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.BorderLayout; |
24 |
|
import java.awt.Color; |
25 |
|
import java.awt.Component; |
26 |
|
import java.awt.Dimension; |
27 |
|
import java.awt.FlowLayout; |
28 |
|
import java.awt.Font; |
29 |
|
import java.awt.Graphics; |
30 |
|
import java.awt.GridLayout; |
31 |
|
import java.awt.Point; |
32 |
|
import java.awt.Rectangle; |
33 |
|
import java.awt.event.ActionEvent; |
34 |
|
import java.awt.event.ActionListener; |
35 |
|
import java.awt.event.ItemEvent; |
36 |
|
import java.awt.event.ItemListener; |
37 |
|
import java.awt.event.MouseAdapter; |
38 |
|
import java.awt.event.MouseEvent; |
39 |
|
import java.awt.event.MouseMotionAdapter; |
40 |
|
import java.beans.PropertyChangeEvent; |
41 |
|
import java.beans.PropertyChangeListener; |
42 |
|
import java.io.File; |
43 |
|
import java.io.FileInputStream; |
44 |
|
import java.io.FileOutputStream; |
45 |
|
import java.io.InputStreamReader; |
46 |
|
import java.io.OutputStreamWriter; |
47 |
|
import java.io.PrintWriter; |
48 |
|
import java.io.Reader; |
49 |
|
import java.util.Arrays; |
50 |
|
import java.util.Comparator; |
51 |
|
import java.util.HashMap; |
52 |
|
import java.util.HashSet; |
53 |
|
import java.util.Hashtable; |
54 |
|
import java.util.Iterator; |
55 |
|
import java.util.List; |
56 |
|
import java.util.Locale; |
57 |
|
import java.util.Map; |
58 |
|
import java.util.Set; |
59 |
|
|
60 |
|
import javax.help.HelpSetException; |
61 |
|
import javax.swing.AbstractCellEditor; |
62 |
|
import javax.swing.BorderFactory; |
63 |
|
import javax.swing.Icon; |
64 |
|
import javax.swing.JButton; |
65 |
|
import javax.swing.JCheckBox; |
66 |
|
import javax.swing.JInternalFrame; |
67 |
|
import javax.swing.JLabel; |
68 |
|
import javax.swing.JLayeredPane; |
69 |
|
import javax.swing.JMenuItem; |
70 |
|
import javax.swing.JPanel; |
71 |
|
import javax.swing.JPopupMenu; |
72 |
|
import javax.swing.JScrollPane; |
73 |
|
import javax.swing.JSlider; |
74 |
|
import javax.swing.JTable; |
75 |
|
import javax.swing.ListSelectionModel; |
76 |
|
import javax.swing.SwingConstants; |
77 |
|
import javax.swing.ToolTipManager; |
78 |
|
import javax.swing.border.Border; |
79 |
|
import javax.swing.event.ChangeEvent; |
80 |
|
import javax.swing.event.ChangeListener; |
81 |
|
import javax.swing.table.AbstractTableModel; |
82 |
|
import javax.swing.table.JTableHeader; |
83 |
|
import javax.swing.table.TableCellEditor; |
84 |
|
import javax.swing.table.TableCellRenderer; |
85 |
|
import javax.swing.table.TableColumn; |
86 |
|
import javax.xml.bind.JAXBContext; |
87 |
|
import javax.xml.bind.JAXBElement; |
88 |
|
import javax.xml.bind.Marshaller; |
89 |
|
import javax.xml.stream.XMLInputFactory; |
90 |
|
import javax.xml.stream.XMLStreamReader; |
91 |
|
|
92 |
|
import jalview.api.AlignViewControllerGuiI; |
93 |
|
import jalview.api.AlignViewportI; |
94 |
|
import jalview.api.FeatureColourI; |
95 |
|
import jalview.api.FeatureSettingsControllerI; |
96 |
|
import jalview.api.SplitContainerI; |
97 |
|
import jalview.api.ViewStyleI; |
98 |
|
import jalview.controller.FeatureSettingsControllerGuiI; |
99 |
|
import jalview.datamodel.AlignmentI; |
100 |
|
import jalview.datamodel.SequenceI; |
101 |
|
import jalview.datamodel.features.FeatureMatcher; |
102 |
|
import jalview.datamodel.features.FeatureMatcherI; |
103 |
|
import jalview.datamodel.features.FeatureMatcherSet; |
104 |
|
import jalview.datamodel.features.FeatureMatcherSetI; |
105 |
|
import jalview.gui.Help.HelpId; |
106 |
|
import jalview.gui.JalviewColourChooser.ColourChooserListener; |
107 |
|
import jalview.io.DataSourceType; |
108 |
|
import jalview.io.FileParse; |
109 |
|
import jalview.io.JalviewFileChooser; |
110 |
|
import jalview.io.JalviewFileView; |
111 |
|
import jalview.schemes.FeatureColour; |
112 |
|
import jalview.util.MessageManager; |
113 |
|
import jalview.util.Platform; |
114 |
|
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; |
115 |
|
import jalview.viewmodel.styles.ViewStyle; |
116 |
|
import jalview.xml.binding.jalview.JalviewUserColours; |
117 |
|
import jalview.xml.binding.jalview.JalviewUserColours.Colour; |
118 |
|
import jalview.xml.binding.jalview.JalviewUserColours.Filter; |
119 |
|
import jalview.xml.binding.jalview.ObjectFactory; |
120 |
|
|
|
|
| 0% |
Uncovered Elements: 812 (812) |
Complexity: 173 |
Complexity Density: 0.3 |
|
121 |
|
public class FeatureSettings extends JPanel |
122 |
|
implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI |
123 |
|
{ |
124 |
|
private static final String SEQUENCE_FEATURE_COLOURS = MessageManager |
125 |
|
.getString("label.sequence_feature_colours"); |
126 |
|
|
127 |
|
|
128 |
|
|
129 |
|
|
130 |
|
static final int TYPE_COLUMN = 0; |
131 |
|
|
132 |
|
static final int COLOUR_COLUMN = 1; |
133 |
|
|
134 |
|
static final int FILTER_COLUMN = 2; |
135 |
|
|
136 |
|
static final int SHOW_COLUMN = 3; |
137 |
|
|
138 |
|
private static final int COLUMN_COUNT = 4; |
139 |
|
|
140 |
|
private static final int MIN_WIDTH = 400; |
141 |
|
|
142 |
|
private static final int MIN_HEIGHT = 400; |
143 |
|
|
144 |
|
private final static String BASE_TOOLTIP = MessageManager |
145 |
|
.getString("label.click_to_edit"); |
146 |
|
|
147 |
|
final FeatureRenderer fr; |
148 |
|
|
149 |
|
public final AlignFrame af; |
150 |
|
|
151 |
|
|
152 |
|
|
153 |
|
|
154 |
|
Object[][] originalData; |
155 |
|
|
156 |
|
private float originalTransparency; |
157 |
|
|
158 |
|
private ViewStyleI originalViewStyle; |
159 |
|
|
160 |
|
private Map<String, FeatureMatcherSetI> originalFilters; |
161 |
|
|
162 |
|
final JInternalFrame frame; |
163 |
|
|
164 |
|
JScrollPane scrollPane = new JScrollPane(); |
165 |
|
|
166 |
|
JTable table; |
167 |
|
|
168 |
|
JPanel groupPanel; |
169 |
|
|
170 |
|
JSlider transparency = new JSlider(); |
171 |
|
|
172 |
|
private JCheckBox showComplementOnTop; |
173 |
|
|
174 |
|
private JCheckBox showComplement; |
175 |
|
|
176 |
|
|
177 |
|
|
178 |
|
|
179 |
|
protected volatile boolean inConstruction = true; |
180 |
|
|
181 |
|
int selectedRow = -1; |
182 |
|
|
183 |
|
boolean resettingTable = false; |
184 |
|
|
185 |
|
|
186 |
|
|
187 |
|
|
188 |
|
private boolean handlingUpdate = false; |
189 |
|
|
190 |
|
|
191 |
|
|
192 |
|
|
193 |
|
|
194 |
|
private PropertyChangeListener change; |
195 |
|
|
196 |
|
|
197 |
|
|
198 |
|
|
199 |
|
Map<String, float[]> typeWidth = null; |
200 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
201 |
0 |
private void storeOriginalSettings()... |
202 |
|
{ |
203 |
|
|
204 |
0 |
originalTransparency = fr.getTransparency(); |
205 |
|
|
206 |
0 |
updateTransparencySliderFromFR(); |
207 |
|
|
208 |
0 |
originalFilters = new HashMap<>(fr.getFeatureFilters()); |
209 |
0 |
originalViewStyle = new ViewStyle(af.viewport.getViewStyle()); |
210 |
|
} |
211 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
212 |
0 |
private void updateTransparencySliderFromFR()... |
213 |
|
{ |
214 |
0 |
boolean incon = inConstruction; |
215 |
0 |
inConstruction = true; |
216 |
|
|
217 |
0 |
int transparencyAsPercent = (int) (fr.getTransparency() * 100); |
218 |
0 |
transparency.setValue(100 - transparencyAsPercent); |
219 |
0 |
inConstruction = incon; |
220 |
|
} |
221 |
|
|
222 |
|
|
223 |
|
|
224 |
|
|
225 |
|
@param |
226 |
|
|
|
|
| 0% |
Uncovered Elements: 62 (62) |
Complexity: 9 |
Complexity Density: 0.17 |
|
227 |
0 |
public FeatureSettings(AlignFrame alignFrame)... |
228 |
|
{ |
229 |
0 |
this.af = alignFrame; |
230 |
0 |
fr = af.getFeatureRenderer(); |
231 |
|
|
232 |
0 |
storeOriginalSettings(); |
233 |
|
|
234 |
0 |
try |
235 |
|
{ |
236 |
0 |
jbInit(); |
237 |
|
} catch (Exception ex) |
238 |
|
{ |
239 |
0 |
ex.printStackTrace(); |
240 |
|
} |
241 |
|
|
242 |
0 |
table = new JTable() |
243 |
|
{ |
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 5 |
Complexity Density: 0.28 |
|
244 |
0 |
@Override... |
245 |
|
public String getToolTipText(MouseEvent e) |
246 |
|
{ |
247 |
0 |
String tip = null; |
248 |
0 |
int column = table.columnAtPoint(e.getPoint()); |
249 |
0 |
int row = table.rowAtPoint(e.getPoint()); |
250 |
|
|
251 |
0 |
switch (column) |
252 |
|
{ |
253 |
0 |
case TYPE_COLUMN: |
254 |
0 |
tip = JvSwingUtils.wrapTooltip(true, MessageManager |
255 |
|
.getString("label.feature_settings_click_drag")); |
256 |
0 |
break; |
257 |
0 |
case COLOUR_COLUMN: |
258 |
0 |
FeatureColourI colour = (FeatureColourI) table.getValueAt(row, |
259 |
|
column); |
260 |
0 |
tip = getColorTooltip(colour, true); |
261 |
0 |
break; |
262 |
0 |
case FILTER_COLUMN: |
263 |
0 |
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row, |
264 |
|
column); |
265 |
0 |
tip = o.isEmpty() |
266 |
|
? MessageManager |
267 |
|
.getString("label.configure_feature_tooltip") |
268 |
|
: o.toString(); |
269 |
0 |
break; |
270 |
0 |
default: |
271 |
0 |
break; |
272 |
|
} |
273 |
|
|
274 |
0 |
return tip; |
275 |
|
} |
276 |
|
|
277 |
|
|
278 |
|
|
279 |
|
|
280 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
281 |
0 |
@Override... |
282 |
|
public Point getToolTipLocation(MouseEvent e) |
283 |
|
{ |
284 |
0 |
Point point = e.getPoint(); |
285 |
0 |
int column = table.columnAtPoint(point); |
286 |
0 |
int row = table.rowAtPoint(point); |
287 |
0 |
Rectangle r = getCellRect(row, column, false); |
288 |
0 |
Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3); |
289 |
0 |
return loc; |
290 |
|
} |
291 |
|
}; |
292 |
0 |
JTableHeader tableHeader = table.getTableHeader(); |
293 |
0 |
tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12)); |
294 |
0 |
tableHeader.setReorderingAllowed(false); |
295 |
0 |
table.setFont(new Font("Verdana", Font.PLAIN, 12)); |
296 |
0 |
ToolTipManager.sharedInstance().registerComponent(table); |
297 |
0 |
table.setDefaultEditor(FeatureColour.class, new ColorEditor()); |
298 |
0 |
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); |
299 |
|
|
300 |
0 |
table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor()); |
301 |
0 |
table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer()); |
302 |
|
|
303 |
0 |
TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75, |
304 |
|
new ColorRenderer(), new ColorEditor()); |
305 |
0 |
table.addColumn(colourColumn); |
306 |
|
|
307 |
0 |
TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75, |
308 |
|
new FilterRenderer(), new FilterEditor()); |
309 |
0 |
table.addColumn(filterColumn); |
310 |
|
|
311 |
0 |
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); |
312 |
|
|
313 |
0 |
table.addMouseListener(new MouseAdapter() |
314 |
|
{ |
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 4 |
Complexity Density: 0.33 |
|
315 |
0 |
@Override... |
316 |
|
public void mousePressed(MouseEvent evt) |
317 |
|
{ |
318 |
0 |
Point pt = evt.getPoint(); |
319 |
0 |
selectedRow = table.rowAtPoint(pt); |
320 |
0 |
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); |
321 |
0 |
if (evt.isPopupTrigger()) |
322 |
|
{ |
323 |
0 |
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); |
324 |
0 |
showPopupMenu(selectedRow, type, colour, evt.getPoint()); |
325 |
|
} |
326 |
0 |
else if (evt.getClickCount() == 2 |
327 |
|
&& table.columnAtPoint(pt) == TYPE_COLUMN) |
328 |
|
{ |
329 |
0 |
boolean invertSelection = evt.isAltDown(); |
330 |
0 |
boolean toggleSelection = Platform.isControlDown(evt); |
331 |
0 |
boolean extendSelection = evt.isShiftDown(); |
332 |
0 |
fr.ap.alignFrame.avc.markColumnsContainingFeatures( |
333 |
|
invertSelection, extendSelection, toggleSelection, type); |
334 |
0 |
fr.ap.av.sendSelection(); |
335 |
|
} |
336 |
|
} |
337 |
|
|
338 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
339 |
0 |
@Override... |
340 |
|
public void mouseReleased(MouseEvent evt) |
341 |
|
{ |
342 |
0 |
selectedRow = table.rowAtPoint(evt.getPoint()); |
343 |
0 |
if (evt.isPopupTrigger()) |
344 |
|
{ |
345 |
0 |
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); |
346 |
0 |
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN); |
347 |
0 |
showPopupMenu(selectedRow, type, colour, evt.getPoint()); |
348 |
|
} |
349 |
|
} |
350 |
|
}); |
351 |
|
|
352 |
0 |
table.addMouseMotionListener(new MouseMotionAdapter() |
353 |
|
{ |
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 6 |
Complexity Density: 0.55 |
|
354 |
0 |
@Override... |
355 |
|
public void mouseDragged(MouseEvent evt) |
356 |
|
{ |
357 |
0 |
int newRow = table.rowAtPoint(evt.getPoint()); |
358 |
0 |
if (newRow != selectedRow && selectedRow != -1 && newRow != -1) |
359 |
|
{ |
360 |
|
|
361 |
|
|
362 |
|
|
363 |
|
|
364 |
|
|
365 |
0 |
Object[][] data = ((FeatureTableModel) table.getModel()) |
366 |
|
.getData(); |
367 |
0 |
int direction = newRow < selectedRow ? -1 : 1; |
368 |
0 |
for (int i = selectedRow; i != newRow; i += direction) |
369 |
|
{ |
370 |
0 |
Object[] temp = data[i]; |
371 |
0 |
data[i] = data[i + direction]; |
372 |
0 |
data[i + direction] = temp; |
373 |
|
} |
374 |
0 |
updateFeatureRenderer(data); |
375 |
0 |
table.repaint(); |
376 |
0 |
selectedRow = newRow; |
377 |
|
} |
378 |
|
} |
379 |
|
}); |
380 |
|
|
381 |
|
|
382 |
0 |
scrollPane.setViewportView(table); |
383 |
|
|
384 |
0 |
if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) |
385 |
|
{ |
386 |
0 |
fr.findAllFeatures(true); |
387 |
|
} |
388 |
|
|
389 |
0 |
discoverAllFeatureData(); |
390 |
0 |
final FeatureSettings fs = this; |
391 |
0 |
fr.addPropertyChangeListener(change = new PropertyChangeListener() |
392 |
|
{ |
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
393 |
0 |
@Override... |
394 |
|
public void propertyChange(PropertyChangeEvent evt) |
395 |
|
{ |
396 |
0 |
if (!fs.resettingTable && !fs.handlingUpdate) |
397 |
|
{ |
398 |
0 |
fs.handlingUpdate = true; |
399 |
0 |
fs.resetTable(null); |
400 |
|
|
401 |
0 |
fs.handlingUpdate = false; |
402 |
|
} |
403 |
|
} |
404 |
|
|
405 |
|
}); |
406 |
|
|
407 |
0 |
SplitContainerI splitframe = af.getSplitViewContainer(); |
408 |
0 |
if (splitframe != null) |
409 |
|
{ |
410 |
0 |
frame = null; |
411 |
0 |
splitframe.addFeatureSettingsUI(this); |
412 |
|
} |
413 |
|
else |
414 |
|
{ |
415 |
0 |
frame = new JInternalFrame(); |
416 |
0 |
frame.setContentPane(this); |
417 |
0 |
frame.setFrameIcon(null); |
418 |
0 |
Rectangle bounds = af.getFeatureSettingsGeometry(); |
419 |
0 |
String title; |
420 |
0 |
if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels( |
421 |
|
af.alignPanel.av.getSequenceSetId()).length > 1) |
422 |
|
{ |
423 |
0 |
title = MessageManager.formatMessage( |
424 |
|
"label.sequence_feature_settings_for_view", |
425 |
|
af.alignPanel.getViewName()); |
426 |
|
} |
427 |
|
else |
428 |
|
{ |
429 |
0 |
title = MessageManager.getString("label.sequence_feature_settings"); |
430 |
|
} |
431 |
0 |
if (bounds == null) |
432 |
|
{ |
433 |
0 |
if (Platform.isAMacAndNotJS()) |
434 |
|
{ |
435 |
0 |
Desktop.addInternalFrame(frame, title, 600, 480); |
436 |
|
} |
437 |
|
else |
438 |
|
{ |
439 |
0 |
Desktop.addInternalFrame(frame, title, 600, 450); |
440 |
|
} |
441 |
|
} |
442 |
|
else |
443 |
|
{ |
444 |
0 |
Desktop.addInternalFrame(frame, title, false, bounds.width, |
445 |
|
bounds.height); |
446 |
0 |
frame.setBounds(bounds); |
447 |
0 |
frame.setVisible(true); |
448 |
|
} |
449 |
0 |
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); |
450 |
|
|
451 |
0 |
frame.addInternalFrameListener( |
452 |
|
new javax.swing.event.InternalFrameAdapter() |
453 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
454 |
0 |
@Override... |
455 |
|
public void internalFrameClosed( |
456 |
|
javax.swing.event.InternalFrameEvent evt) |
457 |
|
{ |
458 |
0 |
featureSettings_isClosed(); |
459 |
|
}; |
460 |
|
}); |
461 |
0 |
frame.setLayer(JLayeredPane.PALETTE_LAYER); |
462 |
|
} |
463 |
0 |
inConstruction = false; |
464 |
|
} |
465 |
|
|
466 |
|
|
467 |
|
|
468 |
|
|
469 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
470 |
0 |
private void updateComplementButtons()... |
471 |
|
{ |
472 |
0 |
showComplement.setSelected(af.getViewport().isShowComplementFeatures()); |
473 |
0 |
showComplementOnTop |
474 |
|
.setSelected(af.getViewport().isShowComplementFeaturesOnTop()); |
475 |
|
} |
476 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
477 |
0 |
@Override... |
478 |
|
public AlignViewControllerGuiI getAlignframe() |
479 |
|
{ |
480 |
0 |
return af; |
481 |
|
} |
482 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
483 |
0 |
@Override... |
484 |
|
public void featureSettings_isClosed() |
485 |
|
{ |
486 |
0 |
fr.removePropertyChangeListener(change); |
487 |
0 |
change = null; |
488 |
|
} |
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
|
493 |
|
|
494 |
|
@param |
495 |
|
@param |
496 |
|
@param |
497 |
|
@param |
498 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 1 |
Complexity Density: 0.05 |
|
499 |
0 |
protected void showPopupMenu(final int rowSelected, final String type,... |
500 |
|
final Object typeCol, final Point pt) |
501 |
|
{ |
502 |
0 |
JPopupMenu men = new JPopupMenu(MessageManager |
503 |
|
.formatMessage("label.settings_for_param", new String[] |
504 |
|
{ type })); |
505 |
|
|
506 |
0 |
JMenuItem scr = new JMenuItem( |
507 |
|
MessageManager.getString("label.sort_by_score")); |
508 |
0 |
men.add(scr); |
509 |
0 |
scr.addActionListener(new ActionListener() |
510 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
511 |
0 |
@Override... |
512 |
|
public void actionPerformed(ActionEvent e) |
513 |
|
{ |
514 |
0 |
sortByScore(Arrays.asList(new String[] { type })); |
515 |
|
} |
516 |
|
}); |
517 |
0 |
JMenuItem dens = new JMenuItem( |
518 |
|
MessageManager.getString("label.sort_by_density")); |
519 |
0 |
dens.addActionListener(new ActionListener() |
520 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
521 |
0 |
@Override... |
522 |
|
public void actionPerformed(ActionEvent e) |
523 |
|
{ |
524 |
0 |
sortByDensity(Arrays.asList(new String[] { type })); |
525 |
|
} |
526 |
|
}); |
527 |
0 |
men.add(dens); |
528 |
|
|
529 |
0 |
JMenuItem selCols = new JMenuItem( |
530 |
|
MessageManager.getString("label.select_columns_containing")); |
531 |
0 |
selCols.addActionListener(new ActionListener() |
532 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
533 |
0 |
@Override... |
534 |
|
public void actionPerformed(ActionEvent arg0) |
535 |
|
{ |
536 |
0 |
fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, |
537 |
|
false, type); |
538 |
0 |
fr.ap.av.sendSelection(); |
539 |
|
} |
540 |
|
}); |
541 |
0 |
JMenuItem clearCols = new JMenuItem(MessageManager |
542 |
|
.getString("label.select_columns_not_containing")); |
543 |
0 |
clearCols.addActionListener(new ActionListener() |
