Coverage Report
File FeatureSettings.java
Coverage histogram
49% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| FeatureSettings | 121 | 570 | 173 | ||
| FeatureSettings.FeatureTableModel | 1660 | 21 | 15 | ||
| FeatureSettings.ColorRenderer | 1749 | 20 | 6 | ||
| FeatureSettings.FilterRenderer | 1804 | 18 | 6 | ||
| FeatureSettings.ColorEditor | 1879 | 53 | 12 | ||
| FeatureSettings.FilterEditor | 2048 | 36 | 8 | ||
| FeatureIcon | 2171 | 26 | 7 |
Contributing tests
This file is covered by 2 tests.
.
Source view
| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.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 | ||
| 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 | * column indices of fields in Feature Settings table | |
| 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 | * 'original' fields hold settings to restore on Cancel | |
| 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 | * when true, constructor is still executing - so ignore UI events | |
| 178 | */ | |
| 179 | protected volatile boolean inConstruction = true; | |
| 180 | ||
| 181 | int selectedRow = -1; | |
| 182 | ||
| 183 | boolean resettingTable = false; | |
| 184 | ||
| 185 | /* | |
| 186 | * true when Feature Settings are updating from feature renderer | |
| 187 | */ | |
| 188 | private boolean handlingUpdate = false; | |
| 189 | ||
| 190 | /* | |
| 191 | * a change listener to ensure the dialog is updated if | |
| 192 | * FeatureRenderer discovers new features | |
| 193 | */ | |
| 194 | private PropertyChangeListener change; | |
| 195 | ||
| 196 | /* | |
| 197 | * holds {featureCount, totalExtent} for each feature type | |
| 198 | */ | |
| 199 | Map<String, float[]> typeWidth = null; | |
| 200 | ||
| 201 | 1 |  private void storeOriginalSettings() |
| 202 | { | |
| 203 | // save transparency for restore on Cancel | |
| 204 | 1 | originalTransparency = fr.getTransparency(); |
| 205 | ||
| 206 | 1 | updateTransparencySliderFromFR(); |
| 207 | ||
| 208 | 1 | originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy |
| 209 | 1 | originalViewStyle = new ViewStyle(af.viewport.getViewStyle()); |
| 210 | } | |
| 211 | ||
| 212 | 1 | private void updateTransparencySliderFromFR() |
| 213 | { | |
| 214 | 1 | boolean incon = inConstruction; |
| 215 | 1 | inConstruction = true; |
| 216 | ||
| 217 | 1 | int transparencyAsPercent = (int) (fr.getTransparency() * 100); |
| 218 | 1 | transparency.setValue(100 - transparencyAsPercent); |
| 219 | 1 | inConstruction = incon; |
| 220 | } | |
| 221 | ||
| 222 | /** | |
| 223 | * Constructor | |
| 224 | * | |
| 225 | * @param af | |
| 226 | */ | |
| 227 | 1 | public FeatureSettings(AlignFrame alignFrame) |
| 228 | { | |
| 229 | 1 | this.af = alignFrame; |
| 230 | 1 | fr = af.getFeatureRenderer(); |
| 231 | ||
| 232 | 1 | storeOriginalSettings(); |
| 233 | ||
| 234 | 1 | try |
| 235 | { | |
| 236 | 1 | jbInit(); |
| 237 | } catch (Exception ex) | |
| 238 | { | |
| 239 | 0 | ex.printStackTrace(); |
| 240 | } | |
| 241 | ||
| 242 | 1 | table = new JTable() |
| 243 | { | |
| 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 | * Position the tooltip near the bottom edge of, and half way across, the | |
| 279 | * current cell | |
| 280 | */ | |
| 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 | 1 | JTableHeader tableHeader = table.getTableHeader(); |
| 293 | 1 | tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12)); |
| 294 | 1 | tableHeader.setReorderingAllowed(false); |
| 295 | 1 | table.setFont(new Font("Verdana", Font.PLAIN, 12)); |
| 296 | 1 | ToolTipManager.sharedInstance().registerComponent(table); |
| 297 | 1 | table.setDefaultEditor(FeatureColour.class, new ColorEditor()); |
| 298 | 1 | table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); |
| 299 | ||
| 300 | 1 | table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor()); |
| 301 | 1 | table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer()); |
| 302 | ||
| 303 | 1 | TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75, |
| 304 | new ColorRenderer(), new ColorEditor()); | |
| 305 | 1 | table.addColumn(colourColumn); |
| 306 | ||
| 307 | 1 | TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75, |
| 308 | new FilterRenderer(), new FilterEditor()); | |
| 309 | 1 | table.addColumn(filterColumn); |
| 310 | ||
| 311 | 1 | table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); |
| 312 | ||
| 313 | 1 | table.addMouseListener(new MouseAdapter() |
| 314 | { | |
| 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 | // isPopupTrigger fires on mouseReleased on Windows | |
| 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 | 1 | table.addMouseMotionListener(new MouseMotionAdapter() |
| 353 | { | |
| 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 | * reposition 'selectedRow' to 'newRow' (the dragged to location) | |
| 362 | * this could be more than one row away for a very fast drag action | |
| 363 | * so just swap it with adjacent rows until we get it there | |
| 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 | // table.setToolTipText(JvSwingUtils.wrapTooltip(true, | |
| 381 | // MessageManager.getString("label.feature_settings_click_drag"))); | |
| 382 | 1 | scrollPane.setViewportView(table); |
| 383 | ||
| 384 | 1 | if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) |
| 385 | { | |
| 386 | 1 | fr.findAllFeatures(true); // display everything! |
| 387 | } | |
| 388 | ||
| 389 | 1 | discoverAllFeatureData(); |
| 390 | 1 | final FeatureSettings fs = this; |
| 391 | 1 | fr.addPropertyChangeListener(change = new PropertyChangeListener() |
| 392 | { | |
| 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 | // new groups may be added with new sequence feature types only | |
| 401 | 0 | fs.handlingUpdate = false; |
| 402 | } | |
| 403 | } | |
| 404 | ||
| 405 | }); | |
| 406 | ||
| 407 | 1 | SplitContainerI splitframe = af.getSplitViewContainer(); |
| 408 | 1 | if (splitframe != null) |
| 409 | { | |
| 410 | 0 | frame = null; // keeps eclipse happy |
