Coverage Report
File AnnotationLabels.java
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49% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AnnotationLabels | 81 | 569 | 238 |
Contributing tests
This file is covered by 209 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.Canvas; | |
| 24 | import java.awt.Color; | |
| 25 | import java.awt.Cursor; | |
| 26 | import java.awt.Dimension; | |
| 27 | import java.awt.Font; | |
| 28 | import java.awt.FontMetrics; | |
| 29 | import java.awt.Graphics; | |
| 30 | import java.awt.Graphics2D; | |
| 31 | import java.awt.RenderingHints; | |
| 32 | import java.awt.Toolkit; | |
| 33 | import java.awt.datatransfer.StringSelection; | |
| 34 | import java.awt.event.ActionEvent; | |
| 35 | import java.awt.event.ActionListener; | |
| 36 | import java.awt.event.MouseEvent; | |
| 37 | import java.awt.event.MouseListener; | |
| 38 | import java.awt.event.MouseMotionListener; | |
| 39 | import java.awt.geom.AffineTransform; | |
| 40 | import java.util.Arrays; | |
| 41 | import java.util.Collections; | |
| 42 | import java.util.Iterator; | |
| 43 | import java.util.List; | |
| 44 | import java.util.Locale; | |
| 45 | ||
| 46 | import javax.swing.JCheckBoxMenuItem; | |
| 47 | import javax.swing.JMenuItem; | |
| 48 | import javax.swing.JPanel; | |
| 49 | import javax.swing.JPopupMenu; | |
| 50 | import javax.swing.SwingUtilities; | |
| 51 | import javax.swing.ToolTipManager; | |
| 52 | ||
| 53 | import jalview.analysis.AlignSeq; | |
| 54 | import jalview.analysis.AlignmentUtils; | |
| 55 | import jalview.api.AlignCalcWorkerI; | |
| 56 | import jalview.bin.Cache; | |
| 57 | import jalview.bin.Jalview; | |
| 58 | import jalview.datamodel.Alignment; | |
| 59 | import jalview.datamodel.AlignmentAnnotation; | |
| 60 | import jalview.datamodel.Annotation; | |
| 61 | import jalview.datamodel.ContactMatrixI; | |
| 62 | import jalview.datamodel.GroupSet; | |
| 63 | import jalview.datamodel.HiddenColumns; | |
| 64 | import jalview.datamodel.Sequence; | |
| 65 | import jalview.datamodel.SequenceGroup; | |
| 66 | import jalview.datamodel.SequenceI; | |
| 67 | import jalview.io.FileFormat; | |
| 68 | import jalview.io.FormatAdapter; | |
| 69 | import jalview.util.Comparison; | |
| 70 | import jalview.util.Constants; | |
| 71 | import jalview.util.MessageManager; | |
| 72 | import jalview.util.ParseHtmlBodyAndLinks; | |
| 73 | import jalview.util.Platform; | |
| 74 | import jalview.workers.SecondaryStructureConsensusThread; | |
| 75 | ||
| 76 | /** | |
| 77 | * The panel that holds the labels for alignment annotations, providing | |
| 78 | * tooltips, context menus, drag to reorder rows, and drag to adjust panel | |
| 79 | * height | |
| 80 | */ | |
| 81 | public class AnnotationLabels extends JPanel | |
| 82 | implements MouseListener, MouseMotionListener, ActionListener | |
| 83 | { | |
| 84 | private static final String HTML_END_TAG = "</html>"; | |
| 85 | ||
| 86 | private static final String HTML_START_TAG = "<html>"; | |
| 87 | ||
| 88 | /** | |
| 89 | * width in pixels within which height adjuster arrows are shown and active | |
| 90 | */ | |
| 91 | private static final int HEIGHT_ADJUSTER_WIDTH = 50; | |
| 92 | ||
| 93 | /** | |
| 94 | * height in pixels for allowing height adjuster to be active | |
| 95 | */ | |
| 96 | public static int HEIGHT_ADJUSTER_HEIGHT = 10; | |
| 97 | ||
| 98 | private static final Font font = new Font("Arial", Font.PLAIN, 11); | |
| 99 | ||
| 100 | private static final String TOGGLE_LABELSCALE = MessageManager | |
| 101 | .getString("label.scale_label_to_column"); | |
| 102 | ||
| 103 | private static final String ADDNEW = MessageManager | |
| 104 | .getString("label.add_new_row"); | |
| 105 | ||
| 106 | private static final String EDITNAME = MessageManager | |
| 107 | .getString("label.edit_label_description"); | |
| 108 | ||
| 109 | private static final String HIDE = MessageManager | |
| 110 | .getString("label.hide_row"); | |
| 111 | ||
| 112 | private static final String DELETE = MessageManager | |
| 113 | .getString("label.delete_row"); | |
| 114 | ||
| 115 | private static final String SHOWALL = MessageManager | |
| 116 | .getString("label.show_all_hidden_rows"); | |
| 117 | ||
| 118 | private static final String OUTPUT_TEXT = MessageManager | |
| 119 | .getString("label.export_annotation"); | |
| 120 | ||
| 121 | private static final String COPYCONS_SEQ = MessageManager | |
| 122 | .getString("label.copy_consensus_sequence"); | |
| 123 | ||
| 124 | private static final String ADJUST_ANNOTATION_LABELS_WIDTH_PREF = "ADJUST_ANNOTATION_LABELS_WIDTH"; | |
| 125 | ||
| 126 | private final boolean debugRedraw = false; | |
| 127 | ||
| 128 | private AlignmentPanel ap; | |
| 129 | ||
| 130 | AlignViewport av; | |
| 131 | ||
| 132 | private MouseEvent dragEvent; | |
| 133 | ||
| 134 | private int oldY; | |
| 135 | ||
| 136 | private int selectedRow; | |
| 137 | ||
| 138 | private int scrollOffset = 0; | |
| 139 | ||
| 140 | private boolean hasHiddenRows; | |
| 141 | ||
| 142 | private boolean resizePanel = false; | |
| 143 | ||
| 144 | private int annotationIdWidth = -1; | |
| 145 | ||
| 146 | public static final String RESIZE_MARGINS_MARK_PREF = "RESIZE_MARGINS_MARK"; | |
| 147 | ||
| 148 | /** | |
| 149 | * Creates a new AnnotationLabels object | |
| 150 | * | |
| 151 | * @param ap | |
| 152 | */ | |
| 153 | 475 |  public AnnotationLabels(AlignmentPanel ap) |
| 154 | { | |
| 155 | 475 | this.ap = ap; |
| 156 | 475 | av = ap.av; |
| 157 | 475 | ToolTipManager.sharedInstance().registerComponent(this); |
| 158 | ||
| 159 | 475 | addMouseListener(this); |
| 160 | 475 | addMouseMotionListener(this); |
| 161 | 475 | addMouseWheelListener(ap.getAnnotationPanel()); |
| 162 | } | |
| 163 | ||
| 164 | 547 | public AnnotationLabels(AlignViewport av) |
| 165 | { | |
| 166 | 547 | this.av = av; |
| 167 | } | |
| 168 | ||
| 169 | /** | |
| 170 | * DOCUMENT ME! | |
| 171 | * | |
| 172 | * @param y | |
| 173 | * DOCUMENT ME! | |
| 174 | */ | |
| 175 | 892 | public void setScrollOffset(int y) |
| 176 | { | |
| 177 | 892 | scrollOffset = y; |
| 178 | 892 | repaint(); |
| 179 | } | |
| 180 | ||
| 181 | /** | |
| 182 | * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at | |
| 183 | * y | |
| 184 | * | |
| 185 | * @param y | |
| 186 | * coordinate position to search for a row | |
| 187 | */ | |
| 188 | 0 | void getSelectedRow(int y) |
| 189 | { | |
| 190 | 0 | int height = 0; |
| 191 | 0 | AlignmentAnnotation[] aa = ap.av.getAlignment() |
| 192 | .getAlignmentAnnotation(); | |
| 193 | 0 | selectedRow = -2; |
| 194 | 0 | if (aa != null) |
| 195 | { | |
| 196 | 0 | for (int i = 0; i < aa.length; i++) |
| 197 | { | |
| 198 | 0 | selectedRow = -1; |
| 199 | 0 | if (!aa[i].isForDisplay()) |
| 200 | { | |
| 201 | 0 | continue; |
| 202 | } | |
| 203 | ||
| 204 | 0 | height += aa[i].height; |
| 205 | ||
| 206 | 0 | if (y < height) |
| 207 | { | |
| 208 | 0 | selectedRow = i; |
| 209 | ||
| 210 | 0 | break; |
| 211 | } | |
| 212 | } | |
| 213 | } | |
| 214 | } | |
| 215 | ||
| 216 | /** | |
| 217 | * DOCUMENT ME! | |
| 218 | * | |
| 219 | * @param evt | |
| 220 | * DOCUMENT ME! | |
| 221 | */ | |
| 222 | 0 | @Override |
| 223 | public void actionPerformed(ActionEvent evt) | |
| 224 | { | |
| 225 | 0 | AlignmentAnnotation[] aa = ap.av.getAlignment() |
| 226 | .getAlignmentAnnotation(); | |
| 227 | ||
| 228 | 0 | String action = evt.getActionCommand(); |
| 229 | 0 | if (ADDNEW.equals(action)) |
| 230 | { | |
| 231 | /* | |