544 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
545 |
0 |
@Override... |
546 |
|
public void actionPerformed(ActionEvent arg0) |
547 |
|
{ |
548 |
0 |
fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, |
549 |
|
false, type); |
550 |
0 |
fr.ap.av.sendSelection(); |
551 |
|
} |
552 |
|
}); |
553 |
0 |
JMenuItem hideCols = new JMenuItem( |
554 |
|
MessageManager.getString("label.hide_columns_containing")); |
555 |
0 |
hideCols.addActionListener(new ActionListener() |
556 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
557 |
0 |
@Override... |
558 |
|
public void actionPerformed(ActionEvent arg0) |
559 |
|
{ |
560 |
0 |
fr.ap.alignFrame.hideFeatureColumns(type, true); |
561 |
0 |
fr.ap.av.sendSelection(); |
562 |
|
} |
563 |
|
}); |
564 |
0 |
JMenuItem hideOtherCols = new JMenuItem( |
565 |
|
MessageManager.getString("label.hide_columns_not_containing")); |
566 |
0 |
hideOtherCols.addActionListener(new ActionListener() |
567 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
568 |
0 |
@Override... |
569 |
|
public void actionPerformed(ActionEvent arg0) |
570 |
|
{ |
571 |
0 |
fr.ap.alignFrame.hideFeatureColumns(type, false); |
572 |
0 |
fr.ap.av.sendSelection(); |
573 |
|
} |
574 |
|
}); |
575 |
0 |
men.add(selCols); |
576 |
0 |
men.add(clearCols); |
577 |
0 |
men.add(hideCols); |
578 |
0 |
men.add(hideOtherCols); |
579 |
0 |
men.show(table, pt.x, pt.y); |
580 |
|
} |
581 |
|
|
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
|
586 |
|
@param |
587 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
588 |
0 |
protected void sortByDensity(List<String> featureTypes)... |
589 |
|
{ |
590 |
0 |
af.avc.sortAlignmentByFeatureDensity(featureTypes); |
591 |
|
} |
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
@param |
598 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
599 |
0 |
protected void sortByScore(List<String> featureTypes)... |
600 |
|
{ |
601 |
0 |
af.avc.sortAlignmentByFeatureScore(featureTypes); |
602 |
|
} |
603 |
|
|
604 |
|
|
605 |
|
|
606 |
|
|
607 |
|
|
608 |
|
@param |
609 |
|
@return |
610 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
611 |
0 |
private boolean canSortBy(String title)... |
612 |
|
{ |
613 |
0 |
if (fr.getDisplayedFeatureTypes().isEmpty()) |
614 |
|
{ |
615 |
0 |
JvOptionPane.showMessageDialog(this, |
616 |
|
MessageManager.getString("label.no_features_to_sort_by"), |
617 |
|
title, JvOptionPane.OK_OPTION); |
618 |
0 |
return false; |
619 |
|
} |
620 |
0 |
return true; |
621 |
|
} |
622 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 4 |
Complexity Density: 0.4 |
|
623 |
0 |
@Override... |
624 |
|
synchronized public void discoverAllFeatureData() |
625 |
|
{ |
626 |
0 |
Set<String> allGroups = new HashSet<>(); |
627 |
0 |
AlignmentI alignment = af.getViewport().getAlignment(); |
628 |
|
|
629 |
0 |
for (int i = 0; i < alignment.getHeight(); i++) |
630 |
|
{ |
631 |
0 |
SequenceI seq = alignment.getSequenceAt(i); |
632 |
0 |
for (String group : seq.getFeatures().getFeatureGroups(true)) |
633 |
|
{ |
634 |
0 |
if (group != null && !allGroups.contains(group)) |
635 |
|
{ |
636 |
0 |
allGroups.add(group); |
637 |
0 |
checkGroupState(group); |
638 |
|
} |
639 |
|
} |
640 |
|
} |
641 |
|
|
642 |
0 |
resetTable(null); |
643 |
|
|
644 |
0 |
validate(); |
645 |
|
} |
646 |
|
|
647 |
|
|
648 |
|
|
649 |
|
|
650 |
|
@param |
651 |
|
@return |
652 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
653 |
0 |
private boolean checkGroupState(String group)... |
654 |
|
{ |
655 |
0 |
boolean visible = fr.checkGroupVisibility(group, true); |
656 |
|
|
657 |
0 |
for (int g = 0; g < groupPanel.getComponentCount(); g++) |
658 |
|
{ |
659 |
0 |
if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) |
660 |
|
{ |
661 |
0 |
((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); |
662 |
0 |
return visible; |
663 |
|
} |
664 |
|
} |
665 |
|
|
666 |
0 |
final String grp = group; |
667 |
0 |
final JCheckBox check = new JCheckBox(group, visible); |
668 |
0 |
check.setFont(new Font("Serif", Font.BOLD, 12)); |
669 |
0 |
check.setToolTipText(group); |
670 |
0 |
check.addItemListener(new ItemListener() |
671 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
672 |
0 |
@Override... |
673 |
|
public void itemStateChanged(ItemEvent evt) |
674 |
|
{ |
675 |
0 |
fr.setGroupVisibility(check.getText(), check.isSelected()); |
676 |
0 |
resetTable(new String[] { grp }); |
677 |
0 |
refreshDisplay(); |
678 |
|
} |
679 |
|
}); |
680 |
0 |
groupPanel.add(check); |
681 |
0 |
return visible; |
682 |
|
} |
683 |
|
|
|
|
| 0% |
Uncovered Elements: 92 (92) |
Complexity: 16 |
Complexity Density: 0.25 |
|
684 |
0 |
synchronized void resetTable(String[] groupChanged)... |
685 |
|
{ |
686 |
0 |
if (resettingTable) |
687 |
|
{ |
688 |
0 |
return; |
689 |
|
} |
690 |
0 |
resettingTable = true; |
691 |
0 |
typeWidth = new Hashtable<>(); |
692 |
|
|
693 |
|
|
694 |
|
|
695 |
0 |
Set<String> displayableTypes = new HashSet<>(); |
696 |
0 |
Set<String> foundGroups = new HashSet<>(); |
697 |
|
|
698 |
|
|
699 |
|
|
700 |
|
|
701 |
|
|
702 |
0 |
for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) |
703 |
|
{ |
704 |
|
|
705 |
0 |
SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); |
706 |
|
|
707 |
|
|
708 |
|
|
709 |
|
|
710 |
|
|
711 |
0 |
Set<String> groups = seq.getFeatures().getFeatureGroups(true); |
712 |
0 |
Set<String> visibleGroups = new HashSet<>(); |
713 |
0 |
for (String group : groups) |
714 |
|
{ |
715 |
0 |
if (group == null || checkGroupState(group)) |
716 |
|
{ |
717 |
0 |
visibleGroups.add(group); |
718 |
|
} |
719 |
|
} |
720 |
0 |
foundGroups.addAll(groups); |
721 |
|
|
722 |
|
|
723 |
|
|
724 |
|
|
725 |
|
|
726 |
0 |
Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true, |
727 |
|
visibleGroups.toArray(new String[visibleGroups.size()])); |
728 |
0 |
for (String type : types) |
729 |
|
{ |
730 |
0 |
displayableTypes.add(type); |
731 |
0 |
float[] avWidth = typeWidth.get(type); |
732 |
0 |
if (avWidth == null) |
733 |
|
{ |
734 |
0 |
avWidth = new float[2]; |
735 |
0 |
typeWidth.put(type, avWidth); |
736 |
|
} |
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
741 |
0 |
avWidth[0] += seq.getFeatures().getFeatureCount(true, type); |
742 |
0 |
avWidth[1] += seq.getFeatures().getTotalFeatureLength(type); |
743 |
|
} |
744 |
|
} |
745 |
|
|
746 |
0 |
Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; |
747 |
0 |
int dataIndex = 0; |
748 |
|
|
749 |
0 |
if (fr.hasRenderOrder()) |
750 |
|
{ |
751 |
0 |
if (!handlingUpdate) |
752 |
|
{ |
753 |
0 |
fr.findAllFeatures(groupChanged != null); |
754 |
|
|
755 |
|
|
756 |
|
|
757 |
|
|
758 |
|
} |
759 |
0 |
List<String> frl = fr.getRenderOrder(); |
760 |
0 |
for (int ro = frl.size() - 1; ro > -1; ro--) |
761 |
|
{ |
762 |
0 |
String type = frl.get(ro); |
763 |
|
|
764 |
0 |
if (!displayableTypes.contains(type)) |
765 |
|
{ |
766 |
0 |
continue; |
767 |
|
} |
768 |
|
|
769 |
0 |
data[dataIndex][TYPE_COLUMN] = type; |
770 |
0 |
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); |
771 |
0 |
FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); |
772 |
0 |
data[dataIndex][FILTER_COLUMN] = featureFilter == null |
773 |
|
? new FeatureMatcherSet() |
774 |
|
: featureFilter; |
775 |
0 |
data[dataIndex][SHOW_COLUMN] = Boolean.valueOf( |
776 |
|
af.getViewport().getFeaturesDisplayed().isVisible(type)); |
777 |
0 |
dataIndex++; |
778 |
0 |
displayableTypes.remove(type); |
779 |
|
} |
780 |
|
} |
781 |
|
|
782 |
|
|
783 |
|
|
784 |
|
|
785 |
|
|
786 |
0 |
while (!displayableTypes.isEmpty()) |
787 |
|
{ |
788 |
0 |
String type = displayableTypes.iterator().next(); |
789 |
0 |
data[dataIndex][TYPE_COLUMN] = type; |
790 |
|
|
791 |
0 |
data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); |
792 |
0 |
if (data[dataIndex][COLOUR_COLUMN] == null) |
793 |
|
{ |
794 |
|
|
795 |
0 |
fr.clearRenderOrder(); |
796 |
0 |
return; |
797 |
|
} |
798 |
0 |
FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); |
799 |
0 |
data[dataIndex][FILTER_COLUMN] = featureFilter == null |
800 |
|
? new FeatureMatcherSet() |
801 |
|
: featureFilter; |
802 |
0 |
data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true); |
803 |
0 |
dataIndex++; |
804 |
0 |
displayableTypes.remove(type); |
805 |
|
} |
806 |
|
|
807 |
0 |
if (originalData == null) |
808 |
|
{ |
809 |
0 |
originalData = new Object[data.length][COLUMN_COUNT]; |
810 |
0 |
for (int i = 0; i < data.length; i++) |
811 |
|
{ |
812 |
0 |
System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); |
813 |
|
} |
814 |
|
} |
815 |
|
else |
816 |
|
{ |
817 |
0 |
updateOriginalData(data); |
818 |
|
} |
819 |
|
|
820 |
0 |
table.setModel(new FeatureTableModel(data)); |
821 |
0 |
table.getColumnModel().getColumn(0).setPreferredWidth(200); |
822 |
|
|
823 |
0 |
groupPanel.setLayout( |
824 |
|
new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); |
825 |
0 |
pruneGroups(foundGroups); |
826 |
0 |
groupPanel.validate(); |
827 |
|
|
828 |
0 |
updateFeatureRenderer(data, groupChanged != null); |
829 |
0 |
resettingTable = false; |
830 |
|
} |
831 |
|
|
832 |
|
|
833 |
|
|
834 |
|
|
835 |
|
|
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
|
840 |
|
@param |
841 |
|
|
|
|
| 0% |
Uncovered Elements: 29 (29) |
Complexity: 6 |
Complexity Density: 0.32 |
|
842 |
0 |
