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.Canvas; |
24 |
|
import java.awt.Color; |
25 |
|
import java.awt.Cursor; |
26 |
|
import java.awt.Dimension; |
27 |
|
import java.awt.Font; |
28 |
|
import java.awt.FontMetrics; |
29 |
|
import java.awt.Graphics; |
30 |
|
import java.awt.Graphics2D; |
31 |
|
import java.awt.RenderingHints; |
32 |
|
import java.awt.Toolkit; |
33 |
|
import java.awt.datatransfer.StringSelection; |
34 |
|
import java.awt.event.ActionEvent; |
35 |
|
import java.awt.event.ActionListener; |
36 |
|
import java.awt.event.MouseEvent; |
37 |
|
import java.awt.event.MouseListener; |
38 |
|
import java.awt.event.MouseMotionListener; |
39 |
|
import java.awt.geom.AffineTransform; |
40 |
|
import java.util.Arrays; |
41 |
|
import java.util.Collections; |
42 |
|
import java.util.Iterator; |
43 |
|
import java.util.Locale; |
44 |
|
|
45 |
|
import javax.swing.JCheckBoxMenuItem; |
46 |
|
import javax.swing.JMenuItem; |
47 |
|
import javax.swing.JPanel; |
48 |
|
import javax.swing.JPopupMenu; |
49 |
|
import javax.swing.SwingUtilities; |
50 |
|
import javax.swing.ToolTipManager; |
51 |
|
|
52 |
|
import jalview.analysis.AlignSeq; |
53 |
|
import jalview.analysis.AlignmentUtils; |
54 |
|
import jalview.bin.Cache; |
55 |
|
import jalview.bin.Jalview; |
56 |
|
import jalview.datamodel.Alignment; |
57 |
|
import jalview.datamodel.AlignmentAnnotation; |
58 |
|
import jalview.datamodel.Annotation; |
59 |
|
import jalview.datamodel.ContactMatrixI; |
60 |
|
import jalview.datamodel.GroupSet; |
61 |
|
import jalview.datamodel.HiddenColumns; |
62 |
|
import jalview.datamodel.Sequence; |
63 |
|
import jalview.datamodel.SequenceGroup; |
64 |
|
import jalview.datamodel.SequenceI; |
65 |
|
import jalview.io.FileFormat; |
66 |
|
import jalview.io.FormatAdapter; |
67 |
|
import jalview.util.Comparison; |
68 |
|
import jalview.util.MessageManager; |
69 |
|
import jalview.util.ParseHtmlBodyAndLinks; |
70 |
|
import jalview.util.Platform; |
71 |
|
|
72 |
|
|
73 |
|
|
74 |
|
|
75 |
|
|
76 |
|
|
|
|
| 33.5% |
Uncovered Elements: 578 (869) |
Complexity: 228 |
Complexity Density: 0.42 |
|
77 |
|
public class AnnotationLabels extends JPanel |
78 |
|
implements MouseListener, MouseMotionListener, ActionListener |
79 |
|
{ |
80 |
|
private static final String HTML_END_TAG = "</html>"; |
81 |
|
|
82 |
|
private static final String HTML_START_TAG = "<html>"; |
83 |
|
|
84 |
|
|
85 |
|
|
86 |
|
|
87 |
|
private static final int HEIGHT_ADJUSTER_WIDTH = 50; |
88 |
|
|
89 |
|
|
90 |
|
|
91 |
|
|
92 |
|
public static int HEIGHT_ADJUSTER_HEIGHT = 10; |
93 |
|
|
94 |
|
private static final Font font = new Font("Arial", Font.PLAIN, 11); |
95 |
|
|
96 |
|
private static final String TOGGLE_LABELSCALE = MessageManager |
97 |
|
.getString("label.scale_label_to_column"); |
98 |
|
|
99 |
|
private static final String ADDNEW = MessageManager |
100 |
|
.getString("label.add_new_row"); |
101 |
|
|
102 |
|
private static final String EDITNAME = MessageManager |
103 |
|
.getString("label.edit_label_description"); |
104 |
|
|
105 |
|
private static final String HIDE = MessageManager |
106 |
|
.getString("label.hide_row"); |
107 |
|
|
108 |
|
private static final String DELETE = MessageManager |
109 |
|
.getString("label.delete_row"); |
110 |
|
|
111 |
|
private static final String SHOWALL = MessageManager |
112 |
|
.getString("label.show_all_hidden_rows"); |
113 |
|
|
114 |
|
private static final String OUTPUT_TEXT = MessageManager |
115 |
|
.getString("label.export_annotation"); |
116 |
|
|
117 |
|
private static final String COPYCONS_SEQ = MessageManager |
118 |
|
.getString("label.copy_consensus_sequence"); |
119 |
|
|
120 |
|
private static final String ADJUST_ANNOTATION_LABELS_WIDTH_PREF = "ADJUST_ANNOTATION_LABELS_WIDTH"; |
121 |
|
|
122 |
|
private final boolean debugRedraw = false; |
123 |
|
|
124 |
|
private AlignmentPanel ap; |
125 |
|
|
126 |
|
AlignViewport av; |
127 |
|
|
128 |
|
private MouseEvent dragEvent; |
129 |
|
|
130 |
|
private int oldY; |
131 |
|
|
132 |
|
private int selectedRow; |
133 |
|
|
134 |
|
private int scrollOffset = 0; |
135 |
|
|
136 |
|
private boolean hasHiddenRows; |
137 |
|
|
138 |
|
private boolean resizePanel = false; |
139 |
|
|
140 |
|
private int annotationIdWidth = -1; |
141 |
|
|
142 |
|
public static final String RESIZE_MARGINS_MARK_PREF = "RESIZE_MARGINS_MARK"; |
143 |
|
|
144 |
|
|
145 |
|
|
146 |
|
|
147 |
|
@param |
148 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
149 |
478 |
public AnnotationLabels(AlignmentPanel ap)... |
150 |
|
{ |
151 |
478 |
this.ap = ap; |
152 |
478 |
av = ap.av; |
153 |
478 |
ToolTipManager.sharedInstance().registerComponent(this); |
154 |
|
|
155 |
478 |
addMouseListener(this); |
156 |
478 |
addMouseMotionListener(this); |
157 |
478 |
addMouseWheelListener(ap.getAnnotationPanel()); |
158 |
|
} |
159 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
160 |
578 |
public AnnotationLabels(AlignViewport av)... |
161 |
|
{ |
162 |
578 |
this.av = av; |
163 |
|
} |
164 |
|
|
165 |
|
|
166 |
|
|
167 |
|
|
168 |
|
@param |
169 |
|
|
170 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
171 |
905 |
public void setScrollOffset(int y)... |
172 |
|
{ |
173 |
905 |
scrollOffset = y; |
174 |
905 |
repaint(); |
175 |
|
} |
176 |
|
|
177 |
|
|
178 |
|
|
179 |
|
|
180 |
|
|
181 |
|
@param |
182 |
|
|
183 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 5 |
Complexity Density: 0.42 |
|
184 |
0 |
void getSelectedRow(int y)... |
185 |
|
{ |
186 |
0 |
int height = 0; |
187 |
0 |
AlignmentAnnotation[] aa = ap.av.getAlignment() |
188 |
|
.getAlignmentAnnotation(); |
189 |
0 |
selectedRow = -2; |
190 |
0 |
if (aa != null) |
191 |
|
{ |
192 |
0 |
for (int i = 0; i < aa.length; i++) |
193 |
|
{ |
194 |
0 |
selectedRow = -1; |
195 |
0 |
if (!aa[i].isForDisplay()) |
196 |
|
{ |
197 |
0 |
continue; |
198 |
|
} |
199 |
|
|
200 |
0 |
height += aa[i].height; |
201 |
|
|
202 |
0 |
if (y < height) |
203 |
|
{ |
204 |
0 |
selectedRow = i; |
205 |
|
|
206 |
0 |
break; |
207 |
|
} |
208 |
|
} |
209 |
|
} |
210 |
|
} |
211 |
|
|
212 |
|
|
213 |
|
|
214 |
|
|
215 |
|
@param |
216 |
|
|
217 |
|
|
|
|
| 0% |
Uncovered Elements: 52 (52) |
Complexity: 14 |
Complexity Density: 0.5 |
|
218 |
0 |
@Override... |
219 |
|
public void actionPerformed(ActionEvent evt) |