| 232 | * non-returning dialog | |
| 233 | */ | |
| 234 | 0 | AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, |
| 235 | null, new Annotation[ap.av.getAlignment().getWidth()]); | |
| 236 | 0 | editLabelDescription(newAnnotation, true); |
| 237 | } | |
| 238 | 0 | else if (EDITNAME.equals(action)) |
| 239 | { | |
| 240 | /* | |
| 241 | * non-returning dialog | |
| 242 | */ | |
| 243 | 0 | editLabelDescription(aa[selectedRow], false); |
| 244 | } | |
| 245 | 0 | else if (HIDE.equals(action)) |
| 246 | { | |
| 247 | 0 | aa[selectedRow].visible = false; |
| 248 | } | |
| 249 | 0 | else if (DELETE.equals(action)) |
| 250 | { | |
| 251 | 0 | ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); |
| 252 | 0 | ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); |
| 253 | ||
| 254 | 0 | List<AlignCalcWorkerI> workers = ap.av.getCalcManager() |
| 255 | .getRegisteredWorkersOfClass( | |
| 256 | SecondaryStructureConsensusThread.class); | |
| 257 | 0 | if (!workers.isEmpty()) |
| 258 | { | |
| 259 | ||
| 260 | 0 | ap.alignFrame.getViewport().getCalcManager() |
| 261 | .startWorker(workers.remove(0)); | |
| 262 | ||
| 263 | } | |
| 264 | } | |
| 265 | 0 | else if (SHOWALL.equals(action)) |
| 266 | { | |
| 267 | 0 | for (int i = 0; i < aa.length; i++) |
| 268 | { | |
| 269 | 0 | if (!aa[i].visible && aa[i].annotations != null) |
| 270 | { | |
| 271 | 0 | aa[i].visible = true; |
| 272 | } | |
| 273 | } | |
| 274 | } | |
| 275 | 0 | else if (OUTPUT_TEXT.equals(action)) |
| 276 | { | |
| 277 | 0 | new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); |
| 278 | } | |
| 279 | 0 | else if (COPYCONS_SEQ.equals(action)) |
| 280 | { | |
| 281 | 0 | SequenceI cons = null; |
| 282 | 0 | if (aa[selectedRow].groupRef != null) |
| 283 | { | |
| 284 | 0 | cons = aa[selectedRow].groupRef.getConsensusSeq(); |
| 285 | } | |
| 286 | else | |
| 287 | { | |
| 288 | 0 | cons = av.getConsensusSeq(); |
| 289 | } | |
| 290 | 0 | if (cons != null) |
| 291 | { | |
| 292 | 0 | copy_annotseqtoclipboard(cons); |
| 293 | } | |
| 294 | } | |
| 295 | 0 | else if (TOGGLE_LABELSCALE.equals(action)) |
| 296 | { | |
| 297 | 0 | aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; |
| 298 | } | |
| 299 | ||
| 300 | 0 | ap.refresh(true); |
| 301 | } | |
| 302 | ||
| 303 | /** | |
| 304 | * Shows a dialog where the annotation name and description may be edited. If | |
| 305 | * parameter addNew is true, then on confirmation, a new AlignmentAnnotation | |
| 306 | * is added, else an existing annotation is updated. | |
| 307 | * | |
| 308 | * @param annotation | |
| 309 | * @param addNew | |
| 310 | */ | |
| 311 | 0 | void editLabelDescription(AlignmentAnnotation annotation, boolean addNew) |
| 312 | { | |
| 313 | 0 | String name = MessageManager.getString("label.annotation_name"); |
| 314 | 0 | String description = MessageManager |
| 315 | .getString("label.annotation_description"); | |
| 316 | 0 | String title = MessageManager |
| 317 | .getString("label.edit_annotation_name_description"); | |
| 318 | 0 | EditNameDialog dialog = new EditNameDialog(annotation.label, |
| 319 | annotation.description, name, description); | |
| 320 | ||
| 321 | 0 | dialog.showDialog(ap.alignFrame, title, () -> { |
| 322 | 0 | annotation.label = dialog.getName(); |
| 323 | 0 | String text = dialog.getDescription(); |
| 324 | 0 | if (text != null && text.length() == 0) |
| 325 | { | |
| 326 | 0 | text = null; |
| 327 | } | |
| 328 | 0 | annotation.description = text; |
| 329 | 0 | if (addNew) |
| 330 | { | |
| 331 | 0 | ap.av.getAlignment().addAnnotation(annotation); |
| 332 | 0 | ap.av.getAlignment().setAnnotationIndex(annotation, 0); |
| 333 | } | |
| 334 | 0 | ap.refresh(true); |
| 335 | }); | |
| 336 | } | |
| 337 | ||
| 338 | 0 | @Override |
| 339 | public void mousePressed(MouseEvent evt) | |
| 340 | { | |
| 341 | 0 | getSelectedRow(evt.getY() - getScrollOffset()); |
| 342 | 0 | oldY = evt.getY(); |
| 343 | 0 | if (evt.isPopupTrigger()) |
| 344 | { | |
| 345 | 0 | showPopupMenu(evt); |
| 346 | } | |
| 347 | } | |
| 348 | ||
| 349 | /** | |
| 350 | * Build and show the Pop-up menu at the right-click mouse position | |
| 351 | * | |
| 352 | * @param evt | |
| 353 | */ | |
| 354 | 0 | void showPopupMenu(MouseEvent evt) |
| 355 | { | |
| 356 | 0 | evt.consume(); |
| 357 | 0 | final AlignmentAnnotation[] aa = ap.av.getAlignment() |
| 358 | .getAlignmentAnnotation(); | |
| 359 | ||
| 360 | 0 | JPopupMenu pop = new JPopupMenu( |
| 361 | MessageManager.getString("label.annotations")); | |
| 362 | 0 | JMenuItem item = new JMenuItem(ADDNEW); |
| 363 | 0 | item.addActionListener(this); |
| 364 | 0 | pop.add(item); |
| 365 | 0 | if (selectedRow < 0) |
| 366 | { | |
| 367 | 0 | if (hasHiddenRows) |
| 368 | { // let the user make everything visible again | |
| 369 | 0 | item = new JMenuItem(SHOWALL); |
| 370 | 0 | item.addActionListener(this); |
| 371 | 0 | pop.add(item); |
| 372 | } | |
| 373 | 0 | pop.show(this, evt.getX(), evt.getY()); |
| 374 | 0 | return; |
| 375 | } | |
| 376 | 0 | item = new JMenuItem(EDITNAME); |
| 377 | 0 | item.addActionListener(this); |
| 378 | 0 | pop.add(item); |
| 379 | 0 | item = new JMenuItem(HIDE); |
| 380 | 0 | item.addActionListener(this); |
| 381 | 0 | pop.add(item); |
| 382 | // JAL-1264 hide all sequence-specific annotations of this type | |
| 383 | 0 | if (selectedRow < aa.length) |
| 384 | { | |
| 385 | 0 | if (aa[selectedRow].sequenceRef != null) |
| 386 | { | |
| 387 | 0 | final String label = aa[selectedRow].label; |
| 388 | 0 | JMenuItem hideType = new JMenuItem(); |
| 389 | 0 | String text = MessageManager.getString("label.hide_all") + " " |
| 390 | + label; | |
| 391 | 0 | hideType.setText(text); |
| 392 | 0 | hideType.addActionListener(new ActionListener() |
| 393 | { | |
| 394 | 0 | @Override |
| 395 | public void actionPerformed(ActionEvent e) | |
| 396 | { | |
| 397 | 0 | AlignmentUtils.showOrHideSequenceAnnotations( |
| 398 | ap.av.getAlignment(), Collections.singleton(label), | |
| 399 | null, false, false); | |
| 400 | 0 | ap.refresh(true); |
| 401 | } | |
| 402 | }); | |
| 403 | 0 | pop.add(hideType); |
| 404 | } | |
| 405 | } | |
| 406 | 0 | item = new JMenuItem(DELETE); |
| 407 | 0 | item.addActionListener(this); |
| 408 | 0 | pop.add(item); |
| 409 | 0 | if (hasHiddenRows) |
| 410 | { | |
| 411 | 0 | item = new JMenuItem(SHOWALL); |
| 412 | 0 | item.addActionListener(this); |
| 413 | 0 | pop.add(item); |
| 414 | } | |
| 415 | 0 | item = new JMenuItem(OUTPUT_TEXT); |
| 416 | 0 | item.addActionListener(this); |
| 417 | 0 | pop.add(item); |
| 418 | // TODO: annotation object should be typed for autocalculated/derived | |
| 419 | // property methods | |
| 420 | 0 | if (selectedRow < aa.length) |
| 421 | { | |
| 422 | 0 | final String label = aa[selectedRow].label; |
| 423 | 0 | if (!aa[selectedRow].autoCalculated) |
| 424 | { | |
| 425 | 0 | if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) |
| 426 | { | |
| 427 | // display formatting settings for this row. | |
| 428 | 0 | pop.addSeparator(); |
| 429 | // av and sequencegroup need to implement same interface for | |
| 430 | 0 | item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, |
| 431 | aa[selectedRow].scaleColLabel); | |
| 432 | 0 | item.addActionListener(this); |
| 433 | 0 | pop.add(item); |
| 434 | } | |
| 435 | } | |
| 436 | 0 | else if (label.indexOf("Consensus") > -1) |
| 437 | { | |
| 438 | 0 | addConsensusMenuOptions(ap, aa[selectedRow], pop); |
| 439 | ||
| 440 | 0 | final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); |