| 411 | 0 | splitframe.addFeatureSettingsUI(this); |
| 412 | } | |
| 413 | else | |
| 414 | { | |
| 415 | 1 | frame = new JInternalFrame(); |
| 416 | 1 | frame.setContentPane(this); |
| 417 | 1 | frame.setFrameIcon(null); |
| 418 | 1 | Rectangle bounds = af.getFeatureSettingsGeometry(); |
| 419 | 1 | String title; |
| 420 | 1 | 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 | 1 | title = MessageManager.getString("label.sequence_feature_settings"); |
| 430 | } | |
| 431 | 1 | if (bounds == null) |
| 432 | { | |
| 433 | 1 | if (Platform.isAMacAndNotJS()) |
| 434 | { | |
| 435 | 0 | Desktop.addInternalFrame(frame, title, 600, 480); |
| 436 | } | |
| 437 | else | |
| 438 | { | |
| 439 | 1 | 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 | 1 | frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); |
| 450 | ||
| 451 | 1 | frame.addInternalFrameListener( |
| 452 | new javax.swing.event.InternalFrameAdapter() | |
| 453 | { | |
| 454 | 1 | @Override |
| 455 | public void internalFrameClosed( | |
| 456 | javax.swing.event.InternalFrameEvent evt) | |
| 457 | { | |
| 458 | 1 | featureSettings_isClosed(); |
| 459 | }; | |
| 460 | }); | |
| 461 | 1 | frame.setLayer(JLayeredPane.PALETTE_LAYER); |
| 462 | } | |
| 463 | 1 | inConstruction = false; |
| 464 | } | |
| 465 | ||
| 466 | /** | |
| 467 | * Sets the state of buttons to show complement features from viewport | |
| 468 | * settings | |
| 469 | */ | |
| 470 | 1 | private void updateComplementButtons() |
| 471 | { | |
| 472 | 1 | showComplement.setSelected(af.getViewport().isShowComplementFeatures()); |
| 473 | 1 | showComplementOnTop |
| 474 | .setSelected(af.getViewport().isShowComplementFeaturesOnTop()); | |
| 475 | } | |
| 476 | ||
| 477 | 0 | @Override |
| 478 | public AlignViewControllerGuiI getAlignframe() | |
| 479 | { | |
| 480 | 0 | return af; |
| 481 | } | |
| 482 | ||
| 483 | 1 | @Override |
| 484 | public void featureSettings_isClosed() | |
| 485 | { | |
| 486 | 1 | fr.removePropertyChangeListener(change); |
| 487 | 1 | change = null; |
| 488 | } | |
| 489 | ||
| 490 | /** | |
| 491 | * Constructs and shows a popup menu of possible actions on the selected row | |
| 492 | * and feature type | |
| 493 | * | |
| 494 | * @param rowSelected | |
| 495 | * @param type | |
| 496 | * @param typeCol | |
| 497 | * @param pt | |
| 498 | */ | |
| 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 | { | |
| 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 | { | |
| 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 | { | |
| 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 | { | |
| 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 | { | |
| 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 | { | |
| 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 | * Sort the sequences in the alignment by the number of features for the given | |
| 584 | * feature types (or all features if null) | |
| 585 | * | |
| 586 | * @param featureTypes | |
| 587 | */ | |
| 588 | 0 | protected void sortByDensity(List<String> featureTypes) |
| 589 | { | |
| 590 | 0 | af.avc.sortAlignmentByFeatureDensity(featureTypes); |
| 591 | } | |
| 592 | ||
| 593 | /** | |
| 594 | * Sort the sequences in the alignment by average score for the given feature | |
| 595 | * types (or all features if null) | |
| 596 | * | |
| 597 | * @param featureTypes | |
| 598 | */ | |
| 599 | 0 | protected void sortByScore(List<String> featureTypes) |
| 600 | { | |
| 601 | 0 | af.avc.sortAlignmentByFeatureScore(featureTypes); |
| 602 | } | |
| 603 | ||
| 604 | /** | |
| 605 | * Returns true if at least one feature type is visible. Else shows a warning | |
| 606 | * dialog and returns false. | |
| 607 | * | |
| 608 | * @param title | |
| 609 | * @return | |
| 610 | */ | |
| 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 | ||
| 623 | 1 | @Override |
| 624 | synchronized public void discoverAllFeatureData() | |
| 625 | { | |
| 626 | 1 | Set<String> allGroups = new HashSet<>(); |
| 627 | 1 | AlignmentI alignment = af.getViewport().getAlignment(); |
| 628 | ||
| 629 | 2 | for (int i = 0; i < alignment.getHeight(); i++) |
| 630 | { | |
| 631 | 1 | SequenceI seq = alignment.getSequenceAt(i); |
| 632 | 1 | for (String group : seq.getFeatures().getFeatureGroups(true)) |
| 633 | { | |
| 634 | 1 | if (group != null && !allGroups.contains(group)) |
| 635 | { | |
| 636 | 1 | allGroups.add(group); |
| 637 | 1 | checkGroupState(group); |
| 638 | } | |
| 639 | } | |
| 640 | } | |
| 641 | ||
| 642 | 1 | resetTable(null); |
| 643 | ||
| 644 | 1 | validate(); |
| 645 | } | |
| 646 | ||
| 647 | /** | |
| 648 | * Synchronise gui group list and check visibility of group | |
| 649 | * | |
| 650 | * @param group | |
| 651 | * @return true if group is visible | |
| 652 | */ | |
| 653 | 3 | private boolean checkGroupState(String group) |
| 654 | { | |
| 655 | 3 | boolean visible = fr.checkGroupVisibility(group, true); |
| 656 | ||
| 657 | 3 | for (int g = 0; g < groupPanel.getComponentCount(); g++) |
| 658 | { | |
| 659 | 2 | if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group)) |
| 660 | { | |
| 661 | 2 | ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible); |
| 662 | 2 | return visible; |
| 663 | } | |
| 664 | } | |
| 665 | ||
| 666 | 1 | final String grp = group; |
| 667 | 1 | final JCheckBox check = new JCheckBox(group, visible); |
| 668 | 1 | check.setFont(new Font("Serif", Font.BOLD, 12)); |
| 669 | 1 | check.setToolTipText(group); |
| 670 | 1 | check.addItemListener(new ItemListener() |
| 671 | { | |
| 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 | 1 | groupPanel.add(check); |
| 681 | 1 | return visible; |
| 682 | } | |
| 683 | ||
| 684 | 2 | synchronized void resetTable(String[] groupChanged) |
| 685 | { | |
| 686 | 2 | if (resettingTable) |
| 687 | { | |
| 688 | 0 | return; |
| 689 | } | |
| 690 | 2 | resettingTable = true; |
| 691 | 2 | typeWidth = new Hashtable<>(); |
| 692 | // TODO: change avWidth calculation to 'per-sequence' average and use long | |
