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SliderPanel | 50 | 140 | 49 |
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 jalview.analysis.Conservation; | |
24 | import jalview.datamodel.SequenceGroup; | |
25 | import jalview.renderer.ResidueShaderI; | |
26 | import jalview.util.MessageManager; | |
27 | ||
28 | import java.awt.BorderLayout; | |
29 | import java.awt.Button; | |
30 | import java.awt.Checkbox; | |
31 | import java.awt.Color; | |
32 | import java.awt.FlowLayout; | |
33 | import java.awt.Frame; | |
34 | import java.awt.Label; | |
35 | import java.awt.Panel; | |
36 | import java.awt.Scrollbar; | |
37 | import java.awt.TextField; | |
38 | import java.awt.event.ActionEvent; | |
39 | import java.awt.event.ActionListener; | |
40 | import java.awt.event.AdjustmentEvent; | |
41 | import java.awt.event.AdjustmentListener; | |
42 | import java.awt.event.FocusAdapter; | |
43 | import java.awt.event.FocusEvent; | |
44 | import java.awt.event.MouseEvent; | |
45 | import java.awt.event.MouseListener; | |
46 | import java.awt.event.WindowAdapter; | |
47 | import java.awt.event.WindowEvent; | |
48 | import java.util.List; | |
49 | ||
50 | public class SliderPanel extends Panel | |
51 | implements ActionListener, AdjustmentListener, MouseListener | |
52 | { | |
53 | private static final String BACKGROUND = "Background"; | |
54 | ||
55 | AlignmentPanel ap; | |
56 | ||
57 | boolean forConservation = true; | |
58 | ||
59 | ResidueShaderI cs; | |
60 | ||
61 | static Frame conservationSlider; | |
62 | ||
63 | static Frame PIDSlider; | |
64 | ||
65 | 0 | public static int setConservationSlider(AlignmentPanel ap, |
66 | ResidueShaderI ccs, String source) | |
67 | { | |
68 | 0 | SliderPanel sp = null; |
69 | ||
70 | 0 | if (conservationSlider == null) |
71 | { | |
72 | 0 | sp = new SliderPanel(ap, ccs.getConservationInc(), true, ccs); |
73 | 0 | conservationSlider = new Frame(); |
74 | 0 | conservationSlider.add(sp); |
75 | } | |
76 | else | |
77 | { | |
78 | 0 | sp = (SliderPanel) conservationSlider.getComponent(0); |
79 | 0 | sp.cs = ccs; |
80 | 0 | sp.valueField.setText(String.valueOf(ccs.getConservationInc())); |
81 | } | |
82 | ||
83 | 0 | conservationSlider.setTitle(MessageManager.formatMessage( |
84 | "label.conservation_colour_increment", new String[] | |
85 | 0 | { source == null ? BACKGROUND : source })); |
86 | 0 | List<SequenceGroup> groups = ap.av.getAlignment().getGroups(); |
87 | 0 | if (groups != null && !groups.isEmpty()) |
88 | { | |
89 | 0 | sp.setAllGroupsCheckEnabled(true); |
90 | } | |
91 | else | |
92 | { | |
93 | 0 | sp.setAllGroupsCheckEnabled(false); |
94 | } | |
95 | ||
96 | 0 | return sp.getValue(); |
97 | } | |
98 | ||
99 | 0 | public static void showConservationSlider() |
100 | { | |
101 | 0 | try |
102 | { | |
103 | 0 | PIDSlider.setVisible(false); |
104 | 0 | PIDSlider = null; |
105 | } catch (Exception ex) | |
106 | { | |
107 | } | |
108 | ||
109 | 0 | if (!conservationSlider.isVisible()) |
110 | { | |
111 | 0 | jalview.bin.JalviewLite.addFrame(conservationSlider, |
112 | conservationSlider.getTitle(), 420, 100); | |
113 | 0 | conservationSlider.addWindowListener(new WindowAdapter() |
114 | { | |
115 | 0 | @Override |
116 | public void windowClosing(WindowEvent e) | |
117 | { | |
118 | 0 | conservationSlider = null; |
119 | } | |
120 | }); | |
121 | ||
122 | } | |
123 | ||
124 | } | |
125 | ||
126 | 0 | public static int setPIDSliderSource(AlignmentPanel ap, |