| 441 | 0 | consclipbrd.addActionListener(this); |
| 442 | 0 | pop.add(consclipbrd); |
| 443 | } | |
| 444 | ||
| 445 | 0 | addColourOrFilterByOptions(ap, aa[selectedRow], pop); |
| 446 | ||
| 447 | 0 | if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP) |
| 448 | { | |
| 449 | 0 | addContactMatrixOptions(ap, aa[selectedRow], pop); |
| 450 | // Set/adjust threshold for grouping ? | |
| 451 | // colour alignment by this [type] | |
| 452 | // select/hide columns by this row | |
| 453 | ||
| 454 | } | |
| 455 | } | |
| 456 | ||
| 457 | 0 | pop.show(this, evt.getX(), evt.getY()); |
| 458 | } | |
| 459 | ||
| 460 | 0 | static void addColourOrFilterByOptions(final AlignmentPanel ap, |
| 461 | final AlignmentAnnotation alignmentAnnotation, | |
| 462 | final JPopupMenu pop) | |
| 463 | { | |
| 464 | 0 | JMenuItem item; |
| 465 | 0 | item = new JMenuItem( |
| 466 | MessageManager.getString("label.colour_by_annotation")); | |
| 467 | 0 | item.addActionListener(new ActionListener() |
| 468 | { | |
| 469 | ||
| 470 | 0 | @Override |
| 471 | public void actionPerformed(ActionEvent e) | |
| 472 | { | |
| 473 | 0 | AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, |
| 474 | false); | |
| 475 | }; | |
| 476 | }); | |
| 477 | 0 | pop.add(item); |
| 478 | 0 | if (alignmentAnnotation.sequenceRef != null) |
| 479 | { | |
| 480 | 0 | item = new JMenuItem( |
| 481 | MessageManager.getString("label.colour_by_annotation") + " (" | |
| 482 | + MessageManager.getString("label.per_seq") + ")"); | |
| 483 | 0 | item.addActionListener(new ActionListener() |
| 484 | { | |
| 485 | 0 | @Override |
| 486 | public void actionPerformed(ActionEvent e) | |
| 487 | { | |
| 488 | 0 | AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, |
| 489 | true); | |
| 490 | }; | |
| 491 | }); | |
| 492 | 0 | pop.add(item); |
| 493 | } | |
| 494 | 0 | item = new JMenuItem( |
| 495 | MessageManager.getString("action.select_by_annotation")); | |
| 496 | 0 | item.addActionListener(new ActionListener() |
| 497 | { | |
| 498 | ||
| 499 | 0 | @Override |
| 500 | public void actionPerformed(ActionEvent e) | |
| 501 | { | |
| 502 | 0 | AnnotationColumnChooser.displayFor(ap.av, ap, alignmentAnnotation); |
| 503 | }; | |
| 504 | }); | |
| 505 | 0 | pop.add(item); |
| 506 | } | |
| 507 | ||
| 508 | 0 | static void addContactMatrixOptions(final AlignmentPanel ap, |
| 509 | final AlignmentAnnotation alignmentAnnotation, | |
| 510 | final JPopupMenu pop) | |
| 511 | { | |
| 512 | ||
| 513 | 0 | final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation); |
| 514 | 0 | JMenuItem item; |
| 515 | 0 | if (cm != null) |
| 516 | { | |
| 517 | 0 | pop.addSeparator(); |
| 518 | ||
| 519 | 0 | if (cm.hasGroups()) |
| 520 | { | |
| 521 | 0 | JCheckBoxMenuItem chitem = new JCheckBoxMenuItem( |
| 522 | MessageManager.getString("action.show_groups_on_matrix")); | |
| 523 | 0 | chitem.setToolTipText(MessageManager |
| 524 | .getString("action.show_groups_on_matrix_tooltip")); | |
| 525 | 0 | boolean showGroups = alignmentAnnotation |
| 526 | .isShowGroupsForContactMatrix(); | |
| 527 | 0 | final AlignmentAnnotation sel_row = alignmentAnnotation; |
| 528 | 0 | chitem.setState(showGroups); |
| 529 | 0 | chitem.addActionListener(new ActionListener() |
| 530 | { | |
| 531 | ||
| 532 | 0 | @Override |
| 533 | public void actionPerformed(ActionEvent e) | |
| 534 | { | |
| 535 | 0 | sel_row.setShowGroupsForContactMatrix(chitem.getState()); |
| 536 | // so any annotation colour changes are propagated - though they | |
| 537 | // probably won't be unless the annotation row colours are removed | |
| 538 | // too! | |
| 539 | 0 | ap.alignmentChanged(); |
| 540 | } | |
| 541 | }); | |
| 542 | 0 | pop.add(chitem); |
| 543 | } | |
| 544 | 0 | if (cm.hasTree()) |
| 545 | { | |
| 546 | 0 | item = new JMenuItem( |
| 547 | MessageManager.getString("action.show_tree_for_matrix")); | |
| 548 | 0 | item.setToolTipText(MessageManager |
| 549 | .getString("action.show_tree_for_matrix_tooltip")); | |
| 550 | 0 | item.addActionListener(new ActionListener() |
| 551 | { | |
| 552 | ||
| 553 | 0 | @Override |
| 554 | public void actionPerformed(ActionEvent e) | |
| 555 | { | |
| 556 | ||
| 557 | 0 | ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); |
| 558 | ||
| 559 | } | |
| 560 | }); | |
| 561 | 0 | pop.add(item); |
| 562 | } | |
| 563 | else | |
| 564 | { | |
| 565 | 0 | item = new JMenuItem( |
| 566 | MessageManager.getString("action.cluster_matrix")); | |
| 567 | 0 | item.setToolTipText( |
| 568 | MessageManager.getString("action.cluster_matrix_tooltip")); | |
| 569 | 0 | item.addActionListener(new ActionListener() |
| 570 | { | |
| 571 | 0 | @Override |
| 572 | public void actionPerformed(ActionEvent e) | |
| 573 | { | |
| 574 | 0 | new Thread(new Runnable() |
| 575 | { | |
| 576 | 0 | @Override |
| 577 | public void run() | |
| 578 | { | |
| 579 | 0 | final long progBar; |
| 580 | 0 | ap.alignFrame.setProgressBar( |
| 581 | MessageManager.formatMessage( | |
| 582 | "action.clustering_matrix_for", | |
| 583 | cm.getAnnotDescr(), 5f), | |
| 584 | progBar = System.currentTimeMillis()); | |
| 585 | 0 | cm.setGroupSet(GroupSet.makeGroups(cm, true)); |
| 586 | 0 | cm.randomlyReColourGroups(); |
| 587 | 0 | cm.transferGroupColorsTo(alignmentAnnotation); |
| 588 | 0 | ap.alignmentChanged(); |
| 589 | 0 | ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); |
| 590 | 0 | ap.alignFrame.setProgressBar(null, progBar); |
| 591 | } | |
| 592 | }).start(); | |
| 593 | } | |
| 594 | }); | |
| 595 | 0 | pop.add(item); |
| 596 | } | |
| 597 | } | |
| 598 | } | |
| 599 | ||
| 600 | /** | |
| 601 | * A helper method that adds menu options for calculation and visualisation of | |
| 602 | * group and/or alignment consensus annotation to a popup menu. This is | |
| 603 | * designed to be reusable for either unwrapped mode (popup menu is shown on | |
| 604 | * component AnnotationLabels), or wrapped mode (popup menu is shown on | |
| 605 | * IdPanel when the mouse is over an annotation label). | |
| 606 | * | |
| 607 | * @param ap | |
| 608 | * @param ann | |
| 609 | * @param pop | |
| 610 | */ | |
| 611 | 0 | static void addConsensusMenuOptions(AlignmentPanel ap, |
| 612 | AlignmentAnnotation ann, JPopupMenu pop) | |
| 613 | { | |
| 614 | 0 | pop.addSeparator(); |
| 615 | ||
| 616 | 0 | final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( |
| 617 | MessageManager.getString("label.ignore_gaps_consensus"), | |
| 618 | 0 | (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus() |
| 619 | : ap.av.isIgnoreGapsConsensus()); | |
| 620 | 0 | final AlignmentAnnotation aaa = ann; |
| 621 | 0 | cbmi.addActionListener(new ActionListener() |
| 622 | { | |
| 623 | 0 | @Override |
| 624 | public void actionPerformed(ActionEvent e) | |
| 625 | { | |
| 626 | 0 | if (aaa.groupRef != null) |
| 627 | { | |
| 628 | 0 | aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); |
| 629 | 0 | ap.getAnnotationPanel() |
| 630 | .paint(ap.getAnnotationPanel().getGraphics()); | |
| 631 | } | |
| 632 | else | |
| 633 | { | |
| 634 | 0 | ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); |
| 635 | } | |
| 636 | 0 | ap.alignmentChanged(); |
| 637 | } | |
| 638 | }); | |
| 639 | 0 | pop.add(cbmi); |
| 640 | ||
| 641 | 0 | if (aaa.groupRef != null) |
| 642 | { | |
| 643 | /* | |
| 644 | * group consensus options | |
| 645 | */ | |
| 646 | 0 | final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( |
| 647 | MessageManager.getString("label.show_group_histogram"), | |
