIDE) |
499 | { | |
500 | 0 | av.hideSelectedColumns(); |
501 | } | |
502 | ||
503 | 0 | filterParams = null; |
504 | 0 | av.setAnnotationColumnSelectionState(this); |
505 | 0 | av.sendSelection(); |
506 | 0 | ap.paintAlignment(true, true); |
507 | } | |
508 | ||
509 | 0 | public HiddenColumns getOldHiddenColumns() |
510 | { | |
511 | 0 | return oldHiddenColumns; |
512 | } | |
513 | ||
514 | 0 | public void setOldHiddenColumns(HiddenColumns currentHiddenColumns) |
515 | { | |
516 | 0 | if (currentHiddenColumns != null) |
517 | { | |
518 | 0 | this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns); |
519 | } | |
520 | } | |
521 | ||
522 | 0 | public FurtherActionPanel getCurrentFutherActionPanel() |
523 | { | |
524 | 0 | return currentFurtherActionPanel; |
525 | } | |
526 | ||
527 | 0 | public void setCurrentFutherActionPanel( |
528 | FurtherActionPanel currentFutherActionPanel) | |
529 | { | |
530 | 0 | this.currentFurtherActionPanel = currentFutherActionPanel; |
531 | } | |
532 | ||
533 | 0 | public SearchPanel getCurrentSearchPanel() |
534 | { | |
535 | 0 | return currentSearchPanel; |
536 | } | |
537 | ||
538 | 0 | public void setCurrentSearchPanel(SearchPanel currentSearchPanel) |
539 | { | |
540 | 0 | this.currentSearchPanel = currentSearchPanel; |
541 | } | |
542 | ||
543 | 0 | public int getActionOption() |
544 | { | |
545 | 0 | return actionOption; |
546 | } | |
547 | ||
548 | 0 | public void setActionOption(int actionOption) |
549 | { | |
550 | 0 | this.actionOption = actionOption; |
551 | } | |
552 | ||
553 | 0 | public StructureFilterPanel getCurrentStructureFilterPanel() |
554 | { | |
555 | 0 | return currentStructureFilterPanel; |
556 | } | |
557 | ||
558 | 0 | public void setCurrentStructureFilterPanel( |
559 | StructureFilterPanel currentStructureFilterPanel) | |
560 | { | |
561 | 0 | this.currentStructureFilterPanel = currentStructureFilterPanel; |
562 | } | |
563 | ||
564 | 0 | @Override |
565 | public void itemStateChanged(ItemEvent e) | |
566 | { | |
567 | 0 | if (e.getSource() == annotations) |
568 | { | |
569 | 0 | selectedAnnotationChanged(); |
570 | } | |
571 | 0 | else if (e.getSource() == threshold) |
572 | { | |
573 | 0 | threshold_actionPerformed(null); |
574 | } | |
575 | 0 | else if (e.getSource() == percentThreshold) |
576 | { | |
577 | 0 | if (!adjusting) |
578 | { | |
579 | 0 | percentageValue_actionPerformed(); |
580 | } | |
581 | ||
582 | } | |
583 | } | |
584 | ||
585 | 0 | public void selectedAnnotationChanged() |
586 | { | |
587 | 0 | String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW; |
588 | 0 | if (av.getAlignment().getAlignmentAnnotation()[getAnnotations() |
589 | .getSelectedIndex()].isQuantitative()) | |
590 | { | |
591 | 0 | currentView = AnnotationColumnChooser.GRAPH_VIEW; |
592 | } | |
593 | ||
594 | 0 | gSearchPanel.syncState(); |
595 | 0 | gFurtherActionPanel.syncState(); |
596 | 0 | gStructureFilterPanel.syncState(); |
597 | ||
598 | 0 | ngSearchPanel.syncState(); |
599 | 0 | ngFurtherActionPanel.syncState(); |
600 | 0 | ngStructureFilterPanel.syncState(); |
601 | ||
602 | 0 | switchableViewsLayout.show(switchableViewsPanel, currentView); |
603 | 0 | updateView(); |
604 | } | |
605 | ||
606 | public class FurtherActionPanel extends Panel implements ItemListener | |