127 | ResidueShaderI ccs, String source) | |
128 | { | |
129 | 0 | SliderPanel pid = null; |
130 | 0 | if (PIDSlider == null) |
131 | { | |
132 | 0 | pid = new SliderPanel(ap, ccs.getThreshold(), false, ccs); |
133 | 0 | PIDSlider = new Frame(); |
134 | 0 | PIDSlider.add(pid); |
135 | } | |
136 | else | |
137 | { | |
138 | 0 | pid = (SliderPanel) PIDSlider.getComponent(0); |
139 | 0 | pid.cs = ccs; |
140 | 0 | pid.valueField.setText(String.valueOf(ccs.getThreshold())); |
141 | } | |
142 | 0 | PIDSlider.setTitle(MessageManager.formatMessage( |
143 | "label.percentage_identity_threshold", new String[] | |
144 | 0 | { source == null ? BACKGROUND : source })); |
145 | ||
146 | 0 | if (ap.av.getAlignment().getGroups() != null) |
147 | { | |
148 | 0 | pid.setAllGroupsCheckEnabled(true); |
149 | } | |
150 | else | |
151 | { | |
152 | 0 | pid.setAllGroupsCheckEnabled(false); |
153 | } | |
154 | ||
155 | 0 | return pid.getValue(); |
156 | ||
157 | } | |
158 | ||
159 | 0 | public static void showPIDSlider() |
160 | { | |
161 | 0 | try |
162 | { | |
163 | 0 | conservationSlider.setVisible(false); |
164 | 0 | conservationSlider = null; |
165 | } catch (Exception ex) | |
166 | { | |
167 | } | |
168 | ||
169 | 0 | if (!PIDSlider.isVisible()) |
170 | { | |
171 | 0 | jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420, |
172 | 100); | |
173 | 0 | PIDSlider.addWindowListener(new WindowAdapter() |
174 | { | |
175 | 0 | @Override |
176 | public void windowClosing(WindowEvent e) | |
177 | { | |
178 | 0 | PIDSlider = null; |
179 | } | |
180 | }); | |
181 | } | |
182 | ||
183 | } | |
184 | ||
185 | /** | |
186 | * Hides the PID slider panel if it is shown | |
187 | */ | |
188 | 0 | public static void hidePIDSlider() |
189 | { | |
190 | 0 | if (PIDSlider != null) |
191 | { | |
192 | 0 | PIDSlider.setVisible(false); |
193 | 0 | PIDSlider = null; |
194 | } | |
195 | } | |
196 | ||
197 | /** | |
198 | * Hides the Conservation slider panel if it is shown | |
199 | */ | |
200 | 0 | public static void hideConservationSlider() |
201 | { | |
202 | 0 | if (conservationSlider != null) |
203 | { | |
204 | 0 | conservationSlider.setVisible(false); |
205 | 0 | conservationSlider = null; |
206 | } | |
207 | } | |
208 | ||
209 | 0 | public SliderPanel(AlignmentPanel ap, int value, boolean forConserve, |
210 | ResidueShaderI shader) | |
211 | { | |
212 | 0 | try |
213 | { | |
214 | 0 | jbInit(); |
215 | } catch (Exception e) | |
216 | { | |
217 | 0 | e.printStackTrace(); |
218 | } | |
219 | 0 | this.ap = ap; |
220 | 0 | this.cs = shader; |
221 | 0 | forConservation = forConserve; |
222 | 0 | undoButton.setVisible(false); |
223 | 0 | applyButton.setVisible(false); |
224 | 0 | if (forConservation) |
225 | { | |
226 | 0 | label.setText(MessageManager |
227 | .getString("label.modify_conservation_visibility")); | |
228 | 0 | slider.setMinimum(0); |
229 | 0 | slider.setMaximum(50 + slider.getVisibleAmount()); |
230 | 0 | slider.setUnitIncrement(1); |
231 | } | |
232 | else | |
233 | { | |
234 | 0 | label.setText(MessageManager |
235 | .getString("label.colour_residues_above_occurrence")); | |
236 | 0 | slider.setMinimum(0); |
237 | 0 | slider.setMaximum(100 + slider.getVisibleAmount()); |
238 | 0 | slider.setBlockIncrement(1); |
239 | } | |
240 | ||
241 | 0 | slider.addAdjustmentListener(this); |
242 | 0 | slider.addMouseListener(this); |
243 | ||
244 | 0 | slider.setValue(value); |
245 | 0 | valueField.setText(value + ""); |
246 | } | |