| 648 | ann.groupRef.isShowConsensusHistogram()); | |
| 649 | 0 | chist.addActionListener(new ActionListener() |
| 650 | { | |
| 651 | 0 | @Override |
| 652 | public void actionPerformed(ActionEvent e) | |
| 653 | { | |
| 654 | 0 | aaa.groupRef.setShowConsensusHistogram(chist.getState()); |
| 655 | 0 | ap.repaint(); |
| 656 | } | |
| 657 | }); | |
| 658 | 0 | pop.add(chist); |
| 659 | 0 | final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( |
| 660 | MessageManager.getString("label.show_group_logo"), | |
| 661 | ann.groupRef.isShowSequenceLogo()); | |
| 662 | 0 | cprofl.addActionListener(new ActionListener() |
| 663 | { | |
| 664 | 0 | @Override |
| 665 | public void actionPerformed(ActionEvent e) | |
| 666 | { | |
| 667 | 0 | aaa.groupRef.setshowSequenceLogo(cprofl.getState()); |
| 668 | 0 | ap.repaint(); |
| 669 | } | |
| 670 | }); | |
| 671 | 0 | pop.add(cprofl); |
| 672 | 0 | final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( |
| 673 | MessageManager.getString("label.normalise_group_logo"), | |
| 674 | ann.groupRef.isNormaliseSequenceLogo()); | |
| 675 | 0 | cproflnorm.addActionListener(new ActionListener() |
| 676 | { | |
| 677 | 0 | @Override |
| 678 | public void actionPerformed(ActionEvent e) | |
| 679 | { | |
| 680 | 0 | aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); |
| 681 | // automatically enable logo display if we're clicked | |
| 682 | 0 | aaa.groupRef.setshowSequenceLogo(true); |
| 683 | 0 | ap.repaint(); |
| 684 | } | |
| 685 | }); | |
| 686 | 0 | pop.add(cproflnorm); |
| 687 | } | |
| 688 | else | |
| 689 | { | |
| 690 | /* | |
| 691 | * alignment consensus options | |
| 692 | */ | |
| 693 | 0 | final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( |
| 694 | MessageManager.getString("label.show_histogram"), | |
| 695 | ap.av.isShowConsensusHistogram()); | |
| 696 | 0 | chist.addActionListener(new ActionListener() |
| 697 | { | |
| 698 | 0 | @Override |
| 699 | public void actionPerformed(ActionEvent e) | |
| 700 | { | |
| 701 | 0 | ap.av.setShowConsensusHistogram(chist.getState()); |
| 702 | 0 | ap.alignFrame.setMenusForViewport(); |
| 703 | 0 | ap.repaint(); |
| 704 | } | |
| 705 | }); | |
| 706 | 0 | pop.add(chist); |
| 707 | 0 | final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( |
| 708 | MessageManager.getString("label.show_logo"), | |
| 709 | ap.av.isShowSequenceLogo()); | |
| 710 | 0 | cprof.addActionListener(new ActionListener() |
| 711 | { | |
| 712 | 0 | @Override |
| 713 | public void actionPerformed(ActionEvent e) | |
| 714 | { | |
| 715 | 0 | ap.av.setShowSequenceLogo(cprof.getState()); |
| 716 | 0 | ap.alignFrame.setMenusForViewport(); |
| 717 | 0 | ap.repaint(); |
| 718 | } | |
| 719 | }); | |
| 720 | 0 | pop.add(cprof); |
| 721 | 0 | final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( |
| 722 | MessageManager.getString("label.normalise_logo"), | |
| 723 | ap.av.isNormaliseSequenceLogo()); | |
| 724 | 0 | cprofnorm.addActionListener(new ActionListener() |
| 725 | { | |
| 726 | 0 | @Override |
| 727 | public void actionPerformed(ActionEvent e) | |
| 728 | { | |
| 729 | 0 | ap.av.setShowSequenceLogo(true); |
| 730 | 0 | ap.av.setNormaliseSequenceLogo(cprofnorm.getState()); |
| 731 | 0 | ap.alignFrame.setMenusForViewport(); |
| 732 | 0 | ap.repaint(); |
| 733 | } | |
| 734 | }); | |
| 735 | 0 | pop.add(cprofnorm); |
| 736 | } | |
| 737 | } | |
| 738 | ||
| 739 | /** | |
| 740 | * Reorders annotation rows after a drag of a label | |
| 741 | * | |
| 742 | * @param evt | |
| 743 | */ | |
| 744 | 0 | @Override |
| 745 | public void mouseReleased(MouseEvent evt) | |
| 746 | { | |
| 747 | 0 | if (evt.isPopupTrigger()) |
| 748 | { | |
| 749 | 0 | showPopupMenu(evt); |
| 750 | 0 | return; |
| 751 | } | |
| 752 | ||
| 753 | 0 | int start = selectedRow; |
| 754 | 0 | getSelectedRow(evt.getY() - getScrollOffset()); |
| 755 | 0 | int end = selectedRow; |
| 756 | ||
| 757 | /* | |
| 758 | * if dragging to resize instead, start == end | |
| 759 | */ | |
| 760 | 0 | if (start != end) |
| 761 | { | |
| 762 | // Swap these annotations | |
| 763 | 0 | AlignmentAnnotation startAA = ap.av.getAlignment() |
| 764 | .getAlignmentAnnotation()[start]; | |
| 765 | 0 | if (end == -1) |
| 766 | { | |
| 767 | 0 | end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; |
| 768 | } | |
| 769 | 0 | AlignmentAnnotation endAA = ap.av.getAlignment() |
| 770 | .getAlignmentAnnotation()[end]; | |
| 771 | ||
| 772 | 0 | ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; |
| 773 | 0 | ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; |
| 774 | } | |
| 775 | ||
| 776 | 0 | resizePanel = false; |
| 777 | 0 | dragEvent = null; |
| 778 | 0 | repaint(); |
| 779 | 0 | ap.getAnnotationPanel().repaint(); |
| 780 | } | |
| 781 | ||
| 782 | /** | |
| 783 | * Removes the height adjuster image on leaving the panel, unless currently | |
| 784 | * dragging it | |
| 785 | */ | |
| 786 | 0 | @Override |
| 787 | public void mouseExited(MouseEvent evt) | |
| 788 | { | |
| 789 | 0 | if (resizePanel && dragEvent == null) |
| 790 | { | |
| 791 | 0 | resizePanel = false; |
| 792 | 0 | repaint(); |
| 793 | } | |
| 794 | } | |
| 795 | ||
| 796 | /** | |
| 797 | * A mouse drag may be either an adjustment of the panel height (if flag | |
| 798 | * resizePanel is set on), or a reordering of the annotation rows. The former | |
| 799 | * is dealt with by this method, the latter in mouseReleased. | |
| 800 | * | |
| 801 | * @param evt | |
| 802 | */ | |
| 803 | 0 | @Override |
| 804 | public void mouseDragged(MouseEvent evt) | |
| 805 | { | |
| 806 | 0 | dragEvent = evt; |
| 807 | ||
| 808 | 0 | if (resizePanel) |
| 809 | { | |
| 810 | 0 | Dimension d = ap.annotationScroller.getPreferredSize(); |
| 811 | 0 | int dif = evt.getY() - oldY; |
| 812 | 0 | dif -= dif % ap.av.getCharHeight(); |
| 813 | ||
| 814 | // don't allow setting an annotation panel height larger than visible | |
| 815 | // (otherwise you can't get back) | |
| 816 | 0 | if (d.height - dif > ap.idPanelHolder.getHeight() |
| 817 | - ap.getIdSpaceFillerPanel1().getHeight()) | |
| 818 | { | |
| 819 | 0 | return; |
| 820 | } | |
| 821 | ||
| 822 | 0 | if ((d.height - dif) > 20) |
| 823 | { | |
| 824 | 0 | ap.annotationScroller |
| 825 | .setPreferredSize(new Dimension(d.width, d.height - dif)); | |
| 826 | 0 | d = ap.annotationSpaceFillerHolder.getPreferredSize(); |
| 827 | 0 | ap.annotationSpaceFillerHolder |
| 828 | .setPreferredSize(new Dimension(d.width, d.height - dif)); | |
| 829 | 0 | ap.paintAlignment(true, false); |
| 830 | } | |
| 831 | ||
| 832 | 0 | ap.addNotify(); |
| 833 | } | |
| 834 | else | |
| 835 | { | |
| 836 | 0 | repaint(); |
| 837 | } | |
| 838 | } | |
| 839 | ||
| 840 | /** | |
| 841 | * Updates the tooltip as the mouse moves over the labels | |
| 842 | * | |
| 843 | * @param evt | |
| 844 | */ | |
| 845 | 0 | @Override |
| 846 | public void mouseMoved(MouseEvent evt) | |
| 847 | { | |
| 848 | 0 | showOrHideAdjuster(evt); |
| 849 | ||
| 850 | 0 | getSelectedRow(evt.getY() - getScrollOffset()); |
| 851 | ||
| 852 | 0 | if (selectedRow > -1 && ap.av.getAlignment() |
| 853 | .getAlignmentAnnotation().length > selectedRow) | |
| 854 | { | |
| 855 | 0 | AlignmentAnnotation[] anns = ap.av.getAlignment() |
| 856 | .getAlignmentAnnotation(); | |
| 857 | 0 | AlignmentAnnotation aa = anns[selectedRow]; |
| 858 | ||
| 859 | 0 | String desc = getTooltip(aa); |
| 860 | 0 | this.setToolTipText(desc); |
| 861 | 0 | String msg = getStatusMessage(aa, anns); |
