1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
|
21 |
|
package jalview.gui; |
22 |
|
|
23 |
|
import java.awt.AlphaComposite; |
24 |
|
import java.awt.Color; |
25 |
|
import java.awt.Dimension; |
26 |
|
import java.awt.FontMetrics; |
27 |
|
import java.awt.Graphics; |
28 |
|
import java.awt.Graphics2D; |
29 |
|
import java.awt.Image; |
30 |
|
import java.awt.Rectangle; |
31 |
|
import java.awt.RenderingHints; |
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.MouseEvent; |
37 |
|
import java.awt.event.MouseListener; |
38 |
|
import java.awt.event.MouseMotionListener; |
39 |
|
import java.awt.event.MouseWheelEvent; |
40 |
|
import java.awt.event.MouseWheelListener; |
41 |
|
import java.awt.image.BufferedImage; |
42 |
|
import java.beans.PropertyChangeEvent; |
43 |
|
import java.util.ArrayList; |
44 |
|
import java.util.BitSet; |
45 |
|
import java.util.Collections; |
46 |
|
import java.util.List; |
47 |
|
|
48 |
|
import javax.swing.JMenuItem; |
49 |
|
import javax.swing.JPanel; |
50 |
|
import javax.swing.JPopupMenu; |
51 |
|
import javax.swing.Scrollable; |
52 |
|
import javax.swing.ToolTipManager; |
53 |
|
|
54 |
|
import jalview.api.AlignViewportI; |
55 |
|
import jalview.datamodel.AlignmentAnnotation; |
56 |
|
import jalview.datamodel.AlignmentI; |
57 |
|
import jalview.datamodel.Annotation; |
58 |
|
import jalview.datamodel.ColumnSelection; |
59 |
|
import jalview.datamodel.ContactListI; |
60 |
|
import jalview.datamodel.ContactMatrixI; |
61 |
|
import jalview.datamodel.ContactRange; |
62 |
|
import jalview.datamodel.GraphLine; |
63 |
|
import jalview.datamodel.HiddenColumns; |
64 |
|
import jalview.datamodel.SequenceI; |
65 |
|
import jalview.gui.JalviewColourChooser.ColourChooserListener; |
66 |
|
import jalview.renderer.AnnotationRenderer; |
67 |
|
import jalview.renderer.AwtRenderPanelI; |
68 |
|
import jalview.renderer.ContactGeometry; |
69 |
|
import jalview.schemes.ResidueProperties; |
70 |
|
import jalview.util.Comparison; |
71 |
|
import jalview.util.Format; |
72 |
|
import jalview.util.MessageManager; |
73 |
|
import jalview.util.Platform; |
74 |
|
import jalview.viewmodel.ViewportListenerI; |
75 |
|
import jalview.viewmodel.ViewportRanges; |
76 |
|
import jalview.ws.datamodel.MappableContactMatrixI; |
77 |
|
import jalview.ws.datamodel.alphafold.PAEContactMatrix; |
78 |
|
|
79 |
|
|
80 |
|
|
81 |
|
|
82 |
|
|
83 |
|
@author |
84 |
|
@version |
85 |
|
|
|
|
| 22.1% |
Uncovered Elements: 742 (952) |
Complexity: 250 |
Complexity Density: 0.42 |
|
86 |
|
public class AnnotationPanel extends JPanel implements AwtRenderPanelI, |
87 |
|
MouseListener, MouseWheelListener, MouseMotionListener, |
88 |
|
ActionListener, AdjustmentListener, Scrollable, ViewportListenerI |
89 |
|
{ |
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 0 |
Complexity Density: - |
|
90 |
|
enum DragMode |
91 |
|
{ |
92 |
|
Select, Resize, Undefined, MatrixSelect |
93 |
|
}; |
94 |
|
|
95 |
|
String HELIX = MessageManager.getString("label.helix"); |
96 |
|
|
97 |
|
String SHEET = MessageManager.getString("label.sheet"); |
98 |
|
|
99 |
|
|
100 |
|
|
101 |
|
|
102 |
|
String STEM = MessageManager.getString("label.rna_helix"); |
103 |
|
|
104 |
|
String LABEL = MessageManager.getString("label.label"); |
105 |
|
|
106 |
|
String REMOVE = MessageManager.getString("label.remove_annotation"); |
107 |
|
|
108 |
|
String COLOUR = MessageManager.getString("action.colour"); |
109 |
|
|
110 |
|
public final Color HELIX_COLOUR = Color.red.darker(); |
111 |
|
|
112 |
|
public final Color SHEET_COLOUR = Color.green.darker().darker(); |
113 |
|
|
114 |
|
public final Color STEM_COLOUR = Color.blue.darker(); |
115 |
|
|
116 |
|
|
117 |
|
public AlignViewport av; |
118 |
|
|
119 |
|
AlignmentPanel ap; |
120 |
|
|
121 |
|
public int activeRow = -1; |
122 |
|
|
123 |
|
public BufferedImage image; |
124 |
|
|
125 |
|
public volatile BufferedImage fadedImage; |
126 |
|
|
127 |
|
|
128 |
|
|
129 |
|
public FontMetrics fm; |
130 |
|
|
131 |
|
public int imgWidth = 0; |
132 |
|
|
133 |
|
boolean fastPaint = false; |
134 |
|
|
135 |
|
|
136 |
|
int graphStretch = -1; |
137 |
|
|
138 |
|
int mouseDragLastX = -1; |
139 |
|
|
140 |
|
int mouseDragLastY = -1; |
141 |
|
|
142 |
|
int firstDragX = -1; |
143 |
|
|
144 |
|
int firstDragY = -1; |
145 |
|
|
146 |
|
DragMode dragMode = DragMode.Undefined; |
147 |
|
|
148 |
|
boolean mouseDragging = false; |
149 |
|
|
150 |
|
|
151 |
|
int cursorX = 0; |
152 |
|
|
153 |
|
int cursorY = 0; |
154 |
|
|
155 |
|
public final AnnotationRenderer renderer; |
156 |
|
|
157 |
|
private MouseWheelListener[] _mwl; |
158 |
|
|
159 |
|
private boolean notJustOne; |
160 |
|
|
161 |
|
|
162 |
|
|
163 |
|
|
164 |
|
@param |
165 |
|
|
166 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
|
167 |
475 |
public AnnotationPanel(AlignmentPanel ap)... |
168 |
|
{ |
169 |
475 |
ToolTipManager.sharedInstance().registerComponent(this); |
170 |
475 |
ToolTipManager.sharedInstance().setInitialDelay(0); |
171 |
475 |
ToolTipManager.sharedInstance().setDismissDelay(10000); |
172 |
475 |
this.ap = ap; |
173 |
475 |
av = ap.av; |
174 |
475 |
this.setLayout(null); |
175 |
475 |
addMouseListener(this); |
176 |
475 |
addMouseMotionListener(this); |
177 |
475 |
ap.annotationScroller.getVerticalScrollBar() |
178 |
|
.addAdjustmentListener(this); |
179 |
|
|
180 |
|
|
181 |
475 |
_mwl = ap.annotationScroller.getMouseWheelListeners(); |
182 |
|
|
183 |
475 |
ap.annotationScroller.addMouseWheelListener(this); |
184 |
475 |
renderer = new AnnotationRenderer(); |
185 |
|
|
186 |
475 |
av.getRanges().addPropertyChangeListener(this); |
187 |
|
} |
188 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
189 |
13 |
public AnnotationPanel(AlignViewport av)... |
190 |
|
{ |
191 |
13 |
this.av = av; |
192 |
13 |
renderer = new AnnotationRenderer(); |
193 |
|
} |
194 |
|
|
195 |
|
|
196 |
|
|
197 |
|
|
198 |
|
|
199 |
|
|
200 |
|
|
201 |
|
|
202 |
|
|
203 |
|
|
204 |
|
|
205 |
|
|
206 |
|
|
207 |
|
|
208 |
|
|
209 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
210 |
0 |
@Override... |
211 |
|
public void mouseWheelMoved(MouseWheelEvent e) |
212 |
|
{ |
213 |
0 |
if (e.isShiftDown()) |
214 |
|
{ |
215 |
0 |
ap.getSeqPanel().mouseWheelMoved(e); |
216 |
|
} |
217 |
|
else |
218 |
|
{ |
219 |
|
|
220 |
|
|
221 |
0 |
for (MouseWheelListener mwl : _mwl) |
222 |
|
{ |
223 |
0 |
if (mwl != null) |
224 |
|
{ |
225 |
0 |
mwl.mouseWheelMoved(e); |
226 |
|
} |
227 |
0 |
if (e.isConsumed()) |
228 |
|
{ |
229 |
0 |
break; |
230 |
|
} |
231 |
|
} |
232 |
|
} |
233 |
|
} |
234 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
235 |
0 |
@Override... |
236 |
|
public Dimension getPreferredScrollableViewportSize() |
237 |
|
{ |
238 |
0 |
Dimension ps = getPreferredSize(); |
239 |
0 |
return new Dimension(ps.width, adjustForAlignFrame(false, ps.height)); |