protected void updateOriginalData(Object[][] foundData)... |
843 |
|
{ |
844 |
|
|
845 |
|
|
846 |
0 |
Object[][] currentData = ((FeatureTableModel) table.getModel()) |
847 |
|
.getData(); |
848 |
0 |
for (Object[] row : foundData) |
849 |
|
{ |
850 |
0 |
String type = (String) row[TYPE_COLUMN]; |
851 |
0 |
boolean found = false; |
852 |
0 |
for (Object[] current : currentData) |
853 |
|
{ |
854 |
0 |
if (type.equals(current[TYPE_COLUMN])) |
855 |
|
{ |
856 |
0 |
found = true; |
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
|
861 |
0 |
if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN])) |
862 |
|
{ |
863 |
|
|
864 |
|
|
865 |
|
|
866 |
0 |
for (Object[] original : originalData) |
867 |
|
{ |
868 |
0 |
if (type.equals(original[TYPE_COLUMN])) |
869 |
|
{ |
870 |
0 |
original[COLOUR_COLUMN] = row[COLOUR_COLUMN]; |
871 |
0 |
break; |
872 |
|
} |
873 |
|
} |
874 |
|
} |
875 |
0 |
break; |
876 |
|
} |
877 |
|
} |
878 |
0 |
if (!found) |
879 |
|
{ |
880 |
|
|
881 |
|
|
882 |
|
|
883 |
0 |
Object[][] newData = new Object[originalData.length |
884 |
|
+ 1][COLUMN_COUNT]; |
885 |
0 |
for (int i = 0; i < originalData.length; i++) |
886 |
|
{ |
887 |
0 |
System.arraycopy(originalData[i], 0, newData[i + 1], 0, |
888 |
|
COLUMN_COUNT); |
889 |
|
} |
890 |
0 |
newData[0] = row; |
891 |
0 |
originalData = newData; |
892 |
|
} |
893 |
|
} |
894 |
|
} |
895 |
|
|
896 |
|
|
897 |
|
|
898 |
|
|
899 |
|
|
900 |
|
|
901 |
|
@param |
902 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
903 |
0 |
protected void pruneGroups(Set<String> foundGroups)... |
904 |
|
{ |
905 |
0 |
for (int g = 0; g < groupPanel.getComponentCount(); g++) |
906 |
|
{ |
907 |
0 |
JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); |
908 |
0 |
if (!foundGroups.contains(checkbox.getText())) |
909 |
|
{ |
910 |
0 |
groupPanel.remove(checkbox); |
911 |
|
} |
912 |
|
} |
913 |
|
} |
914 |
|
|
915 |
|
|
916 |
|
|
917 |
|
|
918 |
|
@param |
919 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 5 |
Complexity Density: 0.5 |
|
920 |
0 |
private void ensureOrder(Object[][] data)... |
921 |
|
{ |
922 |
0 |
boolean sort = false; |
923 |
0 |
float[] order = new float[data.length]; |
924 |
0 |
for (int i = 0; i < order.length; i++) |
925 |
|
{ |
926 |
0 |
order[i] = fr.getOrder(data[i][0].toString()); |
927 |
0 |
if (order[i] < 0) |
928 |
|
{ |
929 |
0 |
order[i] = fr.setOrder(data[i][0].toString(), i / order.length); |
930 |
|
} |
931 |
0 |
if (i > 1) |
932 |
|
{ |
933 |
0 |
sort = sort || order[i - 1] > order[i]; |
934 |
|
} |
935 |
|
} |
936 |
0 |
if (sort) |
937 |
|
{ |
938 |
0 |
jalview.util.QuickSort.sort(order, data); |
939 |
|
} |
940 |
|
} |
941 |
|
|
942 |
|
|
943 |
|
|
944 |
|
|
945 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
|
946 |
0 |
void load()... |
947 |
|
{ |
948 |
0 |
JalviewFileChooser chooser = new JalviewFileChooser("fc", |
949 |
|
SEQUENCE_FEATURE_COLOURS); |
950 |
0 |
chooser.setFileView(new JalviewFileView()); |
951 |
0 |
chooser.setDialogTitle( |
952 |
|
MessageManager.getString("label.load_feature_colours")); |
953 |
0 |
chooser.setToolTipText(MessageManager.getString("action.load")); |
954 |
0 |
chooser.setResponseHandler(0, () -> { |
955 |
0 |
File file = chooser.getSelectedFile(); |
956 |
0 |
load(file); |
957 |
|
}); |
958 |
0 |
chooser.showOpenDialog(this); |
959 |
|
} |
960 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
961 |
0 |
public static boolean loadFeatureSettingsFile(FeatureRenderer fr,... |
962 |
|
File file) throws Exception |
963 |
|
{ |
964 |
0 |
InputStreamReader in = new InputStreamReader(new FileInputStream(file), |
965 |
|
"UTF-8"); |
966 |
0 |
return loadFeatureSettingsFile(fr, in); |
967 |
|
} |
968 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
969 |
0 |
public static void loadFeatureSettingsFile(... |
970 |
|
FeatureRenderer featureRenderer, Object fileObject, |
971 |
|
DataSourceType sourceType) throws Exception |
972 |
|
{ |
973 |
0 |
FileParse fp = new FileParse(fileObject, sourceType); |
974 |
0 |
loadFeatureSettingsFile(featureRenderer, fp.getReader()); |
975 |
|
} |
976 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 4 |
Complexity Density: 0.24 |
|
977 |
0 |
private static boolean loadFeatureSettingsFile(FeatureRenderer fr,... |
978 |
|
Reader in) throws Exception |
979 |
|
{ |
980 |
0 |
JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.jalview"); |
981 |
0 |
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); |
982 |
0 |
XMLStreamReader streamReader = XMLInputFactory.newInstance() |
983 |
|
.createXMLStreamReader(in); |
984 |
0 |
JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader, |
985 |
|
JalviewUserColours.class); |
986 |
0 |
JalviewUserColours jucs = jbe.getValue(); |
987 |
|
|
988 |
|
|
989 |
|
|
990 |
|
|
991 |
|
|
992 |
|
|
993 |
0 |
for (int i = jucs.getColour().size() - 1; i >= 0; i--) |
994 |
|
{ |
995 |
0 |
Colour newcol = jucs.getColour().get(i); |
996 |
0 |
FeatureColourI colour = jalview.project.Jalview2XML |
997 |
|
.parseColour(newcol); |
998 |
0 |
fr.setColour(newcol.getName(), colour); |
999 |
0 |
fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); |
1000 |
|
} |
1001 |
|
|
1002 |
|
|
1003 |
|
|
1004 |
|
|
1005 |
|
|
1006 |
0 |
for (int i = 0; i < jucs.getFilter().size(); i++) |
1007 |
|
{ |
1008 |
0 |
Filter filterModel = jucs.getFilter().get(i); |
1009 |
0 |
String featureType = filterModel.getFeatureType(); |
1010 |
0 |
FeatureMatcherSetI filter = jalview.project.Jalview2XML |
1011 |
|
.parseFilter(featureType, filterModel.getMatcherSet()); |
1012 |
0 |
if (!filter.isEmpty()) |
1013 |
|
{ |
1014 |
0 |
fr.setFeatureFilter(featureType, filter); |
1015 |
|
} |
1016 |
|
} |
1017 |
0 |
return true; |
1018 |
|
} |
1019 |
|
|
1020 |
|
|
1021 |
|
|
1022 |
|
|
1023 |
|
@param |
1024 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1025 |
0 |
void load(File file)... |
1026 |
|
{ |
1027 |
0 |
load(file, DataSourceType.FILE); |
1028 |
|
} |
1029 |
|
|
1030 |
|
|
1031 |
|
|
1032 |
|
|
1033 |
|
@param |
1034 |
|
|
1035 |
|
|
1036 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.33 |
|
1037 |
0 |
void load(Object file, DataSourceType sourceType)... |
1038 |
|
{ |
1039 |
0 |
try |
1040 |
|
{ |
1041 |
0 |
loadFeatureSettingsFile(fr, file, sourceType); |
1042 |
|
|
1043 |
|
|
1044 |
|
|
1045 |
0 |
if (table != null) |
1046 |
|
{ |
1047 |
0 |
resetTable(null); |
1048 |
0 |
Object[][] data = ((FeatureTableModel) table.getModel()).getData(); |
1049 |
0 |
ensureOrder(data); |
1050 |
0 |
updateFeatureRenderer(data, false); |
1051 |
0 |
table.repaint(); |
1052 |
|
} |
1053 |
|
} catch (Exception ex) |
1054 |
|
{ |
1055 |
0 |
jalview.bin.Console |
1056 |
|
.outPrintln("Error loading User Colour File\n" + ex); |
1057 |
|
} |
1058 |
|
} |
1059 |
|
|
1060 |
|
|
1061 |
|
|
1062 |
|
|
1063 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
1064 |
0 |
void save()... |
1065 |
|
{ |
1066 |
0 |
JalviewFileChooser chooser = new JalviewFileChooser("fc", |
1067 |
|
SEQUENCE_FEATURE_COLOURS); |
1068 |
0 |
chooser.setFileView(new JalviewFileView()); |
1069 |
0 |
chooser.setDialogTitle( |
1070 |
|
MessageManager.getString("label.save_feature_colours")); |
1071 |
0 |
chooser.setToolTipText(MessageManager.getString("action.save")); |
1072 |
0 |
int option = chooser.showSaveDialog(this); |
1073 |
0 |
if (option == JalviewFileChooser.APPROVE_OPTION) |
1074 |
|
{ |
1075 |
0 |
File file = chooser.getSelectedFile(); |
1076 |
0 |
save(file); |
1077 |
|
} |
1078 |
|
} |
1079 |
|
|
1080 |
|
|
1081 |
|
|
1082 |
|
|
1083 |
|
@param |
1084 |
|
|
|
|
| 0% |
Uncovered Elements: 29 (29) |
Complexity: 4 |
Complexity Density: 0.15 |
|
1085 |
0 |
void save(File file)... |
1086 |
|
{ |
1087 |
0 |
JalviewUserColours ucs = new JalviewUserColours(); |
1088 |
0 |
ucs.setSchemeName("Sequence Features"); |
1089 |
0 |
try |
1090 |
|
{ |
1091 |
0 |
PrintWriter out = new PrintWriter( |
1092 |
|
new OutputStreamWriter(new FileOutputStream(file), "UTF-8")); |
1093 |
|
|
1094 |
|
|
1095 |
|
|
1096 |
|
|
1097 |
|
|
1098 |
0 |
Set<String> fr_colours = fr.getAllFeatureColours(); |
1099 |
0 |
String[] sortedTypes = fr_colours |
1100 |
|
.toArray(new String[fr_colours.size()]); |
1101 |
0 |
Arrays.sort(sortedTypes, new Comparator<String>() |
1102 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1103 |
0 |
@Override... |
1104 |
|
public int compare(String type1, String type2) |
1105 |
|
{ |
1106 |
0 |
return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); |
1107 |
|
} |
1108 |
|
}); |
1109 |
|
|
1110 |
|
|
1111 |
|
|
1112 |
|
|
1113 |
0 |
for (String featureType : sortedTypes) |
1114 |
|
{ |
1115 |
0 |
FeatureColourI fcol = fr.getFeatureStyle(featureType); |
1116 |
0 |
Colour col = jalview.project.Jalview2XML.marshalColour(featureType, |
1117 |
|
fcol); |
1118 |
0 |
ucs.getColour().add(col); |
1119 |
|
} |
1120 |
|
|
1121 |
|
|
1122 |
|
|
1123 |
|
|
1124 |
0 |
for (String featureType : sortedTypes) |
1125 |
|
{ |
1126 |
0 |
FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); |
1127 |
0 |
if (filter != null && !filter.isEmpty()) |
1128 |
|
{ |
1129 |
0 |
Iterator<FeatureMatcherI> iterator = filter.getMatchers() |
1130 |
|
.iterator(); |
1131 |
0 |
FeatureMatcherI firstMatcher = iterator.next(); |
1132 |
0 |
jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML |
1133 |
|