220 |
|
{ |
221 |
0 |
AlignmentAnnotation[] aa = ap.av.getAlignment() |
222 |
|
.getAlignmentAnnotation(); |
223 |
|
|
224 |
0 |
String action = evt.getActionCommand(); |
225 |
0 |
if (ADDNEW.equals(action)) |
226 |
|
{ |
227 |
|
|
228 |
|
|
229 |
|
|
230 |
0 |
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, |
231 |
|
null, new Annotation[ap.av.getAlignment().getWidth()]); |
232 |
0 |
editLabelDescription(newAnnotation, true); |
233 |
|
} |
234 |
0 |
else if (EDITNAME.equals(action)) |
235 |
|
{ |
236 |
|
|
237 |
|
|
238 |
|
|
239 |
0 |
editLabelDescription(aa[selectedRow], false); |
240 |
|
} |
241 |
0 |
else if (HIDE.equals(action)) |
242 |
|
{ |
243 |
0 |
aa[selectedRow].visible = false; |
244 |
|
} |
245 |
0 |
else if (DELETE.equals(action)) |
246 |
|
{ |
247 |
0 |
ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); |
248 |
0 |
ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); |
249 |
|
} |
250 |
0 |
else if (SHOWALL.equals(action)) |
251 |
|
{ |
252 |
0 |
for (int i = 0; i < aa.length; i++) |
253 |
|
{ |
254 |
0 |
if (!aa[i].visible && aa[i].annotations != null) |
255 |
|
{ |
256 |
0 |
aa[i].visible = true; |
257 |
|
} |
258 |
|
} |
259 |
|
} |
260 |
0 |
else if (OUTPUT_TEXT.equals(action)) |
261 |
|
{ |
262 |
0 |
new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); |
263 |
|
} |
264 |
0 |
else if (COPYCONS_SEQ.equals(action)) |
265 |
|
{ |
266 |
0 |
SequenceI cons = null; |
267 |
0 |
if (aa[selectedRow].groupRef != null) |
268 |
|
{ |
269 |
0 |
cons = aa[selectedRow].groupRef.getConsensusSeq(); |
270 |
|
} |
271 |
|
else |
272 |
|
{ |
273 |
0 |
cons = av.getConsensusSeq(); |
274 |
|
} |
275 |
0 |
if (cons != null) |
276 |
|
{ |
277 |
0 |
copy_annotseqtoclipboard(cons); |
278 |
|
} |
279 |
|
} |
280 |
0 |
else if (TOGGLE_LABELSCALE.equals(action)) |
281 |
|
{ |
282 |
0 |
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; |
283 |
|
} |
284 |
|
|
285 |
0 |
ap.refresh(true); |
286 |
|
} |
287 |
|
|
288 |
|
|
289 |
|
|
290 |
|
|
291 |
|
|
292 |
|
|
293 |
|
@param |
294 |
|
@param |
295 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 4 |
Complexity Density: 0.29 |
|
296 |
0 |
void editLabelDescription(AlignmentAnnotation annotation, boolean addNew)... |
297 |
|
{ |
298 |
0 |
String name = MessageManager.getString("label.annotation_name"); |
299 |
0 |
String description = MessageManager |
300 |
|
.getString("label.annotation_description"); |
301 |
0 |
String title = MessageManager |
302 |
|
.getString("label.edit_annotation_name_description"); |
303 |
0 |
EditNameDialog dialog = new EditNameDialog(annotation.label, |
304 |
|
annotation.description, name, description); |
305 |
|
|
306 |
0 |
dialog.showDialog(ap.alignFrame, title, () -> { |
307 |
0 |
annotation.label = dialog.getName(); |
308 |
0 |
String text = dialog.getDescription(); |
309 |
0 |
if (text != null && text.length() == 0) |
310 |
|
{ |
311 |
0 |
text = null; |
312 |
|
} |
313 |
0 |
annotation.description = text; |
314 |
0 |
if (addNew) |
315 |
|
{ |
316 |
0 |
ap.av.getAlignment().addAnnotation(annotation); |
317 |
0 |
ap.av.getAlignment().setAnnotationIndex(annotation, 0); |
318 |
|
} |
319 |
0 |
ap.refresh(true); |
320 |
|
}); |
321 |
|
} |
322 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
323 |
0 |
@Override... |
324 |
|
public void mousePressed(MouseEvent evt) |
325 |
|
{ |
326 |
0 |
getSelectedRow(evt.getY() - getScrollOffset()); |
327 |
0 |
oldY = evt.getY(); |
328 |
0 |
if (evt.isPopupTrigger()) |
329 |
|
{ |
330 |
0 |
showPopupMenu(evt); |
331 |
|
} |
332 |
|
} |
333 |
|
|
334 |
|
|
335 |
|
|
336 |
|
|
337 |
|
@param |
338 |
|
|
|
|
| 0% |
Uncovered Elements: 74 (74) |
Complexity: 11 |
Complexity Density: 0.2 |
|
339 |
0 |
void showPopupMenu(MouseEvent evt)... |
340 |
|
{ |
341 |
0 |
evt.consume(); |
342 |
0 |
final AlignmentAnnotation[] aa = ap.av.getAlignment() |
343 |
|
.getAlignmentAnnotation(); |
344 |
|
|
345 |
0 |
JPopupMenu pop = new JPopupMenu( |
346 |
|
MessageManager.getString("label.annotations")); |
347 |
0 |
JMenuItem item = new JMenuItem(ADDNEW); |
348 |
0 |
item.addActionListener(this); |
349 |
0 |
pop.add(item); |
350 |
0 |
if (selectedRow < 0) |
351 |
|
{ |
352 |
0 |
if (hasHiddenRows) |
353 |
|
{ |
354 |
0 |
item = new JMenuItem(SHOWALL); |
355 |
0 |
item.addActionListener(this); |
356 |
0 |
pop.add(item); |
357 |
|
} |
358 |
0 |
pop.show(this, evt.getX(), evt.getY()); |
359 |
0 |
return; |
360 |
|
} |
361 |
0 |
item = new JMenuItem(EDITNAME); |
362 |
0 |
item.addActionListener(this); |
363 |
0 |
pop.add(item); |
364 |
0 |
item = new JMenuItem(HIDE); |
365 |
0 |
item.addActionListener(this); |
366 |
0 |
pop.add(item); |
367 |
|
|
368 |
0 |
if (selectedRow < aa.length) |
369 |
|
{ |
370 |
0 |
if (aa[selectedRow].sequenceRef != null) |
371 |
|
{ |
372 |
0 |
final String label = aa[selectedRow].label; |
373 |
0 |
JMenuItem hideType = new JMenuItem(); |
374 |
0 |
String text = MessageManager.getString("label.hide_all") + " " |
375 |
|
+ label; |
376 |
0 |
hideType.setText(text); |
377 |
0 |
hideType.addActionListener(new ActionListener() |
378 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
379 |
0 |
@Override... |
380 |
|
public void actionPerformed(ActionEvent e) |
381 |
|
{ |
382 |
0 |
AlignmentUtils.showOrHideSequenceAnnotations( |
383 |
|
ap.av.getAlignment(), Collections.singleton(label), |
384 |
|
null, false, false); |
385 |
0 |
ap.refresh(true); |
386 |
|
} |
387 |
|
}); |
388 |
0 |
pop.add(hideType); |
389 |
|
} |
390 |
|
} |
391 |
0 |
item = new JMenuItem(DELETE); |
392 |
0 |
item.addActionListener(this); |
393 |
0 |
pop.add(item); |
394 |
0 |
if (hasHiddenRows) |
395 |
|
{ |
396 |
0 |
item = new JMenuItem(SHOWALL); |
397 |
0 |
item.addActionListener(this); |
398 |
0 |
pop.add(item); |
399 |
|
} |
400 |
0 |
item = new JMenuItem(OUTPUT_TEXT); |
401 |
0 |
item.addActionListener(this); |
402 |
0 |
pop.add(item); |
403 |
|
|
404 |
|
|
405 |
0 |
if (selectedRow < aa.length) |
406 |
|
{ |
407 |
0 |
final String label = aa[selectedRow].label; |
408 |
0 |
if (!aa[selectedRow].autoCalculated) |
409 |
|
{ |
410 |
0 |
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) |
411 |
|
{ |
412 |
|
|
413 |
0 |
pop.addSeparator(); |
414 |
|
|
415 |
0 |
item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, |
416 |
|
aa[selectedRow].scaleColLabel); |
417 |
0 |