607 | { | |
608 | private AnnotationColumnChooser aColChooser; | |
609 | ||
610 | private Choice furtherAction = new Choice(); | |
611 | ||
612 | 0 | public FurtherActionPanel(AnnotationColumnChooser aColChooser) |
613 | { | |
614 | 0 | this.aColChooser = aColChooser; |
615 | 0 | furtherAction.addItem("Select"); |
616 | 0 | furtherAction.addItem("Hide"); |
617 | 0 | furtherAction.addItemListener(this); |
618 | 0 | syncState(); |
619 | ||
620 | // this.setTitle("Filter Actions"); | |
621 | // this.setFont(JvSwingUtils.getLabelFont()); | |
622 | ||
623 | 0 | this.add(furtherAction); |
624 | } | |
625 | ||
626 | 0 | public void syncState() |
627 | { | |
628 | 0 | if (aColChooser |
629 | .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE) | |
630 | { | |
631 | 0 | furtherAction.select("Hide"); |
632 | } | |
633 | else | |
634 | { | |
635 | 0 | furtherAction.select("Select"); |
636 | } | |
637 | } | |
638 | ||
639 | 0 | @Override |
640 | public void itemStateChanged(ItemEvent e) | |
641 | { | |
642 | 0 | aColChooser.setCurrentFutherActionPanel(this); |
643 | 0 | if (furtherAction.getSelectedItem().equalsIgnoreCase("Select")) |
644 | { | |
645 | 0 | setActionOption(ACTION_OPTION_SELECT); |
646 | 0 | updateView(); |
647 | } | |
648 | else | |
649 | { | |
650 | 0 | setActionOption(ACTION_OPTION_HIDE); |
651 | 0 | updateView(); |
652 | } | |
653 | ||
654 | } | |
655 | } | |
656 | ||
657 | public class StructureFilterPanel extends TitledPanel | |
658 | implements ItemListener | |
659 | { | |
660 | private AnnotationColumnChooser aColChooser; | |
661 | ||
662 | private Checkbox alphaHelix = new Checkbox(); | |
663 | ||
664 | private Checkbox betaStrand = new Checkbox(); | |
665 | ||
666 | private Checkbox turn = new Checkbox(); | |
667 | ||
668 | private Checkbox all = new Checkbox(); | |
669 | ||
670 | 0 | public StructureFilterPanel(AnnotationColumnChooser aColChooser) |
671 | { | |
672 | 0 | this.aColChooser = aColChooser; |
673 | ||
674 | 0 | alphaHelix.setLabel(MessageManager.getString("label.alpha_helix")); |
675 | 0 | alphaHelix.setBackground(Color.white); |
676 | ||
677 | 0 | alphaHelix.addItemListener(this); |
678 | ||
679 | 0 | betaStrand.setLabel(MessageManager.getString("label.beta_strand")); |
680 | 0 | betaStrand.setBackground(Color.white); |
681 | 0 | betaStrand.addItemListener(this); |
682 | ||
683 | 0 | turn.setLabel(MessageManager.getString("label.turn")); |
684 | 0 | turn.setBackground(Color.white); |
685 | 0 | turn.addItemListener(this); |
686 | ||
687 | 0 | all.setLabel(MessageManager.getString("label.select_all")); |
688 | 0 | all.setBackground(Color.white); |
689 | 0 | all.addItemListener(this); |
690 | ||
691 | 0 | this.setBackground(Color.white); |
692 | 0 | this.setTitle("Structure Filter"); |
693 | // this.setFont(JvSwingUtils.getLabelFont()); | |
694 | ||
695 | 0 | this.add(all); |
696 | 0 | this.add(alphaHelix); |
697 | 0 | this.add(betaStrand); |
698 | 0 | this.add(turn); |
699 | } | |
700 | ||
701 | 0 | public void alphaHelix_actionPerformed() |
702 | { | |
703 | 0 | updateSelectAllState(); |
704 | 0 | aColChooser.setCurrentStructureFilterPanel(this); |
705 | 0 | aColChooser.updateView(); |
706 | } | |
707 | ||
708 | 0 | public void betaStrand_actionPerformed() |