240 |
|
} |
241 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
242 |
0 |
@Override... |
243 |
|
public int getScrollableBlockIncrement(Rectangle visibleRect, |
244 |
|
int orientation, int direction) |
245 |
|
{ |
246 |
0 |
return 30; |
247 |
|
} |
248 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
249 |
6801 |
@Override... |
250 |
|
public boolean getScrollableTracksViewportHeight() |
251 |
|
{ |
252 |
6801 |
return false; |
253 |
|
} |
254 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
255 |
6801 |
@Override... |
256 |
|
public boolean getScrollableTracksViewportWidth() |
257 |
|
{ |
258 |
6801 |
return true; |
259 |
|
} |
260 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
261 |
0 |
@Override... |
262 |
|
public int getScrollableUnitIncrement(Rectangle visibleRect, |
263 |
|
int orientation, int direction) |
264 |
|
{ |
265 |
0 |
return 30; |
266 |
|
} |
267 |
|
|
268 |
|
|
269 |
|
|
270 |
|
|
271 |
|
@see |
272 |
|
|
273 |
|
|
274 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
275 |
892 |
@Override... |
276 |
|
public void adjustmentValueChanged(AdjustmentEvent evt) |
277 |
|
{ |
278 |
|
|
279 |
892 |
ap.getAlabels().setScrollOffset(-evt.getValue()); |
280 |
|
} |
281 |
|
|
282 |
|
|
283 |
|
|
284 |
|
|
285 |
|
|
286 |
|
|
287 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
288 |
4734 |
public int adjustPanelHeight()... |
289 |
|
{ |
290 |
4734 |
int height = av.calcPanelHeight(); |
291 |
4734 |
this.setPreferredSize(new Dimension(1, height)); |
292 |
4734 |
if (ap != null) |
293 |
|
{ |
294 |
|
|
295 |
4151 |
ap.validate(); |
296 |
|
} |
297 |
|
|
298 |
4734 |
return height; |
299 |
|
} |
300 |
|
|
301 |
|
|
302 |
|
|
303 |
|
|
304 |
|
@param |
305 |
|
|
306 |
|
|
|
|
| 0% |
Uncovered Elements: 107 (107) |
Complexity: 24 |
Complexity Density: 0.37 |
|
307 |
0 |
@Override... |
308 |
|
public void actionPerformed(ActionEvent evt) |
309 |
|
{ |
310 |
0 |
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); |
311 |
0 |
if (aa == null) |
312 |
|
{ |
313 |
0 |
return; |
314 |
|
} |
315 |
0 |
Annotation[] anot = aa[activeRow].annotations; |
316 |
|
|
317 |
0 |
if (anot.length < av.getColumnSelection().getMax()) |
318 |
|
{ |
319 |
0 |
Annotation[] temp = new Annotation[av.getColumnSelection().getMax() |
320 |
|
+ 2]; |
321 |
0 |
System.arraycopy(anot, 0, temp, 0, anot.length); |
322 |
0 |
anot = temp; |
323 |
0 |
aa[activeRow].annotations = anot; |
324 |
|
} |
325 |
|
|
326 |
0 |
String action = evt.getActionCommand(); |
327 |
0 |
if (action.equals(REMOVE)) |
328 |
|
{ |
329 |
0 |
for (int index : av.getColumnSelection().getSelected()) |
330 |
|
{ |
331 |
0 |
if (av.getAlignment().getHiddenColumns().isVisible(index)) |
332 |
|
{ |
333 |
0 |
anot[index] = null; |
334 |
|
} |
335 |
|
} |
336 |
|
} |
337 |
0 |
else if (action.equals(LABEL)) |
338 |
|
{ |
339 |
0 |
String exMesg = collectAnnotVals(anot, LABEL); |
340 |
0 |
String label = JvOptionPane.showInputDialog( |
341 |
|
MessageManager.getString("label.enter_label"), exMesg); |
342 |
|
|
343 |
0 |
if (label == null) |
344 |
|
{ |
345 |
0 |
return; |
346 |
|
} |
347 |
|
|
348 |
0 |
if ((label.length() > 0) && !aa[activeRow].hasText) |
349 |
|
{ |
350 |
0 |
aa[activeRow].hasText = true; |
351 |
|
} |
352 |
|
|
353 |
0 |
for (int index : av.getColumnSelection().getSelected()) |
354 |
|
{ |
355 |
0 |
if (!av.getAlignment().getHiddenColumns().isVisible(index)) |
356 |
|
{ |
357 |
0 |
continue; |
358 |
|
} |
359 |
|
|
360 |
0 |
if (anot[index] == null) |
361 |
|
{ |
362 |
0 |
anot[index] = new Annotation(label, "", ' ', 0); |
363 |
|
} |
364 |
|
else |
365 |
|
{ |
366 |
0 |
anot[index].displayCharacter = label; |
367 |
|
} |
368 |
|
} |
369 |
|
} |
370 |
0 |
else if (action.equals(COLOUR)) |
371 |
|
{ |
372 |
0 |
final Annotation[] fAnot = anot; |
373 |
0 |
String title = MessageManager |
374 |
|
.getString("label.select_foreground_colour"); |
375 |
0 |
ColourChooserListener listener = new ColourChooserListener() |
376 |
|
{ |
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
377 |
0 |
@Override... |
378 |
|
public void colourSelected(Color c) |
379 |
|
{ |
380 |
0 |
HiddenColumns hiddenColumns = av.getAlignment() |
381 |
|
.getHiddenColumns(); |
382 |
0 |
for (int index : av.getColumnSelection().getSelected()) |
383 |
|
{ |
384 |
0 |
if (hiddenColumns.isVisible(index)) |
385 |
|
{ |
386 |
0 |
if (fAnot[index] == null) |
387 |
|
{ |
388 |
0 |
fAnot[index] = new Annotation("", "", ' ', 0); |
389 |
|
} |
390 |
0 |
fAnot[index].colour = c; |
391 |
|
} |
392 |
|
} |
393 |
|
}; |
394 |
|
}; |
395 |
0 |
JalviewColourChooser.showColourChooser(this, title, Color.black, |
396 |
|
listener); |
397 |
|
} |
398 |
|
else |
399 |
|
|
400 |
|
{ |
401 |
0 |
char type = 0; |
402 |
0 |
String symbol = "\u03B1"; |
403 |
|
|
404 |
0 |
if (action.equals(HELIX)) |
405 |
|
{ |
406 |
0 |
type = 'H'; |
407 |
|
} |
408 |
0 |
else if (action.equals(SHEET)) |
409 |
|
{ |
410 |
0 |
type = 'E'; |
411 |
0 |
symbol = "\u03B2"; |
412 |
|
} |
413 |
|
|
414 |
|
|
415 |
0 |
else if (action.equals(STEM)) |
416 |
|
{ |
417 |
0 |
type = 'S'; |
418 |
0 |
int column = av.getColumnSelection().getSelectedRanges().get(0)[0]; |
419 |
0 |
symbol = aa[activeRow].getDefaultRnaHelixSymbol(column); |
420 |
|
} |
421 |
|
|
422 |
0 |
if (!aa[activeRow].hasIcons) |
423 |
|
{ |
424 |
0 |
aa[activeRow].hasIcons = true; |
425 |
|
} |
426 |
|
|
427 |
0 |
String label = JvOptionPane.showInputDialog(MessageManager |
428 |
|
.getString("label.enter_label_for_the_structure"), symbol); |
429 |
|
|
430 |
0 |
if (label == null) |
431 |
|
{ |
432 |
0 |
return; |
433 |
|
} |
434 |
|
|
435 |
0 |
if ((label.length() > 0) && !aa[activeRow].hasText) |
436 |
|
{ |
437 |
0 |
aa[activeRow].hasText = true; |
438 |
0 |
if (action.equals(STEM)) |
439 |
|
{ |
440 |
0 |
aa[activeRow].showAllColLabels = true; |
441 |
|
} |
442 |
|
} |
443 |
0 |
for (int index : av.getColumnSelection().getSelected()) |
444 |
|
{ |
445 |
0 |
if (!av.getAlignment().getHiddenColumns().isVisible(index)) |
446 |
|
{ |
447 |
0 |
continue; |
448 |
|
} |
449 |
|
|
450 |
0 |
if (anot[index] == null) |
451 |
|
{ |
452 |
0 |
anot[index] = new Annotation(label, "", type, 0); |
453 |
|
} |
454 |
|
|
455 |
0 |
anot[index].secondaryStructure = type != 'S' ? type |
456 |
0 |
: label.length() == 0 ? ' ' : label.charAt(0); |
457 |
0 |
anot[index].displayCharacter = label; |
458 |
|
|
459 |
|
} |
460 |
|
} |
461 |
|
|
462 |
0 |
av.getAlignment().validateAnnotation(aa[activeRow]); |
463 |
0 |
ap.alignmentChanged(); |
464 |
0 |
ap.alignFrame.setMenusForViewport(); |
465 |
0 |
adjustPanelHeight(); |
466 |
0 |
repaint(); |
467 |
|
|
468 |
0 |
return; |
469 |
|
} |
470 |
|
|
471 |
|
|
472 |
|
|
473 |
|
|
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
@param |
478 |
|
@param |
479 |
|
@return |
480 |
|
|
|
|
| 0% |