item.addActionListener(this); |
418 |
0 |
pop.add(item); |
419 |
|
} |
420 |
|
} |
421 |
0 |
else if (label.indexOf("Consensus") > -1) |
422 |
|
{ |
423 |
0 |
addConsensusMenuOptions(ap, aa[selectedRow], pop); |
424 |
|
|
425 |
0 |
final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); |
426 |
0 |
consclipbrd.addActionListener(this); |
427 |
0 |
pop.add(consclipbrd); |
428 |
|
} |
429 |
|
|
430 |
0 |
addColourOrFilterByOptions(ap, aa[selectedRow], pop); |
431 |
|
|
432 |
0 |
if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP) |
433 |
|
{ |
434 |
0 |
addContactMatrixOptions(ap, aa[selectedRow], pop); |
435 |
|
|
436 |
|
|
437 |
|
|
438 |
|
|
439 |
|
} |
440 |
|
} |
441 |
|
|
442 |
0 |
pop.show(this, evt.getX(), evt.getY()); |
443 |
|
} |
444 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 2 |
Complexity Density: 0.18 |
|
445 |
0 |
static void addColourOrFilterByOptions(final AlignmentPanel ap,... |
446 |
|
final AlignmentAnnotation alignmentAnnotation, |
447 |
|
final JPopupMenu pop) |
448 |
|
{ |
449 |
0 |
JMenuItem item; |
450 |
0 |
item = new JMenuItem( |
451 |
|
MessageManager.getString("label.colour_by_annotation")); |
452 |
0 |
item.addActionListener(new ActionListener() |
453 |
|
{ |
454 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
455 |
0 |
@Override... |
456 |
|
public void actionPerformed(ActionEvent e) |
457 |
|
{ |
458 |
0 |
AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, |
459 |
|
false); |
460 |
|
}; |
461 |
|
}); |
462 |
0 |
pop.add(item); |
463 |
0 |
if (alignmentAnnotation.sequenceRef != null) |
464 |
|
{ |
465 |
0 |
item = new JMenuItem( |
466 |
|
MessageManager.getString("label.colour_by_annotation") + " (" |
467 |
|
+ MessageManager.getString("label.per_seq") + ")"); |
468 |
0 |
item.addActionListener(new ActionListener() |
469 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
470 |
0 |
@Override... |
471 |
|
public void actionPerformed(ActionEvent e) |
472 |
|
{ |
473 |
0 |
AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, |
474 |
|
true); |
475 |
|
}; |
476 |
|
}); |
477 |
0 |
pop.add(item); |
478 |
|
} |
479 |
0 |
item = new JMenuItem( |
480 |
|
MessageManager.getString("action.select_by_annotation")); |
481 |
0 |
item.addActionListener(new ActionListener() |
482 |
|
{ |
483 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
484 |
0 |
@Override... |
485 |
|
public void actionPerformed(ActionEvent e) |
486 |
|
{ |
487 |
0 |
AnnotationColumnChooser.displayFor(ap.av, ap, alignmentAnnotation); |
488 |
|
}; |
489 |
|
}); |
490 |
0 |
pop.add(item); |
491 |
|
} |
492 |
|
|
|
|
| 0% |
Uncovered Elements: 27 (27) |
Complexity: 4 |
Complexity Density: 0.19 |
|
493 |
0 |
static void addContactMatrixOptions(final AlignmentPanel ap,... |
494 |
|
final AlignmentAnnotation alignmentAnnotation, |
495 |
|
final JPopupMenu pop) |
496 |
|
{ |
497 |
|
|
498 |
0 |
final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation); |
499 |
0 |
JMenuItem item; |
500 |
0 |
if (cm != null) |
501 |
|
{ |
502 |
0 |
pop.addSeparator(); |
503 |
|
|
504 |
0 |
if (cm.hasGroups()) |
505 |
|
{ |
506 |
0 |
JCheckBoxMenuItem chitem = new JCheckBoxMenuItem( |
507 |
|
MessageManager.getString("action.show_groups_on_matrix")); |
508 |
0 |
chitem.setToolTipText(MessageManager |
509 |
|
.getString("action.show_groups_on_matrix_tooltip")); |
510 |
0 |
boolean showGroups = alignmentAnnotation |
511 |
|
.isShowGroupsForContactMatrix(); |
512 |
0 |
final AlignmentAnnotation sel_row = alignmentAnnotation; |
513 |
0 |
chitem.setState(showGroups); |
514 |
0 |
chitem.addActionListener(new ActionListener() |
515 |
|
{ |
516 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
517 |
0 |
@Override... |
518 |
|
public void actionPerformed(ActionEvent e) |
519 |
|
{ |
520 |
0 |
sel_row.setShowGroupsForContactMatrix(chitem.getState()); |
521 |
|
|
522 |
|
|
523 |
|
|
524 |
0 |
ap.alignmentChanged(); |
525 |
|
} |
526 |
|
}); |
527 |
0 |
pop.add(chitem); |
528 |
|
} |
529 |
0 |
if (cm.hasTree()) |
530 |
|
{ |
531 |
0 |
item = new JMenuItem( |
532 |
|
MessageManager.getString("action.show_tree_for_matrix")); |
533 |
0 |
item.setToolTipText(MessageManager |
534 |
|
.getString("action.show_tree_for_matrix_tooltip")); |
535 |
0 |
item.addActionListener(new ActionListener() |
536 |
|
{ |
537 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
538 |
0 |
@Override... |
539 |
|
public void actionPerformed(ActionEvent e) |
540 |
|
{ |
541 |
|
|
542 |
0 |
ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); |
543 |
|
|
544 |
|
} |
545 |
|
}); |
546 |
0 |
pop.add(item); |
547 |
|
} |
548 |
|
else |
549 |
|
{ |
550 |
0 |
item = new JMenuItem( |
551 |
|
MessageManager.getString("action.cluster_matrix")); |
552 |
0 |
item.setToolTipText( |
553 |
|
MessageManager.getString("action.cluster_matrix_tooltip")); |
554 |
0 |
item.addActionListener(new ActionListener() |
555 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
556 |
0 |
@Override... |
557 |
|
public void actionPerformed(ActionEvent e) |
558 |
|
{ |
559 |
0 |
new Thread(new Runnable() |
560 |
|
{ |
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
|
561 |
0 |
@Override... |
562 |
|
public void run() |
563 |
|
{ |
564 |
0 |
final long progBar; |
565 |
0 |
ap.alignFrame.setProgressBar( |
566 |
|
MessageManager.formatMessage( |
567 |
|
"action.clustering_matrix_for", |
568 |
|
cm.getAnnotDescr(), 5f), |
569 |
|
progBar = System.currentTimeMillis()); |
570 |
0 |
cm.setGroupSet(GroupSet.makeGroups(cm, true)); |
571 |
0 |
cm.randomlyReColourGroups(); |
572 |
0 |
cm.transferGroupColorsTo(alignmentAnnotation); |
573 |
0 |
ap.alignmentChanged(); |
574 |
0 |
ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); |
575 |
0 |
ap.alignFrame.setProgressBar(null, progBar); |
576 |
|
} |
577 |
|
}).start(); |
578 |
|
} |
579 |
|
}); |
580 |
0 |
pop.add(item); |
581 |
|
} |
582 |
|
} |
583 |
|
} |
584 |
|
|
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
|
592 |
|
@param |
593 |
|
@param |
594 |
|
@param |
595 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 3 |
Complexity Density: 0.12 |
|
596 |
0 |
static void addConsensusMenuOptions(AlignmentPanel ap,... |
597 |
|
AlignmentAnnotation ann, JPopupMenu pop) |
598 |
|
{ |
599 |
0 |
pop.addSeparator(); |
600 |
|
|
601 |
0 |
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( |
602 |