709 | { | |
710 | 0 | updateSelectAllState(); |
711 | 0 | aColChooser.setCurrentStructureFilterPanel(this); |
712 | 0 | aColChooser.updateView(); |
713 | } | |
714 | ||
715 | 0 | public void turn_actionPerformed() |
716 | { | |
717 | 0 | updateSelectAllState(); |
718 | 0 | aColChooser.setCurrentStructureFilterPanel(this); |
719 | 0 | aColChooser.updateView(); |
720 | } | |
721 | ||
722 | 0 | public void all_actionPerformed() |
723 | { | |
724 | 0 | if (all.getState()) |
725 | { | |
726 | 0 | alphaHelix.setState(true); |
727 | 0 | betaStrand.setState(true); |
728 | 0 | turn.setState(true); |
729 | } | |
730 | else | |
731 | { | |
732 | 0 | alphaHelix.setState(false); |
733 | 0 | betaStrand.setState(false); |
734 | 0 | turn.setState(false); |
735 | } | |
736 | 0 | aColChooser.setCurrentStructureFilterPanel(this); |
737 | 0 | aColChooser.updateView(); |
738 | } | |
739 | ||
740 | 0 | public void updateSelectAllState() |
741 | { | |
742 | 0 | if (alphaHelix.getState() && betaStrand.getState() && turn.getState()) |
743 | { | |
744 | 0 | all.setState(true); |
745 | } | |
746 | else | |
747 | { | |
748 | 0 | all.setState(false); |
749 | } | |
750 | } | |
751 | ||
752 | 0 | public void syncState() |
753 | { | |
754 | 0 | StructureFilterPanel sfp = aColChooser |
755 | .getCurrentStructureFilterPanel(); | |
756 | 0 | if (sfp != null) |
757 | { | |
758 | 0 | alphaHelix.setState(sfp.alphaHelix.getState()); |
759 | 0 | betaStrand.setState(sfp.betaStrand.getState()); |
760 | 0 | turn.setState(sfp.turn.getState()); |
761 | 0 | if (sfp.all.getState()) |
762 | { | |
763 | 0 | all.setState(true); |
764 | 0 | alphaHelix.setState(true); |
765 | 0 | betaStrand.setState(true); |
766 | 0 | turn.setState(true); |
767 | } | |
768 | } | |
769 | ||
770 | } | |
771 | ||
772 | 0 | @Override |
773 | public void itemStateChanged(ItemEvent e) | |
774 | { | |
775 | 0 | if (e.getSource() == alphaHelix) |
776 | { | |
777 | 0 | alphaHelix_actionPerformed(); |
778 | } | |
779 | 0 | else if (e.getSource() == betaStrand) |
780 | { | |
781 | 0 | betaStrand_actionPerformed(); |
782 | } | |
783 | 0 | else if (e.getSource() == turn) |
784 | { | |
785 | 0 | turn_actionPerformed(); |
786 | } | |
787 | 0 | else if (e.getSource() == all) |
788 | { | |
789 | 0 | all_actionPerformed(); |
790 | } | |
791 | } | |
792 | } | |
793 | ||
794 | public class SearchPanel extends TitledPanel implements ItemListener | |
795 | { | |
796 | private AnnotationColumnChooser aColChooser; | |
797 | ||
798 | private Checkbox displayName = new Checkbox(); | |
799 | ||
800 | private Checkbox description = new Checkbox(); | |
801 | ||
802 | private TextField searchBox = new TextField(10); | |
803 | ||
804 | 0 | public SearchPanel(AnnotationColumnChooser aColChooser) |
805 | { | |
806 | ||
807 | 0 | this.aColChooser = aColChooser; |
808 | 0 | searchBox.addTextListener(new TextListener() |
809 | { | |
810 | ||
811 | 0 | @Override |
812 | public void textValueChanged(TextEvent e) | |
813 | { | |
814 | 0 | searchStringAction(); |
815 | ||
816 | } | |
817 | ||
818 | }); | |
819 | ||
820 | 0 | displayName.setLabel(MessageManager.getString("label.label")); |
821 | 0 | displayName.setEnabled(false); |
822 | 0 | displayName.addItemListener(this); |
823 | ||