| 693 | // rather than float | |
| 694 | ||
| 695 | 2 | Set<String> displayableTypes = new HashSet<>(); |
| 696 | 2 | Set<String> foundGroups = new HashSet<>(); |
| 697 | ||
| 698 | /* | |
| 699 | * determine which feature types may be visible depending on | |
| 700 | * which groups are selected, and recompute average width data | |
| 701 | */ | |
| 702 | 4 | for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) |
| 703 | { | |
| 704 | ||
| 705 | 2 | SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i); |
| 706 | ||
| 707 | /* | |
| 708 | * get the sequence's groups for positional features | |
| 709 | * and keep track of which groups are visible | |
| 710 | */ | |
| 711 | 2 | Set<String> groups = seq.getFeatures().getFeatureGroups(true); |
| 712 | 2 | Set<String> visibleGroups = new HashSet<>(); |
| 713 | 2 | for (String group : groups) |
| 714 | { | |
| 715 | 2 | if (group == null || checkGroupState(group)) |
| 716 | { | |
| 717 | 2 | visibleGroups.add(group); |
| 718 | } | |
| 719 | } | |
| 720 | 2 | foundGroups.addAll(groups); |
| 721 | ||
| 722 | /* | |
| 723 | * get distinct feature types for visible groups | |
| 724 | * record distinct visible types, and their count and total length | |
| 725 | */ | |
| 726 | 2 | Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true, |
| 727 | visibleGroups.toArray(new String[visibleGroups.size()])); | |
| 728 | 2 | for (String type : types) |
| 729 | { | |
| 730 | 10 | displayableTypes.add(type); |
| 731 | 10 | float[] avWidth = typeWidth.get(type); |
| 732 | 10 | if (avWidth == null) |
| 733 | { | |
| 734 | 10 | avWidth = new float[2]; |
| 735 | 10 | typeWidth.put(type, avWidth); |
| 736 | } | |
| 737 | // todo this could include features with a non-visible group | |
| 738 | // - do we greatly care? | |
| 739 | // todo should we include non-displayable features here, and only | |
| 740 | // update when features are added? | |
| 741 | 10 | avWidth[0] += seq.getFeatures().getFeatureCount(true, type); |
| 742 | 10 | avWidth[1] += seq.getFeatures().getTotalFeatureLength(type); |
| 743 | } | |
| 744 | } | |
| 745 | ||
| 746 | 2 | Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; |
| 747 | 2 | int dataIndex = 0; |
| 748 | ||
| 749 | 2 | if (fr.hasRenderOrder()) |
| 750 | { | |
| 751 | 2 | if (!handlingUpdate) |
| 752 | { | |
| 753 | 2 | fr.findAllFeatures(groupChanged != null); // prod to update |
| 754 | // colourschemes. but don't | |
| 755 | // affect display | |
| 756 | // First add the checks in the previous render order, | |
| 757 | // in case the window has been closed and reopened | |
| 758 | } | |
| 759 | 2 | List<String> frl = fr.getRenderOrder(); |
| 760 | 12 | for (int ro = frl.size() - 1; ro > -1; ro--) |
| 761 | { | |
| 762 | 10 | String type = frl.get(ro); |
| 763 | ||
| 764 | 10 | if (!displayableTypes.contains(type)) |
| 765 | { | |
| 766 | 0 | continue; |
| 767 | } | |
| 768 | ||
| 769 | 10 | data[dataIndex][TYPE_COLUMN] = type; |
| 770 | 10 | data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type); |
| 771 | 10 | FeatureMatcherSetI featureFilter = fr.getFeatureFilter(type); |
| 772 | 10 | data[dataIndex][FILTER_COLUMN] = featureFilter == null |
| 773 | ? new FeatureMatcherSet() | |
| 774 | : featureFilter; | |
| 775 | 10 | data[dataIndex][SHOW_COLUMN] = Boolean.valueOf( |
| 776 | af.getViewport().getFeaturesDisplayed().isVisible(type)); | |
| 777 | 10 | dataIndex++; |
| 778 | 10 | displayableTypes.remove(type); |
| 779 | } | |
| 780 | } | |
| 781 | ||
| 782 | /* | |
| 783 | * process any extra features belonging only to | |
| 784 | * a group which was just selected | |
| 785 | */ | |
| 786 | 2 | 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 | // "Colour has been updated in another view!!" | |
| 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 | 2 | if (originalData == null) |
| 808 | { | |
| 809 | 1 | originalData = new Object[data.length][COLUMN_COUNT]; |
| 810 | 6 | for (int i = 0; i < data.length; i++) |
| 811 | { | |
| 812 | 5 | System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); |
| 813 | } | |
| 814 | } | |
| 815 | else | |
| 816 | { | |
| 817 | 1 | updateOriginalData(data); |
| 818 | } | |
| 819 | ||
| 820 | 2 | table.setModel(new FeatureTableModel(data)); |
| 821 | 2 | table.getColumnModel().getColumn(0).setPreferredWidth(200); |
| 822 | ||
| 823 | 2 | groupPanel.setLayout( |
| 824 | new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4)); | |
| 825 | 2 | pruneGroups(foundGroups); |
| 826 | 2 | groupPanel.validate(); |
| 827 | ||
| 828 | 2 | updateFeatureRenderer(data, groupChanged != null); |
| 829 | 2 | resettingTable = false; |
| 830 | } | |
| 831 | ||
| 832 | /** | |
| 833 | * Updates 'originalData' (used for restore on Cancel) if we detect that | |
| 834 | * changes have been made outwith this dialog | |
| 835 | * <ul> | |
| 836 | * <li>a new feature type added (and made visible)</li> | |
| 837 | * <li>a feature colour changed (in the Amend Features dialog)</li> | |
| 838 | * </ul> | |
| 839 | * | |
| 840 | * @param foundData | |
| 841 | */ | |
| 842 | 1 | protected void updateOriginalData(Object[][] foundData) |
| 843 | { | |
| 844 | // todo LinkedHashMap instead of Object[][] would be nice | |
| 845 | ||
| 846 | 1 | Object[][] currentData = ((FeatureTableModel) table.getModel()) |
| 847 | .getData(); | |
| 848 | 1 | for (Object[] row : foundData) |
| 849 | { | |
| 850 | 5 | String type = (String) row[TYPE_COLUMN]; |
| 851 | 5 | boolean found = false; |
| 852 | 5 | for (Object[] current : currentData) |
| 853 | { | |
| 854 | 15 | if (type.equals(current[TYPE_COLUMN])) |
| 855 | { | |
| 856 | 5 | found = true; |
| 857 | /* | |
| 858 | * currently dependent on object equality here; | |
| 859 | * really need an equals method on FeatureColour | |
| 860 | */ | |
| 861 | 5 | if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN])) |
| 862 | { | |
| 863 | /* | |
| 864 | * feature colour has changed externally - update originalData | |