|
MessageManager.getString("label.ignore_gaps_consensus"), |
603 |
0 |
(ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus() |
604 |
|
: ap.av.isIgnoreGapsConsensus()); |
605 |
0 |
final AlignmentAnnotation aaa = ann; |
606 |
0 |
cbmi.addActionListener(new ActionListener() |
607 |
|
{ |
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
608 |
0 |
@Override... |
609 |
|
public void actionPerformed(ActionEvent e) |
610 |
|
{ |
611 |
0 |
if (aaa.groupRef != null) |
612 |
|
{ |
613 |
0 |
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); |
614 |
0 |
ap.getAnnotationPanel() |
615 |
|
.paint(ap.getAnnotationPanel().getGraphics()); |
616 |
|
} |
617 |
|
else |
618 |
|
{ |
619 |
0 |
ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); |
620 |
|
} |
621 |
0 |
ap.alignmentChanged(); |
622 |
|
} |
623 |
|
}); |
624 |
0 |
pop.add(cbmi); |
625 |
|
|
626 |
0 |
if (aaa.groupRef != null) |
627 |
|
{ |
628 |
|
|
629 |
|
|
630 |
|
|
631 |
0 |
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( |
632 |
|
MessageManager.getString("label.show_group_histogram"), |
633 |
|
ann.groupRef.isShowConsensusHistogram()); |
634 |
0 |
chist.addActionListener(new ActionListener() |
635 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
636 |
0 |
@Override... |
637 |
|
public void actionPerformed(ActionEvent e) |
638 |
|
{ |
639 |
0 |
aaa.groupRef.setShowConsensusHistogram(chist.getState()); |
640 |
0 |
ap.repaint(); |
641 |
|
} |
642 |
|
}); |
643 |
0 |
pop.add(chist); |
644 |
0 |
final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( |
645 |
|
MessageManager.getString("label.show_group_logo"), |
646 |
|
ann.groupRef.isShowSequenceLogo()); |
647 |
0 |
cprofl.addActionListener(new ActionListener() |
648 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
649 |
0 |
@Override... |
650 |
|
public void actionPerformed(ActionEvent e) |
651 |
|
{ |
652 |
0 |
aaa.groupRef.setshowSequenceLogo(cprofl.getState()); |
653 |
0 |
ap.repaint(); |
654 |
|
} |
655 |
|
}); |
656 |
0 |
pop.add(cprofl); |
657 |
0 |
final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( |
658 |
|
MessageManager.getString("label.normalise_group_logo"), |
659 |
|
ann.groupRef.isNormaliseSequenceLogo()); |
660 |
0 |
cproflnorm.addActionListener(new ActionListener() |
661 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
662 |
0 |
@Override... |
663 |
|
public void actionPerformed(ActionEvent e) |
664 |
|
{ |
665 |
0 |
aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); |
666 |
|
|
667 |
0 |
aaa.groupRef.setshowSequenceLogo(true); |
668 |
0 |
ap.repaint(); |
669 |
|
} |
670 |
|
}); |
671 |
0 |
pop.add(cproflnorm); |
672 |
|
} |
673 |
|
else |
674 |
|
{ |
675 |
|
|
676 |
|
|
677 |
|
|
678 |
0 |
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( |
679 |
|
MessageManager.getString("label.show_histogram"), |
680 |
|
ap.av.isShowConsensusHistogram()); |
681 |
0 |
chist.addActionListener(new ActionListener() |
682 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
683 |
0 |
@Override... |
684 |
|
public void actionPerformed(ActionEvent e) |
685 |
|
{ |
686 |
0 |
ap.av.setShowConsensusHistogram(chist.getState()); |
687 |
0 |
ap.alignFrame.setMenusForViewport(); |
688 |
0 |
ap.repaint(); |
689 |
|
} |
690 |
|
}); |
691 |
0 |
pop.add(chist); |
692 |
0 |
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( |
693 |
|
MessageManager.getString("label.show_logo"), |
694 |
|
ap.av.isShowSequenceLogo()); |
695 |
0 |
cprof.addActionListener(new ActionListener() |
696 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
697 |
0 |
@Override... |
698 |
|
public void actionPerformed(ActionEvent e) |
699 |
|
{ |
700 |
0 |
ap.av.setShowSequenceLogo(cprof.getState()); |
701 |
0 |
ap.alignFrame.setMenusForViewport(); |
702 |
0 |
ap.repaint(); |
703 |
|
} |
704 |
|
}); |
705 |
0 |
pop.add(cprof); |
706 |
0 |
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( |
707 |
|
MessageManager.getString("label.normalise_logo"), |
708 |
|
ap.av.isNormaliseSequenceLogo()); |
709 |
0 |
cprofnorm.addActionListener(new ActionListener() |
710 |
|
{ |
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
711 |
0 |
@Override... |
712 |
|
public void actionPerformed(ActionEvent e) |
713 |
|
{ |
714 |
0 |
ap.av.setShowSequenceLogo(true); |
715 |
0 |
ap.av.setNormaliseSequenceLogo(cprofnorm.getState()); |
716 |
0 |
ap.alignFrame.setMenusForViewport(); |
717 |
0 |
ap.repaint(); |
718 |
|
} |
719 |
|
}); |
720 |
0 |
pop.add(cprofnorm); |
721 |
|
} |
722 |
|
} |
723 |
|
|
724 |
|
|
725 |
|
|
726 |
|
|
727 |
|
@param |
728 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 4 |
Complexity Density: 0.24 |
|
729 |
0 |
@Override... |
730 |
|
public void mouseReleased(MouseEvent evt) |
731 |
|
{ |
732 |
0 |
if (evt.isPopupTrigger()) |
733 |
|
{ |
734 |
0 |
showPopupMenu(evt); |
735 |
0 |
return; |
736 |
|
} |
737 |
|
|
738 |
0 |
int start = selectedRow; |
739 |
0 |
getSelectedRow(evt.getY() - getScrollOffset()); |
740 |
0 |
int end = selectedRow; |
741 |
|
|
742 |
|
|
743 |
|
|
744 |
|
|
745 |
0 |
if (start != end) |
746 |
|
{ |
747 |
|
|
748 |
0 |
AlignmentAnnotation startAA = ap.av.getAlignment() |
749 |
|
.getAlignmentAnnotation()[start]; |
750 |
0 |
if (end == -1) |
751 |
|
{ |
752 |
0 |
end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; |
753 |
|
} |
754 |
0 |
AlignmentAnnotation endAA = ap.av.getAlignment() |
755 |
|
.getAlignmentAnnotation()[end]; |
756 |
|
|
757 |
0 |
ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; |
758 |
0 |
ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; |
759 |
|
} |
760 |
|
|
761 |
0 |
resizePanel = false; |
762 |
0 |
dragEvent = null; |
763 |
0 |
repaint(); |
764 |
0 |
ap.getAnnotationPanel().repaint(); |
765 |
|
} |
766 |
|
|
767 |
|
|
768 |
|
|
769 |
|
|
770 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
771 |
0 |
@Override... |
772 |
|
public void mouseExited(MouseEvent evt) |
773 |
|
{ |
774 |
0 |
if (resizePanel && dragEvent == null) |
775 |
|
{ |
776 |
0 |
resizePanel = false; |
777 |
0 |
repaint(); |
778 |
|
} |
779 |
|
} |
780 |
|
|
781 |
|
|
782 |
|
|
783 |
|
|
784 |
|
|
785 |
|
|
786 |
|
@param |
787 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 4 |
Complexity Density: 0.29 |
|
788 |
0 |
@Override... |
789 |
|
public void mouseDragged(MouseEvent evt) |
790 |
|
{ |
791 |
0 |