Uncovered Elements: 36 (36) |
Complexity: 15 |
Complexity Density: 0.68 |
|
481 |
0 |
private String collectAnnotVals(Annotation[] anots, String type)... |
482 |
|
{ |
483 |
|
|
484 |
|
|
485 |
0 |
StringBuilder collatedInput = new StringBuilder(64); |
486 |
0 |
String last = ""; |
487 |
0 |
ColumnSelection viscols = av.getColumnSelection(); |
488 |
0 |
HiddenColumns hidden = av.getAlignment().getHiddenColumns(); |
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
|
493 |
|
|
494 |
0 |
List<Integer> selected = new ArrayList<>(viscols.getSelected()); |
495 |
0 |
Collections.sort(selected); |
496 |
0 |
for (int index : selected) |
497 |
|
{ |
498 |
|
|
499 |
0 |
if (!hidden.isVisible(index)) |
500 |
|
{ |
501 |
0 |
continue; |
502 |
|
} |
503 |
0 |
String tlabel = null; |
504 |
0 |
if (anots[index] != null) |
505 |
|
{ |
506 |
0 |
if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM) |
507 |
|
|| type.equals(LABEL)) |
508 |
|
{ |
509 |
0 |
tlabel = anots[index].description; |
510 |
0 |
if (tlabel == null || tlabel.length() < 1) |
511 |
|
{ |
512 |
0 |
if (type.equals(HELIX) || type.equals(SHEET) |
513 |
|
|| type.equals(STEM)) |
514 |
|
{ |
515 |
0 |
tlabel = "" + anots[index].secondaryStructure; |
516 |
|
} |
517 |
|
else |
518 |
|
{ |
519 |
0 |
tlabel = "" + anots[index].displayCharacter; |
520 |
|
} |
521 |
|
} |
522 |
|
} |
523 |
0 |
if (tlabel != null && !tlabel.equals(last)) |
524 |
|
{ |
525 |
0 |
if (last.length() > 0) |
526 |
|
{ |
527 |
0 |
collatedInput.append(" "); |
528 |
|
} |
529 |
0 |
collatedInput.append(tlabel); |
530 |
|
} |
531 |
|
} |
532 |
|
} |
533 |
0 |
return collatedInput.toString(); |
534 |
|
} |
535 |
|
|
536 |
|
|
537 |
|
|
538 |
|
|
539 |
|
|
540 |
|
|
541 |
|
@param |
542 |
|
|
|
|
| 0% |
Uncovered Elements: 49 (49) |
Complexity: 13 |
Complexity Density: 0.45 |
|
543 |
0 |
@Override... |
544 |
|
public void mousePressed(MouseEvent evt) |
545 |
|
{ |
546 |
|
|
547 |
0 |
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); |
548 |
0 |
if (aa == null) |
549 |
|
{ |
550 |
0 |
return; |
551 |
|
} |
552 |
0 |
mouseDragLastX = evt.getX(); |
553 |
0 |
mouseDragLastY = evt.getY(); |
554 |
|
|
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
559 |
0 |
int height = 0; |
560 |
0 |
activeRow = -1; |
561 |
0 |
int yOffset = 0; |
562 |
|
|
563 |
0 |
final int y = evt.getY(); |
564 |
|
|
565 |
0 |
for (int i = 0; i < aa.length; i++) |
566 |
|
{ |
567 |
0 |
if (aa[i].isForDisplay()) |
568 |
|
{ |
569 |
0 |
height += aa[i].height; |
570 |
|
} |
571 |
|
|
572 |
0 |
if (y < height) |
573 |
|
{ |
574 |
0 |
if (aa[i].editable) |
575 |
|
{ |
576 |
0 |
activeRow = i; |
577 |
|
} |
578 |
0 |
else if (aa[i].graph != 0) |
579 |
|
{ |
580 |
|
|
581 |
|
|
582 |
|
|
583 |
0 |
graphStretch = i; |
584 |
0 |
yOffset = height - y; |
585 |
|
} |
586 |
0 |
break; |
587 |
|
} |
588 |
|
} |
589 |
|
|
590 |
|
|
591 |
|
|
592 |
|
|
593 |
|
|
594 |
0 |
if (evt.isPopupTrigger() && activeRow != -1) |
595 |
|
{ |
596 |
0 |
showPopupMenu(y, evt.getX()); |
597 |
0 |
return; |
598 |
|
} |
599 |
|
|
600 |
0 |
if (graphStretch != -1) |
601 |
|
{ |
602 |
|
|
603 |
0 |
if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP) |
604 |
|
{ |
605 |
|
|
606 |
0 |
if (evt.isAltDown() || evt.isAltGraphDown()) |
607 |
|
{ |
608 |
0 |
dragMode = DragMode.MatrixSelect; |
609 |
0 |
firstDragX = mouseDragLastX; |
610 |
0 |
firstDragY = mouseDragLastY; |
611 |
|
} |
612 |
|
} |
613 |
|
} |
614 |
|
else |
615 |
|
{ |
616 |
|
|
617 |
|
|
618 |
0 |
ap.getScalePanel().mousePressed(evt); |
619 |
|
} |
620 |
|
} |
621 |
|
|
622 |
|
|
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
@param |
627 |
|
@return |
628 |
|
|
|
|
| 0% |
Uncovered Elements: 124 (124) |
Complexity: 31 |
Complexity Density: 0.41 |
|
629 |
0 |
boolean matrix_clicked(MouseEvent evt)... |
630 |
|
{ |
631 |
0 |
int[] rowIndex = getRowIndexAndOffset(evt.getY(), |
632 |
|
av.getAlignment().getAlignmentAnnotation()); |
633 |
0 |
if (rowIndex == null) |
634 |
|
{ |
635 |
0 |
jalview.bin.Console |
636 |
|
.error("IMPLEMENTATION ERROR: matrix click out of range."); |
637 |
0 |
return false; |
638 |
|
} |
639 |
0 |
int yOffset = rowIndex[1]; |
640 |
0 |
AlignmentAnnotation[] allAnnotation = av.getAlignment() |
641 |
|
.getAlignmentAnnotation(); |
642 |
0 |
if (allAnnotation == null || rowIndex[0] < 0 |
643 |
|
|| rowIndex[0] >= allAnnotation.length) |
644 |
|
{ |
645 |
0 |
return false; |
646 |
|
} |
647 |
0 |
AlignmentAnnotation clicked = av.getAlignment() |
648 |
|
.getAlignmentAnnotation()[rowIndex[0]]; |
649 |
0 |
if (clicked.graph != AlignmentAnnotation.CONTACT_MAP) |
650 |
|
{ |
651 |
0 |
return false; |
652 |
|
} |
653 |
|
|
654 |
|
|
655 |
0 |
GraphLine thr = clicked.getThreshold(); |
656 |
|
|
657 |
0 |
int currentX = getColumnForXPos(evt.getX()); |
658 |
0 |
ContactListI forCurrentX = av.getContactList(clicked, currentX); |
659 |
0 |
if (forCurrentX != null) |
660 |
|
{ |
661 |
0 |
ContactGeometry cXcgeom = new ContactGeometry(forCurrentX, |
662 |
|
clicked.graphHeight); |
663 |
0 |
ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset); |
664 |
0 |
if (cXci != null) |
665 |
|
{ |
666 |
|
|
667 |
|
|
668 |
|
|
669 |
|
|
670 |
0 |
int fr, to; |
671 |
0 |
fr = Math.min(cXci.cStart, cXci.cEnd); |
672 |
0 |
to = Math.max(cXci.cStart, cXci.cEnd); |
673 |
|
|
674 |
|
|
675 |
0 |
if (evt.getClickCount() == 2) |
676 |
|
{ |
677 |
0 |
ContactMatrixI matrix = av.getContactMatrix(clicked); |
678 |
|
|
679 |
0 |
if (matrix != null) |
680 |
|
{ |
681 |
|
|
682 |
0 |
if (matrix.hasGroups()) |
683 |
|
{ |
684 |
0 |
SequenceI rseq = clicked.sequenceRef; |
685 |
0 |
BitSet grp = new BitSet(); |
686 |
0 |
grp.or(matrix.getGroupsFor(forCurrentX.getPosition())); |
687 |
|
|
688 |
0 |
for (int c = fr; c <= to; c++) |
689 |
|
{ |
690 |
0 |
BitSet additionalGrp = matrix.getGroupsFor(c); |
691 |
0 |
grp.or(additionalGrp); |
692 |
|
} |
693 |
|
|
694 |
0 |
HiddenColumns hc = av.getAlignment().getHiddenColumns(); |
695 |
0 |
ColumnSelection cs = av.getColumnSelection(); |
696 |
|
|
697 |
0 |
for (int p = grp.nextSetBit(0); p >= 0; p = grp |
698 |
|
.nextSetBit(p + 1)) |
699 |
|
{ |
700 |
0 |
if (matrix instanceof MappableContactMatrixI) |
701 |
|
{ |
702 |
|
|
703 |
0 |
int nextp = grp.nextClearBit(p) - 1; |
704 |
0 |
int[] pos = ((MappableContactMatrixI) matrix) |
705 |
|
.getMappedPositionsFor(rseq, p, nextp); |
706 |
0 |
p = nextp; |
707 |
|
|
708 |
0 |
if (pos != null) |
709 |
|
{ |
710 |
0 |
for (int pos_p = pos[0]; pos_p <= pos[1]; pos_p++) |
711 |
|
{ |
712 |
0 |
int col = rseq.findIndex(pos_p) - 1; |
713 |
0 |
if (col >= 0 && (!av.hasHiddenColumns() |
714 |
|
|| hc.isVisible(col))) |
715 |
|
{ |
716 |
0 |
cs.addElement(col); |
717 |
|
} |
718 |
|
} |
719 |
|
} |
720 |
|
} |
721 |
|
else |
722 |
|
{ |
723 |
0 |
int offp = (rseq != null) |
724 |
|
? rseq.findIndex(rseq.getStart() - 1 + p) |