| 865 | */ | |
| 866 | 5 | for (Object[] original : originalData) |
| 867 | { | |
| 868 | 15 | if (type.equals(original[TYPE_COLUMN])) |
| 869 | { | |
| 870 | 5 | original[COLOUR_COLUMN] = row[COLOUR_COLUMN]; |
| 871 | 5 | break; |
| 872 | } | |
| 873 | } | |
| 874 | } | |
| 875 | 5 | break; |
| 876 | } | |
| 877 | } | |
| 878 | 5 | if (!found) |
| 879 | { | |
| 880 | /* | |
| 881 | * new feature detected - add to original data (on top) | |
| 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 | * Remove from the groups panel any checkboxes for groups that are not in the | |
| 898 | * foundGroups set. This enables removing a group from the display when the | |
| 899 | * last feature in that group is deleted. | |
| 900 | * | |
| 901 | * @param foundGroups | |
| 902 | */ | |
| 903 | 2 | protected void pruneGroups(Set<String> foundGroups) |
| 904 | { | |
| 905 | 4 | for (int g = 0; g < groupPanel.getComponentCount(); g++) |
| 906 | { | |
| 907 | 2 | JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g); |
| 908 | 2 | if (!foundGroups.contains(checkbox.getText())) |
| 909 | { | |
| 910 | 0 | groupPanel.remove(checkbox); |
| 911 | } | |
| 912 | } | |
| 913 | } | |
| 914 | ||
| 915 | /** | |
| 916 | * reorder data based on the featureRenderers global priority list. | |
| 917 | * | |
| 918 | * @param data | |
| 919 | */ | |
| 920 | 1 | private void ensureOrder(Object[][] data) |
| 921 | { | |
| 922 | 1 | boolean sort = false; |
| 923 | 1 | float[] order = new float[data.length]; |
| 924 | 6 | for (int i = 0; i < order.length; i++) |
| 925 | { | |
| 926 | 5 | order[i] = fr.getOrder(data[i][0].toString()); |
| 927 | 5 | if (order[i] < 0) |
| 928 | { | |
| 929 | 0 | order[i] = fr.setOrder(data[i][0].toString(), i / order.length); |
| 930 | } | |
| 931 | 5 | if (i > 1) |
| 932 | { | |
| 933 | 3 | sort = sort || order[i - 1] > order[i]; |
| 934 | } | |
| 935 | } | |
| 936 | 1 | if (sort) |
| 937 | { | |
| 938 | 0 | jalview.util.QuickSort.sort(order, data); |
| 939 | } | |
| 940 | } | |
| 941 | ||
| 942 | /** | |
| 943 | * Offers a file chooser dialog, and then loads the feature colours and | |
| 944 | * filters from file in XML format and unmarshals to Jalview feature settings | |
| 945 | */ | |
| 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 | ||
| 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 | ||
| 969 | 1 | public static void loadFeatureSettingsFile( |
| 970 | FeatureRenderer featureRenderer, Object fileObject, | |
| 971 | DataSourceType sourceType) throws Exception | |
| 972 | { | |
| 973 | 1 | FileParse fp = new FileParse(fileObject, sourceType); |
| 974 | 1 | loadFeatureSettingsFile(featureRenderer, fp.getReader()); |
| 975 | } | |
| 976 | ||
| 977 | 1 | private static boolean loadFeatureSettingsFile(FeatureRenderer fr, |
| 978 | Reader in) throws Exception | |
| 979 | { | |
| 980 | 1 | JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.jalview"); |
| 981 | 1 | javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); |
| 982 | 1 | XMLStreamReader streamReader = XMLInputFactory.newInstance() |
| 983 | .createXMLStreamReader(in); | |
| 984 | 1 | JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader, |
| 985 | JalviewUserColours.class); | |
| 986 | 1 | JalviewUserColours jucs = jbe.getValue(); |
| 987 | ||
| 988 | // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); | |
| 989 | ||
| 990 | /* | |
| 991 | * load feature colours | |
| 992 | */ | |
| 993 | 6 | for (int i = jucs.getColour().size() - 1; i >= 0; i--) |
| 994 | { | |
| 995 | 5 | Colour newcol = jucs.getColour().get(i); |
| 996 | 5 | FeatureColourI colour = jalview.project.Jalview2XML |
| 997 | .parseColour(newcol); | |
| 998 | 5 | fr.setColour(newcol.getName(), colour); |
| 999 | 5 | fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); |
| 1000 | } | |
| 1001 | ||
| 1002 | /* | |
| 1003 | * load feature filters; loaded filters will replace any that are | |
| 1004 | * currently defined, other defined filters are left unchanged | |
| 1005 | */ | |
| 1006 | 4 | for (int i = 0; i < jucs.getFilter().size(); i++) |
| 1007 | { | |
| 1008 | 3 | Filter filterModel = jucs.getFilter().get(i); |
| 1009 | 3 | String featureType = filterModel.getFeatureType(); |
| 1010 | 3 | FeatureMatcherSetI filter = jalview.project.Jalview2XML |
| 1011 | .parseFilter(featureType, filterModel.getMatcherSet()); | |
| 1012 | 3 | if (!filter.isEmpty()) |
| 1013 | { | |
| 1014 | 3 | fr.setFeatureFilter(featureType, filter); |
| 1015 | } | |
| 1016 | } | |
| 1017 | 1 | return true; |
| 1018 | } | |
| 1019 | ||
| 1020 | /** | |
| 1021 | * Loads feature colours and filters from XML stored in the given file | |
| 1022 | * | |
| 1023 | * @param file | |
| 1024 | */ | |
| 1025 | 1 | void load(File file) |
| 1026 | { | |
| 1027 | 1 | load(file, DataSourceType.FILE); |
| 1028 | } | |
| 1029 | ||
| 1030 | /** | |
| 1031 | * Loads feature colours and filters from XML at a specified source | |
| 1032 | * | |
| 1033 | * @param file | |
| 1034 | * - string or file or other object that allows FileParse to be | |
| 1035 | * created | |
| 1036 | */ | |
| 1037 | 1 | void load(Object file, DataSourceType sourceType) |
| 1038 | { | |
| 1039 | 1 | try |
| 1040 | { | |
| 1041 | 1 | loadFeatureSettingsFile(fr, file, sourceType); |
| 1042 | /* | |
| 1043 | * update feature settings table | |
| 1044 | */ | |
| 1045 | 1 | if (table != null) |
| 1046 | { | |
| 1047 | 1 | resetTable(null); |
| 1048 | 1 | Object[][] data = ((FeatureTableModel) table.getModel()).getData(); |
| 1049 | 1 | ensureOrder(data); |
| 1050 | 1 | updateFeatureRenderer(data, false); |
| 1051 | 1 | 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 | * Offers a file chooser dialog, and then saves the current feature colours | |
| 1062 | * and any filters to the selected file in XML format | |
| 1063 | */ | |
| 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 | * Saves feature colours and filters to the given file | |
| 1082 | * | |
| 1083 | * @param file | |