dragEvent = evt; |
792 |
|
|
793 |
0 |
if (resizePanel) |
794 |
|
{ |
795 |
0 |
Dimension d = ap.annotationScroller.getPreferredSize(); |
796 |
0 |
int dif = evt.getY() - oldY; |
797 |
0 |
dif -= dif % ap.av.getCharHeight(); |
798 |
|
|
799 |
|
|
800 |
|
|
801 |
0 |
if (d.height - dif > ap.idPanelHolder.getHeight() |
802 |
|
- ap.getIdSpaceFillerPanel1().getHeight()) |
803 |
|
{ |
804 |
0 |
return; |
805 |
|
} |
806 |
|
|
807 |
0 |
if ((d.height - dif) > 20) |
808 |
|
{ |
809 |
0 |
ap.annotationScroller |
810 |
|
.setPreferredSize(new Dimension(d.width, d.height - dif)); |
811 |
0 |
d = ap.annotationSpaceFillerHolder.getPreferredSize(); |
812 |
0 |
ap.annotationSpaceFillerHolder |
813 |
|
.setPreferredSize(new Dimension(d.width, d.height - dif)); |
814 |
0 |
ap.paintAlignment(true, false); |
815 |
|
} |
816 |
|
|
817 |
0 |
ap.addNotify(); |
818 |
|
} |
819 |
|
else |
820 |
|
{ |
821 |
0 |
repaint(); |
822 |
|
} |
823 |
|
} |
824 |
|
|
825 |
|
|
826 |
|
|
827 |
|
|
828 |
|
@param |
829 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.33 |
|
830 |
0 |
@Override... |
831 |
|
public void mouseMoved(MouseEvent evt) |
832 |
|
{ |
833 |
0 |
showOrHideAdjuster(evt); |
834 |
|
|
835 |
0 |
getSelectedRow(evt.getY() - getScrollOffset()); |
836 |
|
|
837 |
0 |
if (selectedRow > -1 && ap.av.getAlignment() |
838 |
|
.getAlignmentAnnotation().length > selectedRow) |
839 |
|
{ |
840 |
0 |
AlignmentAnnotation[] anns = ap.av.getAlignment() |
841 |
|
.getAlignmentAnnotation(); |
842 |
0 |
AlignmentAnnotation aa = anns[selectedRow]; |
843 |
|
|
844 |
0 |
String desc = getTooltip(aa); |
845 |
0 |
this.setToolTipText(desc); |
846 |
0 |
String msg = getStatusMessage(aa, anns); |
847 |
0 |
ap.alignFrame.setStatus(msg); |
848 |
|
} |
849 |
|
} |
850 |
|
|
851 |
|
|
852 |
|
|
853 |
|
|
854 |
|
|
855 |
|
|
856 |
|
@param |
857 |
|
@param |
858 |
|
@return |
859 |
|
|
|
|
| 96.7% |
Uncovered Elements: 1 (30) |
Complexity: 8 |
Complexity Density: 0.5 |
|
860 |
6 |
static String getStatusMessage(AlignmentAnnotation aa,... |
861 |
|
AlignmentAnnotation[] anns) |
862 |
|
{ |
863 |
6 |
if (aa == null) |
864 |
|
{ |
865 |
1 |
return null; |
866 |
|
} |
867 |
|
|
868 |
5 |
StringBuilder msg = new StringBuilder(32); |
869 |
5 |
if (aa.sequenceRef != null) |
870 |
|
{ |
871 |
3 |
msg.append(aa.sequenceRef.getName()).append(" : "); |
872 |
|
} |
873 |
|
|
874 |
5 |
if (aa.graphGroup == -1) |
875 |
|
{ |
876 |
2 |
msg.append(aa.label); |
877 |
|
} |
878 |
3 |
else if (anns != null) |
879 |
|
{ |
880 |
3 |
boolean first = true; |
881 |
9 |
for (int i = anns.length - 1; i >= 0; i--) |
882 |
|
{ |
883 |
6 |
if (anns[i].graphGroup == aa.graphGroup) |
884 |
|
{ |
885 |
5 |
if (!first) |
886 |
|
{ |
887 |
2 |
msg.append(", "); |
888 |
|
} |
889 |
5 |
msg.append(anns[i].label); |
890 |
5 |
first = false; |
891 |
|
} |
892 |
|
} |
893 |
|
} |
894 |
|
|
895 |
5 |
return msg.toString(); |
896 |
|
} |
897 |
|
|
898 |
|
|
899 |
|
|
900 |
|
|
901 |
|
|
902 |
|
|
903 |
|
|
904 |
|
@param |
905 |
|
@return |
906 |
|
|
|
|
| 97% |
Uncovered Elements: 1 (33) |
Complexity: 9 |
Complexity Density: 0.47 |
|
907 |
13 |
static String getTooltip(AlignmentAnnotation aa)... |
908 |
|
{ |
909 |
13 |
if (aa == null) |
910 |
|
{ |
911 |
1 |
return null; |
912 |
|
} |
913 |
12 |
StringBuilder tooltip = new StringBuilder(); |
914 |
12 |
if (aa.description != null && !aa.description.equals("New description")) |
915 |
|
{ |
916 |
|
|
917 |
|
|
918 |
|
|
919 |
10 |
String desc = aa.getDescription(true).trim(); |
920 |
10 |
if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG)) |
921 |
|
{ |
922 |
7 |
tooltip.append(HTML_START_TAG); |
923 |
7 |
desc = desc.replace("<", "<"); |
924 |
|
} |
925 |
3 |
else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG)) |
926 |
|
{ |
927 |
3 |
desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); |
928 |
|
} |
929 |
10 |
tooltip.append(desc); |
930 |
|
} |
931 |
|
else |
932 |
|
{ |
933 |
|
|
934 |
2 |
tooltip.append(HTML_START_TAG); |
935 |
|
} |
936 |
12 |
if (aa.hasScore()) |
937 |
|
{ |
938 |
5 |
if (tooltip.length() > HTML_START_TAG.length()) |
939 |
|
{ |
940 |
3 |
tooltip.append("<br/>"); |
941 |
|
} |
942 |
|
|
943 |
|
|
944 |
|
|
945 |
5 |
tooltip.append(" Score: ").append(String.valueOf(aa.score)); |
946 |
|
} |
947 |
|
|
948 |
12 |
if (tooltip.length() > HTML_START_TAG.length()) |
949 |
|
{ |
950 |
10 |
return tooltip.append(HTML_END_TAG).toString(); |
951 |
|
} |
952 |
|
|
953 |
|
|
954 |
|
|
955 |
|
|
956 |
2 |
return null; |
957 |
|
} |
958 |
|
|
959 |
|
|
960 |
|
|
961 |
|
|
962 |
|
|
963 |
|
@param |
964 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
965 |
0 |
protected void showOrHideAdjuster(MouseEvent evt)... |
966 |
|
{ |
967 |
0 |
boolean was = resizePanel; |
968 |
0 |
resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT |
969 |
|
&& evt.getX() < HEIGHT_ADJUSTER_WIDTH; |
970 |
|
|
971 |
0 |
if (resizePanel != was) |
972 |
|
{ |
973 |
0 |
setCursor(Cursor |
974 |
0 |
.getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR |
975 |
|
: Cursor.DEFAULT_CURSOR)); |
976 |
0 |
repaint(); |
977 |
|
} |
978 |
|
} |
979 |
|
|
|
|
| 0% |
Uncovered Elements: 70 (70) |
Complexity: 21 |
Complexity Density: 0.48 |
|
980 |
0 |
@Override... |
981 |
|
public void mouseClicked(MouseEvent evt) |
982 |
|
{ |
983 |
0 |
final AlignmentAnnotation[] aa = ap.av.getAlignment() |
984 |
|
.getAlignmentAnnotation(); |
985 |
0 |
if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) |
986 |
|
{ |
987 |
0 |
if (selectedRow > -1 && selectedRow < aa.length) |
988 |
|
{ |
989 |
0 |
if (aa[selectedRow].groupRef != null) |
990 |
|
{ |
991 |
0 |
if (evt.getClickCount() >= 2) |
992 |
|
{ |
993 |
|
|
994 |
|
|
995 |
0 |
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); |
996 |
|
|
997 |
0 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
998 |
0 |
if (sg == null || sg == aa[selectedRow].groupRef |
999 |
|
|| !(Platform.isControlDown(evt) || evt.isShiftDown())) |
1000 |
|
{ |
1001 |
0 |
if (Platform.isControlDown(evt) || evt.isShiftDown()) |
1002 |
|
{ |
1003 |
|
|
1004 |
0 |
ap.av.setSelectionGroup( |
1005 |
|
new SequenceGroup(aa[selectedRow].groupRef)); |
1006 |
|
} |
1007 |
|
else |
1008 |
|
{ |
1009 |
|
|
1010 |
0 |
ap.av.setSelectionGroup(aa[selectedRow].groupRef); |
1011 |
|
} |
1012 |
|
} |
1013 |
|
else |