725 |
|
: p; |
726 |
|
|
727 |
0 |
if (!av.hasHiddenColumns() || hc.isVisible(offp)) |
728 |
|
{ |
729 |
0 |
cs.addElement(offp); |
730 |
|
} |
731 |
|
} |
732 |
|
} |
733 |
|
} |
734 |
|
|
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
|
739 |
|
} |
740 |
|
} |
741 |
|
else |
742 |
|
{ |
743 |
|
|
744 |
|
{ |
745 |
0 |
int[] rng = forCurrentX.getMappedPositionsFor(fr, to); |
746 |
0 |
if (rng != null) |
747 |
|
{ |
748 |
0 |
av.getColumnSelection().addRangeOfElements(rng, true); |
749 |
|
} |
750 |
0 |
av.getColumnSelection().addElement(currentX); |
751 |
|
} |
752 |
|
|
753 |
|
|
754 |
|
|
755 |
0 |
if (evt.isControlDown() |
756 |
|
&& PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId())) |
757 |
|
{ |
758 |
0 |
int c = fr; |
759 |
0 |
ContactRange cr = forCurrentX.getRangeFor(fr, to); |
760 |
0 |
double cval; |
761 |
|
|
762 |
|
|
763 |
|
|
764 |
|
|
765 |
|
|
766 |
|
|
767 |
0 |
double thresh = cr.getMean() |
768 |
|
+ (cr.getMax() - cr.getMean()) * .15; |
769 |
0 |
while (c >= 0) |
770 |
|
{ |
771 |
0 |
cval = forCurrentX.getContactAt(c); |
772 |
0 |
if ( |
773 |
0 |
cval <= thresh) |
774 |
|
{ |
775 |
0 |
int[] cols = forCurrentX.getMappedPositionsFor(c, c); |
776 |
0 |
if (cols != null) |
777 |
|
{ |
778 |
0 |
av.getColumnSelection().addRangeOfElements(cols, true); |
779 |
|
} |
780 |
|
else |
781 |
|
{ |
782 |
0 |
break; |
783 |
|
} |
784 |
|
} |
785 |
0 |
c--; |
786 |
|
} |
787 |
0 |
c = to; |
788 |
0 |
while (c < forCurrentX.getContactHeight()) |
789 |
|
{ |
790 |
0 |
cval = forCurrentX.getContactAt(c); |
791 |
0 |
if ( |
792 |
0 |
cval <= thresh) |
793 |
|
{ |
794 |
0 |
int[] cols = forCurrentX.getMappedPositionsFor(c, c); |
795 |
0 |
if (cols != null) |
796 |
|
{ |
797 |
0 |
av.getColumnSelection().addRangeOfElements(cols, true); |
798 |
|
} |
799 |
|
} |
800 |
|
else |
801 |
|
{ |
802 |
0 |
break; |
803 |
|
} |
804 |
0 |
c++; |
805 |
|
|
806 |
|
} |
807 |
|
} |
808 |
|
|
809 |
|
} |
810 |
|
} |
811 |
|
} |
812 |
0 |
ap.paintAlignment(false, false); |
813 |
0 |
PaintRefresher.Refresh(ap, av.getSequenceSetId()); |
814 |
0 |
av.sendSelection(); |
815 |
0 |
return true; |
816 |
|
} |
817 |
|
|
818 |
|
|
819 |
|
|
820 |
|
|
821 |
|
@param |
822 |
|
@param |
823 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 4 |
Complexity Density: 0.17 |
|
824 |
0 |
void showPopupMenu(final int y, int x)... |
825 |
|
{ |
826 |
0 |
if (av.getColumnSelection() == null |
827 |
|
|| av.getColumnSelection().isEmpty()) |
828 |
|
{ |
829 |
0 |
return; |
830 |
|
} |
831 |
|
|
832 |
0 |
JPopupMenu pop = new JPopupMenu( |
833 |
|
MessageManager.getString("label.structure_type")); |
834 |
0 |
JMenuItem item; |
835 |
|
|
836 |
|
|
837 |
|
|
838 |
0 |
if (av.getAlignment().isNucleotide()) |
839 |
|
{ |
840 |
0 |
item = new JMenuItem(STEM); |
841 |
0 |
item.addActionListener(this); |
842 |
0 |
pop.add(item); |
843 |
|
} |
844 |
|
else |
845 |
|
{ |
846 |
0 |
item = new JMenuItem(HELIX); |
847 |
0 |
item.addActionListener(this); |
848 |
0 |
pop.add(item); |
849 |
0 |
item = new JMenuItem(SHEET); |
850 |
0 |
item.addActionListener(this); |
851 |
0 |
pop.add(item); |
852 |
|
} |
853 |
0 |
item = new JMenuItem(LABEL); |
854 |
0 |
item.addActionListener(this); |
855 |
0 |
pop.add(item); |
856 |
0 |
item = new JMenuItem(COLOUR); |
857 |
0 |
item.addActionListener(this); |
858 |
0 |
pop.add(item); |
859 |
0 |
item = new JMenuItem(REMOVE); |
860 |
0 |
item.addActionListener(this); |
861 |
0 |
pop.add(item); |
862 |
0 |
pop.show(this, x, y); |
863 |
|
} |
864 |
|
|
865 |
|
|
866 |
|
|
867 |
|
|
868 |
|
|
869 |
|
|
870 |
|
@param |
871 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 6 |
Complexity Density: 0.4 |
|
872 |
0 |
@Override... |
873 |
|
public void mouseReleased(MouseEvent evt) |
874 |
|
{ |
875 |
0 |
if (dragMode == DragMode.MatrixSelect) |
876 |
|
{ |
877 |
0 |
matrixSelectRange(evt); |
878 |
|
} |
879 |
0 |
graphStretch = -1; |
880 |
0 |
mouseDragLastX = -1; |
881 |
0 |
mouseDragLastY = -1; |
882 |
0 |
firstDragX = -1; |
883 |
0 |
firstDragY = -1; |
884 |
0 |
mouseDragging = false; |
885 |
0 |
if (dragMode == DragMode.Resize) |
886 |
|
{ |
887 |
0 |
ap.adjustAnnotationHeight(); |
888 |
|
} |
889 |
0 |
dragMode = DragMode.Undefined; |
890 |
0 |
if (!matrix_clicked(evt)) |
891 |
|
{ |
892 |
0 |
ap.getScalePanel().mouseReleased(evt); |
893 |
|
} |
894 |
|
|
895 |
|
|
896 |
|
|
897 |
|
|
898 |
|
|
899 |
0 |
if (evt.isPopupTrigger() && activeRow != -1) |
900 |
|
{ |
901 |
0 |
showPopupMenu(evt.getY(), evt.getX()); |
902 |
|
} |
903 |
|
|
904 |
|
} |
905 |
|
|
906 |
|
|
907 |
|
|
908 |
|
|
909 |
|
@param |
910 |
|
|
911 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
912 |
0 |
@Override... |
913 |
|
public void mouseEntered(MouseEvent evt) |
914 |
|
{ |
915 |
0 |
this.mouseDragging = false; |
916 |
0 |
ap.getScalePanel().mouseEntered(evt); |
917 |
|
} |
918 |
|
|
919 |
|
|
920 |
|
|
921 |
|
|
922 |
|
|
923 |
|
@param |
924 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
925 |
0 |
@Override... |
926 |
|
public void mouseExited(MouseEvent evt) |
927 |
|
{ |
928 |
0 |
ap.getScalePanel().mouseExited(evt); |
929 |
|
} |
930 |
|
|
931 |
|
|
932 |
|
|
933 |
|
|
934 |
|
|
935 |
|
|
936 |
|
|
937 |
|
|
938 |
|
|
939 |
|
|
940 |
|
|
941 |
|
|
942 |
|
|
943 |
|
|
944 |
|
@param |
945 |
|
|
|
|
| 0% |
Uncovered Elements: 53 (53) |
Complexity: 13 |
Complexity Density: 0.37 |
|
946 |
0 |
@Override... |
947 |
|
public void mouseDragged(MouseEvent evt) |
948 |
|
{ |
949 |
|
|
950 |
|
|
951 |
|
|
952 |
|
|
953 |
|
|
954 |
|
|
955 |
0 |
final int x = evt.getX(); |
956 |
0 |
final int y = evt.getY(); |
957 |
0 |
if (dragMode == DragMode.Undefined) |
958 |
|
{ |
959 |
0 |
int dx = Math.abs(x - mouseDragLastX); |
960 |
0 |
int dy = Math.abs(y - mouseDragLastY); |
961 |
0 |
if (graphStretch == -1 || dx > dy) |
962 |
|
{ |
963 |
|
|
964 |
|
|
965 |
|
|
966 |
0 |
dragMode = DragMode.Select; |
967 |
|
} |
968 |
0 |
else if (dy > dx) |
969 |
|
{ |
970 |
|
|
971 |
|
|
972 |
|
|
973 |
0 |
dragMode = DragMode.Resize; |
974 |
0 |
notJustOne = evt.isShiftDown(); |
975 |
|
|
976 |
|
|
977 |
|
|
978 |
|
|
979 |
0 |
if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment() |
980 |
|
.getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)) |
981 |
|
{ |
982 |
|
|
983 |
|
|
984 |
|
|
985 |
0 |
dragMode = DragMode.MatrixSelect; |
986 |
0 |
firstDragX = mouseDragLastX; |
987 |
0 |
firstDragY = mouseDragLastY; |
988 |
|
} |
989 |
|
} |
990 |
|
} |
991 |
|
|
992 |
0 |
if (dragMode == DragMode.Undefined) |
993 |
|
|
994 |
|
{ |
995 |
|
|
996 |
|
|
997 |
|
|
998 |
|
|
999 |
0 |
return; |
1000 |
|
} |
1001 |
|
|
1002 |
0 |
try |
1003 |
|
{ |
1004 |
0 |
if (dragMode == DragMode.Resize) |
1005 |
|
{ |
1006 |
|
|
1007 |
|
|
1008 |
|
|
1009 |
0 |
int deltaY = mouseDragLastY - evt.getY(); |
1010 |
0 |
if (deltaY != 0) |
1011 |