| 1084 | */ | |
| 1085 | 1 | void save(File file) |
| 1086 | { | |
| 1087 | 1 | JalviewUserColours ucs = new JalviewUserColours(); |
| 1088 | 1 | ucs.setSchemeName("Sequence Features"); |
| 1089 | 1 | try |
| 1090 | { | |
| 1091 | 1 | PrintWriter out = new PrintWriter( |
| 1092 | new OutputStreamWriter(new FileOutputStream(file), "UTF-8")); | |
| 1093 | ||
| 1094 | /* | |
| 1095 | * sort feature types by colour order, from 0 (highest) | |
| 1096 | * to 1 (lowest) | |
| 1097 | */ | |
| 1098 | 1 | Set<String> fr_colours = fr.getAllFeatureColours(); |
| 1099 | 1 | String[] sortedTypes = fr_colours |
| 1100 | .toArray(new String[fr_colours.size()]); | |
| 1101 | 1 | Arrays.sort(sortedTypes, new Comparator<String>() |
| 1102 | { | |
| 1103 | 4 | @Override |
| 1104 | public int compare(String type1, String type2) | |
| 1105 | { | |
| 1106 | 4 | return Float.compare(fr.getOrder(type1), fr.getOrder(type2)); |
| 1107 | } | |
| 1108 | }); | |
| 1109 | ||
| 1110 | /* | |
| 1111 | * save feature colours | |
| 1112 | */ | |
| 1113 | 1 | for (String featureType : sortedTypes) |
| 1114 | { | |
| 1115 | 5 | FeatureColourI fcol = fr.getFeatureStyle(featureType); |
| 1116 | 5 | Colour col = jalview.project.Jalview2XML.marshalColour(featureType, |
| 1117 | fcol); | |
| 1118 | 5 | ucs.getColour().add(col); |
| 1119 | } | |
| 1120 | ||
| 1121 | /* | |
| 1122 | * save any feature filters | |
| 1123 | */ | |
| 1124 | 1 | for (String featureType : sortedTypes) |
| 1125 | { | |
| 1126 | 5 | FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); |
| 1127 | 5 | if (filter != null && !filter.isEmpty()) |
| 1128 | { | |
| 1129 | 3 | Iterator<FeatureMatcherI> iterator = filter.getMatchers() |
| 1130 | .iterator(); | |
| 1131 | 3 | FeatureMatcherI firstMatcher = iterator.next(); |
| 1132 | 3 | jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML |
| 1133 | .marshalFilter(firstMatcher, iterator, filter.isAnded()); | |
| 1134 | 3 | Filter filterModel = new Filter(); |
| 1135 | 3 | filterModel.setFeatureType(featureType); |
| 1136 | 3 | filterModel.setMatcherSet(ms); |
| 1137 | 3 | ucs.getFilter().add(filterModel); |
| 1138 | } | |
| 1139 | } | |
| 1140 | 1 | JAXBContext jaxbContext = JAXBContext |
| 1141 | .newInstance(JalviewUserColours.class); | |
| 1142 | 1 | Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); |
| 1143 | 1 | jaxbMarshaller.marshal( |
| 1144 | new ObjectFactory().createJalviewUserColours(ucs), out); | |
| 1145 | ||
| 1146 | // jaxbMarshaller.marshal(object, pout); | |
| 1147 | // marshaller.marshal(object); | |
| 1148 | 1 | out.flush(); |
| 1149 | ||
| 1150 | // ucs.marshal(out); | |
| 1151 | 1 | out.close(); |
| 1152 | } catch (Exception ex) | |
| 1153 | { | |
| 1154 | 0 | ex.printStackTrace(); |
| 1155 | } | |
| 1156 | } | |
| 1157 | ||
| 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 | ||
| 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];// *awidth[0]*awidth[2]; - better |
| 1186 | // weight - but have to make per | |
| 1187 | // sequence, too (awidth[2]) | |
| 1188 | // if (width[i]==1) // hack to distinguish single width sequences. | |
| 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 | // awidth = (float[]) typeWidth.get(data[i][0]); | |
| 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; // normalize |
| 1215 | 0 | fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for |
| 1216 | // later | |
| 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 | // update global priority order | |
| 1227 | } | |
| 1228 | ||
| 1229 | 0 | updateFeatureRenderer(data, false); |
| 1230 | 0 | table.repaint(); |
| 1231 | } | |
| 1232 | ||
| 1233 | /** | |
| 1234 | * close ourselves but leave any existing UI handlers (e.g a CDS/Protein | |
| 1235 | * tabbed feature settings dialog) intact | |
| 1236 | */ | |
| 1237 | 0 | public void closeOldSettings() |
| 1238 | { | |
| 1239 | 0 | closeDialog(false); |
| 1240 | } | |
| 1241 | ||
| 1242 | /** | |
| 1243 | * close the feature settings dialog (and any containing frame) | |
| 1244 | */ | |
| 1245 | 0 | public void close() |
| 1246 | { | |
| 1247 | 0 | closeDialog(true); |
| 1248 | } | |
| 1249 | ||
| 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 | ||
| 1271 | 0 | public void updateFeatureRenderer(Object[][] data) |
| 1272 | { | |
| 1273 | 0 | updateFeatureRenderer(data, true); |
| 1274 | } | |
| 1275 | ||
| 1276 | /** | |
| 1277 | * Update the priority order of features; only repaint if this changed the | |
| 1278 | * order of visible features | |
| 1279 | * | |
| 1280 | * @param data | |
| 1281 | * @param visibleNew | |
| 1282 | */ | |
| 1283 | 3 | void updateFeatureRenderer(Object[][] data, boolean visibleNew) |
| 1284 | { | |
| 1285 | 3 | FeatureSettingsBean[] rowData = getTableAsBeans(data); |
| 1286 | ||
| 1287 | 3 | if (fr.setFeaturePriority(rowData, visibleNew)) |
| 1288 | { | |
| 1289 | 0 | refreshDisplay(); |
| 1290 | } | |
| 1291 | } | |
| 1292 | ||
| 1293 | /** | |
| 1294 | * Converts table data into an array of data beans | |
| 1295 | */ | |
| 1296 | 3 | private FeatureSettingsBean[] getTableAsBeans(Object[][] data) |
| 1297 | { | |
| 1298 | 3 | FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; |
| 1299 | 18 | for (int i = 0; i < data.length; i++) |
| 1300 | { | |
| 1301 | 15 | String type = (String) data[i][TYPE_COLUMN]; |
| 1302 | 15 | FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; |
| 1303 | 15 | FeatureMatcherSetI theFilter = (FeatureMatcherSetI) data[i][FILTER_COLUMN]; |
| 1304 | 15 | Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; |
| 1305 | 15 | rowData[i] = new FeatureSettingsBean(type, colour, theFilter, |
| 1306 | isShown); | |
| 1307 | } | |
| 1308 | 3 | return rowData; |
| 1309 | } | |
| 1310 | ||
| 1311 | 1 | private void jbInit() throws Exception |
| 1312 | { | |
| 1313 | 1 | this.setLayout(new BorderLayout()); |
| 1314 | ||
| 1315 | 1 | final boolean hasComplement = af.getViewport() |
| 1316 | .getCodingComplement() != null; | |
| 1317 | ||