824 | 0 | description.setLabel(MessageManager.getString("label.description")); |
825 | 0 | description.setEnabled(false); |
826 | 0 | description.addItemListener(this); |
827 | 0 | this.setTitle("Search Filter"); |
828 | // this.setFont(JvSwingUtils.getLabelFont()); | |
829 | ||
830 | 0 | syncState(); |
831 | 0 | this.add(searchBox); |
832 | 0 | this.add(displayName); |
833 | 0 | this.add(description); |
834 | } | |
835 | ||
836 | 0 | public void displayNameCheckboxAction() |
837 | { | |
838 | 0 | aColChooser.setCurrentSearchPanel(this); |
839 | 0 | aColChooser.updateView(); |
840 | } | |
841 | ||
842 | 0 | public void discriptionCheckboxAction() |
843 | { | |
844 | 0 | aColChooser.setCurrentSearchPanel(this); |
845 | 0 | aColChooser.updateView(); |
846 | } | |
847 | ||
848 | 0 | public void searchStringAction() |
849 | { | |
850 | 0 | aColChooser.setCurrentSearchPanel(this); |
851 | 0 | aColChooser.updateView(); |
852 | } | |
853 | ||
854 | 0 | public void syncState() |
855 | { | |
856 | 0 | SearchPanel sp = aColChooser.getCurrentSearchPanel(); |
857 | 0 | if (sp != null) |
858 | { | |
859 | 0 | description.setEnabled(sp.description.isEnabled()); |
860 | 0 | description.setState(sp.description.getState()); |
861 | ||
862 | 0 | displayName.setEnabled(sp.displayName.isEnabled()); |
863 | 0 | displayName.setState(sp.displayName.getState()); |
864 | ||
865 | 0 | searchBox.setText(sp.searchBox.getText()); |
866 | } | |
867 | } | |
868 | ||
869 | 0 | @Override |
870 | public void itemStateChanged(ItemEvent e) | |
871 | { | |
872 | 0 | if (e.getSource() == displayName) |
873 | { | |
874 | 0 | displayNameCheckboxAction(); |
875 | } | |
876 | 0 | else if (e.getSource() == description) |
877 | { | |
878 | 0 | discriptionCheckboxAction(); |
879 | } | |
880 | ||
881 | } | |
882 | } | |
883 | ||
884 | 0 | @Override |
885 | public void actionPerformed(ActionEvent evt) | |
886 | { | |
887 | ||
888 | 0 | if (evt.getSource() == ok) |
889 | { | |
890 | 0 | ok_actionPerformed(null); |
891 | } | |
892 | 0 | else if (evt.getSource() == cancel) |
893 | { | |
894 | 0 | cancel_actionPerformed(null); |
895 | } | |
896 | 0 | else if (evt.getSource() == thresholdValue) |
897 | { | |
898 | 0 | thresholdValue_actionPerformed(null); |
899 | } | |
900 | else | |
901 | { | |
902 | 0 | updateView(); |
903 | } | |
904 | } | |
905 | ||
906 | 0 | @Override |
907 | public void mouseClicked(MouseEvent e) | |
908 | { | |
909 | // TODO Auto-generated method stub | |
910 | ||
911 | } | |
912 | ||
913 | 0 | @Override |
914 | public void mousePressed(MouseEvent e) | |
915 | { | |
916 | 0 | if (e.getSource() == slider) |
917 | { | |
918 | 0 | updateView(); |
919 | } | |
920 | ||
921 | } | |
922 | ||
923 | 0 | @Override |
924 | public void mouseReleased(MouseEvent e) | |
925 | { | |
926 | 0 | if (e.getSource() == slider) |
927 | { | |
928 | 0 | updateView(); |
929 | } | |
930 | } | |
931 | ||
932 | 0 | @Override |
933 | public void mouseEntered(MouseEvent e) | |
934 | { | |
935 | 0 | if (e.getSource() == slider) |
936 | { | |
937 | 0 | updateView(); |
938 | } | |
939 | } | |
940 | ||
941 | 0 | @Override |
942 | public void mouseExited(MouseEvent e) | |
943 | { | |
944 | 0 | if (e.getSource() == slider) |
945 | { | |
946 | 0 | updateView(); |
947 | } | |
948 | } | |
949 | ||
950 | } |