|
{ |
1012 |
0 |
AlignmentAnnotation graphAnnotation = av.getAlignment() |
1013 |
|
.getAlignmentAnnotation()[graphStretch]; |
1014 |
0 |
int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY); |
1015 |
0 |
if (notJustOne) |
1016 |
|
{ |
1017 |
0 |
for (AlignmentAnnotation similar : av.getAlignment() |
1018 |
|
.findAnnotations(null, graphAnnotation.getCalcId(), |
1019 |
|
graphAnnotation.label)) |
1020 |
|
{ |
1021 |
0 |
similar.graphHeight = newHeight; |
1022 |
|
} |
1023 |
|
|
1024 |
|
} |
1025 |
|
else |
1026 |
|
{ |
1027 |
0 |
graphAnnotation.graphHeight = newHeight; |
1028 |
|
} |
1029 |
0 |
adjustPanelHeight(); |
1030 |
0 |
ap.paintAlignment(false, false); |
1031 |
|
} |
1032 |
|
} |
1033 |
0 |
else if (dragMode == DragMode.MatrixSelect) |
1034 |
|
{ |
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
0 |
mouseDragLastX = x; |
1039 |
0 |
mouseDragLastY = y; |
1040 |
0 |
ap.paintAlignment(false, false); |
1041 |
|
} |
1042 |
|
else |
1043 |
|
{ |
1044 |
|
|
1045 |
|
|
1046 |
|
|
1047 |
|
|
1048 |
0 |
ap.getScalePanel().mouseDragged(evt); |
1049 |
|
} |
1050 |
|
} finally |
1051 |
|
{ |
1052 |
0 |
mouseDragLastX = x; |
1053 |
0 |
mouseDragLastY = y; |
1054 |
|
} |
1055 |
|
} |
1056 |
|
|
|
|
| 0% |
Uncovered Elements: 52 (52) |
Complexity: 10 |
Complexity Density: 0.26 |
|
1057 |
0 |
public void matrixSelectRange(MouseEvent evt)... |
1058 |
|
{ |
1059 |
|
|
1060 |
|
|
1061 |
|
|
1062 |
0 |
int fromY = Math.min(firstDragY, evt.getY()); |
1063 |
0 |
int toY = Math.max(firstDragY, evt.getY()); |
1064 |
0 |
int fromX = Math.min(firstDragX, evt.getX()); |
1065 |
0 |
int toX = Math.max(firstDragX, evt.getX()); |
1066 |
|
|
1067 |
0 |
int deltaY = toY - fromY; |
1068 |
0 |
int deltaX = toX - fromX; |
1069 |
|
|
1070 |
0 |
int[] rowIndex = getRowIndexAndOffset(fromY, |
1071 |
|
av.getAlignment().getAlignmentAnnotation()); |
1072 |
0 |
int[] toRowIndex = getRowIndexAndOffset(toY, |
1073 |
|
av.getAlignment().getAlignmentAnnotation()); |
1074 |
|
|
1075 |
0 |
if (rowIndex == null || toRowIndex == null) |
1076 |
|
{ |
1077 |
0 |
jalview.bin.Console.trace("Drag out of range. needs to be clipped"); |
1078 |
|
|
1079 |
|
} |
1080 |
0 |
if (rowIndex[0] != toRowIndex[0]) |
1081 |
|
{ |
1082 |
0 |
jalview.bin.Console |
1083 |
|
.trace("Drag went to another row. needs to be clipped"); |
1084 |
|
} |
1085 |
|
|
1086 |
|
|
1087 |
0 |
AlignmentAnnotation cma = av.getAlignment() |
1088 |
|
.getAlignmentAnnotation()[rowIndex[0]]; |
1089 |
|
|
1090 |
0 |
int lastX = getColumnForXPos(fromX); |
1091 |
0 |
int currentX = getColumnForXPos(toX); |
1092 |
0 |
int fromXc = Math.min(lastX, currentX); |
1093 |
0 |
int toXc = Math.max(lastX, currentX); |
1094 |
0 |
ContactListI forFromX = av.getContactList(cma, fromXc); |
1095 |
0 |
ContactListI forToX = av.getContactList(cma, toXc); |
1096 |
|
|
1097 |
0 |
if (forFromX != null && forToX != null) |
1098 |
|
{ |
1099 |
|
|
1100 |
|
|
1101 |
|
|
1102 |
0 |
ContactGeometry xcgeom = new ContactGeometry(forFromX, |
1103 |
|
cma.graphHeight); |
1104 |
0 |
ContactGeometry.contactInterval lastXci = xcgeom.mapFor(rowIndex[1]); |
1105 |
0 |
ContactGeometry.contactInterval cXci = xcgeom |
1106 |
|
.mapFor(rowIndex[1] + deltaY); |
1107 |
|
|
1108 |
|
|
1109 |
0 |
jalview.bin.Console.trace("Matrix Selection from last(" + fromXc |
1110 |
|
+ ",[" + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" |
1111 |
|
+ toXc + ",[" + cXci.cStart + "," + cXci.cEnd + "])"); |
1112 |
0 |
int fr, to; |
1113 |
0 |
fr = Math.min(lastXci.cStart, cXci.cStart); |
1114 |
0 |
to = Math.max(lastXci.cEnd, cXci.cEnd); |
1115 |
0 |
int[] mappedPos = forFromX.getMappedPositionsFor(fr, to); |
1116 |
0 |
if (mappedPos != null) |
1117 |
|
{ |
1118 |
0 |
jalview.bin.Console.trace("Marking " + fr + " to " + to |
1119 |
|
+ " mapping to sequence positions " + mappedPos[0] + " to " |
1120 |
|
+ mappedPos[1]); |
1121 |
0 |
for (int pair = 0; pair < mappedPos.length; pair += 2) |
1122 |
|
{ |
1123 |
0 |
for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++) |
1124 |
|
|
1125 |
|
|
1126 |
|
|
1127 |
|
|
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
|
{ |
1132 |
0 |
av.getColumnSelection().addElement(c - 1); |
1133 |
|
} |
1134 |
|
} |
1135 |
|
} |
1136 |
0 |
fr = Math.min(lastX, currentX); |
1137 |
0 |
to = Math.max(lastX, currentX); |
1138 |
|
|
1139 |
0 |
jalview.bin.Console.trace("Marking " + fr + " to " + to); |
1140 |
0 |
for (int c = fr; c <= to; c++) |
1141 |
|
{ |
1142 |
0 |
av.getColumnSelection().addElement(c); |
1143 |
|
} |
1144 |
|
} |
1145 |
|
|
1146 |
|
} |
1147 |
|
|
1148 |
|
|
1149 |
|
|
1150 |
|
|
1151 |
|
|
1152 |
|
@param |
1153 |
|
|
|
|
| 0% |
Uncovered Elements: 22 (22) |
Complexity: 6 |
Complexity Density: 0.38 |
|
1154 |
0 |
@Override... |
1155 |
|
public void mouseMoved(MouseEvent evt) |
1156 |
|
{ |
1157 |
0 |
int yPos = evt.getY(); |
1158 |
0 |
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); |
1159 |
0 |
int rowAndOffset[] = getRowIndexAndOffset(yPos, aa); |
1160 |
0 |
int row = rowAndOffset[0]; |
1161 |
|
|
1162 |
0 |
if (row == -1) |
1163 |
|
{ |
1164 |
0 |
this.setToolTipText(null); |
1165 |
0 |
return; |
1166 |
|
} |
1167 |
|
|
1168 |
0 |
int column = getColumnForXPos(evt.getX()); |
1169 |
|
|
1170 |
0 |
AlignmentAnnotation ann = aa[row]; |
1171 |
0 |
if (row > -1 && ann.annotations != null |
1172 |
|
&& column < ann.annotations.length) |
1173 |
|
{ |
1174 |
0 |
String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av, |
1175 |
|
ap); |
1176 |
0 |
setToolTipText(toolTip == null ? null |
1177 |
|
: JvSwingUtils.wrapTooltip(true, toolTip)); |
1178 |
0 |
String msg = getStatusMessage(av.getAlignment(), column, ann, |
1179 |
|
rowAndOffset[1], av); |
1180 |
0 |
ap.alignFrame.setStatus(msg); |
1181 |
|
} |
1182 |
|
else |
1183 |
|
{ |
1184 |
0 |
this.setToolTipText(null); |
1185 |
0 |
ap.alignFrame.setStatus(" "); |
1186 |
|
} |
1187 |
|
} |
1188 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1189 |
0 |
private int getColumnForXPos(int x)... |
1190 |
|
{ |
1191 |
0 |
int column = (x / av.getCharWidth()) + av.getRanges().getStartRes(); |
1192 |
0 |
column = Math.min(column, av.getRanges().getEndRes()); |
1193 |
|
|
1194 |
0 |
if (av.hasHiddenColumns()) |
1195 |
|
{ |
1196 |
0 |
column = av.getAlignment().getHiddenColumns() |
1197 |
|
.visibleToAbsoluteColumn(column); |
1198 |
|
} |
1199 |
0 |
return column; |
1200 |
|
} |
1201 |
|
|
1202 |
|
|
1203 |
|
|
1204 |
|
|
1205 |
|
|
1206 |
|
|
1207 |
|
|
1208 |
|
@param |
1209 |
|
@param |
1210 |
|
@return |
1211 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1212 |
33 |
static int getRowIndex(int yPos, AlignmentAnnotation[] aa)... |
1213 |
|
{ |
1214 |
33 |
if (aa == null) |
1215 |
|
{ |
1216 |
1 |
return -1; |
1217 |
|
} |
1218 |
32 |
return getRowIndexAndOffset(yPos, aa)[0]; |
1219 |
|
} |
1220 |
|
|
|
|
| 92% |