| 1318 | 1 | JPanel settingsPane = new JPanel(); |
| 1319 | 1 | settingsPane.setLayout(new BorderLayout()); |
| 1320 | ||
| 1321 | 1 | JPanel bigPanel = new JPanel(); |
| 1322 | 1 | bigPanel.setLayout(new BorderLayout()); |
| 1323 | ||
| 1324 | 1 | groupPanel = new JPanel(); |
| 1325 | 1 | bigPanel.add(groupPanel, BorderLayout.NORTH); |
| 1326 | ||
| 1327 | 1 | JButton invert = new JButton( |
| 1328 | MessageManager.getString("label.invert_selection")); | |
| 1329 | 1 | invert.setFont(JvSwingUtils.getLabelFont()); |
| 1330 | 1 | invert.addActionListener(new ActionListener() |
| 1331 | { | |
| 1332 | 0 | @Override |
| 1333 | public void actionPerformed(ActionEvent e) | |
| 1334 | { | |
| 1335 | 0 | invertSelection(); |
| 1336 | } | |
| 1337 | }); | |
| 1338 | ||
| 1339 | 1 | JButton optimizeOrder = new JButton( |
| 1340 | MessageManager.getString("label.optimise_order")); | |
| 1341 | 1 | optimizeOrder.setFont(JvSwingUtils.getLabelFont()); |
| 1342 | 1 | optimizeOrder.addActionListener(new ActionListener() |
| 1343 | { | |
| 1344 | 0 | @Override |
| 1345 | public void actionPerformed(ActionEvent e) | |
| 1346 | { | |
| 1347 | 0 | orderByAvWidth(); |
| 1348 | } | |
| 1349 | }); | |
| 1350 | ||
| 1351 | 1 | final String byScoreLabel = MessageManager |
| 1352 | .getString("label.seq_sort_by_score"); | |
| 1353 | 1 | JButton sortByScore = new JButton(byScoreLabel); |
| 1354 | 1 | sortByScore.setFont(JvSwingUtils.getLabelFont()); |
| 1355 | 1 | sortByScore.addActionListener(new ActionListener() |
| 1356 | { | |
| 1357 | 0 | @Override |
| 1358 | public void actionPerformed(ActionEvent e) | |
| 1359 | { | |
| 1360 | 0 | if (canSortBy(byScoreLabel)) |
| 1361 | { | |
| 1362 | 0 | sortByScore(null); |
| 1363 | } | |
| 1364 | } | |
| 1365 | }); | |
| 1366 | 1 | final String byDensityLabel = MessageManager |
| 1367 | .getString("label.sequence_sort_by_density"); | |
| 1368 | 1 | JButton sortByDens = new JButton(byDensityLabel); |
| 1369 | 1 | sortByDens.setFont(JvSwingUtils.getLabelFont()); |
| 1370 | 1 | sortByDens.addActionListener(new ActionListener() |
| 1371 | { | |
| 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 | 1 | JButton help = new JButton(MessageManager.getString("action.help")); |
| 1383 | 1 | help.setFont(JvSwingUtils.getLabelFont()); |
| 1384 | 1 | help.addActionListener(new ActionListener() |
| 1385 | { | |
| 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 | // Cancel for a SplitFrame should just revert changes to the currently | |
| 1399 | // displayed | |
| 1400 | // settings. May want to do this for either or both - so need a splitview | |
| 1401 | // feature settings cancel/OK. | |
| 1402 | 1 | JButton cancel = new JButton(MessageManager |
| 1403 | 1 | .getString(hasComplement ? "action.revert" : "action.cancel")); |
| 1404 | 1 | cancel.setToolTipText(MessageManager.getString(hasComplement |
| 1405 | ? "action.undo_changes_to_feature_settings" | |
| 1406 | : "action.undo_changes_to_feature_settings_and_close_the_dialog")); | |
| 1407 | 1 | cancel.setFont(JvSwingUtils.getLabelFont()); |
| 1408 | // TODO: disable cancel (and apply!) until current settings are different | |
| 1409 | 1 | cancel.addActionListener(new ActionListener() |
| 1410 | { | |
| 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 | // Cancel for the whole dialog should cancel both CDS and Protein. | |
| 1423 | // OK for an individual feature settings just applies changes, but dialog | |
| 1424 | // remains open | |
| 1425 | 1 | JButton ok = new JButton(MessageManager |
| 1426 | 1 | .getString(hasComplement ? "action.apply" : "action.ok")); |
| 1427 | 1 | ok.setFont(JvSwingUtils.getLabelFont()); |
| 1428 | 1 | ok.addActionListener(new ActionListener() |
| 1429 | { | |
| 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 | 1 | JButton loadColours = new JButton( |
| 1445 | MessageManager.getString("label.load_colours")); | |
| 1446 | 1 | loadColours.setFont(JvSwingUtils.getLabelFont()); |
| 1447 | 1 | loadColours.setToolTipText( |
| 1448 | MessageManager.getString("label.load_colours_tooltip")); | |
| 1449 | 1 | loadColours.addActionListener(new ActionListener() |
| 1450 | { | |
| 1451 | 0 | @Override |
| 1452 | public void actionPerformed(ActionEvent e) | |
| 1453 | { | |
| 1454 | 0 | load(); |
| 1455 | } | |
| 1456 | }); | |
| 1457 | ||
| 1458 | 1 | JButton saveColours = new JButton( |
| 1459 | MessageManager.getString("label.save_colours")); | |
| 1460 | 1 | saveColours.setFont(JvSwingUtils.getLabelFont()); |
| 1461 | 1 | saveColours.setToolTipText( |
| 1462 | MessageManager.getString("label.save_colours_tooltip")); | |
| 1463 | 1 | saveColours.addActionListener(new ActionListener() |
| 1464 | { | |
| 1465 | 0 | @Override |
| 1466 | public void actionPerformed(ActionEvent e) | |
| 1467 | { | |
| 1468 | 0 | save(); |
| 1469 | } | |
| 1470 | }); | |
| 1471 | 1 | transparency.addChangeListener(new ChangeListener() |
| 1472 | { | |
| 1473 | 1 | @Override |
| 1474 | public void stateChanged(ChangeEvent evt) | |
| 1475 | { | |
| 1476 | 1 | if (!inConstruction) |
| 1477 | { | |
| 1478 | 0 | fr.setTransparency((100 - transparency.getValue()) / 100f); |
| 1479 | 0 | refreshDisplay(); |
| 1480 | } | |
| 1481 | } | |
| 1482 | }); | |
| 1483 | ||
| 1484 | 1 | transparency.setMaximum(70); |
| 1485 | 1 | transparency.setToolTipText( |
| 1486 | MessageManager.getString("label.transparency_tip")); | |
| 1487 | ||
| 1488 | 1 | boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); |
| 1489 | 1 | String text = MessageManager |
| 1490 | .formatMessage("label.show_linked_features", | |
| 1491 | 1 | nucleotide |
| 1492 | ? MessageManager.getString("label.protein") | |
| 1493 | .toLowerCase(Locale.ROOT) | |
| 1494 | : "CDS"); | |
| 1495 | 1 | showComplement = new JCheckBox(text); |
| 1496 | 1 | showComplement.addActionListener(new ActionListener() |
| 1497 | { | |
| 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 | 1 | showComplementOnTop = new JCheckBox( |
| 1508 | MessageManager.getString("label.on_top")); | |