1014 |
|
{ |
1015 |
|
|
1016 |
0 |
int remainToAdd = aa[selectedRow].groupRef.getSize(); |
1017 |
0 |
for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) |
1018 |
|
{ |
1019 |
0 |
if (jalview.util.Platform.isControlDown(evt)) |
1020 |
|
{ |
1021 |
0 |
sg.addOrRemove(sgs, --remainToAdd == 0); |
1022 |
|
} |
1023 |
|
else |
1024 |
|
{ |
1025 |
|
|
1026 |
|
|
1027 |
0 |
sg.addSequence(sgs, --remainToAdd == 0); |
1028 |
|
} |
1029 |
|
} |
1030 |
|
} |
1031 |
|
|
1032 |
0 |
ap.paintAlignment(false, false); |
1033 |
0 |
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); |
1034 |
0 |
ap.av.sendSelection(); |
1035 |
|
} |
1036 |
|
else |
1037 |
|
{ |
1038 |
0 |
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( |
1039 |
|
aa[selectedRow].groupRef.getSequences(null)); |
1040 |
|
} |
1041 |
0 |
return; |
1042 |
|
} |
1043 |
0 |
else if (aa[selectedRow].sequenceRef != null) |
1044 |
|
{ |
1045 |
0 |
if (evt.getClickCount() == 1) |
1046 |
|
{ |
1047 |
0 |
ap.getSeqPanel().ap.getIdPanel() |
1048 |
|
.highlightSearchResults(Arrays.asList(new SequenceI[] |
1049 |
|
{ aa[selectedRow].sequenceRef })); |
1050 |
|
} |
1051 |
0 |
else if (evt.getClickCount() >= 2) |
1052 |
|
{ |
1053 |
0 |
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); |
1054 |
0 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
1055 |
0 |
if (sg != null) |
1056 |
|
{ |
1057 |
|
|
1058 |
|
|
1059 |
|
|
1060 |
0 |
if (!(Platform.isControlDown(evt) || evt.isShiftDown())) |
1061 |
|
{ |
1062 |
0 |
sg = new SequenceGroup(sg); |
1063 |
0 |
sg.clear(); |
1064 |
0 |
sg.addSequence(aa[selectedRow].sequenceRef, false); |
1065 |
|
} |
1066 |
|
else |
1067 |
|
{ |
1068 |
0 |
if (Platform.isControlDown(evt)) |
1069 |
|
{ |
1070 |
0 |
sg.addOrRemove(aa[selectedRow].sequenceRef, true); |
1071 |
|
} |
1072 |
|
else |
1073 |
|
{ |
1074 |
|
|
1075 |
|
|
1076 |
0 |
sg.addSequence(aa[selectedRow].sequenceRef, true); |
1077 |
|
} |
1078 |
|
} |
1079 |
|
} |
1080 |
|
else |
1081 |
|
{ |
1082 |
0 |
sg = new SequenceGroup(); |
1083 |
0 |
sg.setStartRes(0); |
1084 |
0 |
sg.setEndRes(ap.av.getAlignment().getWidth() - 1); |
1085 |
0 |
sg.addSequence(aa[selectedRow].sequenceRef, false); |
1086 |
|
} |
1087 |
0 |
ap.av.setSelectionGroup(sg); |
1088 |
0 |
ap.paintAlignment(false, false); |
1089 |
0 |
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); |
1090 |
0 |
ap.av.sendSelection(); |
1091 |
|
} |
1092 |
|
|
1093 |
|
} |
1094 |
|
} |
1095 |
0 |
return; |
1096 |
|
} |
1097 |
|
} |
1098 |
|
|
1099 |
|
|
1100 |
|
|
1101 |
|
|
1102 |
|
@param |
1103 |
|
|
1104 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 5 |
Complexity Density: 0.25 |
|
1105 |
0 |
protected void copy_annotseqtoclipboard(SequenceI sq)... |
1106 |
|
{ |
1107 |
0 |
SequenceI[] seqs = new SequenceI[] { sq }; |
1108 |
0 |
String[] omitHidden = null; |
1109 |
0 |
SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() }; |
1110 |
0 |
if (dseqs[0] == null) |
1111 |
|
{ |
1112 |
0 |
dseqs[0] = new Sequence(sq); |
1113 |
0 |
dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, |
1114 |
|
sq.getSequenceAsString())); |
1115 |
|
|
1116 |
0 |
sq.setDatasetSequence(dseqs[0]); |
1117 |
|
} |
1118 |
0 |
Alignment ds = new Alignment(dseqs); |
1119 |
0 |
if (av.hasHiddenColumns()) |
1120 |
|
{ |
1121 |
0 |
Iterator<int[]> it = av.getAlignment().getHiddenColumns() |
1122 |
|
.getVisContigsIterator(0, sq.getLength() + 1, false); |
1123 |
0 |
omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; |
1124 |
|
} |
1125 |
|
|
1126 |
0 |
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; |
1127 |
0 |
if (av.hasHiddenColumns()) |
1128 |
|
{ |
1129 |
0 |
alignmentStartEnd = av.getAlignment().getHiddenColumns() |
1130 |
|
.getVisibleStartAndEndIndex(av.getAlignment().getWidth()); |
1131 |
|
} |
1132 |
|
|
1133 |
0 |
String output = new FormatAdapter().formatSequences(FileFormat.Fasta, |
1134 |
|
seqs, omitHidden, alignmentStartEnd); |
1135 |
|
|
1136 |
0 |
Toolkit.getDefaultToolkit().getSystemClipboard() |
1137 |
|
.setContents(new StringSelection(output), Desktop.instance); |
1138 |
|
|
1139 |
0 |
HiddenColumns hiddenColumns = null; |
1140 |
|
|
1141 |
0 |
if (av.hasHiddenColumns()) |
1142 |
|
{ |
1143 |
0 |
hiddenColumns = new HiddenColumns( |
1144 |
|
av.getAlignment().getHiddenColumns()); |
1145 |
|
} |
1146 |
|
|
1147 |
0 |
Desktop.jalviewClipboard = new Object[] { seqs, ds, |
1148 |
|
|
1149 |
|
|
1150 |
|
|
1151 |
|
|
1152 |
|
hiddenColumns }; |
1153 |
|
} |
1154 |
|
|
1155 |
|
|
1156 |
|
|
1157 |
|
|
1158 |
|
@param |
1159 |
|
|
1160 |
|
|
|
|
| 81.8% |
Uncovered Elements: 2 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
1161 |
2247 |
@Override... |
1162 |
|
public void paintComponent(Graphics g) |
1163 |
|
{ |
1164 |
|
|
1165 |
2247 |
int width = getWidth(); |
1166 |
2247 |
if (width == 0) |
1167 |
|
{ |
1168 |
0 |
width = ap.calculateIdWidth().width; |
1169 |
|
} |
1170 |
|
|
1171 |
2247 |
Graphics2D g2 = (Graphics2D) g; |
1172 |
2247 |
if (av.antiAlias) |
1173 |
|
{ |
1174 |
847 |
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
1175 |
|
RenderingHints.VALUE_ANTIALIAS_ON); |
1176 |
|
} |
1177 |
|
|
1178 |
2247 |
drawComponent(g2, true, width, true); |
1179 |
|
} |
1180 |
|
|
1181 |
|
|
1182 |
|
|
1183 |
|
|
1184 |
|
|
1185 |
|
@param |
1186 |
|
|
1187 |
|
@param |
1188 |
|
|
1189 |
|
|
1190 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1191 |
0 |
public void drawComponent(Graphics g, int width)... |
1192 |
|
{ |
1193 |
0 |
drawComponent(g, false, width, true); |
1194 |
|
} |
1195 |
|
|
1196 |
|
|
1197 |
|
|
1198 |
|
|
1199 |
|
|
1200 |
|
@param |
1201 |
|
|
1202 |
|
@param |
1203 |
|
|
1204 |
|
|
1205 |
|
@param |
1206 |
|
|
1207 |
|
|
|
|
| 92.1% |
Uncovered Elements: 3 (38) |
Complexity: 14 |
Complexity Density: 0.58 |
|
1208 |
2856 |
public void drawComponent(Graphics g, boolean clip, int givenWidth,... |
1209 |
|
boolean forGUI) |
1210 |
|
{ |
1211 |
2856 |
int width = givenWidth; |
1212 |
2856 |
IdwidthAdjuster iwa = null; |
1213 |
2856 |
if (ap != null) |
1214 |
|
{ |
1215 |
2285 |
iwa = ap.idwidthAdjuster; |
1216 |
2285 |
if (Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true) |
1217 |
|
|| Jalview.isHeadlessMode()) |
1218 |
|
{ |
1219 |
2285 |
Graphics2D g2d = (Graphics2D) g; |
1220 |
2285 |
Graphics dummy = g2d.create(); |
1221 |
2285 |