247 | ||
248 | 0 | public void valueChanged(int i) |
249 | { | |
250 | 0 | if (cs == null) |
251 | { | |
252 | 0 | return; |
253 | } | |
254 | 0 | if (forConservation) |
255 | { | |
256 | 0 | cs.setConservationApplied(true); |
257 | 0 | cs.setConservationInc(i); |
258 | } | |
259 | else | |
260 | { | |
261 | 0 | cs.setThreshold(i, ap.av.isIgnoreGapsConsensus()); |
262 | } | |
263 | ||
264 | 0 | if (allGroupsCheck.getState()) |
265 | { | |
266 | 0 | for (SequenceGroup group : ap.av.getAlignment().getGroups()) |
267 | { | |
268 | 0 | ResidueShaderI groupColourScheme = group.getGroupColourScheme(); |
269 | 0 | if (forConservation) |
270 | { | |
271 | 0 | if (!groupColourScheme.conservationApplied()) |
272 | { | |
273 | /* | |
274 | * first time the colour scheme has had Conservation shading applied | |
275 | * - compute conservation | |
276 | */ | |
277 | 0 | Conservation c = new Conservation("Group", |
278 | group.getSequences(null), group.getStartRes(), | |
279 | group.getEndRes()); | |
280 | 0 | c.calculate(); |
281 | 0 | c.verdict(false, ap.av.getConsPercGaps()); |
282 | 0 | group.cs.setConservation(c); |
283 | ||
284 | } | |
285 | 0 | groupColourScheme.setConservationApplied(true); |
286 | 0 | groupColourScheme.setConservationInc(i); |
287 | } | |
288 | else | |
289 | { | |
290 | 0 | groupColourScheme.setThreshold(i, ap.av.isIgnoreGapsConsensus()); |
291 | } | |
292 | } | |
293 | } | |
294 | ||
295 | 0 | ap.seqPanel.seqCanvas.repaint(); |
296 | } | |
297 | ||
298 | 0 | public void setAllGroupsCheckEnabled(boolean b) |
299 | { | |
300 | 0 | allGroupsCheck.setState(ap.av.getColourAppliesToAllGroups()); |
301 | 0 | allGroupsCheck.setEnabled(b); |
302 | } | |
303 | ||
304 | 0 | @Override |
305 | public void actionPerformed(ActionEvent evt) | |
306 | { | |
307 | 0 | if (evt.getSource() == applyButton) |
308 | { | |
309 | 0 | applyButton_actionPerformed(); |
310 | } | |
311 | 0 | else if (evt.getSource() == undoButton) |
312 | { | |
313 | 0 | undoButton_actionPerformed(); |
314 | } | |
315 | 0 | else if (evt.getSource() == valueField) |
316 | { | |
317 | 0 | valueField_actionPerformed(); |
318 | } | |
319 | } | |
320 | ||
321 | 0 | @Override |
322 | public void adjustmentValueChanged(AdjustmentEvent evt) | |
323 | { | |
324 | 0 | valueField.setText(slider.getValue() + ""); |
325 | 0 | valueChanged(slider.getValue()); |
326 | } | |
327 | ||
328 | 0 | public void valueField_actionPerformed() |
329 | { | |
330 | 0 | try |
331 | { | |
332 | 0 | int i = Integer.valueOf(valueField.getText()); |
333 | 0 | slider.setValue(i); |
334 | } catch (NumberFormatException ex) | |
335 | { | |
336 | 0 | valueField.setText(String.valueOf(slider.getValue())); |
337 | } | |
338 | } | |
339 | ||
340 | 0 | public void setValue(int value) |
341 | { | |
342 | 0 | slider.setValue(value); |
343 | } | |
344 | ||
345 | 0 | public int getValue() |
346 | { | |
347 | 0 | return Integer.parseInt(valueField.getText()); |
348 | } | |
349 | ||
350 | // this is used for conservation colours, PID colours and redundancy threshold | |
351 | protected Scrollbar slider = new Scrollbar(); | |
352 | ||
353 | protected TextField valueField = new TextField(); | |
354 | ||
355 | protected Label label = new Label(); | |
356 | ||
357 | Panel jPanel1 = new Panel(); | |
358 | ||
359 | Panel jPanel2 = new Panel(); | |
360 | ||
361 | protected Button applyButton = new Button(); | |
362 | ||
363 | protected Button undoButton = new Button(); | |
364 | ||