Uncovered Elements: 2 (25) |
Complexity: 5 |
Complexity Density: 0.29 |
|
1221 |
32 |
static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)... |
1222 |
|
{ |
1223 |
32 |
int[] res = new int[2]; |
1224 |
32 |
res[0] = -1; |
1225 |
32 |
res[1] = 0; |
1226 |
32 |
if (aa == null) |
1227 |
|
{ |
1228 |
0 |
return res; |
1229 |
|
} |
1230 |
32 |
int row = -1; |
1231 |
32 |
int height = 0, lheight = 0; |
1232 |
79 |
for (int i = 0; i < aa.length; i++) |
1233 |
|
{ |
1234 |
75 |
if (aa[i].isForDisplay()) |
1235 |
|
{ |
1236 |
66 |
lheight = height; |
1237 |
66 |
height += aa[i].height; |
1238 |
|
} |
1239 |
|
|
1240 |
75 |
if (height > yPos) |
1241 |
|
{ |
1242 |
28 |
row = i; |
1243 |
28 |
res[0] = row; |
1244 |
28 |
res[1] = yPos - lheight; |
1245 |
28 |
break; |
1246 |
|
} |
1247 |
|
} |
1248 |
32 |
return res; |
1249 |
|
} |
1250 |
|
|
1251 |
|
|
1252 |
|
|
1253 |
|
|
1254 |
|
|
1255 |
|
|
1256 |
|
@param |
1257 |
|
@param |
1258 |
|
@param |
1259 |
|
@param |
1260 |
|
|
|
|
| 0% |
Uncovered Elements: 66 (66) |
Complexity: 18 |
Complexity Density: 0.45 |
|
1261 |
0 |
static String buildToolTip(AlignmentAnnotation ann, int column,... |
1262 |
|
AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av, |
1263 |
|
AlignmentPanel ap) |
1264 |
|
{ |
1265 |
0 |
String tooltip = null; |
1266 |
0 |
if (ann.graphGroup > -1) |
1267 |
|
{ |
1268 |
0 |
StringBuilder tip = new StringBuilder(32); |
1269 |
0 |
boolean first = true; |
1270 |
0 |
for (int i = 0; i < anns.length; i++) |
1271 |
|
{ |
1272 |
0 |
if (anns[i].graphGroup == ann.graphGroup |
1273 |
|
&& anns[i].annotations[column] != null) |
1274 |
|
{ |
1275 |
0 |
if (!first) |
1276 |
|
{ |
1277 |
0 |
tip.append("<br>"); |
1278 |
0 |
first = false; |
1279 |
|
} |
1280 |
0 |
tip.append(anns[i].label); |
1281 |
0 |
String description = anns[i].annotations[column].description; |
1282 |
0 |
if (description != null && description.length() > 0) |
1283 |
|
{ |
1284 |
0 |
tip.append(" ").append(description); |
1285 |
|
} |
1286 |
|
} |
1287 |
|
} |
1288 |
0 |
tooltip = first ? null : tip.toString(); |
1289 |
|
} |
1290 |
0 |
else if (column < ann.annotations.length |
1291 |
|
&& ann.annotations[column] != null) |
1292 |
|
{ |
1293 |
0 |
tooltip = getAnnotationBriefSummary(ann.annotations[column]); |
1294 |
|
} |
1295 |
|
|
1296 |
0 |
if (ann.graph == AlignmentAnnotation.CONTACT_MAP) |
1297 |
|
{ |
1298 |
0 |
if (rowAndOffset >= ann.graphHeight) |
1299 |
|
{ |
1300 |
0 |
return null; |
1301 |
|
} |
1302 |
0 |
ContactListI clist = av.getContactList(ann, column); |
1303 |
0 |
if (clist != null) |
1304 |
|
{ |
1305 |
0 |
ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight); |
1306 |
0 |
ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset); |
1307 |
0 |
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd); |
1308 |
0 |
StringBuilder tooltipb = new StringBuilder(); |
1309 |
0 |
tooltipb.append("Contact from ").append(clist.getPosition()) |
1310 |
|
.append(", [").append(ci.cStart).append(" - ") |
1311 |
|
.append(ci.cEnd).append("]").append("<br/>Mean:"); |
1312 |
0 |
Format.appendPercentage(tooltipb, (float) cr.getMean(), 2); |
1313 |
0 |
tooltip = tooltipb.toString(); |
1314 |
0 |
int col = ann.sequenceRef.findPosition(column); |
1315 |
0 |
int[][] highlightPos; |
1316 |
0 |
int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd); |
1317 |
0 |
if (mappedPos != null) |
1318 |
|
{ |
1319 |
0 |
highlightPos = new int[1 + mappedPos.length][2]; |
1320 |
0 |
highlightPos[0] = new int[] { col, col }; |
1321 |
0 |
for (int p = 0, h = 0; p < mappedPos.length; h++, p += 2) |
1322 |
|
{ |
1323 |
0 |
highlightPos[h][0] = ann.sequenceRef |
1324 |
|
.findPosition(mappedPos[p] - 1); |
1325 |
0 |
highlightPos[h][1] = ann.sequenceRef |
1326 |
|
.findPosition(mappedPos[p + 1] - 1); |
1327 |
|
} |
1328 |
|
} |
1329 |
|
else |
1330 |
|
{ |
1331 |
0 |
highlightPos = new int[][] { new int[] { col, col } }; |
1332 |
|
} |
1333 |
0 |
ap.getStructureSelectionManager() |
1334 |
|
.highlightPositionsOn(ann.sequenceRef, highlightPos, null); |
1335 |
|
} |
1336 |
|
} |
1337 |
0 |
return tooltip == null || tooltip.length() == 0 ? null : tooltip; |
1338 |
|
} |
1339 |
|
|
|
|
| 0% |
Uncovered Elements: 22 (22) |
Complexity: 9 |
Complexity Density: 0.75 |
|
1340 |
0 |
private static String getAnnotationBriefSummary(Annotation a)... |
1341 |
|
{ |
1342 |
0 |
StringBuilder ttSB = new StringBuilder(); |
1343 |
0 |
if (a.secondaryStructure != 0 && a.secondaryStructure != ' ') |
1344 |
|
{ |
1345 |
0 |
ttSB.append(a.secondaryStructure); |
1346 |
|
} |
1347 |
0 |
else if (a.description != null && a.description.trim().length() > 0) |
1348 |
|
{ |
1349 |
0 |
ttSB.append(a.description); |
1350 |
|
} |
1351 |
0 |
else if (a.displayCharacter != null |
1352 |
|
&& a.displayCharacter.trim().length() > 0) |
1353 |
|
{ |
1354 |
0 |
ttSB.append(a.displayCharacter); |
1355 |
|
} |
1356 |
0 |
else if (!Float.isNaN(a.value)) |
1357 |
|
{ |
1358 |
0 |
if (a.value == Math.floor(a.value)) |
1359 |
|
{ |
1360 |
0 |
ttSB.append(String.format("%.0f", a.value)); |
1361 |
|
} |
1362 |
|
else |
1363 |
|
{ |
1364 |
0 |
ttSB.append(String.valueOf(a.value)); |
1365 |
|
} |
1366 |
|
} |
1367 |
0 |
return ttSB.toString(); |
1368 |
|
} |
1369 |
|
|
1370 |
|
|
1371 |
|
|
1372 |
|
|
1373 |
|
@param |
1374 |
|
@param |
1375 |
|
@param |
1376 |
|
@param |
1377 |
|
|
|
|
| 0% |
Uncovered Elements: 43 (43) |
Complexity: 13 |
Complexity Density: 0.57 |
|
1378 |
0 |
static String getStatusMessage(AlignmentI al, int column,... |
1379 |
|
AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av) |
1380 |
|
{ |
1381 |
|
|
1382 |
|
|
1383 |
|
|
1384 |
0 |
StringBuilder text = new StringBuilder(32); |
1385 |
0 |
text.append(MessageManager.getString("label.column")).append(" ") |
1386 |
|
.append(column + 1); |
1387 |
|
|
1388 |
0 |
if (column < ann.annotations.length && ann.annotations[column] != null) |
1389 |
|
{ |
1390 |
0 |
String description = getAnnotationBriefSummary( |
1391 |
|
ann.annotations[column]); |
1392 |
0 |
if (description != null && description.trim().length() > 0) |
1393 |
|
{ |
1394 |
0 |
text.append(" ").append(description); |
1395 |
|
} |
1396 |
|
} |
1397 |
|
|
1398 |
|
|
1399 |
|
|
1400 |
|
|
1401 |
|
|
1402 |
0 |
SequenceI seqref = ann.sequenceRef; |
1403 |
0 |
if (seqref != null) |
1404 |
|
{ |
1405 |
0 |
int seqIndex = al.findIndex(seqref); |
1406 |
0 |
if (seqIndex != -1) |
1407 |
|
{ |
1408 |
0 |
text.append(", ").append(MessageManager.getString("label.sequence")) |
1409 |
|
.append(" ").append(seqIndex + 1); |
1410 |
0 |
char residue = seqref.getCharAt(column); |
1411 |
0 |
if (!Comparison.isGap(residue)) |
1412 |
|
{ |
1413 |
0 |
text.append(" "); |
1414 |
0 |
String name; |
1415 |
0 |
if (al.isNucleotide()) |
1416 |
|
{ |
1417 |
0 |
name = ResidueProperties.nucleotideName |
1418 |
|
.get(String.valueOf(residue)); |