| 862 | 0 | ap.alignFrame.setStatus(msg); |
| 863 | } | |
| 864 | } | |
| 865 | ||
| 866 | /** | |
| 867 | * Constructs suitable text to show in the status bar when over an annotation | |
| 868 | * label, containing the associated sequence name (if any), and the annotation | |
| 869 | * labels (or all labels for a graph group annotation) | |
| 870 | * | |
| 871 | * @param aa | |
| 872 | * @param anns | |
| 873 | * @return | |
| 874 | */ | |
| 875 | 6 | static String getStatusMessage(AlignmentAnnotation aa, |
| 876 | AlignmentAnnotation[] anns) | |
| 877 | { | |
| 878 | 6 | if (aa == null) |
| 879 | { | |
| 880 | 1 | return null; |
| 881 | } | |
| 882 | ||
| 883 | 5 | StringBuilder msg = new StringBuilder(32); |
| 884 | 5 | if (aa.sequenceRef != null) |
| 885 | { | |
| 886 | 3 | msg.append(aa.sequenceRef.getName()).append(" : "); |
| 887 | } | |
| 888 | ||
| 889 | 5 | if (aa.graphGroup == -1) |
| 890 | { | |
| 891 | 2 | msg.append(aa.label); |
| 892 | 2 | if (aa.getNoOfSequencesIncluded() >= 0) |
| 893 | { | |
| 894 | 0 | msg.append(" ("); |
| 895 | 0 | msg.append(MessageManager.getString("label.sequence_count")); |
| 896 | 0 | msg.append(aa.getNoOfSequencesIncluded()); |
| 897 | 0 | msg.append(")"); |
| 898 | } | |
| 899 | } | |
| 900 | ||
| 901 | 3 | else if (anns != null) |
| 902 | { | |
| 903 | 3 | boolean first = true; |
| 904 | 9 | for (int i = anns.length - 1; i >= 0; i--) |
| 905 | { | |
| 906 | 6 | if (anns[i].graphGroup == aa.graphGroup) |
| 907 | { | |
| 908 | 5 | if (!first) |
| 909 | { | |
| 910 | 2 | msg.append(", "); |
| 911 | } | |
| 912 | 5 | msg.append(anns[i].label); |
| 913 | 5 | first = false; |
| 914 | } | |
| 915 | } | |
| 916 | } | |
| 917 | ||
| 918 | 5 | return msg.toString(); |
| 919 | } | |
| 920 | ||
| 921 | /** | |
| 922 | * Answers a tooltip, formatted as html, containing the annotation description | |
| 923 | * (prefixed by associated sequence id if applicable), and the annotation | |
| 924 | * (non-positional) score if it has one. Answers null if neither description | |
| 925 | * nor score is found. | |
| 926 | * | |
| 927 | * @param aa | |
| 928 | * @return | |
| 929 | */ | |
| 930 | 13 | static String getTooltip(AlignmentAnnotation aa) |
| 931 | { | |
| 932 | 13 | if (aa == null) |
| 933 | { | |
| 934 | 1 | return null; |
| 935 | } | |
| 936 | 12 | StringBuilder tooltip = new StringBuilder(); |
| 937 | 12 | if (aa.description != null && !aa.description.equals("New description")) |
| 938 | { | |
| 939 | // TODO: we could refactor and merge this code with the code in | |
| 940 | // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature | |
| 941 | // tooltips | |
| 942 | 10 | String desc = aa.getDescription(true).trim(); |
| 943 | 10 | if (aa.getNoOfSequencesIncluded() >= 0) |
| 944 | { | |
| 945 | 0 | desc += " (" + MessageManager.getString("label.sequence_count") |
| 946 | + aa.getNoOfSequencesIncluded() + ")"; | |
| 947 | } | |
| 948 | 10 | if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG)) |
| 949 | { | |
| 950 | 7 | tooltip.append(HTML_START_TAG); |
| 951 | 7 | desc = desc.replace("<", "<"); |
| 952 | } | |
| 953 | 3 | else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG)) |
| 954 | { | |
| 955 | 3 | desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); |
| 956 | } | |
| 957 | 10 | tooltip.append(desc); |
| 958 | } | |
| 959 | else | |
| 960 | { | |
| 961 | // begin the tooltip's html fragment | |
| 962 | 2 | tooltip.append(HTML_START_TAG); |
| 963 | } | |
| 964 | 12 | if (aa.hasScore()) |
| 965 | { | |
| 966 | 5 | if (tooltip.length() > HTML_START_TAG.length()) |
| 967 | { | |
| 968 | 3 | tooltip.append("<br/>"); |
| 969 | } | |
| 970 | // TODO: limit precision of score to avoid noise from imprecise | |
| 971 | // doubles | |
| 972 | // (64.7 becomes 64.7+/some tiny value). | |
| 973 | 5 | tooltip.append(" Score: ").append(String.valueOf(aa.score)); |
| 974 | } | |
| 975 | ||
| 976 | 12 | if (tooltip.length() > HTML_START_TAG.length()) |
| 977 | { | |
| 978 | 10 | return tooltip.append(HTML_END_TAG).toString(); |
| 979 | } | |
| 980 | ||
| 981 | /* | |
| 982 | * nothing in the tooltip (except "<html>") | |
| 983 | */ | |
| 984 | 2 | return null; |
| 985 | } | |
| 986 | ||
| 987 | /** | |
| 988 | * Shows the height adjuster image if the mouse moves into the top left | |
| 989 | * region, or hides it if the mouse leaves the regio | |
| 990 | * | |
| 991 | * @param evt | |
| 992 | */ | |
| 993 | 0 | protected void showOrHideAdjuster(MouseEvent evt) |
| 994 | { | |
| 995 | 0 | boolean was = resizePanel; |
| 996 | 0 | resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT |
| 997 | && evt.getX() < HEIGHT_ADJUSTER_WIDTH; | |
| 998 | ||
| 999 | 0 | if (resizePanel != was) |
| 1000 | { | |
| 1001 | 0 | setCursor(Cursor |
| 1002 | 0 | .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR |
| 1003 | : Cursor.DEFAULT_CURSOR)); | |
| 1004 | 0 | repaint(); |
| 1005 | } | |
| 1006 | } | |
| 1007 | ||
| 1008 | 0 | @Override |
| 1009 | public void mouseClicked(MouseEvent evt) | |
| 1010 | { | |
| 1011 | 0 | final AlignmentAnnotation[] aa = ap.av.getAlignment() |
| 1012 | .getAlignmentAnnotation(); | |
| 1013 | 0 | if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) |
| 1014 | { | |
| 1015 | 0 | if (selectedRow > -1 && selectedRow < aa.length) |
| 1016 | { | |
| 1017 | 0 | if (aa[selectedRow].groupRef != null) |
| 1018 | { | |
| 1019 | 0 | if (evt.getClickCount() >= 2) |
| 1020 | { | |
| 1021 | // todo: make the ap scroll to the selection - not necessary, first | |
| 1022 | // click highlights/scrolls, second selects | |
| 1023 | 0 | ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); |
| 1024 | // process modifiers | |
| 1025 | 0 | SequenceGroup sg = ap.av.getSelectionGroup(); |
| 1026 | 0 | if (sg == null || sg == aa[selectedRow].groupRef |
| 1027 | || !(Platform.isControlDown(evt) || evt.isShiftDown())) | |
| 1028 | { | |
| 1029 | 0 | if (Platform.isControlDown(evt) || evt.isShiftDown()) |
| 1030 | { | |
| 1031 | // clone a new selection group from the associated group | |
| 1032 | 0 | ap.av.setSelectionGroup( |
| 1033 | new SequenceGroup(aa[selectedRow].groupRef)); | |
| 1034 | } | |
| 1035 | else | |
| 1036 | { | |
| 1037 | // set selection to the associated group so it can be edited | |
| 1038 | 0 | ap.av.setSelectionGroup(aa[selectedRow].groupRef); |
| 1039 | } | |
| 1040 | } | |
| 1041 | else | |
| 1042 | { | |
| 1043 | // modify current selection with associated group | |
| 1044 | 0 | int remainToAdd = aa[selectedRow].groupRef.getSize(); |
| 1045 | 0 | for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) |
| 1046 | { | |
| 1047 | 0 | if (jalview.util.Platform.isControlDown(evt)) |
| 1048 | { | |
| 1049 | 0 | sg.addOrRemove(sgs, --remainToAdd == 0); |
| 1050 | } | |
| 1051 | else | |
| 1052 | { | |
| 1053 | // notionally, we should also add intermediate sequences from | |
| 1054 | // last added sequence ? | |
| 1055 | 0 | sg.addSequence(sgs, --remainToAdd == 0); |
| 1056 | } | |
| 1057 | } | |
| 1058 | } | |
| 1059 | ||
| 1060 | 0 | ap.paintAlignment(false, false); |
| 1061 | 0 | PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); |
| 1062 | 0 | ap.av.sendSelection(); |
| 1063 | } | |
| 1064 | else | |
| 1065 | { | |
| 1066 | 0 | ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( |
| 1067 | aa[selectedRow].groupRef.getSequences(null)); | |
| 1068 | } | |
| 1069 | 0 | return; |
| 1070 | } | |
| 1071 | 0 | else if (aa[selectedRow].sequenceRef != null) |
| 1072 | { | |
| 1073 | 0 | if (evt.getClickCount() == 1) |