int newAnnotationIdWidth = drawLabels(dummy, clip, width, false, |
1222 |
|
forGUI, null, false); |
1223 |
2285 |
dummy.dispose(); |
1224 |
2285 |
Dimension d = ap.calculateDefaultAlignmentIdWidth(); |
1225 |
2285 |
int alignmentIdWidth = d.width; |
1226 |
2285 |
if (iwa != null && !iwa.manuallyAdjusted()) |
1227 |
|
{ |
1228 |
|
|
1229 |
|
|
1230 |
1150 |
boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH", |
1231 |
|
false); |
1232 |
1150 |
width = Math.max(alignmentIdWidth, newAnnotationIdWidth); |
1233 |
1150 |
if (clip && width < givenWidth && !allowShrink) |
1234 |
|
{ |
1235 |
0 |
width = givenWidth; |
1236 |
|
} |
1237 |
|
} |
1238 |
1135 |
else if (newAnnotationIdWidth != annotationIdWidth |
1239 |
|
&& newAnnotationIdWidth > givenWidth |
1240 |
|
&& newAnnotationIdWidth > alignmentIdWidth) |
1241 |
|
{ |
1242 |
|
|
1243 |
|
|
1244 |
12 |
width = newAnnotationIdWidth; |
1245 |
12 |
annotationIdWidth = newAnnotationIdWidth; |
1246 |
|
} |
1247 |
|
|
1248 |
2285 |
if (width != ap.av.getIdWidth()) |
1249 |
|
{ |
1250 |
113 |
iwa.setWidth(width); |
1251 |
|
} |
1252 |
|
} |
1253 |
|
} |
1254 |
|
else |
1255 |
|
{ |
1256 |
571 |
int newAnnotationIdWidth = drawLabels(g, clip, width, false, forGUI, |
1257 |
|
null, false); |
1258 |
571 |
width = newAnnotationIdWidth < givenWidth ? givenWidth |
1259 |
|
: Math.min(newAnnotationIdWidth, givenWidth); |
1260 |
|
} |
1261 |
2856 |
drawLabels(g, clip, width, true, forGUI, null, false); |
1262 |
|
} |
1263 |
|
|
1264 |
|
|
1265 |
|
|
1266 |
|
|
1267 |
|
|
1268 |
|
|
1269 |
|
|
1270 |
|
@param |
1271 |
|
|
1272 |
|
|
1273 |
|
@param |
1274 |
|
|
1275 |
|
|
1276 |
|
@param |
1277 |
|
|
1278 |
|
@param |
1279 |
|
|
1280 |
|
@param |
1281 |
|
|
1282 |
|
|
1283 |
|
@param |
1284 |
|
|
1285 |
|
@param |
1286 |
|
|
1287 |
|
|
1288 |
|
@return |
1289 |
|
|
|
|
| 64% |
Uncovered Elements: 93 (258) |
Complexity: 83 |
Complexity Density: 0.55 |
|
1290 |
6102 |
public int drawLabels(Graphics g0, boolean clip, int width,... |
1291 |
|
boolean actuallyDraw, boolean forGUI, FontMetrics fmetrics, |
1292 |
|
boolean includeHidden) |
1293 |
|
{ |
1294 |
6102 |
if (clip) |
1295 |
|
{ |
1296 |
4494 |
clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS", |
1297 |
|
true); |
1298 |
|
} |
1299 |
6102 |
Graphics g = null; |
1300 |
|
|
1301 |
6102 |
if (g0 != null) |
1302 |
|
{ |
1303 |
6019 |
if (!actuallyDraw) |
1304 |
|
{ |
1305 |
3163 |
Graphics2D g2d = (Graphics2D) g0; |
1306 |
3163 |
g = g2d.create(); |
1307 |
|
} |
1308 |
|
else |
1309 |
|
{ |
1310 |
2856 |
g = g0; |
1311 |
|
} |
1312 |
|
} |
1313 |
6102 |
int actualWidth = 0; |
1314 |
6102 |
if (g != null) |
1315 |
|
{ |
1316 |
6019 |
if (av.getFont().getSize() < 10) |
1317 |
|
{ |
1318 |
0 |
g.setFont(font); |
1319 |
|
} |
1320 |
|
else |
1321 |
|
{ |
1322 |
6019 |
g.setFont(av.getFont()); |
1323 |
|
} |
1324 |
|
} |
1325 |
|
|
1326 |
6102 |
FontMetrics fm = fmetrics == null ? g.getFontMetrics(g.getFont()) |
1327 |
|
: fmetrics; |
1328 |
6102 |
if (actuallyDraw) |
1329 |
|
{ |
1330 |
2856 |
g.setColor(Color.white); |
1331 |
2856 |
g.fillRect(0, 0, getWidth(), getHeight()); |
1332 |
|
|
1333 |
2856 |
if (!Cache.getDefault(RESIZE_MARGINS_MARK_PREF, false) |
1334 |
|
&& !av.getWrapAlignment() && forGUI) |
1335 |
|
{ |
1336 |
2247 |
g.setColor(Color.LIGHT_GRAY); |
1337 |
2247 |
g.drawLine(0, HEIGHT_ADJUSTER_HEIGHT / 4, HEIGHT_ADJUSTER_WIDTH / 4, |
1338 |
|
HEIGHT_ADJUSTER_HEIGHT / 4); |
1339 |
2247 |
g.drawLine(0, 3 * HEIGHT_ADJUSTER_HEIGHT / 4, |
1340 |
|
HEIGHT_ADJUSTER_WIDTH / 4, 3 * HEIGHT_ADJUSTER_HEIGHT / 4); |
1341 |
|
|
1342 |
|
} |
1343 |
|
} |
1344 |
|
|
1345 |
6102 |
if (actuallyDraw) |
1346 |
|
{ |
1347 |
2856 |
g.translate(0, getScrollOffset()); |
1348 |
2856 |
g.setColor(Color.black); |
1349 |
|
} |
1350 |
6102 |
SequenceI lastSeqRef = null; |
1351 |
6102 |
String lastLabel = null; |
1352 |
6102 |
String lastDescription = null; |
1353 |
6102 |
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); |
1354 |
6102 |
int fontHeight = g != null ? g.getFont().getSize() |
1355 |
|
: fm.getFont().getSize(); |
1356 |
6102 |
int y = 0; |
1357 |
6102 |
int x = 0; |
1358 |
6102 |
int graphExtras = 0; |
1359 |
6102 |
int offset = 0; |
1360 |
6102 |
Font baseFont = g != null ? g.getFont() : fm.getFont(); |
1361 |
6102 |
FontMetrics baseMetrics = fm; |
1362 |
6102 |
int ofontH = fontHeight; |
1363 |
6102 |
int sOffset = 0; |
1364 |
6102 |
int visHeight = 0; |
1365 |
6102 |
int[] visr = (ap != null && ap.getAnnotationPanel() != null) |
1366 |
|
? ap.getAnnotationPanel().getVisibleVRange() |
1367 |
|
: null; |
1368 |
6102 |
if (clip && visr != null) |
1369 |
|
{ |
1370 |
4494 |
sOffset = visr[0]; |
1371 |
4494 |
visHeight = visr[1]; |
1372 |
|
} |
1373 |
6102 |
boolean visible = true, before = false, after = false; |
1374 |
6102 |
if (aa != null) |
1375 |
|
{ |
1376 |
6102 |
hasHiddenRows = false; |
1377 |
6102 |
int olY = 0; |
1378 |
6102 |
int nexAA = 0; |
1379 |
40237 |
for (int i = 0; i < aa.length; i++) |
1380 |
|
{ |
1381 |
34136 |
visible = true; |
1382 |
34136 |
if (!aa[i].isForDisplay() && !includeHidden) |
1383 |
|
{ |
1384 |
2394 |
hasHiddenRows = true; |
1385 |
2394 |
continue; |
1386 |
|
} |
1387 |
31742 |
olY = y; |
1388 |
|
|
1389 |
31742 |
for (nexAA = i + 1; nexAA < aa.length |
1390 |
|
&& (!aa[nexAA].isForDisplay() && includeHidden); nexAA++) |
1391 |
0 |
; |
1392 |
31742 |
y += aa[i].height; |
1393 |
31742 |
if (clip) |
1394 |
|
{ |
1395 |
22125 |
if (y < sOffset) |
1396 |
|
{ |
1397 |
0 |
if (!before) |
1398 |
|
{ |
1399 |
0 |
if (debugRedraw) |
1400 |
|
{ |
1401 |
0 |
jalview.bin.Console.outPrintln("before vis: " + i); |
1402 |
|
} |
1403 |
0 |
before = true; |
1404 |
|
} |
1405 |
|
|
1406 |
0 |
continue; |
1407 |
|
} |
1408 |
22125 |
if (olY > visHeight) |
1409 |
|
{ |
1410 |
|
|
1411 |
1349 |
if (!after) |
1412 |
|
{ |
1413 |
619 |
if (debugRedraw) |
1414 |
|
{ |
1415 |
0 |
jalview.bin.Console.outPrintln( |
1416 |
|
"Scroll offset: " + sOffset + " after vis: " + i); |
1417 |
|
} |
1418 |
619 |
after = true; |
1419 |
|
} |
1420 |
|
|
1421 |
1349 |
continue; |
1422 |
|
} |
1423 |
|
} |
1424 |
30394 |
if (actuallyDraw && g != null) |
1425 |
|
{ |
1426 |
13982 |
g.setColor(Color.black); |
1427 |
|
} |
1428 |
30394 |
offset = -aa[i].height / 2; |
1429 |
|
|
1430 |
30394 |
if (aa[i].hasText) |