1419 |
0 |
text.append(" Nucleotide: ") |
1420 |
0 |
.append(name != null ? name : residue); |
1421 |
|
} |
1422 |
|
else |
1423 |
|
{ |
1424 |
0 |
name = 'X' == residue ? "X" |
1425 |
0 |
: ('*' == residue ? "STOP" |
1426 |
|
: ResidueProperties.aa2Triplet |
1427 |
|
.get(String.valueOf(residue))); |
1428 |
0 |
text.append(" Residue: ").append(name != null ? name : residue); |
1429 |
|
} |
1430 |
0 |
int residuePos = seqref.findPosition(column); |
1431 |
0 |
text.append(" (").append(residuePos).append(")"); |
1432 |
|
} |
1433 |
|
} |
1434 |
|
} |
1435 |
|
|
1436 |
0 |
return text.toString(); |
1437 |
|
} |
1438 |
|
|
1439 |
|
|
1440 |
|
|
1441 |
|
|
1442 |
|
@param |
1443 |
|
|
1444 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1445 |
0 |
@Override... |
1446 |
|
public void mouseClicked(MouseEvent evt) |
1447 |
|
{ |
1448 |
|
|
1449 |
|
|
1450 |
|
|
1451 |
|
|
1452 |
|
|
1453 |
|
} |
1454 |
|
|
1455 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
|
1456 |
0 |
public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,... |
1457 |
|
int y1) |
1458 |
|
{ |
1459 |
0 |
int pady = av.getCharHeight() / 5; |
1460 |
0 |
int charOffset = 0; |
1461 |
0 |
graphics.setColor(Color.black); |
1462 |
0 |
graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); |
1463 |
|
|
1464 |
0 |
if (av.validCharWidth) |
1465 |
|
{ |
1466 |
0 |
graphics.setColor(Color.white); |
1467 |
|
|
1468 |
0 |
char s = seq.getCharAt(res); |
1469 |
|
|
1470 |
0 |
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; |
1471 |
0 |
graphics.drawString(String.valueOf(s), charOffset + x1, |
1472 |
|
(y1 + av.getCharHeight()) - pady); |
1473 |
|
} |
1474 |
|
|
1475 |
|
} |
1476 |
|
|
1477 |
|
private volatile boolean imageFresh = false; |
1478 |
|
|
1479 |
|
private Rectangle visibleRect = new Rectangle(), |
1480 |
|
clipBounds = new Rectangle(); |
1481 |
|
|
1482 |
|
|
1483 |
|
|
1484 |
|
|
1485 |
|
@param |
1486 |
|
|
1487 |
|
|
|
|
| 78.4% |
Uncovered Elements: 11 (51) |
Complexity: 15 |
Complexity Density: 0.38 |
|
1488 |
2137 |
@Override... |
1489 |
|
public void paintComponent(Graphics g) |
1490 |
|
{ |
1491 |
|
|
1492 |
|
|
1493 |
|
|
1494 |
|
|
1495 |
|
|
1496 |
|
|
1497 |
|
|
1498 |
2137 |
computeVisibleRect(visibleRect); |
1499 |
|
|
1500 |
2137 |
g.setColor(Color.white); |
1501 |
2137 |
g.fillRect(0, 0, visibleRect.width, visibleRect.height); |
1502 |
|
|
1503 |
2137 |
if (image != null) |
1504 |
|
{ |
1505 |
|
|
1506 |
? |
if (fastPaint |
1507 |
|
|| (visibleRect.width != (clipBounds = g |
1508 |
|
.getClipBounds(clipBounds)).width) |
1509 |
|
|| (visibleRect.height != clipBounds.height)) |
1510 |
|
{ |
1511 |
|
|
1512 |
87 |
g.drawImage(image, 0, 0, this); |
1513 |
87 |
fastPaint = false; |
1514 |
87 |
return; |
1515 |
|
} |
1516 |
|
} |
1517 |
2050 |
updateFadedImageWidth(); |
1518 |
2050 |
if (imgWidth < 1) |
1519 |
|
{ |
1520 |
0 |
return; |
1521 |
|
} |
1522 |
2050 |
Graphics2D gg; |
1523 |
2050 |
if (image == null || imgWidth != image.getWidth(this) |
1524 |
|
|| image.getHeight(this) != getHeight()) |
1525 |
|
{ |
1526 |
207 |
boolean tried = false; |
1527 |
207 |
image = null; |
1528 |
414 |
while (image == null && !tried) |
1529 |
|
{ |
1530 |
207 |
try |
1531 |
|
{ |
1532 |
207 |
image = new BufferedImage(imgWidth, |
1533 |
|
ap.getAnnotationPanel().getHeight(), |
1534 |
|
BufferedImage.TYPE_INT_RGB); |
1535 |
207 |
tried = true; |
1536 |
|
} catch (IllegalArgumentException exc) |
1537 |
|
{ |
1538 |
0 |
jalview.bin.Console.errPrintln( |
1539 |
|
"Serious issue with viewport geometry imgWidth requested was " |
1540 |
|
+ imgWidth); |
1541 |
0 |
return; |
1542 |
|
} catch (OutOfMemoryError oom) |
1543 |
|
{ |
1544 |
0 |
try |
1545 |
|
{ |
1546 |
0 |
System.gc(); |
1547 |
|
} catch (Exception x) |
1548 |
|
{ |
1549 |
|
} |
1550 |
0 |
; |
1551 |
0 |
new OOMWarning( |
1552 |
|
"Couldn't allocate memory to redraw screen. Please restart Jalview", |
1553 |
|
oom); |
1554 |
0 |
return; |
1555 |
|
} |
1556 |
|
|
1557 |
|
} |
1558 |
207 |
gg = (Graphics2D) image.getGraphics(); |
1559 |
|
|
1560 |
207 |
if (av.antiAlias) |
1561 |
|
{ |
1562 |
121 |
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
1563 |
|
RenderingHints.VALUE_ANTIALIAS_ON); |
1564 |
|
} |
1565 |
|
|
1566 |
207 |
gg.setFont(av.getFont()); |
1567 |
207 |
fm = gg.getFontMetrics(); |
1568 |
207 |
gg.setColor(Color.white); |
1569 |
207 |
gg.fillRect(0, 0, imgWidth, image.getHeight()); |
1570 |
207 |
imageFresh = true; |
1571 |
|
} |
1572 |
|
else |
1573 |
|
{ |
1574 |
1843 |
gg = (Graphics2D) image.getGraphics(); |
1575 |
|
|
1576 |
|
} |
1577 |
|
|
1578 |
2050 |
drawComponent(gg, av.getRanges().getStartRes(), |
1579 |
|
av.getRanges().getEndRes() + 1); |
1580 |
2049 |
gg.dispose(); |
1581 |
2049 |
imageFresh = false; |
1582 |
2049 |
g.drawImage(image, 0, 0, this); |
1583 |
|
} |
1584 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1585 |
4378 |
public void updateFadedImageWidth()... |
1586 |
|
{ |
1587 |
4378 |
imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() |
1588 |
|
+ 1) * av.getCharWidth(); |
1589 |
|
|
1590 |
|
} |
1591 |
|
|
1592 |
|
|
1593 |
|
|
1594 |
|
|
1595 |
|
private final boolean debugRedraw = false; |
1596 |
|
|
1597 |
|
|
1598 |
|
|
1599 |
|
|
1600 |
|
@param |
1601 |
|
|
1602 |
|
|
|
|
| 60.7% |
Uncovered Elements: 11 (28) |
Complexity: 9 |
Complexity Density: 0.45 |
|
1603 |
32 |
public void fastPaint(int horizontal)... |
1604 |
|
{ |
1605 |
32 |
if ((horizontal == 0) || image == null |
1606 |
|
|| av.getAlignment().getAlignmentAnnotation() == null |
1607 |
|
|| av.getAlignment().getAlignmentAnnotation().length < 1 |
1608 |
|
|| av.isCalcInProgress()) |
1609 |
|
{ |
1610 |
31 |
repaint(); |
1611 |
31 |
return; |
1612 |
|
} |
1613 |
|
|
1614 |
1 |
int sr = av.getRanges().getStartRes(); |
1615 |
1 |
int er = av.getRanges().getEndRes() + 1; |
1616 |
1 |
int transX = 0; |
1617 |
|
|
1618 |
1 |
Graphics2D gg = (Graphics2D) image.getGraphics(); |
1619 |
|
|
1620 |
1 |
if (imgWidth > Math.abs(horizontal * av.getCharWidth())) |
1621 |
|
{ |
1622 |
|
|
1623 |
0 |
gg.copyArea(0, 0, imgWidth, getHeight(), |
1624 |
|
-horizontal * av.getCharWidth(), 0); |
1625 |
|
|
1626 |
0 |
if (horizontal > 0) |
1627 |
|
{ |
1628 |
0 |
transX = (er - sr - horizontal) * av.getCharWidth(); |
1629 |
0 |
sr = er - horizontal; |
1630 |
|
} |
1631 |
0 |
else if (horizontal < 0) |
1632 |
|
{ |
1633 |
0 |
er = sr - horizontal; |
1634 |
|
} |
1635 |
|
} |
1636 |
1 |
gg.translate(transX, 0); |
1637 |
|
|
1638 |
1 |
drawComponent(gg, sr, er); |
1639 |
|
|
1640 |
1 |
gg.translate(-transX, 0); |
1641 |
|
|
1642 |
1 |
gg.dispose(); |
1643 |
|
|
1644 |
1 |
fastPaint = true; |
1645 |
|
|
1646 |
|
|
1647 |
|
|
1648 |
|
|
1649 |
1 |
av.getAlignPanel().repaint(); |
1650 |
|
} |
1651 |
|
|
1652 |
|
private volatile boolean lastImageGood = false; |
1653 |
|
|
1654 |