.marshalFilter(firstMatcher, iterator, filter.isAnded()); |
1134 |
0 |
Filter filterModel = new Filter(); |
1135 |
0 |
filterModel.setFeatureType(featureType); |
1136 |
0 |
filterModel.setMatcherSet(ms); |
1137 |
0 |
ucs.getFilter().add(filterModel); |
1138 |
|
} |
1139 |
|
} |
1140 |
0 |
JAXBContext jaxbContext = JAXBContext |
1141 |
|
.newInstance(JalviewUserColours.class); |
1142 |
0 |
Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); |
1143 |
0 |
jaxbMarshaller.marshal( |
1144 |
|
new ObjectFactory().createJalviewUserColours(ucs), out); |
1145 |
|
|
1146 |
|
|
1147 |
|
|
1148 |
0 |
out.flush(); |
1149 |
|
|
1150 |
|
|
1151 |
0 |
out.close(); |
1152 |
|
} catch (Exception ex) |
1153 |
|
{ |
1154 |
0 |
ex.printStackTrace(); |
1155 |
|
} |
1156 |
|
} |
1157 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1158 |
0 |
public void invertSelection()... |
1159 |
|
{ |
1160 |
0 |
Object[][] data = ((FeatureTableModel) table.getModel()).getData(); |
1161 |
0 |
for (int i = 0; i < data.length; i++) |
1162 |
|
{ |
1163 |
0 |
data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN]; |
1164 |
|
} |
1165 |
0 |
updateFeatureRenderer(data, true); |
1166 |
0 |
table.repaint(); |
1167 |
|
} |
1168 |
|
|
|
|
| 0% |
Uncovered Elements: 45 (45) |
Complexity: 11 |
Complexity Density: 0.41 |
|
1169 |
0 |
public void orderByAvWidth()... |
1170 |
|
{ |
1171 |
0 |
if (table == null || table.getModel() == null) |
1172 |
|
{ |
1173 |
0 |
return; |
1174 |
|
} |
1175 |
0 |
Object[][] data = ((FeatureTableModel) table.getModel()).getData(); |
1176 |
0 |
float[] width = new float[data.length]; |
1177 |
0 |
float[] awidth; |
1178 |
0 |
float max = 0; |
1179 |
|
|
1180 |
0 |
for (int i = 0; i < data.length; i++) |
1181 |
|
{ |
1182 |
0 |
awidth = typeWidth.get(data[i][TYPE_COLUMN]); |
1183 |
0 |
if (awidth[0] > 0) |
1184 |
|
{ |
1185 |
0 |
width[i] = awidth[1] / awidth[0]; |
1186 |
|
|
1187 |
|
|
1188 |
|
|
1189 |
|
} |
1190 |
|
else |
1191 |
|
{ |
1192 |
0 |
width[i] = 0; |
1193 |
|
} |
1194 |
0 |
if (max < width[i]) |
1195 |
|
{ |
1196 |
0 |
max = width[i]; |
1197 |
|
} |
1198 |
|
} |
1199 |
0 |
boolean sort = false; |
1200 |
0 |
for (int i = 0; i < width.length; i++) |
1201 |
|
{ |
1202 |
|
|
1203 |
0 |
if (width[i] == 0) |
1204 |
|
{ |
1205 |
0 |
width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString()); |
1206 |
0 |
if (width[i] < 0) |
1207 |
|
{ |
1208 |
0 |
width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(), |
1209 |
|
i / data.length); |
1210 |
|
} |
1211 |
|
} |
1212 |
|
else |
1213 |
|
{ |
1214 |
0 |
width[i] /= max; |
1215 |
0 |
fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); |
1216 |
|
|
1217 |
|
} |
1218 |
0 |
if (i > 0) |
1219 |
|
{ |
1220 |
0 |
sort = sort || width[i - 1] > width[i]; |
1221 |
|
} |
1222 |
|
} |
1223 |
0 |
if (sort) |
1224 |
|
{ |
1225 |
0 |
jalview.util.QuickSort.sort(width, data); |
1226 |
|
|
1227 |
|
} |
1228 |
|
|
1229 |
0 |
updateFeatureRenderer(data, false); |
1230 |
0 |
table.repaint(); |
1231 |
|
} |
1232 |
|
|
1233 |
|
|
1234 |
|
|
1235 |
|
|
1236 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1237 |
0 |
public void closeOldSettings()... |
1238 |
|
{ |
1239 |
0 |
closeDialog(false); |
1240 |
|
} |
1241 |
|
|
1242 |
|
|
1243 |
|
|
1244 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1245 |
0 |
public void close()... |
1246 |
|
{ |
1247 |
0 |
closeDialog(true); |
1248 |
|
} |
1249 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
1250 |
0 |
private void closeDialog(boolean closeContainingFrame)... |
1251 |
|
{ |
1252 |
0 |
try |
1253 |
|
{ |
1254 |
0 |
if (frame != null) |
1255 |
|
{ |
1256 |
0 |
af.setFeatureSettingsGeometry(frame.getBounds()); |
1257 |
0 |
frame.setClosed(true); |
1258 |
|
} |
1259 |
|
else |
1260 |
|
{ |
1261 |
0 |
SplitContainerI sc = af.getSplitViewContainer(); |
1262 |
0 |
sc.closeFeatureSettings(this, closeContainingFrame); |
1263 |
0 |
af.featureSettings = null; |
1264 |
|
} |
1265 |
|
} catch (Exception exe) |
1266 |
|
{ |
1267 |
|
} |
1268 |
|
|
1269 |
|
} |
1270 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1271 |
0 |
public void updateFeatureRenderer(Object[][] data)... |
1272 |
|
{ |
1273 |
0 |
updateFeatureRenderer(data, true); |
1274 |
|
} |
1275 |
|
|
1276 |
|
|
1277 |
|
|
1278 |
|
|
1279 |
|
|
1280 |
|
@param |
1281 |
|
@param |
1282 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1283 |
0 |
void updateFeatureRenderer(Object[][] data, boolean visibleNew)... |
1284 |
|
{ |
1285 |
0 |
FeatureSettingsBean[] rowData = getTableAsBeans(data); |
1286 |
|
|
1287 |
0 |
if (fr.setFeaturePriority(rowData, visibleNew)) |
1288 |
|
{ |
1289 |
0 |
refreshDisplay(); |
1290 |
|
} |
1291 |
|
} |
1292 |
|
|
1293 |
|
|
1294 |
|
|
1295 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
1296 |
0 |
private FeatureSettingsBean[] getTableAsBeans(Object[][] data)... |
1297 |
|
{ |
1298 |
0 |
FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; |
1299 |
0 |
for (int i = 0; i < data.length; i++) |
1300 |
|
{ |
1301 |
0 |
String type = (String) data[i][TYPE_COLUMN]; |
1302 |
0 |
FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; |
1303 |
0 |
FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN]; |
1304 |
0 |
Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; |
1305 |
0 |
rowData[i] = new FeatureSettingsBean(type, colour, theFilter, |
1306 |
|
isShown); |
1307 |
|
} |
1308 |
0 |
return rowData; |
1309 |
|
} |
1310 |
|
|
|
|
| 0% |
Uncovered Elements: 89 (89) |
Complexity: 7 |
Complexity Density: 0.09 |
|
1311 |
0 |
private void jbInit() throws Exception... |
1312 |
|
{ |
1313 |
0 |
this.setLayout(new BorderLayout()); |
1314 |
|
|
1315 |
0 |
final boolean hasComplement = af.getViewport() |
1316 |
|
.getCodingComplement() != null; |
1317 |
|
|
1318 |
0 |
JPanel settingsPane = new JPanel(); |
1319 |
0 |
settingsPane.setLayout(new BorderLayout()); |
1320 |
|
|
1321 |
0 |
JPanel bigPanel = new JPanel(); |
1322 |
0 |
bigPanel.setLayout(new BorderLayout()); |
1323 |
|
|
1324 |
0 |
groupPanel = new JPanel(); |
1325 |
0 |
bigPanel.add(groupPanel, BorderLayout.NORTH); |
1326 |
|
|
1327 |
0 |
JButton invert = new JButton( |
1328 |
|
MessageManager.getString("label.invert_selection")); |
1329 |
0 |
invert.setFont(JvSwingUtils.getLabelFont()); |
1330 |
0 |
invert.addActionListener(new ActionListener() |
1331 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1332 |
0 |
@Override... |
1333 |
|
public void actionPerformed(ActionEvent e) |
1334 |
|
{ |
1335 |
0 |
invertSelection(); |
1336 |
|
} |
1337 |
|
}); |
1338 |
|
|
1339 |
0 |
JButton optimizeOrder = new JButton( |
1340 |
|
MessageManager.getString("label.optimise_order")); |
1341 |
0 |
optimizeOrder.setFont(JvSwingUtils.getLabelFont()); |
1342 |
0 |
optimizeOrder.addActionListener(new ActionListener() |
1343 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1344 |
0 |
@Override... |
1345 |
|
public void actionPerformed(ActionEvent e) |
1346 |
|
{ |
1347 |
0 |
orderByAvWidth(); |
1348 |
|
} |
1349 |
|
}); |
1350 |
|
|
1351 |
0 |
final String byScoreLabel = MessageManager |
1352 |
|
.getString("label.seq_sort_by_score"); |
1353 |
0 |
JButton sortByScore = new JButton(byScoreLabel); |
1354 |
0 |
sortByScore.setFont(JvSwingUtils.getLabelFont()); |
1355 |
0 |
sortByScore.addActionListener(new ActionListener() |
1356 |
|
{ |
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1357 |
0 |
@Override... |
1358 |
|
public void actionPerformed(ActionEvent e) |
1359 |
|
{ |
1360 |
0 |
if (canSortBy(byScoreLabel)) |
1361 |
|
{ |
1362 |
0 |
sortByScore(null); |
1363 |
|
} |
1364 |
|
} |
1365 |
|
}); |
1366 |
0 |
final String byDensityLabel = MessageManager |
1367 |
|
.getString("label.sequence_sort_by_density"); |
1368 |
0 |
JButton sortByDens = new JButton(byDensityLabel); |
1369 |
0 |
sortByDens.setFont(JvSwingUtils.getLabelFont()); |
1370 |
0 |
sortByDens.addActionListener(new ActionListener() |
1371 |
|
{ |
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1372 |
0 |
@Override... |
1373 |
|
public void actionPerformed(ActionEvent e) |
1374 |
|
{ |
1375 |
0 |
if (canSortBy(byDensityLabel)) |
1376 |
|
{ |
1377 |
0 |
sortByDensity(null); |
1378 |
|
} |
1379 |
|
} |
1380 |
|
}); |
1381 |
|
|
1382 |
0 |
JButton help = new JButton(MessageManager.getString("action.help")); |
1383 |
0 |
help.setFont(JvSwingUtils.getLabelFont()); |
1384 |
0 |
help.addActionListener(new ActionListener() |
1385 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1386 |
0 |
@Override... |
1387 |
|
public void actionPerformed(ActionEvent e) |
1388 |
|
{ |
1389 |
0 |
try |
1390 |
|
{ |
1391 |
0 |
Help.showHelpWindow(HelpId.SequenceFeatureSettings); |
1392 |
|
} catch (HelpSetException e1) |
1393 |
|
{ |
1394 |
0 |
e1.printStackTrace(); |
1395 |
|
} |
1396 |
|
} |
1397 |
|
}); |
1398 |
|
|
1399 |
|
|
1400 |
|
|
1401 |
|
|
1402 |
0 |
JButton cancel = new JButton(MessageManager |
1403 |
0 |
.getString(hasComplement ? "action.revert" : "action.cancel")); |
1404 |
0 |
cancel.setToolTipText(MessageManager.getString(hasComplement |
1405 |
|
? "action.undo_changes_to_feature_settings" |
1406 |
|
: "action.undo_changes_to_feature_settings_and_close_the_dialog")); |
1407 |
0 |
cancel.setFont(JvSwingUtils.getLabelFont()); |
1408 |
|
|
1409 |
0 |
cancel.addActionListener(new ActionListener() |
1410 |
|
{ |