| 1074 | { | |
| 1075 | 0 | ap.getSeqPanel().ap.getIdPanel() |
| 1076 | .highlightSearchResults(Arrays.asList(new SequenceI[] | |
| 1077 | { aa[selectedRow].sequenceRef })); | |
| 1078 | } | |
| 1079 | 0 | else if (evt.getClickCount() >= 2) |
| 1080 | { | |
| 1081 | 0 | ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); |
| 1082 | 0 | SequenceGroup sg = ap.av.getSelectionGroup(); |
| 1083 | 0 | if (sg != null) |
| 1084 | { | |
| 1085 | // we make a copy rather than edit the current selection if no | |
| 1086 | // modifiers pressed | |
| 1087 | // see Enhancement JAL-1557 | |
| 1088 | 0 | if (!(Platform.isControlDown(evt) || evt.isShiftDown())) |
| 1089 | { | |
| 1090 | 0 | sg = new SequenceGroup(sg); |
| 1091 | 0 | sg.clear(); |
| 1092 | 0 | sg.addSequence(aa[selectedRow].sequenceRef, false); |
| 1093 | } | |
| 1094 | else | |
| 1095 | { | |
| 1096 | 0 | if (Platform.isControlDown(evt)) |
| 1097 | { | |
| 1098 | 0 | sg.addOrRemove(aa[selectedRow].sequenceRef, true); |
| 1099 | } | |
| 1100 | else | |
| 1101 | { | |
| 1102 | // notionally, we should also add intermediate sequences from | |
| 1103 | // last added sequence ? | |
| 1104 | 0 | sg.addSequence(aa[selectedRow].sequenceRef, true); |
| 1105 | } | |
| 1106 | } | |
| 1107 | } | |
| 1108 | else | |
| 1109 | { | |
| 1110 | 0 | sg = new SequenceGroup(); |
| 1111 | 0 | sg.setStartRes(0); |
| 1112 | 0 | sg.setEndRes(ap.av.getAlignment().getWidth() - 1); |
| 1113 | 0 | sg.addSequence(aa[selectedRow].sequenceRef, false); |
| 1114 | } | |
| 1115 | 0 | ap.av.setSelectionGroup(sg); |
| 1116 | 0 | ap.paintAlignment(false, false); |
| 1117 | 0 | PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); |
| 1118 | 0 | ap.av.sendSelection(); |
| 1119 | } | |
| 1120 | ||
| 1121 | } | |
| 1122 | } | |
| 1123 | 0 | return; |
| 1124 | } | |
| 1125 | } | |
| 1126 | ||
| 1127 | /** | |
| 1128 | * do a single sequence copy to jalview and the system clipboard | |
| 1129 | * | |
| 1130 | * @param sq | |
| 1131 | * sequence to be copied to clipboard | |
| 1132 | */ | |
| 1133 | 0 | protected void copy_annotseqtoclipboard(SequenceI sq) |
| 1134 | { | |
| 1135 | 0 | SequenceI[] seqs = new SequenceI[] { sq }; |
| 1136 | 0 | String[] omitHidden = null; |
| 1137 | 0 | SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() }; |
| 1138 | 0 | if (dseqs[0] == null) |
| 1139 | { | |
| 1140 | 0 | dseqs[0] = new Sequence(sq); |
| 1141 | 0 | dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, |
| 1142 | sq.getSequenceAsString())); | |
| 1143 | ||
| 1144 | 0 | sq.setDatasetSequence(dseqs[0]); |
| 1145 | } | |
| 1146 | 0 | Alignment ds = new Alignment(dseqs); |
| 1147 | 0 | if (av.hasHiddenColumns()) |
| 1148 | { | |
| 1149 | 0 | Iterator<int[]> it = av.getAlignment().getHiddenColumns() |
| 1150 | .getVisContigsIterator(0, sq.getLength() + 1, false); | |
| 1151 | 0 | omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; |
| 1152 | } | |
| 1153 | ||
| 1154 | 0 | int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; |
| 1155 | 0 | if (av.hasHiddenColumns()) |
| 1156 | { | |
| 1157 | 0 | alignmentStartEnd = av.getAlignment().getHiddenColumns() |
| 1158 | .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); | |
| 1159 | } | |
| 1160 | ||
| 1161 | 0 | String output = new FormatAdapter().formatSequences(FileFormat.Fasta, |
| 1162 | seqs, omitHidden, alignmentStartEnd); | |
| 1163 | ||
| 1164 | 0 | Toolkit.getDefaultToolkit().getSystemClipboard() |
| 1165 | .setContents(new StringSelection(output), Desktop.instance); | |
| 1166 | ||
| 1167 | 0 | HiddenColumns hiddenColumns = null; |
| 1168 | ||
| 1169 | 0 | if (av.hasHiddenColumns()) |
| 1170 | { | |
| 1171 | 0 | hiddenColumns = new HiddenColumns( |
| 1172 | av.getAlignment().getHiddenColumns()); | |
| 1173 | } | |
| 1174 | ||
| 1175 | 0 | Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset |
| 1176 | // of a consensus | |
| 1177 | // sequence ? need to | |
| 1178 | // flag | |
| 1179 | // sequence as special. | |
| 1180 | hiddenColumns }; | |
| 1181 | } | |
| 1182 | ||
| 1183 | /** | |
| 1184 | * DOCUMENT ME! | |
| 1185 | * | |
| 1186 | * @param g1 | |
| 1187 | * DOCUMENT ME! | |
| 1188 | */ | |
| 1189 | 2109 | @Override |
| 1190 | public void paintComponent(Graphics g) | |
| 1191 | { | |
| 1192 | ||
| 1193 | 2109 | int width = getWidth(); |
| 1194 | 2109 | if (width == 0) |
| 1195 | { | |
| 1196 | 0 | width = ap.calculateIdWidth().width; |
| 1197 | } | |
| 1198 | ||
| 1199 | 2109 | Graphics2D g2 = (Graphics2D) g; |
| 1200 | 2109 | if (av.antiAlias) |
| 1201 | { | |
| 1202 | 766 | g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
| 1203 | RenderingHints.VALUE_ANTIALIAS_ON); | |
| 1204 | } | |
| 1205 | ||
| 1206 | 2109 | drawComponent(g2, true, width, true); |
| 1207 | } | |
| 1208 | ||
| 1209 | /** | |
| 1210 | * Draw the full set of annotation Labels for the alignment at the given | |
| 1211 | * cursor | |
| 1212 | * | |
| 1213 | * @param g | |
| 1214 | * Graphics2D instance (needed for font scaling) | |
| 1215 | * @param width | |
| 1216 | * Width for scaling labels | |
| 1217 | * | |
| 1218 | */ | |
| 1219 | 0 | public void drawComponent(Graphics g, int width) |
| 1220 | { | |
| 1221 | 0 | drawComponent(g, false, width, true); |
| 1222 | } | |
| 1223 | ||
| 1224 | /** | |
| 1225 | * Draw the full set of annotation Labels for the alignment at the given | |
| 1226 | * cursor | |
| 1227 | * | |
| 1228 | * @param g | |
| 1229 | * Graphics2D instance (needed for font scaling) | |
| 1230 | * @param clip | |
| 1231 | * - true indicates that only current visible area needs to be | |
| 1232 | * rendered | |
| 1233 | * @param width | |
| 1234 | * Width for scaling labels | |
| 1235 | */ | |
| 1236 | 2687 | public void drawComponent(Graphics g, boolean clip, int givenWidth, |
| 1237 | boolean forGUI) | |
| 1238 | { | |
| 1239 | 2687 | int width = givenWidth; |
| 1240 | 2687 | IdwidthAdjuster iwa = null; |
| 1241 | 2687 | if (ap != null) |
| 1242 | { | |
| 1243 | 2147 | iwa = ap.idwidthAdjuster; |
| 1244 | 2147 | if (Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true) |
| 1245 | || Jalview.isHeadlessMode()) | |
| 1246 | { | |
| 1247 | 2147 | Graphics2D g2d = (Graphics2D) g; |
| 1248 | 2147 | Graphics dummy = g2d.create(); |
| 1249 | 2147 | int newAnnotationIdWidth = drawLabels(dummy, clip, width, false, |
| 1250 | forGUI, null, false); | |
| 1251 | 2147 | dummy.dispose(); |
| 1252 | 2147 | Dimension d = ap.calculateDefaultAlignmentIdWidth(); |
| 1253 | 2147 | int alignmentIdWidth = d.width; |
| 1254 | 2147 | if (iwa != null && !iwa.manuallyAdjusted()) |
| 1255 | { | |
| 1256 | // If no manual adjustment to ID column with has been made then adjust | |
| 1257 | // width match widest of alignment or annotation id widths | |
| 1258 | 1141 | boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH", |
| 1259 | false); | |
| 1260 | 1141 | width = Math.max(alignmentIdWidth, newAnnotationIdWidth); |
| 1261 | 1141 | if (clip && width < givenWidth && !allowShrink) |
| 1262 | { | |
| 1263 | 0 | width = givenWidth; |
| 1264 | } | |
| 1265 | } | |
| 1266 | 1006 | else if (newAnnotationIdWidth != annotationIdWidth |
| 1267 | && newAnnotationIdWidth > givenWidth | |
| 1268 | && newAnnotationIdWidth > alignmentIdWidth) | |
| 1269 | { | |
| 1270 | // otherwise if the annotation id width has become larger than the | |
| 1271 | // current id width, increase | |
| 1272 | 13 | width = newAnnotationIdWidth; |
| 1273 | 13 | annotationIdWidth = newAnnotationIdWidth; |
| 1274 | } | |