| 1509 | 1 | showComplementOnTop.addActionListener(new ActionListener() |
| 1510 | { | |
| 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 | 1 | updateComplementButtons(); |
| 1521 | ||
| 1522 | 1 | JPanel lowerPanel = new JPanel(new GridLayout(1, 2)); |
| 1523 | 1 | bigPanel.add(lowerPanel, BorderLayout.SOUTH); |
| 1524 | ||
| 1525 | 1 | JPanel transbuttons = new JPanel(new GridLayout(5, 1)); |
| 1526 | 1 | transbuttons.add(optimizeOrder); |
| 1527 | 1 | transbuttons.add(invert); |
| 1528 | 1 | transbuttons.add(sortByScore); |
| 1529 | 1 | transbuttons.add(sortByDens); |
| 1530 | 1 | transbuttons.add(help); |
| 1531 | ||
| 1532 | 1 | JPanel transPanelLeft = new JPanel( |
| 1533 | 1 | new GridLayout(hasComplement ? 4 : 2, 1)); |
| 1534 | 1 | transPanelLeft.add(new JLabel(" Colour transparency" + ":")); |
| 1535 | 1 | transPanelLeft.add(transparency); |
| 1536 | 1 | 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 | 1 | lowerPanel.add(transPanelLeft); |
| 1544 | 1 | lowerPanel.add(transbuttons); |
| 1545 | ||
| 1546 | 1 | JPanel buttonPanel = new JPanel(); |
| 1547 | 1 | buttonPanel.add(ok); |
| 1548 | 1 | buttonPanel.add(cancel); |
| 1549 | 1 | buttonPanel.add(loadColours); |
| 1550 | 1 | buttonPanel.add(saveColours); |
| 1551 | 1 | bigPanel.add(scrollPane, BorderLayout.CENTER); |
| 1552 | 1 | settingsPane.add(bigPanel, BorderLayout.CENTER); |
| 1553 | 1 | settingsPane.add(buttonPanel, BorderLayout.SOUTH); |
| 1554 | 1 | this.add(settingsPane); |
| 1555 | } | |
| 1556 | ||
| 1557 | /** | |
| 1558 | * Repaints alignment, structure and overview (if shown). If there is a | |
| 1559 | * complementary view which is showing this view's features, then also | |
| 1560 | * repaints that. | |
| 1561 | */ | |
| 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 | * Answers a suitable tooltip to show on the colour cell of the table | |
| 1575 | * | |
| 1576 | * @param fcol | |
| 1577 | * @param withHint | |
| 1578 | * if true include 'click to edit' and similar text | |
| 1579 | * @return | |
| 1580 | */ | |
| 1581 | 9 | public static String getColorTooltip(FeatureColourI fcol, |
| 1582 | boolean withHint) | |
| 1583 | { | |
| 1584 | 9 | if (fcol == null) |
| 1585 | { | |
| 1586 | 1 | return null; |
| 1587 | } | |
| 1588 | 8 | if (fcol.isSimpleColour()) |
| 1589 | { | |
| 1590 | 2 | return withHint ? BASE_TOOLTIP : null; |
| 1591 | } | |
| 1592 | 6 | String description = fcol.getDescription(); |
| 1593 | 6 | description = description.replaceAll("<", "<"); |
| 1594 | 6 | description = description.replaceAll(">", ">"); |
| 1595 | 6 | StringBuilder tt = new StringBuilder(description); |
| 1596 | 6 | if (withHint) |
| 1597 | { | |
| 1598 | 3 | tt.append("<br>").append(BASE_TOOLTIP).append("</br>"); |
| 1599 | } | |
| 1600 | 6 | return JvSwingUtils.wrapTooltip(true, tt.toString()); |
| 1601 | } | |
| 1602 | ||
| 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 | // jalview.bin.Console.errPrintln("Width is " + w / 2); | |
| 1646 | 0 | Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); |
| 1647 | 0 | comp.setIcon(ficon); |
| 1648 | // tt+="RGB value: Max (" + newColor.getRed() + ", " | |
| 1649 | // + newColor.getGreen() + ", " + newColor.getBlue() | |
| 1650 | // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen() | |
| 1651 | // + ", " + minCol.getBlue() + ")"); | |
| 1652 | } | |
| 1653 | 0 | comp.setHorizontalAlignment(SwingConstants.CENTER); |
| 1654 | 0 | comp.setText(tx.toString()); |
| 1655 | } | |
| 1656 | ||
| 1657 | // /////////////////////////////////////////////////////////////////////// | |
| 1658 | // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html | |
| 1659 | // /////////////////////////////////////////////////////////////////////// | |
| 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 | ||
| 1670 | 2 | FeatureTableModel(Object[][] data) |
| 1671 | { | |
| 1672 | 2 | this.data = data; |
| 1673 | } | |
| 1674 | ||
| 1675 | 2 | public Object[][] getData() |
| 1676 | { | |
| 1677 | 2 | return data; |
| 1678 | } | |
| 1679 | ||
| 1680 | 0 | public void setData(Object[][] data) |
| 1681 | { | |
| 1682 | 0 | this.data = data; |
| 1683 | } | |
| 1684 | ||
| 1685 | 10 | @Override |
| 1686 | public int getColumnCount() | |
| 1687 | { | |
| 1688 | 10 | return columnNames.length; |
| 1689 | } | |
| 1690 | ||
| 1691 | 0 | public Object[] getRow(int row) |
| 1692 | { | |
| 1693 | 0 | return data[row]; |
| 1694 | } | |
| 1695 | ||
| 1696 | 14 | @Override |
| 1697 | public int getRowCount() | |
| 1698 | { | |
| 1699 | 14 | return data.length; |
| 1700 | } | |
| 1701 | ||
| 1702 | 8 | @Override |
| 1703 | public String getColumnName(int col) | |
| 1704 | { | |
| 1705 | 8 | return columnNames[col]; |
| 1706 | } | |
| 1707 | ||
| 1708 | 0 | @Override |
| 1709 | public Object getValueAt(int row, int col) | |
| 1710 | { | |
| 1711 | 0 | return data[row][col]; |
| 1712 | } | |
| 1713 | ||
| 1714 | /** | |
| 1715 | * Answers the class of column c of the table | |
| 1716 | */ | |
| 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 | ||
| 1733 | 0 | @Override |
| 1734 | public boolean isCellEditable(int row, int col) | |
| 1735 | { | |
| 1736 | 0 | return col == 0 ? false : true; |
| 1737 | } | |
| 1738 | ||
| 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 | ||
| 1749 | class ColorRenderer extends JLabel implements TableCellRenderer | |
| 1750 | { | |
| 1751 | Border unselectedBorder = null; | |
| 1752 | ||
| 1753 | Border selectedBorder = null; | |
| 1754 | ||
| 1755 | 2 | public ColorRenderer() |
| 1756 | { | |
| 1757 | 2 | setOpaque(true); // MUST do this for background to show up. |
| 1758 | 2 | setHorizontalTextPosition(SwingConstants.CENTER); |
| 1759 | 2 | setVerticalTextPosition(SwingConstants.CENTER); |
| 1760 | } | |
| 1761 | ||
| 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 | ||
| 1804 | class FilterRenderer extends JLabel implements TableCellRenderer | |
| 1805 | { | |
| 1806 | javax.swing.border.Border unselectedBorder = null; | |