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1411 |
0 |
@Override... |
1412 |
|
public void actionPerformed(ActionEvent e) |
1413 |
|
{ |
1414 |
0 |
revert(); |
1415 |
0 |
refreshDisplay(); |
1416 |
0 |
if (!hasComplement) |
1417 |
|
{ |
1418 |
0 |
close(); |
1419 |
|
} |
1420 |
|
} |
1421 |
|
}); |
1422 |
|
|
1423 |
|
|
1424 |
|
|
1425 |
0 |
JButton ok = new JButton(MessageManager |
1426 |
0 |
.getString(hasComplement ? "action.apply" : "action.ok")); |
1427 |
0 |
ok.setFont(JvSwingUtils.getLabelFont()); |
1428 |
0 |
ok.addActionListener(new ActionListener() |
1429 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1430 |
0 |
@Override... |
1431 |
|
public void actionPerformed(ActionEvent e) |
1432 |
|
{ |
1433 |
0 |
if (!hasComplement) |
1434 |
|
{ |
1435 |
0 |
close(); |
1436 |
|
} |
1437 |
|
else |
1438 |
|
{ |
1439 |
0 |
storeOriginalSettings(); |
1440 |
|
} |
1441 |
|
} |
1442 |
|
}); |
1443 |
|
|
1444 |
0 |
JButton loadColours = new JButton( |
1445 |
|
MessageManager.getString("label.load_colours")); |
1446 |
0 |
loadColours.setFont(JvSwingUtils.getLabelFont()); |
1447 |
0 |
loadColours.setToolTipText( |
1448 |
|
MessageManager.getString("label.load_colours_tooltip")); |
1449 |
0 |
loadColours.addActionListener(new ActionListener() |
1450 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1451 |
0 |
@Override... |
1452 |
|
public void actionPerformed(ActionEvent e) |
1453 |
|
{ |
1454 |
0 |
load(); |
1455 |
|
} |
1456 |
|
}); |
1457 |
|
|
1458 |
0 |
JButton saveColours = new JButton( |
1459 |
|
MessageManager.getString("label.save_colours")); |
1460 |
0 |
saveColours.setFont(JvSwingUtils.getLabelFont()); |
1461 |
0 |
saveColours.setToolTipText( |
1462 |
|
MessageManager.getString("label.save_colours_tooltip")); |
1463 |
0 |
saveColours.addActionListener(new ActionListener() |
1464 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1465 |
0 |
@Override... |
1466 |
|
public void actionPerformed(ActionEvent e) |
1467 |
|
{ |
1468 |
0 |
save(); |
1469 |
|
} |
1470 |
|
}); |
1471 |
0 |
transparency.addChangeListener(new ChangeListener() |
1472 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1473 |
0 |
@Override... |
1474 |
|
public void stateChanged(ChangeEvent evt) |
1475 |
|
{ |
1476 |
0 |
if (!inConstruction) |
1477 |
|
{ |
1478 |
0 |
fr.setTransparency((100 - transparency.getValue()) / 100f); |
1479 |
0 |
refreshDisplay(); |
1480 |
|
} |
1481 |
|
} |
1482 |
|
}); |
1483 |
|
|
1484 |
0 |
transparency.setMaximum(70); |
1485 |
0 |
transparency.setToolTipText( |
1486 |
|
MessageManager.getString("label.transparency_tip")); |
1487 |
|
|
1488 |
0 |
boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); |
1489 |
0 |
String text = MessageManager |
1490 |
|
.formatMessage("label.show_linked_features", |
1491 |
0 |
nucleotide |
1492 |
|
? MessageManager.getString("label.protein") |
1493 |
|
.toLowerCase(Locale.ROOT) |
1494 |
|
: "CDS"); |
1495 |
0 |
showComplement = new JCheckBox(text); |
1496 |
0 |
showComplement.addActionListener(new ActionListener() |
1497 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1498 |
0 |
@Override... |
1499 |
|
public void actionPerformed(ActionEvent e) |
1500 |
|
{ |
1501 |
0 |
af.getViewport() |
1502 |
|
.setShowComplementFeatures(showComplement.isSelected()); |
1503 |
0 |
refreshDisplay(); |
1504 |
|
} |
1505 |
|
}); |
1506 |
|
|
1507 |
0 |
showComplementOnTop = new JCheckBox( |
1508 |
|
MessageManager.getString("label.on_top")); |
1509 |
0 |
showComplementOnTop.addActionListener(new ActionListener() |
1510 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1511 |
0 |
@Override... |
1512 |
|
public void actionPerformed(ActionEvent e) |
1513 |
|
{ |
1514 |
0 |
af.getViewport().setShowComplementFeaturesOnTop( |
1515 |
|
showComplementOnTop.isSelected()); |
1516 |
0 |
refreshDisplay(); |
1517 |
|
} |
1518 |
|
}); |
1519 |
|
|
1520 |
0 |
updateComplementButtons(); |
1521 |
|
|
1522 |
0 |
JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); |
1523 |
0 |
bigPanel.add(lowerPanel, BorderLayout.SOUTH); |
1524 |
|
|
1525 |
0 |
JPanel transbuttons = new JPanel(new GridLayout(5, 1)); |
1526 |
0 |
transbuttons.add(optimizeOrder); |
1527 |
0 |
transbuttons.add(invert); |
1528 |
0 |
transbuttons.add(sortByScore); |
1529 |
0 |
transbuttons.add(sortByDens); |
1530 |
0 |
transbuttons.add(help); |
1531 |
|
|
1532 |
0 |
JPanel transPanelLeft = new JPanel( |
1533 |
0 |
new GridLayout(hasComplement ? 4 : 2, 1)); |
1534 |
0 |
transPanelLeft.add(new JLabel(" Colour transparency" + ":")); |
1535 |
0 |
transPanelLeft.add(transparency); |
1536 |
0 |
if (hasComplement) |
1537 |
|
{ |
1538 |
0 |
JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT)); |
1539 |
0 |
cp.add(showComplement); |
1540 |
0 |
cp.add(showComplementOnTop); |
1541 |
0 |
transPanelLeft.add(cp); |
1542 |
|
} |
1543 |
0 |
lowerPanel.add(transPanelLeft); |
1544 |
0 |
lowerPanel.add(transbuttons); |
1545 |
|
|
1546 |
0 |
JPanel buttonPanel = new JPanel(); |
1547 |
0 |
buttonPanel.add(ok); |
1548 |
0 |
buttonPanel.add(cancel); |
1549 |
0 |
buttonPanel.add(loadColours); |
1550 |
0 |
buttonPanel.add(saveColours); |
1551 |
0 |
bigPanel.add(scrollPane, BorderLayout.CENTER); |
1552 |
0 |
settingsPane.add(bigPanel, BorderLayout.CENTER); |
1553 |
0 |
settingsPane.add(buttonPanel, BorderLayout.SOUTH); |
1554 |
0 |
this.add(settingsPane); |
1555 |
|
} |
1556 |
|
|
1557 |
|
|
1558 |
|
|
1559 |
|
|
1560 |
|
|
1561 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1562 |
0 |
void refreshDisplay()... |
1563 |
|
{ |
1564 |
0 |
af.alignPanel.paintAlignment(true, true); |
1565 |
0 |
AlignViewportI complement = af.getViewport().getCodingComplement(); |
1566 |
0 |
if (complement != null && complement.isShowComplementFeatures()) |
1567 |
|
{ |
1568 |
0 |
AlignFrame af2 = Desktop.getAlignFrameFor(complement); |
1569 |
0 |
af2.alignPanel.paintAlignment(true, true); |
1570 |
|
} |
1571 |
|
} |
1572 |
|
|
1573 |
|
|
1574 |
|
|
1575 |
|
|
1576 |
|
@param |
1577 |
|
@param |
1578 |
|
|
1579 |
|
@return |
1580 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 5 |
Complexity Density: 0.45 |
|
1581 |
0 |
public static String getColorTooltip(FeatureColourI fcol,... |
1582 |
|
boolean withHint) |
1583 |
|
{ |
1584 |
0 |
if (fcol == null) |
1585 |
|
{ |
1586 |
0 |
return null; |
1587 |
|
} |
1588 |
0 |
if (fcol.isSimpleColour()) |
1589 |
|
{ |
1590 |
0 |
return withHint ? BASE_TOOLTIP : null; |
1591 |
|
} |
1592 |
0 |
String description = fcol.getDescription(); |
1593 |
0 |
description = description.replaceAll("<", "<"); |
1594 |
0 |
description = description.replaceAll(">", ">"); |
1595 |
0 |
StringBuilder tt = new StringBuilder(description); |
1596 |
0 |
if (withHint) |
1597 |
|
{ |
1598 |
0 |
tt.append("<br>").append(BASE_TOOLTIP).append("</br>"); |
1599 |
|
} |
1600 |
0 |
return JvSwingUtils.wrapTooltip(true, tt.toString()); |
1601 |
|
} |
1602 |
|
|
|
|
| 0% |
Uncovered Elements: 39 (39) |
Complexity: 8 |
Complexity Density: 0.32 |
|
1603 |
0 |
public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,... |
1604 |
|
int w, int h) |
1605 |
|
{ |
1606 |
0 |
boolean thr = false; |
1607 |
0 |
StringBuilder tx = new StringBuilder(); |
1608 |
|
|
1609 |
0 |
if (gcol.isColourByAttribute()) |
1610 |
|
{ |
1611 |
0 |
tx.append(FeatureMatcher |
1612 |
|
.toAttributeDisplayName(gcol.getAttributeName())); |
1613 |
|
} |
1614 |
0 |
else if (!gcol.isColourByLabel()) |
1615 |
|
{ |
1616 |
0 |
tx.append(MessageManager.getString("label.score")); |
1617 |
|
} |
1618 |
0 |
tx.append(" "); |
1619 |
0 |
if (gcol.isAboveThreshold()) |
1620 |
|
{ |
1621 |
0 |
thr = true; |
1622 |
0 |
tx.append(">"); |
1623 |
|
} |
1624 |
0 |
if (gcol.isBelowThreshold()) |
1625 |
|
{ |
1626 |
0 |
thr = true; |
1627 |
0 |
tx.append("<"); |
1628 |
|
} |
1629 |
0 |
if (gcol.isColourByLabel()) |
1630 |
|
{ |
1631 |
0 |
if (thr) |
1632 |
|
{ |
1633 |
0 |
tx.append(" "); |
1634 |
|
} |
1635 |
0 |
if (!gcol.isColourByAttribute()) |
1636 |
|
{ |
1637 |
0 |
tx.append("Label"); |
1638 |
|
} |
1639 |
0 |
comp.setIcon(null); |
1640 |
|
} |
1641 |
|
else |
1642 |
|
{ |
1643 |
0 |
Color newColor = gcol.getMaxColour(); |
1644 |
0 |
comp.setBackground(newColor); |
1645 |
|
|
1646 |
0 |
Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); |
1647 |
0 |
comp.setIcon(ficon); |
1648 |
|
|
1649 |
|
|
1650 |
|
|
1651 |
|
|
1652 |
|
} |
1653 |
0 |
comp.setHorizontalAlignment(SwingConstants.CENTER); |
1654 |
0 |
comp.setText(tx.toString()); |
1655 |
|
} |
1656 |
|
|
1657 |
|
|
1658 |
|
|
1659 |
|
|
|
|
| 0% |
Uncovered Elements: 34 (34) |
Complexity: 15 |
Complexity Density: 0.71 |
|
1660 |
|
class FeatureTableModel extends AbstractTableModel |
1661 |
|
{ |
1662 |
|
private String[] columnNames = { |
1663 |
|
MessageManager.getString("label.feature_type"), |
1664 |
|
MessageManager.getString("action.colour"), |
1665 |
|
MessageManager.getString("label.configuration"), |
1666 |
|
MessageManager.getString("label.show") }; |
1667 |
|
|
1668 |
|
private Object[][] data; |
1669 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1670 |
0 |
FeatureTableModel(Object[][] data)... |
1671 |
|
{ |
1672 |
0 |
this.data = data; |
1673 |
|
} |
1674 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1675 |
0 |
public Object[][] getData()... |
1676 |
|
{ |
1677 |
0 |
return data; |
1678 |
|
} |
1679 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1680 |