365 | FlowLayout flowLayout1 = new FlowLayout(); | |
366 | ||
367 | protected Checkbox allGroupsCheck = new Checkbox(); | |
368 | ||
369 | BorderLayout borderLayout1 = new BorderLayout(); | |
370 | ||
371 | BorderLayout borderLayout2 = new BorderLayout(); | |
372 | ||
373 | FlowLayout flowLayout2 = new FlowLayout(); | |
374 | ||
375 | 0 | private void jbInit() throws Exception |
376 | { | |
377 | 0 | this.setLayout(borderLayout2); |
378 | ||
379 | // slider.setMajorTickSpacing(10); | |
380 | // slider.setMinorTickSpacing(1); | |
381 | // slider.setPaintTicks(true); | |
382 | 0 | slider.setBackground(Color.white); |
383 | 0 | slider.setFont(new java.awt.Font("Verdana", 0, 11)); |
384 | 0 | slider.setOrientation(0); |
385 | 0 | valueField.setFont(new java.awt.Font("Verdana", 0, 11)); |
386 | 0 | valueField.setText(" "); |
387 | 0 | valueField.addActionListener(this); |
388 | 0 | valueField.setColumns(3); |
389 | 0 | valueField.addFocusListener(new FocusAdapter() |
390 | { | |
391 | 0 | @Override |
392 | public void focusLost(FocusEvent e) | |
393 | { | |
394 | 0 | valueField_actionPerformed(); |
395 | 0 | valueChanged(slider.getValue()); |
396 | } | |
397 | }); | |
398 | ||
399 | 0 | label.setFont(new java.awt.Font("Verdana", 0, 11)); |
400 | 0 | label.setText(MessageManager.getString("label.set_this_label_text")); |
401 | 0 | jPanel1.setLayout(borderLayout1); |
402 | 0 | jPanel2.setLayout(flowLayout1); |
403 | 0 | applyButton.setFont(new java.awt.Font("Verdana", 0, 11)); |
404 | 0 | applyButton.setLabel(MessageManager.getString("action.apply")); |
405 | 0 | applyButton.addActionListener(this); |
406 | 0 | undoButton.setEnabled(false); |
407 | 0 | undoButton.setFont(new java.awt.Font("Verdana", 0, 11)); |
408 | 0 | undoButton.setLabel(MessageManager.getString("action.undo")); |
409 | 0 | undoButton.addActionListener(this); |
410 | 0 | allGroupsCheck.setEnabled(false); |
411 | 0 | allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11)); |
412 | 0 | allGroupsCheck.setLabel( |
413 | MessageManager.getString("action.apply_threshold_all_groups")); | |
414 | 0 | allGroupsCheck |
415 | .setName(MessageManager.getString("action.apply_all_groups")); | |
416 | 0 | this.setBackground(Color.white); |
417 | 0 | this.setForeground(Color.black); |
418 | 0 | jPanel2.add(label, null); |
419 | 0 | jPanel2.add(applyButton, null); |
420 | 0 | jPanel2.add(undoButton, null); |
421 | 0 | jPanel2.add(allGroupsCheck); |
422 | 0 | jPanel1.add(valueField, java.awt.BorderLayout.EAST); |
423 | 0 | jPanel1.add(slider, java.awt.BorderLayout.CENTER); |
424 | 0 | this.add(jPanel1, java.awt.BorderLayout.SOUTH); |
425 | 0 | this.add(jPanel2, java.awt.BorderLayout.CENTER); |
426 | } | |
427 | ||
428 | 0 | protected void applyButton_actionPerformed() |
429 | { | |
430 | } | |
431 | ||
432 | 0 | protected void undoButton_actionPerformed() |
433 | { | |
434 | } | |
435 | ||
436 | 0 | @Override |
437 | public void mousePressed(MouseEvent evt) | |
438 | { | |
439 | } | |
440 | ||
441 | 0 | @Override |
442 | public void mouseReleased(MouseEvent evt) | |
443 | { | |
444 | 0 | ap.paintAlignment(true, true); |
445 | } | |
446 | ||
447 | 0 | @Override |
448 | public void mouseClicked(MouseEvent evt) | |
449 | { | |
450 | } | |
451 | ||
452 | 0 | @Override |
453 | public void mouseEntered(MouseEvent evt) | |
454 | { | |
455 | } | |
456 | ||
457 | 0 | @Override |
458 | public void mouseExited(MouseEvent evt) | |
459 | { | |
460 | } | |
461 | } |