| 1807 | ||
| 1808 | javax.swing.border.Border selectedBorder = null; | |
| 1809 | ||
| 1810 | 2 | public FilterRenderer() |
| 1811 | { | |
| 1812 | 2 | setOpaque(true); // MUST do this for background to show up. |
| 1813 | 2 | setHorizontalTextPosition(SwingConstants.CENTER); |
| 1814 | 2 | setVerticalTextPosition(SwingConstants.CENTER); |
| 1815 | } | |
| 1816 | ||
| 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 | * update comp using rendering settings from gcol | |
| 1858 | * | |
| 1859 | * @param comp | |
| 1860 | * @param gcol | |
| 1861 | */ | |
| 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") | |
| 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 | ||
| 1894 | 2 | public ColorEditor() |
| 1895 | { | |
| 1896 | // Set up the editor (from the table's point of view), | |
| 1897 | // which is a button. | |
| 1898 | // This button brings up the color chooser dialog, | |
| 1899 | // which is the editor from the user's point of view. | |
| 1900 | 2 | button = new JButton(); |
| 1901 | 2 | button.setActionCommand(EDIT); |
| 1902 | 2 | button.addActionListener(this); |
| 1903 | 2 | button.setBorderPainted(false); |
| 1904 | } | |
| 1905 | ||
| 1906 | /** | |
| 1907 | * Handles events from the editor button, and from the colour/filters | |
| 1908 | * dialog's OK button | |
| 1909 | */ | |
| 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 | * simple colour chooser | |
| 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 | { | |
| 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 | ||
| 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 | * variable colour and filters dialog | |
| 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 | * Java only | |
| 1958 | * | |
| 1959 | * @j2sIgnore | |
| 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 | * after OK in variable colour dialog, any changes to colour | |
| 1973 | * (or filters!) are already set in FeatureRenderer, so just | |
| 1974 | * update table data without triggering updateFeatureRenderer | |
| 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 | // SwingJS needs an explicit repaint() here, | |
| 1988 | // rather than relying upon no validation having | |
| 1989 | // occurred since the stopEditing call was made. | |
| 1990 | // Its laying out has not been stopped by the modal frame | |
| 1991 | 0 | table.validate(); |
| 1992 | 0 | table.repaint(); |
| 1993 | } | |
| 1994 | } | |
| 1995 | ||
| 1996 | /** | |
| 1997 | * Override allows access to this method from anonymous inner classes | |
| 1998 | */ | |
| 1999 | 0 | @Override |
| 2000 | protected void fireEditingStopped() | |
| 2001 | { | |
| 2002 | 0 | super.fireEditingStopped(); |
| 2003 | } | |
| 2004 | ||
| 2005 | // Implement the one CellEditor method that AbstractCellEditor doesn't. | |
| 2006 | 0 | @Override |
| 2007 | public Object getCellEditorValue() | |
| 2008 | { | |
| 2009 | 0 | return currentColor; |
| 2010 | } | |
| 2011 | ||
| 2012 | // Implement the one method defined by TableCellEditor. | |
| 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 | * The cell editor for the Filter column. It displays the text of any filters | |
| 2043 | * for the feature type in that row (in full as a tooltip, possible | |
| 2044 | * abbreviated as display text). On click in the cell, opens the Feature | |
| 2045 | * Display Settings dialog at the Filters tab. | |
| 2046 | */ | |
| 2047 | @SuppressWarnings("serial") | |
| 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 | ||
| 2064 | 2 | public FilterEditor() |
| 2065 | { | |
| 2066 | 2 | button = new JButton(); |
| 2067 | 2 | button.setActionCommand(EDIT); |
| 2068 | 2 | button.addActionListener(this); |
| 2069 | 2 | button.setBorderPainted(false); |
| 2070 | } | |
| 2071 | ||
| 2072 | /** | |
| 2073 | * Handles events from the editor button | |
| 2074 | */ | |
| 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 | // todo open at its last position on screen | |
| 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 | * after OK in variable colour dialog, any changes to filter | |
| 2102 | * (or colours!) are already set in FeatureRenderer, so just | |
| 2103 | * update table data without triggering updateFeatureRenderer | |
| 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 | // SwingJS needs an explicit repaint() here, | |
| 2120 | // rather than relying upon no validation having | |
| 2121 | // occurred since the stopEditing call was made. | |
| 2122 | // Its laying out has not been stopped by the modal frame | |
| 2123 | 0 | table.validate(); |
| 2124 | 0 | table.repaint(); |
| 2125 | } | |
| 2126 | } | |
| 2127 | ||
| 2128 | 0 | @Override |
| 2129 | public Object getCellEditorValue() | |
| 2130 | { | |
| 2131 | 0 | return currentFilter; |
| 2132 | } | |
| 2133 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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; // start and end of midpoint band for thresholded symbol | |
| 2182 | ||
| 2183 | Color mpcolour = Color.white; | |
| 2184 | ||
| 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 | ||
| 2204 | 0 | @Override |
| 2205 | public int getIconWidth() | |
| 2206 | { | |
| 2207 | 0 | return width; |
| 2208 | } | |
| 2209 | ||
| 2210 | 0 | @Override |
| 2211 | public int getIconHeight() | |
| 2212 | { | |
| 2213 | 0 | return height; |
| 2214 | } | |
| 2215 | ||
| 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 | // need an icon here. | |
| 2225 | 0 | g.setColor(gcol.getMaxColour()); |
| 2226 | ||
| 2227 | 0 | g.setFont(new Font("Verdana", Font.PLAIN, 9)); |
| 2228 | ||
| 2229 | // g.setFont(g.getFont().deriveFont( | |
| 2230 | // AffineTransform.getScaleInstance( | |
| 2231 | // width/g.getFontMetrics().stringWidth("Label"), | |
| 2232 | // height/g.getFontMetrics().getHeight()))); | |
| 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 | // g.fillRect(0, e1, width - e1, height); // BH 2018 | |
| 2249 | 0 | g.fillRect(e1, 0, width - e1, height); |
| 2250 | } | |
| 2251 | } | |
| 2252 | } |