0 |
public void setData(Object[][] data)... |
1681 |
|
{ |
1682 |
0 |
this.data = data; |
1683 |
|
} |
1684 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1685 |
0 |
@Override... |
1686 |
|
public int getColumnCount() |
1687 |
|
{ |
1688 |
0 |
return columnNames.length; |
1689 |
|
} |
1690 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1691 |
0 |
public Object[] getRow(int row)... |
1692 |
|
{ |
1693 |
0 |
return data[row]; |
1694 |
|
} |
1695 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1696 |
0 |
@Override... |
1697 |
|
public int getRowCount() |
1698 |
|
{ |
1699 |
0 |
return data.length; |
1700 |
|
} |
1701 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1702 |
0 |
@Override... |
1703 |
|
public String getColumnName(int col) |
1704 |
|
{ |
1705 |
0 |
return columnNames[col]; |
1706 |
|
} |
1707 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1708 |
0 |
@Override... |
1709 |
|
public Object getValueAt(int row, int col) |
1710 |
|
{ |
1711 |
0 |
return data[row][col]; |
1712 |
|
} |
1713 |
|
|
1714 |
|
|
1715 |
|
|
1716 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 4 |
Complexity Density: 0.44 |
|
1717 |
0 |
@Override... |
1718 |
|
public Class<?> getColumnClass(int c) |
1719 |
|
{ |
1720 |
0 |
switch (c) |
1721 |
|
{ |
1722 |
0 |
case TYPE_COLUMN: |
1723 |
0 |
return String.class; |
1724 |
0 |
case COLOUR_COLUMN: |
1725 |
0 |
return FeatureColour.class; |
1726 |
0 |
case FILTER_COLUMN: |
1727 |
0 |
return FeatureMatcherSet.class; |
1728 |
0 |
default: |
1729 |
0 |
return Boolean.class; |
1730 |
|
} |
1731 |
|
} |
1732 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1733 |
0 |
@Override... |
1734 |
|
public boolean isCellEditable(int row, int col) |
1735 |
|
{ |
1736 |
0 |
return col == 0 ? false : true; |
1737 |
|
} |
1738 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1739 |
0 |
@Override... |
1740 |
|
public void setValueAt(Object value, int row, int col) |
1741 |
|
{ |
1742 |
0 |
data[row][col] = value; |
1743 |
0 |
fireTableCellUpdated(row, col); |
1744 |
0 |
updateFeatureRenderer(data); |
1745 |
|
} |
1746 |
|
|
1747 |
|
} |
1748 |
|
|
|
|
| 0% |
Uncovered Elements: 30 (30) |
Complexity: 6 |
Complexity Density: 0.3 |
|
1749 |
|
class ColorRenderer extends JLabel implements TableCellRenderer |
1750 |
|
{ |
1751 |
|
Border unselectedBorder = null; |
1752 |
|
|
1753 |
|
Border selectedBorder = null; |
1754 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1755 |
0 |
public ColorRenderer()... |
1756 |
|
{ |
1757 |
0 |
setOpaque(true); |
1758 |
0 |
setHorizontalTextPosition(SwingConstants.CENTER); |
1759 |
0 |
setVerticalTextPosition(SwingConstants.CENTER); |
1760 |
|
} |
1761 |
|
|
|
|
| 0% |
Uncovered Elements: 25 (25) |
Complexity: 5 |
Complexity Density: 0.29 |
|
1762 |
0 |
@Override... |
1763 |
|
public Component getTableCellRendererComponent(JTable tbl, Object color, |
1764 |
|
boolean isSelected, boolean hasFocus, int row, int column) |
1765 |
|
{ |
1766 |
0 |
FeatureColourI cellColour = (FeatureColourI) color; |
1767 |
0 |
setOpaque(true); |
1768 |
0 |
setBackground(tbl.getBackground()); |
1769 |
0 |
if (!cellColour.isSimpleColour()) |
1770 |
|
{ |
1771 |
0 |
Rectangle cr = tbl.getCellRect(row, column, false); |
1772 |
0 |
FeatureSettings.renderGraduatedColor(this, cellColour, |
1773 |
|
(int) cr.getWidth(), (int) cr.getHeight()); |
1774 |
|
} |
1775 |
|
else |
1776 |
|
{ |
1777 |
0 |
this.setText(""); |
1778 |
0 |
this.setIcon(null); |
1779 |
0 |
setBackground(cellColour.getColour()); |
1780 |
|
} |
1781 |
0 |
if (isSelected) |
1782 |
|
{ |
1783 |
0 |
if (selectedBorder == null) |
1784 |
|
{ |
1785 |
0 |
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1786 |
|
tbl.getSelectionBackground()); |
1787 |
|
} |
1788 |
0 |
setBorder(selectedBorder); |
1789 |
|
} |
1790 |
|
else |
1791 |
|
{ |
1792 |
0 |
if (unselectedBorder == null) |
1793 |
|
{ |
1794 |
0 |
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1795 |
|
tbl.getBackground()); |
1796 |
|
} |
1797 |
0 |
setBorder(unselectedBorder); |
1798 |
|
} |
1799 |
|
|
1800 |
0 |
return this; |
1801 |
|
} |
1802 |
|
} |
1803 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 6 |
Complexity Density: 0.33 |
|
1804 |
|
class FilterRenderer extends JLabel implements TableCellRenderer |
1805 |
|
{ |
1806 |
|
javax.swing.border.Border unselectedBorder = null; |
1807 |
|
|
1808 |
|
javax.swing.border.Border selectedBorder = null; |
1809 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1810 |
0 |
public FilterRenderer()... |
1811 |
|
{ |
1812 |
0 |
setOpaque(true); |
1813 |
0 |
setHorizontalTextPosition(SwingConstants.CENTER); |
1814 |
0 |
setVerticalTextPosition(SwingConstants.CENTER); |
1815 |
|
} |
1816 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 5 |
Complexity Density: 0.33 |
|
1817 |
0 |
@Override... |
1818 |
|
public Component getTableCellRendererComponent(JTable tbl, |
1819 |
|
Object filter, boolean isSelected, boolean hasFocus, int row, |
1820 |
|
int column) |
1821 |
|
{ |
1822 |
0 |
FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; |
1823 |
0 |
setOpaque(true); |
1824 |
0 |
setBackground(tbl.getBackground()); |
1825 |
0 |
this.setIcon(null); |
1826 |
|
|
1827 |
0 |
if (theFilter != null) |
1828 |
|
{ |
1829 |
0 |
String asText = theFilter.toString(); |
1830 |
0 |
this.setText(asText); |
1831 |
|
} |
1832 |
|
|
1833 |
0 |
if (isSelected) |
1834 |
|
{ |
1835 |
0 |
if (selectedBorder == null) |
1836 |
|
{ |
1837 |
0 |
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1838 |
|
tbl.getSelectionBackground()); |
1839 |
|
} |
1840 |
0 |
setBorder(selectedBorder); |
1841 |
|
} |
1842 |
|
else |
1843 |
|
{ |
1844 |
0 |
if (unselectedBorder == null) |
1845 |
|
{ |
1846 |
0 |
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, |
1847 |
|
tbl.getBackground()); |
1848 |
|
} |
1849 |
0 |
setBorder(unselectedBorder); |
1850 |
|
} |
1851 |
|
|
1852 |
0 |
return this; |
1853 |
|
} |
1854 |
|
} |
1855 |
|
|
1856 |
|
|
1857 |
|
|
1858 |
|
|
1859 |
|
@param |
1860 |
|
@param |
1861 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
1862 |
0 |
public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)... |
1863 |
|
{ |
1864 |
0 |
int w = comp.getWidth(), h = comp.getHeight(); |
1865 |
0 |
if (w < 20) |
1866 |
|
{ |
1867 |
0 |
w = (int) comp.getPreferredSize().getWidth(); |
1868 |
0 |
h = (int) comp.getPreferredSize().getHeight(); |
1869 |
0 |
if (w < 20) |
1870 |
|
{ |
1871 |
0 |
w = 80; |
1872 |
0 |
h = 12; |
1873 |
|
} |
1874 |
|
} |
1875 |
0 |
renderGraduatedColor(comp, gcol, w, h); |
1876 |
|
} |
1877 |
|
|
1878 |
|
@SuppressWarnings("serial") |
|
|
| 0% |
Uncovered Elements: 70 (70) |
Complexity: 12 |
Complexity Density: 0.23 |
|
1879 |
|
class ColorEditor extends AbstractCellEditor |
1880 |
|
implements TableCellEditor, ActionListener |
1881 |
|
{ |
1882 |
|
FeatureColourI currentColor; |
1883 |
|
|
1884 |
|
FeatureTypeSettings chooser; |
1885 |
|
|
1886 |
|
String type; |
1887 |
|
|
1888 |
|
JButton button; |
1889 |
|
|
1890 |
|
protected static final String EDIT = "edit"; |
1891 |
|
|
1892 |
|
int rowSelected = 0; |
1893 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
1894 |
0 |
public ColorEditor()... |
1895 |
|
{ |
1896 |
|
|
1897 |
|
|
1898 |
|
|
1899 |
|
|
1900 |
0 |
button = new JButton(); |
1901 |
0 |
button.setActionCommand(EDIT); |
1902 |
0 |
button.addActionListener(this); |
1903 |
0 |
button.setBorderPainted(false); |
1904 |
|
} |
1905 |
|
|
1906 |
|
|
1907 |
|
|
1908 |
|
|
1909 |
|
|
|
|
| 0% |
Uncovered Elements: 33 (33) |
Complexity: 5 |
Complexity Density: 0.2 |
|
1910 |
0 |
@Override... |
1911 |
|
public void actionPerformed(ActionEvent e) |
1912 |
|
{ |
1913 |
0 |
if (button == e.getSource()) |
1914 |
|
{ |
1915 |
0 |
if (currentColor.isSimpleColour()) |
1916 |
|
{ |
1917 |
|
|
1918 |
|
|
1919 |
|
|
1920 |
0 |
String ttl = MessageManager |
1921 |
|
.formatMessage("label.select_colour_for", type); |
1922 |
0 |
Object last = (Boolean) table.getValueAt(selectedRow, |
1923 |
|
SHOW_COLUMN); |
1924 |
0 |
table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); |
1925 |
0 |
ColourChooserListener listener = new ColourChooserListener() |
1926 |
|
{ |
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
1927 |
0 |
@Override... |
1928 |
|
public void colourSelected(Color c) |
1929 |
|
{ |
1930 |
0 |
currentColor = new FeatureColour(c); |
1931 |
0 |
table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); |
1932 |
0 |
table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); |
1933 |
0 |
fireEditingStopped(); |
1934 |
|
} |
1935 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1936 |
0 |
@Override... |
1937 |
|
public void cancel() |
1938 |
|
{ |
1939 |
0 |
table.setValueAt(last, selectedRow, SHOW_COLUMN); |
1940 |
0 |
fireEditingStopped(); |
1941 |
|
} |
1942 |
|
}; |
1943 |
0 |
JalviewColourChooser.showColourChooser(button, ttl, |
1944 |
|
currentColor.getColour(), listener); |
1945 |
|
} |
1946 |
|
else |
1947 |
|
{ |
1948 |
|
|
1949 |
|
|
1950 |
|
|
1951 |
0 |
boolean last = (Boolean) table.getValueAt(selectedRow, |
1952 |
|
SHOW_COLUMN); |
1953 |
0 |
table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); |
1954 |
0 |
chooser = new FeatureTypeSettings(fr, type, last); |
1955 |
0 |
if (!Platform.isJS()) |
1956 |
|
|
1957 |