| 1275 | // set the width if it's changed | |
| 1276 | 2147 | if (width != ap.av.getIdWidth()) |
| 1277 | { | |
| 1278 | 117 | iwa.setWidth(width); |
| 1279 | } | |
| 1280 | } | |
| 1281 | } | |
| 1282 | else | |
| 1283 | { | |
| 1284 | 540 | int newAnnotationIdWidth = drawLabels(g, clip, width, false, forGUI, |
| 1285 | null, false); | |
| 1286 | 540 | width = newAnnotationIdWidth < givenWidth ? givenWidth |
| 1287 | : Math.min(newAnnotationIdWidth, givenWidth); | |
| 1288 | } | |
| 1289 | 2687 | drawLabels(g, clip, width, true, forGUI, null, false); |
| 1290 | } | |
| 1291 | ||
| 1292 | /** | |
| 1293 | * Render the full set of annotation Labels for the alignment at the given | |
| 1294 | * cursor. If actuallyDraw is false or g is null then no actual drawing will | |
| 1295 | * occur, but the widest label width will be returned. If g is null then | |
| 1296 | * fmetrics must be supplied. | |
| 1297 | * | |
| 1298 | * @param g | |
| 1299 | * Graphics2D instance (used for rendering and font scaling if no | |
| 1300 | * fmetrics supplied) | |
| 1301 | * @param clip | |
| 1302 | * - true indicates that only current visible area needs to be | |
| 1303 | * rendered | |
| 1304 | * @param width | |
| 1305 | * Width for scaling labels | |
| 1306 | * @param actuallyDraw | |
| 1307 | * - when false, no graphics are rendered to g0 | |
| 1308 | * @param forGUI | |
| 1309 | * - when false, GUI relevant marks like indicators for dragging | |
| 1310 | * annotation panel height are not rendered | |
| 1311 | * @param fmetrics | |
| 1312 | * FontMetrics if Graphics object g is null | |
| 1313 | * @param includeHidden | |
| 1314 | * - when true returned width includes labels in hidden row width | |
| 1315 | * calculation | |
| 1316 | * @return the width of the annotation labels. | |
| 1317 | */ | |
| 1318 | 5742 | public int drawLabels(Graphics g0, boolean clip, int width, |
| 1319 | boolean actuallyDraw, boolean forGUI, FontMetrics fmetrics, | |
| 1320 | boolean includeHidden) | |
| 1321 | { | |
| 1322 | 5742 | if (clip) |
| 1323 | { | |
| 1324 | 4218 | clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS", |
| 1325 | true); | |
| 1326 | } | |
| 1327 | 5742 | Graphics g = null; |
| 1328 | // create a dummy Graphics object if not drawing and one is supplied | |
| 1329 | 5742 | if (g0 != null) |
| 1330 | { | |
| 1331 | 5659 | if (!actuallyDraw) |
| 1332 | { | |
| 1333 | 2972 | Graphics2D g2d = (Graphics2D) g0; |
| 1334 | 2972 | g = g2d.create(); |
| 1335 | } | |
| 1336 | else | |
| 1337 | { | |
| 1338 | 2687 | g = g0; |
| 1339 | } | |
| 1340 | } | |
| 1341 | 5742 | int actualWidth = 0; |
| 1342 | 5742 | if (g != null) |
| 1343 | { | |
| 1344 | 5659 | if (av.getFont().getSize() < 10) |
| 1345 | { | |
| 1346 | 0 | g.setFont(font); |
| 1347 | } | |
| 1348 | else | |
| 1349 | { | |
| 1350 | 5659 | g.setFont(av.getFont()); |
| 1351 | } | |
| 1352 | } | |
| 1353 | ||
| 1354 | 5742 | FontMetrics fm = fmetrics == null ? g.getFontMetrics(g.getFont()) |
| 1355 | : fmetrics; | |
| 1356 | 5742 | if (actuallyDraw) |
| 1357 | { | |
| 1358 | 2687 | g.setColor(Color.white); |
| 1359 | 2687 | g.fillRect(0, 0, getWidth(), getHeight()); |
| 1360 | ||
| 1361 | 2687 | if (!Cache.getDefault(RESIZE_MARGINS_MARK_PREF, false) |
| 1362 | && !av.getWrapAlignment() && forGUI) | |
| 1363 | { | |
| 1364 | 2109 | g.setColor(Color.LIGHT_GRAY); |
| 1365 | 2109 | g.drawLine(0, HEIGHT_ADJUSTER_HEIGHT / 4, HEIGHT_ADJUSTER_WIDTH / 4, |
| 1366 | HEIGHT_ADJUSTER_HEIGHT / 4); | |
| 1367 | 2109 | g.drawLine(0, 3 * HEIGHT_ADJUSTER_HEIGHT / 4, |
| 1368 | HEIGHT_ADJUSTER_WIDTH / 4, 3 * HEIGHT_ADJUSTER_HEIGHT / 4); | |
| 1369 | ||
| 1370 | } | |
| 1371 | } | |
| 1372 | ||
| 1373 | 5742 | if (actuallyDraw) |
| 1374 | { | |
| 1375 | 2687 | g.translate(0, getScrollOffset()); |
| 1376 | 2687 | g.setColor(Color.black); |
| 1377 | } | |
| 1378 | 5742 | SequenceI lastSeqRef = null; |
| 1379 | 5742 | String lastLabel = null; |
| 1380 | 5742 | String lastDescription = null; |
| 1381 | 5742 | AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); |
| 1382 | 5742 | boolean isShowStructureProvider = av.isShowStructureProvider(); |
| 1383 | 5742 | int fontHeight = g != null ? g.getFont().getSize() |
| 1384 | : fm.getFont().getSize(); | |
| 1385 | 5742 | int y = 0; |
| 1386 | 5742 | int x = 0; |
| 1387 | 5742 | int graphExtras = 0; |
| 1388 | 5742 | int offset = 0; |
| 1389 | 5742 | Font baseFont = g != null ? g.getFont() : fm.getFont(); |
| 1390 | 5742 | FontMetrics baseMetrics = fm; |
| 1391 | 5742 | int ofontH = fontHeight; |
| 1392 | 5742 | int sOffset = 0; |
| 1393 | 5742 | int visHeight = 0; |
| 1394 | 5742 | int[] visr = (ap != null && ap.getAnnotationPanel() != null) |
| 1395 | ? ap.getAnnotationPanel().getVisibleVRange() | |
| 1396 | : null; | |
| 1397 | 5742 | if (clip && visr != null) |
| 1398 | { | |
| 1399 | 4218 | sOffset = visr[0]; |
| 1400 | 4218 | visHeight = visr[1]; |
| 1401 | } | |
| 1402 | 5742 | boolean visible = true, before = false, after = false; |
| 1403 | 5742 | if (aa != null) |
| 1404 | { | |
| 1405 | 5742 | hasHiddenRows = false; |
| 1406 | 5742 | int olY = 0; |
| 1407 | 5742 | int nexAA = 0; |
| 1408 | 38277 | for (int i = 0; i < aa.length; i++) |
| 1409 | { | |
| 1410 | 32535 | visible = true; |
| 1411 | 32535 | if (!aa[i].isForDisplay() && !includeHidden) |
| 1412 | { | |
| 1413 | 2108 | hasHiddenRows = true; |
| 1414 | 2108 | continue; |
| 1415 | } | |
| 1416 | 30427 | olY = y; |
| 1417 | // look ahead to next annotation | |
| 1418 | 30427 | for (nexAA = i + 1; nexAA < aa.length |
| 1419 | && (!aa[nexAA].isForDisplay() && includeHidden); nexAA++) | |
| 1420 | 0 | ; |
| 1421 | 30427 | y += aa[i].height; |
| 1422 | 30427 | if (clip) |
| 1423 | { | |
| 1424 | 21362 | if (y < sOffset) |
| 1425 | { | |
| 1426 | 0 | if (!before) |
| 1427 | { | |
| 1428 | 0 | if (debugRedraw) |
| 1429 | { | |
| 1430 | 0 | jalview.bin.Console.outPrintln("before vis: " + i); |
| 1431 | } | |
| 1432 | 0 | before = true; |
| 1433 | } | |
| 1434 | // don't draw what isn't visible | |
| 1435 | 0 | continue; |
| 1436 | } | |
| 1437 | 21362 | if (olY > visHeight) |
| 1438 | { | |
| 1439 | ||
| 1440 | 1604 | if (!after) |
| 1441 | { | |
| 1442 | 744 | if (debugRedraw) |
| 1443 | { | |
| 1444 | 0 | jalview.bin.Console.outPrintln( |
| 1445 | "Scroll offset: " + sOffset + " after vis: " + i); | |
| 1446 | } | |
| 1447 | 744 | after = true; |
| 1448 | } | |
| 1449 | // don't draw what isn't visible | |
| 1450 | 1604 | continue; |
| 1451 | } | |
| 1452 | } | |
| 1453 | 28823 | if (actuallyDraw && g != null) |
| 1454 | { | |
| 1455 | 13275 | g.setColor(Color.black); |
| 1456 | } | |
| 1457 | 28823 | offset = -aa[i].height / 2; |
| 1458 | ||
| 1459 | 28823 | if (aa[i].hasText) |
| 1460 | { | |
| 1461 | 23848 | offset += fm.getHeight() / 2; |
| 1462 | 23848 | offset -= fm.getDescent(); |
| 1463 | } | |
| 1464 | else | |
| 1465 | { | |
| 1466 | 4975 | offset += fm.getDescent(); |
| 1467 | } | |
| 1468 | 28823 | String label = aa[i].label; |
| 1469 | 28823 | ParseHtmlBodyAndLinks phbDecription = new ParseHtmlBodyAndLinks( |
| 1470 | aa[i].description, true, "\n"); | |
| 1471 | 28823 | String description = phbDecription.getNonHtmlContent(); |
| 1472 | 28823 | boolean vertBar = false; |
| 1473 | 28823 | if (lastLabel != null && lastLabel.equals(label) && |
| 1474 | lastDescription != null && lastDescription.equals(description)) | |
| 1475 | { | |
| 1476 | //JAL-4427 | |
| 1477 | 1 | label = aa[i].label; // No change in label |
| 1478 | } | |