1431 |
|
{ |
1432 |
25754 |
offset += fm.getHeight() / 2; |
1433 |
25754 |
offset -= fm.getDescent(); |
1434 |
|
} |
1435 |
|
else |
1436 |
|
{ |
1437 |
4640 |
offset += fm.getDescent(); |
1438 |
|
} |
1439 |
30394 |
String label = aa[i].label; |
1440 |
30394 |
ParseHtmlBodyAndLinks phbDecription = new ParseHtmlBodyAndLinks( |
1441 |
|
aa[i].description, true, "\n"); |
1442 |
30393 |
String description = phbDecription.getNonHtmlContent(); |
1443 |
30393 |
boolean vertBar = false; |
1444 |
30393 |
if (lastLabel != null && lastLabel.equals(label) && |
1445 |
|
lastDescription != null && lastDescription.equals(description)) |
1446 |
|
{ |
1447 |
|
|
1448 |
1 |
label = aa[i].label; |
1449 |
|
} |
1450 |
30392 |
else if (lastLabel != null && lastLabel.equals(label)) |
1451 |
|
{ |
1452 |
|
|
1453 |
5 |
if(!(lastDescription != null && lastDescription.equals(description)) |
1454 |
|
&& (aa[i].sequenceRef == lastSeqRef)) { |
1455 |
4 |
label = description; |
1456 |
4 |
lastDescription = description; |
1457 |
|
} |
1458 |
|
} |
1459 |
|
else |
1460 |
|
{ |
1461 |
30387 |
if (nexAA < aa.length && label.equals(aa[nexAA].label)) |
1462 |
|
|
1463 |
|
{ |
1464 |
5 |
lastLabel = label; |
1465 |
|
|
1466 |
|
|
1467 |
5 |
if((lastDescription != null && !lastDescription.equals(description))) { |
1468 |
0 |
if(aa[nexAA].sequenceRef == aa[i].sequenceRef) { |
1469 |
0 |
label = description; |
1470 |
|
} |
1471 |
0 |
lastDescription = description; |
1472 |
|
} |
1473 |
|
} |
1474 |
|
else |
1475 |
|
{ |
1476 |
30382 |
lastLabel = label; |
1477 |
30382 |
lastDescription = description; |
1478 |
|
} |
1479 |
|
} |
1480 |
30393 |
if (aa[i].sequenceRef != null) |
1481 |
|
{ |
1482 |
4111 |
if (aa[i].sequenceRef != lastSeqRef) |
1483 |
|
{ |
1484 |
1296 |
label = aa[i].sequenceRef.getName() + " " + label; |
1485 |
|
|
1486 |
|
|
1487 |
|
} |
1488 |
|
else |
1489 |
|
{ |
1490 |
2815 |
vertBar = true; |
1491 |
|
} |
1492 |
|
} |
1493 |
|
|
1494 |
30393 |
int labelWidth = fm.stringWidth(label) + 3; |
1495 |
30393 |
x = width - labelWidth; |
1496 |
|
|
1497 |
30393 |
if (aa[i].graphGroup > -1) |
1498 |
|
{ |
1499 |
0 |
int groupSize = 0; |
1500 |
|
|
1501 |
|
|
1502 |
0 |
for (int gg = 0; gg < aa.length; gg++) |
1503 |
|
{ |
1504 |
0 |
if (aa[gg].graphGroup == aa[i].graphGroup) |
1505 |
|
{ |
1506 |
0 |
groupSize++; |
1507 |
|
} |
1508 |
|
} |
1509 |
0 |
if (groupSize * (fontHeight + 8) < aa[i].height) |
1510 |
|
{ |
1511 |
0 |
graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) |
1512 |
|
/ 2; |
1513 |
|
} |
1514 |
|
else |
1515 |
|
{ |
1516 |
|
|
1517 |
0 |
float h = aa[i].height / (float) groupSize, s; |
1518 |
0 |
if (h < 9) |
1519 |
|
{ |
1520 |
0 |
visible = false; |
1521 |
|
} |
1522 |
|
else |
1523 |
|
{ |
1524 |
0 |
fontHeight = -8 + (int) h; |
1525 |
0 |
s = ((float) fontHeight) / (float) ofontH; |
1526 |
0 |
Font f = baseFont |
1527 |
|
.deriveFont(AffineTransform.getScaleInstance(s, s)); |
1528 |
0 |
Canvas c = new Canvas(); |
1529 |
0 |
fm = c.getFontMetrics(f); |
1530 |
0 |
if (actuallyDraw && g != null) |
1531 |
|
{ |
1532 |
0 |
g.setFont(f); |
1533 |
|
|
1534 |
0 |
graphExtras = (aa[i].height |
1535 |
|
- (groupSize * (fontHeight + 8))) / 2; |
1536 |
|
} |
1537 |
|
} |
1538 |
|
} |
1539 |
0 |
if (visible) |
1540 |
|
{ |
1541 |
0 |
for (int gg = 0; gg < aa.length; gg++) |
1542 |
|
{ |
1543 |
0 |
if (aa[gg].graphGroup == aa[i].graphGroup) |
1544 |
|
{ |
1545 |
0 |
labelWidth = fm.stringWidth(aa[gg].label) + 3; |
1546 |
0 |
x = width - labelWidth; |
1547 |
0 |
if (actuallyDraw && g != null) |
1548 |
|
{ |
1549 |
0 |
g.drawString(aa[gg].label, x, y - graphExtras); |
1550 |
|
|
1551 |
0 |
if (aa[gg]._linecolour != null) |
1552 |
|
{ |
1553 |
|
|
1554 |
0 |
g.setColor(aa[gg]._linecolour); |
1555 |
0 |
g.drawLine(x, y - graphExtras + 3, |
1556 |
|
x + fm.stringWidth(aa[gg].label), |
1557 |
|
y - graphExtras + 3); |
1558 |
|
} |
1559 |
|
|
1560 |
0 |
g.setColor(Color.black); |
1561 |
|
} |
1562 |
0 |
graphExtras += fontHeight + 8; |
1563 |
|
} |
1564 |
|
} |
1565 |
|
} |
1566 |
0 |
if (actuallyDraw && g != null) |
1567 |
|
{ |
1568 |
0 |
g.setFont(baseFont); |
1569 |
|
} |
1570 |
0 |
fm = baseMetrics; |
1571 |
0 |
fontHeight = ofontH; |
1572 |
|
} |
1573 |
|
else |
1574 |
|
{ |
1575 |
30393 |
if (actuallyDraw && g != null) |
1576 |
|
{ |
1577 |
13981 |
if (vertBar) |
1578 |
|
{ |
1579 |
1086 |
g.drawLine(width - 3, y + offset - fontHeight, width - 3, |
1580 |
|
(int) (y - 1.5 * aa[i].height - offset - fontHeight)); |
1581 |
|
|
1582 |
|
|
1583 |
|
} |
1584 |
13981 |
g.drawString(label, x, y + offset); |
1585 |
|
} |
1586 |
|
} |
1587 |
30393 |
lastSeqRef = aa[i].sequenceRef; |
1588 |
|
|
1589 |
30393 |
if (labelWidth > actualWidth) |
1590 |
|
{ |
1591 |
8362 |
actualWidth = labelWidth; |
1592 |
|
} |
1593 |
|
} |
1594 |
|
} |
1595 |
|
|
1596 |
6101 |
if (!resizePanel && dragEvent != null && aa != null && selectedRow > -1 |
1597 |
|
&& selectedRow < aa.length) |
1598 |
|
{ |
1599 |
0 |
if (actuallyDraw && g != null) |
1600 |
|
{ |
1601 |
0 |
g.setColor(Color.lightGray); |
1602 |
0 |
g.drawString( |
1603 |
0 |
(aa[selectedRow].sequenceRef == null ? "" |
1604 |
|
: aa[selectedRow].sequenceRef.getName()) |
1605 |
|
+ aa[selectedRow].label, |
1606 |
|
dragEvent.getX(), dragEvent.getY() - getScrollOffset()); |
1607 |
|
} |
1608 |
|
} |
1609 |
|
|
1610 |
6101 |
if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) |
1611 |
|
{ |
1612 |
0 |
if (actuallyDraw && g != null) |
1613 |
|
{ |
1614 |
0 |
g.drawString(MessageManager.getString("label.right_click"), 2, 8); |
1615 |
0 |
g.drawString(MessageManager.getString("label.to_add_annotation"), 2, |
1616 |
|
18); |
1617 |
|
} |
1618 |
|
} |
1619 |
|
|
1620 |
6101 |
return actualWidth; |
1621 |
|
} |
1622 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1623 |
9750 |
public int getScrollOffset()... |
1624 |
|
{ |
1625 |
9750 |
return scrollOffset; |
1626 |
|
} |
1627 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1628 |
0 |
@Override... |
1629 |
|
public void mouseEntered(MouseEvent e) |
1630 |
|
{ |
1631 |
|
} |
1632 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1633 |
38 |
public void drawComponentNotGUI(Graphics idGraphics, int idWidth)... |
1634 |
|
{ |
1635 |
38 |
drawComponent(idGraphics, false, idWidth, false); |
1636 |
|
} |
1637 |
|
} |