|
|
1958 |
|
|
1959 |
|
|
1960 |
|
|
1961 |
|
{ |
1962 |
0 |
chooser.setRequestFocusEnabled(true); |
1963 |
0 |
chooser.requestFocus(); |
1964 |
|
} |
1965 |
0 |
chooser.addActionListener(this); |
1966 |
0 |
fireEditingStopped(); |
1967 |
|
} |
1968 |
|
} |
1969 |
|
else |
1970 |
|
{ |
1971 |
|
|
1972 |
|
|
1973 |
|
|
1974 |
|
|
1975 |
|
|
1976 |
0 |
currentColor = fr.getFeatureColours().get(type); |
1977 |
0 |
FeatureMatcherSetI currentFilter = fr.getFeatureFilter(type); |
1978 |
0 |
if (currentFilter == null) |
1979 |
|
{ |
1980 |
0 |
currentFilter = new FeatureMatcherSet(); |
1981 |
|
} |
1982 |
0 |
Object[] data = ((FeatureTableModel) table.getModel()) |
1983 |
|
.getData()[rowSelected]; |
1984 |
0 |
data[COLOUR_COLUMN] = currentColor; |
1985 |
0 |
data[FILTER_COLUMN] = currentFilter; |
1986 |
0 |
fireEditingStopped(); |
1987 |
|
|
1988 |
|
|
1989 |
|
|
1990 |
|
|
1991 |
0 |
table.validate(); |
1992 |
0 |
table.repaint(); |
1993 |
|
} |
1994 |
|
} |
1995 |
|
|
1996 |
|
|
1997 |
|
|
1998 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1999 |
0 |
@Override... |
2000 |
|
protected void fireEditingStopped() |
2001 |
|
{ |
2002 |
0 |
super.fireEditingStopped(); |
2003 |
|
} |
2004 |
|
|
2005 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2006 |
0 |
@Override... |
2007 |
|
public Object getCellEditorValue() |
2008 |
|
{ |
2009 |
0 |
return currentColor; |
2010 |
|
} |
2011 |
|
|
2012 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 2 |
Complexity Density: 0.12 |
|
2013 |
0 |
@Override... |
2014 |
|
public Component getTableCellEditorComponent(JTable theTable, |
2015 |
|
Object value, boolean isSelected, int row, int column) |
2016 |
|
{ |
2017 |
0 |
currentColor = (FeatureColourI) value; |
2018 |
0 |
this.rowSelected = row; |
2019 |
0 |
type = table.getValueAt(row, TYPE_COLUMN).toString(); |
2020 |
0 |
button.setOpaque(true); |
2021 |
0 |
button.setBackground(FeatureSettings.this.getBackground()); |
2022 |
0 |
if (!currentColor.isSimpleColour()) |
2023 |
|
{ |
2024 |
0 |
JLabel btn = new JLabel(); |
2025 |
0 |
btn.setSize(button.getSize()); |
2026 |
0 |
FeatureSettings.renderGraduatedColor(btn, currentColor); |
2027 |
0 |
button.setBackground(btn.getBackground()); |
2028 |
0 |
button.setIcon(btn.getIcon()); |
2029 |
0 |
button.setText(btn.getText()); |
2030 |
|
} |
2031 |
|
else |
2032 |
|
{ |
2033 |
0 |
button.setText(""); |
2034 |
0 |
button.setIcon(null); |
2035 |
0 |
button.setBackground(currentColor.getColour()); |
2036 |
|
} |
2037 |
0 |
return button; |
2038 |
|
} |
2039 |
|
} |
2040 |
|
|
2041 |
|
|
2042 |
|
|
2043 |
|
|
2044 |
|
|
2045 |
|
|
2046 |
|
|
2047 |
|
@SuppressWarnings("serial") |
|
|
| 0% |
Uncovered Elements: 48 (48) |
Complexity: 8 |
Complexity Density: 0.22 |
|
2048 |
|
class FilterEditor extends AbstractCellEditor |
2049 |
|
implements TableCellEditor, ActionListener |
2050 |
|
{ |
2051 |
|
|
2052 |
|
FeatureMatcherSetI currentFilter; |
2053 |
|
|
2054 |
|
Point lastLocation; |
2055 |
|
|
2056 |
|
String type; |
2057 |
|
|
2058 |
|
JButton button; |
2059 |
|
|
2060 |
|
protected static final String EDIT = "edit"; |
2061 |
|
|
2062 |
|
int rowSelected = 0; |
2063 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2064 |
0 |
public FilterEditor()... |
2065 |
|
{ |
2066 |
0 |
button = new JButton(); |
2067 |
0 |
button.setActionCommand(EDIT); |
2068 |
0 |
button.addActionListener(this); |
2069 |
0 |
button.setBorderPainted(false); |
2070 |
|
} |
2071 |
|
|
2072 |
|
|
2073 |
|
|
2074 |
|
|
|
|
| 0% |
Uncovered Elements: 31 (31) |
Complexity: 5 |
Complexity Density: 0.22 |
|
2075 |
0 |
@Override... |
2076 |
|
public void actionPerformed(ActionEvent e) |
2077 |
|
{ |
2078 |
0 |
if (button == e.getSource()) |
2079 |
|
{ |
2080 |
0 |
boolean last = fr.getFeaturesDisplayed().isVisible(type); |
2081 |
0 |
((FeatureTableModel) table.getModel()).setValueAt(Boolean.TRUE, |
2082 |
|
rowSelected, SHOW_COLUMN); |
2083 |
0 |
FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type, |
2084 |
|
last); |
2085 |
0 |
chooser.addActionListener(this); |
2086 |
0 |
chooser.setRequestFocusEnabled(true); |
2087 |
0 |
chooser.requestFocus(); |
2088 |
0 |
if (lastLocation != null) |
2089 |
|
{ |
2090 |
|
|
2091 |
0 |
chooser.setBounds(lastLocation.x, lastLocation.y, |
2092 |
|
chooser.getWidth(), chooser.getHeight()); |
2093 |
0 |
chooser.validate(); |
2094 |
|
} |
2095 |
0 |
fireEditingStopped(); |
2096 |
|
} |
2097 |
0 |
else if (e.getSource() instanceof Component) |
2098 |
|
{ |
2099 |
|
|
2100 |
|
|
2101 |
|
|
2102 |
|
|
2103 |
|
|
2104 |
|
|
2105 |
0 |
FeatureColourI currentColor = fr.getFeatureColours().get(type); |
2106 |
0 |
currentFilter = fr.getFeatureFilter(type); |
2107 |
0 |
if (currentFilter == null) |
2108 |
|
{ |
2109 |
0 |
currentFilter = new FeatureMatcherSet(); |
2110 |
|
} |
2111 |
|
|
2112 |
0 |
Object[] data = ((FeatureTableModel) table.getModel()) |
2113 |
|
.getData()[rowSelected]; |
2114 |
0 |
data[COLOUR_COLUMN] = currentColor; |
2115 |
0 |
data[FILTER_COLUMN] = currentFilter; |
2116 |
0 |
data[SHOW_COLUMN] = fr.getFeaturesDisplayed().isVisible(type); |
2117 |
|
|
2118 |
0 |
fireEditingStopped(); |
2119 |
|
|
2120 |
|
|
2121 |
|
|
2122 |
|
|
2123 |
0 |
table.validate(); |
2124 |
0 |
table.repaint(); |
2125 |
|
} |
2126 |
|
} |
2127 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2128 |
0 |
@Override... |
2129 |
|
public Object getCellEditorValue() |
2130 |
|
{ |
2131 |
0 |
return currentFilter; |
2132 |
|
} |
2133 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
|
2134 |
0 |
@Override... |
2135 |
|
public Component getTableCellEditorComponent(JTable theTable, |
2136 |
|
Object value, boolean isSelected, int row, int column) |
2137 |
|
{ |
2138 |
0 |
currentFilter = (FeatureMatcherSetI) value; |
2139 |
0 |
this.rowSelected = row; |
2140 |
0 |
type = table.getValueAt(row, TYPE_COLUMN).toString(); |
2141 |
0 |
button.setOpaque(true); |
2142 |
0 |
button.setBackground(FeatureSettings.this.getBackground()); |
2143 |
0 |
button.setText(currentFilter.toString()); |
2144 |
0 |
button.setIcon(null); |
2145 |
0 |
return button; |
2146 |
|
} |
2147 |
|
} |
2148 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
2149 |
0 |
public boolean isOpen()... |
2150 |
|
{ |
2151 |
0 |
if (af.getSplitViewContainer() != null) |
2152 |
|
{ |
2153 |
0 |
return af.getSplitViewContainer().isFeatureSettingsOpen(); |
2154 |
|
} |
2155 |
0 |
return frame != null && !frame.isClosed(); |
2156 |
|
} |
2157 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
|
2158 |
0 |
@Override... |
2159 |
|
public void revert() |
2160 |
|
{ |
2161 |
0 |
fr.setTransparency(originalTransparency); |
2162 |
0 |
fr.setFeatureFilters(originalFilters); |
2163 |
0 |
updateFeatureRenderer(originalData); |
2164 |
0 |
af.getViewport().setViewStyle(originalViewStyle); |
2165 |
0 |
updateTransparencySliderFromFR(); |
2166 |
0 |
updateComplementButtons(); |
2167 |
0 |
refreshDisplay(); |
2168 |
|
} |
2169 |
|
} |
2170 |
|
|
|
|
| 0% |
Uncovered Elements: 36 (36) |
Complexity: 7 |
Complexity Density: 0.27 |
|
2171 |
|
class FeatureIcon implements Icon |
2172 |
|
{ |
2173 |
|
FeatureColourI gcol; |
2174 |
|
|
2175 |
|
Color backg; |
2176 |
|
|
2177 |
|
boolean midspace = false; |
2178 |
|
|
2179 |
|
int width = 50, height = 20; |
2180 |
|
|
2181 |
|
int s1, e1; |
2182 |
|
|
2183 |
|
Color mpcolour = Color.white; |
2184 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 2 |
Complexity Density: 0.2 |
|
2185 |
0 |
FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)... |
2186 |
|
{ |
2187 |
0 |
gcol = gfc; |
2188 |
0 |
backg = bg; |
2189 |
0 |
width = w; |
2190 |
0 |
height = h; |
2191 |
0 |
midspace = mspace; |
2192 |
0 |
if (midspace) |
2193 |
|
{ |
2194 |
0 |
s1 = width / 3; |
2195 |
0 |
e1 = s1 * 2; |
2196 |
|
} |
2197 |
|
else |
2198 |
|
{ |
2199 |
0 |
s1 = width / 2; |
2200 |
0 |
e1 = s1; |
2201 |
|
} |
2202 |
|
} |
2203 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2204 |
0 |
@Override... |
2205 |
|
public int getIconWidth() |
2206 |
|
{ |
2207 |
0 |
return width; |
2208 |
|
} |
2209 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2210 |
0 |
@Override... |
2211 |
|
public int getIconHeight() |
2212 |
|
{ |
2213 |
0 |
return height; |
2214 |
|
} |
2215 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 3 |
Complexity Density: 0.21 |
|
2216 |
0 |
@Override... |
2217 |
|
public void paintIcon(Component c, Graphics g, int x, int y) |
2218 |
|
{ |
2219 |
|
|
2220 |
0 |
if (gcol.isColourByLabel()) |
2221 |
|
{ |
2222 |
0 |
g.setColor(backg); |
2223 |
0 |
g.fillRect(0, 0, width, height); |
2224 |
|
|
2225 |
0 |
g.setColor(gcol.getMaxColour()); |
2226 |
|
|
2227 |
0 |
g.setFont(new Font("Verdana", Font.PLAIN, 9)); |
2228 |
|
|
2229 |
|
|
2230 |
|
|
2231 |
|
|
2232 |
|
|
2233 |
|
|
2234 |
0 |
g.drawString(MessageManager.getString("label.label"), 0, 0); |
2235 |
|
|
2236 |
|
} |
2237 |
|
else |
2238 |
|
{ |
2239 |
0 |
Color minCol = gcol.getMinColour(); |
2240 |
0 |
g.setColor(minCol); |
2241 |
0 |
g.fillRect(0, 0, s1, height); |
2242 |
0 |
if (midspace) |
2243 |
|
{ |
2244 |
0 |
g.setColor(Color.white); |
2245 |
0 |
g.fillRect(s1, 0, e1 - s1, height); |
2246 |
|
} |
2247 |
0 |
g.setColor(gcol.getMaxColour()); |
2248 |
|
|
2249 |
0 |
g.fillRect(e1, 0, width - e1, height); |
2250 |
|
} |
2251 |
|
} |
2252 |
|
} |