| 1479 | 28822 | else if (lastLabel != null && lastLabel.equals(label)) |
| 1480 | { | |
| 1481 | //JAL-4427 | |
| 1482 | 5 | if(!(lastDescription != null && lastDescription.equals(description)) |
| 1483 | && (aa[i].sequenceRef == lastSeqRef)) { | |
| 1484 | 4 | label = description; |
| 1485 | 4 | lastDescription = description; |
| 1486 | } | |
| 1487 | } | |
| 1488 | else | |
| 1489 | { | |
| 1490 | 28817 | if (nexAA < aa.length && label.equals(aa[nexAA].label)) // && |
| 1491 | // aa[nexY].sequenceRef==aa[i].sequenceRef) | |
| 1492 | { | |
| 1493 | 5 | lastLabel = label; |
| 1494 | // next label is the same as this label | |
| 1495 | //JAL-4427 | |
| 1496 | 5 | if((lastDescription != null && !lastDescription.equals(description))) { |
| 1497 | 0 | if(aa[nexAA].sequenceRef == aa[i].sequenceRef) { |
| 1498 | 0 | label = description; |
| 1499 | } | |
| 1500 | 0 | lastDescription = description; |
| 1501 | } | |
| 1502 | } | |
| 1503 | else | |
| 1504 | { | |
| 1505 | 28812 | lastLabel = label; |
| 1506 | 28812 | lastDescription = description; |
| 1507 | } | |
| 1508 | } | |
| 1509 | 28823 | if (aa[i].sequenceRef != null) |
| 1510 | { | |
| 1511 | 4465 | if (aa[i].sequenceRef != lastSeqRef) |
| 1512 | { | |
| 1513 | 1506 | label = aa[i].sequenceRef.getName() + " " + label; |
| 1514 | // TODO record relationship between sequence and this annotation and | |
| 1515 | // display it here | |
| 1516 | } | |
| 1517 | else | |
| 1518 | { | |
| 1519 | 2959 | vertBar = true; |
| 1520 | } | |
| 1521 | } | |
| 1522 | ||
| 1523 | 28823 | if (isShowStructureProvider && aa[i].hasIcons |
| 1524 | && Constants.SECONDARY_STRUCTURE_LABELS.keySet() | |
| 1525 | .contains(aa[i].label)) | |
| 1526 | { | |
| 1527 | 0 | String ssSource = AlignmentUtils |
| 1528 | .extractSSSourceFromAnnotationDescription(aa[i]); | |
| 1529 | 0 | if (ssSource != null && ssSource.length() > 0) |
| 1530 | 0 | label += " (" + ssSource + ")"; |
| 1531 | } | |
| 1532 | ||
| 1533 | 28823 | int labelWidth = fm.stringWidth(label) + 3; |
| 1534 | 28823 | x = width - labelWidth; |
| 1535 | ||
| 1536 | 28823 | if (aa[i].graphGroup > -1) |
| 1537 | { | |
| 1538 | 0 | int groupSize = 0; |
| 1539 | // TODO: JAL-1291 revise rendering model so the graphGroup map is | |
| 1540 | // computed efficiently for all visible labels | |
| 1541 | 0 | for (int gg = 0; gg < aa.length; gg++) |
| 1542 | { | |
| 1543 | 0 | if (aa[gg].graphGroup == aa[i].graphGroup) |
| 1544 | { | |
| 1545 | 0 | groupSize++; |
| 1546 | } | |
| 1547 | } | |
| 1548 | 0 | if (groupSize * (fontHeight + 8) < aa[i].height) |
| 1549 | { | |
| 1550 | 0 | graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) |
| 1551 | / 2; | |
| 1552 | } | |
| 1553 | else | |
| 1554 | { | |
| 1555 | // scale font to fit | |
| 1556 | 0 | float h = aa[i].height / (float) groupSize, s; |
| 1557 | 0 | if (h < 9) |
| 1558 | { | |
| 1559 | 0 | visible = false; |
| 1560 | } | |
| 1561 | else | |
| 1562 | { | |
| 1563 | 0 | fontHeight = -8 + (int) h; |
| 1564 | 0 | s = ((float) fontHeight) / (float) ofontH; |
| 1565 | 0 | Font f = baseFont |
| 1566 | .deriveFont(AffineTransform.getScaleInstance(s, s)); | |
| 1567 | 0 | Canvas c = new Canvas(); |
| 1568 | 0 | fm = c.getFontMetrics(f); |
| 1569 | 0 | if (actuallyDraw && g != null) |
| 1570 | { | |
| 1571 | 0 | g.setFont(f); |
| 1572 | // fm = g.getFontMetrics(); | |
| 1573 | 0 | graphExtras = (aa[i].height |
| 1574 | - (groupSize * (fontHeight + 8))) / 2; | |
| 1575 | } | |
| 1576 | } | |
| 1577 | } | |
| 1578 | 0 | if (visible) |
| 1579 | { | |
| 1580 | 0 | for (int gg = 0; gg < aa.length; gg++) |
| 1581 | { | |
| 1582 | 0 | if (aa[gg].graphGroup == aa[i].graphGroup) |
| 1583 | { | |
| 1584 | 0 | labelWidth = fm.stringWidth(aa[gg].label) + 3; |
| 1585 | 0 | x = width - labelWidth; |
| 1586 | 0 | if (actuallyDraw && g != null) |
| 1587 | { | |
| 1588 | 0 | g.drawString(aa[gg].label, x, y - graphExtras); |
| 1589 | ||
| 1590 | 0 | if (aa[gg]._linecolour != null) |
| 1591 | { | |
| 1592 | ||
| 1593 | 0 | g.setColor(aa[gg]._linecolour); |
| 1594 | 0 | g.drawLine(x, y - graphExtras + 3, |
| 1595 | x + fm.stringWidth(aa[gg].label), | |
| 1596 | y - graphExtras + 3); | |
| 1597 | } | |
| 1598 | ||
| 1599 | 0 | g.setColor(Color.black); |
| 1600 | } | |
| 1601 | 0 | graphExtras += fontHeight + 8; |
| 1602 | } | |
| 1603 | } | |
| 1604 | } | |
| 1605 | 0 | if (actuallyDraw && g != null) |
| 1606 | { | |
| 1607 | 0 | g.setFont(baseFont); |
| 1608 | } | |
| 1609 | 0 | fm = baseMetrics; |
| 1610 | 0 | fontHeight = ofontH; |
| 1611 | } | |
| 1612 | else | |
| 1613 | { | |
| 1614 | 28823 | if (actuallyDraw && g != null) |
| 1615 | { | |
| 1616 | 13275 | if (vertBar) |
| 1617 | { | |
| 1618 | 1182 | g.drawLine(width - 3, y + offset - fontHeight, width - 3, |
| 1619 | (int) (y - 1.5 * aa[i].height - offset - fontHeight)); | |
| 1620 | // g.drawLine(20, y + offset, x - 20, y + offset); | |
| 1621 | ||
| 1622 | } | |
| 1623 | 13275 | if(label.contains("Secondary Structure Consensus")) { |
| 1624 | //label.replace("Secondary Structure Consensus", "Secondary Structure Consensus" + "\n"); | |
| 1625 | // Split the string into lines using the newline character | |
| 1626 | 0 | String[] lines = label.split("(?<=Secondary Structure Consensus)", 2); |
| 1627 | ||
| 1628 | // Set the starting y position | |
| 1629 | 0 | int lineHeight = g.getFontMetrics().getHeight(); |
| 1630 | 0 | labelWidth = Math.max(fm.stringWidth(lines[0]), fm.stringWidth(lines[1])) + 3; |
| 1631 | ||
| 1632 | 0 | x = width - labelWidth; |
| 1633 | 0 | for (int k = 0; k < lines.length; k++) { |
| 1634 | // Draw each line, offsetting the y position by lineHeight for each line | |
| 1635 | 0 | g.drawString(lines[k].trim(), x, y + offset +(k * lineHeight)); |
| 1636 | } | |
| 1637 | } | |
| 1638 | else { | |
| 1639 | 13275 | g.drawString(label, x, y + offset); |
| 1640 | } | |
| 1641 | } | |
| 1642 | } | |
| 1643 | 28823 | lastSeqRef = aa[i].sequenceRef; |
| 1644 | ||
| 1645 | 28823 | if (labelWidth > actualWidth) |
| 1646 | { | |
| 1647 | 7838 | actualWidth = labelWidth; |
| 1648 | } | |
| 1649 | } | |
| 1650 | } | |
| 1651 | ||
| 1652 | 5742 | if (!resizePanel && dragEvent != null && aa != null && selectedRow > -1 |
| 1653 | && selectedRow < aa.length) | |
| 1654 | { | |
| 1655 | 0 | if (actuallyDraw && g != null) |
| 1656 | { | |
| 1657 | 0 | g.setColor(Color.lightGray); |
| 1658 | 0 | g.drawString( |
| 1659 | 0 | (aa[selectedRow].sequenceRef == null ? "" |
| 1660 | : aa[selectedRow].sequenceRef.getName()) | |
| 1661 | + aa[selectedRow].label, | |
| 1662 | dragEvent.getX(), dragEvent.getY() - getScrollOffset()); | |
| 1663 | } | |
| 1664 | } | |
| 1665 | ||
| 1666 | 5742 | if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) |
| 1667 | { | |
| 1668 | 0 | if (actuallyDraw && g != null) |
| 1669 | { | |
| 1670 | 0 | g.drawString(MessageManager.getString("label.right_click"), 2, 8); |
| 1671 | 0 | g.drawString(MessageManager.getString("label.to_add_annotation"), 2, |
| 1672 | 18); | |
| 1673 | } | |
| 1674 | } | |
| 1675 | ||
| 1676 | 5742 | return actualWidth; |
| 1677 | } | |
| 1678 | ||
| 1679 | 9184 | public int getScrollOffset() |
| 1680 | { | |
| 1681 | 9184 | return scrollOffset; |
| 1682 | } | |
| 1683 | ||
| 1684 | 0 | @Override |
| 1685 | public void mouseEntered(MouseEvent e) | |
| 1686 | { | |
| 1687 | } | |
| 1688 | ||
| 1689 | 38 | public void drawComponentNotGUI(Graphics idGraphics, int idWidth) |
| 1690 | { | |
| 1691 | 38 | drawComponent(idGraphics, false, idWidth, false); |
| 1692 | } | |
| 1693 | } |