|
|
1655 |
|
|
1656 |
|
|
1657 |
|
@param |
1658 |
|
|
1659 |
|
@param |
1660 |
|
|
1661 |
|
@param |
1662 |
|
|
1663 |
|
|
|
|
| 67.3% |
Uncovered Elements: 17 (52) |
Complexity: 15 |
Complexity Density: 0.44 |
|
1664 |
2051 |
public void drawComponent(Graphics g, int startRes, int endRes)... |
1665 |
|
{ |
1666 |
2051 |
BufferedImage oldFaded = fadedImage; |
1667 |
2051 |
if (av.isCalcInProgress()) |
1668 |
|
{ |
1669 |
146 |
if (image == null) |
1670 |
|
{ |
1671 |
0 |
lastImageGood = false; |
1672 |
0 |
return; |
1673 |
|
} |
1674 |
|
|
1675 |
|
|
1676 |
|
|
1677 |
146 |
if (lastImageGood |
1678 |
|
&& (fadedImage == null || fadedImage.getWidth() != imgWidth |
1679 |
|
|| fadedImage.getHeight() != image.getHeight())) |
1680 |
|
{ |
1681 |
|
|
1682 |
|
|
1683 |
|
|
1684 |
68 |
fadedImage = new BufferedImage(imgWidth, image.getHeight(), |
1685 |
|
BufferedImage.TYPE_INT_RGB); |
1686 |
|
|
1687 |
68 |
Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics(); |
1688 |
|
|
1689 |
68 |
fadedG.setColor(Color.white); |
1690 |
68 |
fadedG.fillRect(0, 0, imgWidth, image.getHeight()); |
1691 |
|
|
1692 |
68 |
fadedG.setComposite( |
1693 |
|
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f)); |
1694 |
68 |
fadedG.drawImage(image, 0, 0, this); |
1695 |
|
|
1696 |
|
} |
1697 |
|
|
1698 |
|
|
1699 |
146 |
lastImageGood = false; |
1700 |
|
|
1701 |
|
} |
1702 |
|
else |
1703 |
|
{ |
1704 |
1905 |
if (fadedImage != null) |
1705 |
|
{ |
1706 |
65 |
oldFaded = fadedImage; |
1707 |
|
} |
1708 |
1905 |
fadedImage = null; |
1709 |
|
} |
1710 |
|
|
1711 |
2051 |
g.setColor(Color.white); |
1712 |
2051 |
g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight()); |
1713 |
|
|
1714 |
2051 |
g.setFont(av.getFont()); |
1715 |
2051 |
if (fm == null) |
1716 |
|
{ |
1717 |
0 |
fm = g.getFontMetrics(); |
1718 |
|
} |
1719 |
|
|
1720 |
2051 |
if ((av.getAlignment().getAlignmentAnnotation() == null) |
1721 |
|
|| (av.getAlignment().getAlignmentAnnotation().length < 1)) |
1722 |
|
{ |
1723 |
0 |
g.setColor(Color.white); |
1724 |
0 |
g.fillRect(0, 0, getWidth(), getHeight()); |
1725 |
0 |
g.setColor(Color.black); |
1726 |
0 |
if (av.validCharWidth) |
1727 |
|
{ |
1728 |
0 |
g.drawString(MessageManager |
1729 |
|
.getString("label.alignment_has_no_annotations"), 20, 15); |
1730 |
|
} |
1731 |
|
|
1732 |
0 |
return; |
1733 |
|
} |
1734 |
2051 |
lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes, |
1735 |
|
endRes); |
1736 |
2050 |
if (!lastImageGood && fadedImage == null) |
1737 |
|
{ |
1738 |
51 |
fadedImage = oldFaded; |
1739 |
|
} |
1740 |
2050 |
if (dragMode == DragMode.MatrixSelect) |
1741 |
|
{ |
1742 |
0 |
g.setColor(Color.yellow); |
1743 |
0 |
g.drawRect(Math.min(firstDragX, mouseDragLastX), |
1744 |
|
Math.min(firstDragY, mouseDragLastY), |
1745 |
|
Math.max(firstDragX, mouseDragLastX) |
1746 |
|
- Math.min(firstDragX, mouseDragLastX), |
1747 |
|
Math.max(firstDragY, mouseDragLastY) |
1748 |
|
- Math.min(firstDragY, mouseDragLastY)); |
1749 |
|
|
1750 |
|
} |
1751 |
|
} |
1752 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1753 |
2328 |
@Override... |
1754 |
|
public FontMetrics getFontMetrics() |
1755 |
|
{ |
1756 |
2328 |
return fm; |
1757 |
|
} |
1758 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1759 |
2328 |
@Override... |
1760 |
|
public Image getFadedImage() |
1761 |
|
{ |
1762 |
2328 |
return fadedImage; |
1763 |
|
} |
1764 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1765 |
2328 |
@Override... |
1766 |
|
public int getFadedImageWidth() |
1767 |
|
{ |
1768 |
2328 |
updateFadedImageWidth(); |
1769 |
2328 |
return imgWidth; |
1770 |
|
} |
1771 |
|
|
1772 |
|
private int[] bounds = new int[2]; |
1773 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
1774 |
6698 |
@Override... |
1775 |
|
public int[] getVisibleVRange() |
1776 |
|
{ |
1777 |
6698 |
if (ap != null && ap.getAlabels() != null) |
1778 |
|
{ |
1779 |
6459 |
int sOffset = -ap.getAlabels().getScrollOffset(); |
1780 |
6459 |
int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight(); |
1781 |
6459 |
bounds[0] = sOffset; |
1782 |
6459 |
bounds[1] = visHeight; |
1783 |
6459 |
return bounds; |
1784 |
|
} |
1785 |
|
else |
1786 |
|
{ |
1787 |
239 |
return null; |
1788 |
|
} |
1789 |
|
} |
1790 |
|
|
1791 |
|
|
1792 |
|
|
1793 |
|
|
|
|
| 88.9% |
Uncovered Elements: 1 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
1794 |
252 |
public void dispose()... |
1795 |
|
{ |
1796 |
252 |
av = null; |
1797 |
252 |
ap = null; |
1798 |
252 |
image = null; |
1799 |
252 |
fadedImage = null; |
1800 |
|
|
1801 |
252 |
_mwl = null; |
1802 |
|
|
1803 |
|
|
1804 |
|
|
1805 |
|
|
1806 |
252 |
if (renderer != null) |
1807 |
|
{ |
1808 |
252 |
renderer.dispose(); |
1809 |
|
} |
1810 |
|
} |
1811 |
|
|
|
|
| 66.7% |
Uncovered Elements: 4 (12) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1812 |
610 |
@Override... |
1813 |
|
public void propertyChange(PropertyChangeEvent evt) |
1814 |
|
{ |
1815 |
|
|
1816 |
|
|
1817 |
|
|
1818 |
|
|
1819 |
|
|
1820 |
|
|
1821 |
610 |
if (evt.getPropertyName().equals(ViewportRanges.STARTRES)) |
1822 |
|
{ |
1823 |
32 |
fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); |
1824 |
|
} |
1825 |
578 |
else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)) |
1826 |
|
{ |
1827 |
0 |
fastPaint(((int[]) evt.getNewValue())[0] |
1828 |
|
- ((int[]) evt.getOldValue())[0]); |
1829 |
|
} |
1830 |
578 |
else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) |
1831 |
|
{ |
1832 |
0 |
repaint(); |
1833 |
|
} |
1834 |
|
} |
1835 |
|
|
1836 |
|
|
1837 |
|
|
1838 |
|
|
1839 |
|
@param |
1840 |
|
|
1841 |
|
|
1842 |
|
@param |
1843 |
|
@return |
1844 |
|
|
|
|
| 94.1% |
Uncovered Elements: 1 (17) |
Complexity: 5 |
Complexity Density: 0.56 |
|
1845 |
2598 |
public int adjustForAlignFrame(boolean adjustPanelHeight,... |
1846 |
|
int annotationHeight) |
1847 |
|
{ |
1848 |
|
|
1849 |
|
|
1850 |
|
|
1851 |
|
|
1852 |
|
|
1853 |
2598 |
int stuff = (ap.getViewName() != null ? 30 : 0) |
1854 |
2598 |
+ (Platform.isAMacAndNotJS() ? 120 : 140); |
1855 |
2598 |
int availableHeight = ap.alignFrame.getHeight() - stuff; |
1856 |
2598 |
int rowHeight = av.getCharHeight(); |
1857 |
|
|
1858 |
2598 |
if (adjustPanelHeight) |
1859 |
|
{ |
1860 |
2017 |
int alignmentHeight = rowHeight * av.getAlignment().getHeight(); |
1861 |
|
|
1862 |
|
|
1863 |
|
|
1864 |
|
|
1865 |
|
|
1866 |
2017 |
if (annotationHeight + alignmentHeight > availableHeight) |
1867 |
|
{ |
1868 |
1226 |
annotationHeight = Math.min(annotationHeight, |
1869 |
|
availableHeight - 2 * rowHeight); |
1870 |
|
} |
1871 |
|
} |
1872 |
|
else |
1873 |
|
{ |
1874 |
|
|
1875 |
581 |
annotationHeight = Math.min(ap.annotationScroller.getSize().height, |
1876 |
|
availableHeight - 2 * rowHeight); |
1877 |
|
} |
1878 |
2598 |
return annotationHeight; |
1879 |
|
} |
1880 |
|
} |