Coverage Report
File AlignmentViewport.java
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20% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignmentViewport | 110 | 867 | 531 |
Contributing tests
This file is covered by 545 tests.
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| 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.viewmodel; | |
| 22 | ||
| 23 | import java.awt.Color; | |
| 24 | import java.beans.PropertyChangeSupport; | |
| 25 | import java.util.ArrayDeque; | |
| 26 | import java.util.ArrayList; | |
| 27 | import java.util.BitSet; | |
| 28 | import java.util.Deque; | |
| 29 | import java.util.HashMap; | |
| 30 | import java.util.Hashtable; | |
| 31 | import java.util.Iterator; | |
| 32 | import java.util.List; | |
| 33 | import java.util.Map; | |
| 34 | ||
| 35 | import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; | |
| 36 | import jalview.analysis.AlignmentUtils; | |
| 37 | import jalview.analysis.Conservation; | |
| 38 | import jalview.analysis.TreeModel; | |
| 39 | import jalview.api.AlignCalcManagerI2; | |
| 40 | import jalview.api.AlignCalcWorkerI; | |
| 41 | import jalview.api.AlignExportSettingsI; | |
| 42 | import jalview.api.AlignViewportI; | |
| 43 | import jalview.api.AlignmentViewPanel; | |
| 44 | import jalview.api.FeaturesDisplayedI; | |
| 45 | import jalview.api.ViewStyleI; | |
| 46 | import jalview.bin.Console; | |
| 47 | import jalview.commands.CommandI; | |
| 48 | import jalview.datamodel.AlignedCodonFrame; | |
| 49 | import jalview.datamodel.AlignmentAnnotation; | |
| 50 | import jalview.datamodel.AlignmentExportData; | |
| 51 | import jalview.datamodel.AlignmentI; | |
| 52 | import jalview.datamodel.AlignmentView; | |
| 53 | import jalview.datamodel.Annotation; | |
| 54 | import jalview.datamodel.ColumnSelection; | |
| 55 | import jalview.datamodel.ContactListI; | |
| 56 | import jalview.datamodel.ContactMatrixI; | |
| 57 | import jalview.datamodel.HiddenColumns; | |
| 58 | import jalview.datamodel.HiddenSequences; | |
| 59 | import jalview.datamodel.ProfilesI; | |
| 60 | import jalview.datamodel.SearchResultsI; | |
| 61 | import jalview.datamodel.Sequence; | |
| 62 | import jalview.datamodel.SequenceCollectionI; | |
| 63 | import jalview.datamodel.SequenceGroup; | |
| 64 | import jalview.datamodel.SequenceI; | |
| 65 | import jalview.gui.QuitHandler; | |
| 66 | import jalview.project.Jalview2XML; | |
| 67 | import jalview.renderer.ResidueShader; | |
| 68 | import jalview.renderer.ResidueShaderI; | |
| 69 | import jalview.schemes.ColourSchemeI; | |
| 70 | import jalview.structure.CommandListener; | |
| 71 | import jalview.structure.StructureSelectionManager; | |
| 72 | import jalview.structure.VamsasSource; | |
| 73 | import jalview.util.Comparison; | |
| 74 | import jalview.util.Constants; | |
| 75 | import jalview.util.MapList; | |
| 76 | import jalview.util.MappingUtils; | |
| 77 | import jalview.util.MessageManager; | |
| 78 | import jalview.viewmodel.styles.ViewStyle; | |
| 79 | import jalview.workers.AlignCalcManager2; | |
| 80 | import jalview.workers.ComplementConsensusThread; | |
| 81 | import jalview.workers.ConsensusThread; | |
| 82 | import jalview.workers.SecondaryStructureConsensusThread; | |
| 83 | import jalview.workers.InformationThread; | |
| 84 | import jalview.workers.StrucConsensusThread; | |
| 85 | ||
| 86 | import java.awt.Color; | |
| 87 | import java.beans.PropertyChangeSupport; | |
| 88 | import java.util.ArrayDeque; | |
| 89 | import java.util.ArrayList; | |
| 90 | import java.util.BitSet; | |
| 91 | import java.util.Deque; | |
| 92 | import java.util.HashMap; | |
| 93 | import java.util.Hashtable; | |
| 94 | import java.util.Iterator; | |
| 95 | import java.util.List; | |
| 96 | import java.util.Map; | |
| 97 | import java.util.concurrent.Executors; | |
| 98 | import java.util.concurrent.ScheduledExecutorService; | |
| 99 | import java.util.concurrent.ScheduledThreadPoolExecutor; | |
| 100 | ||
| 101 | /** | |
| 102 | * base class holding visualization and analysis attributes and common logic for | |
| 103 | * an active alignment view displayed in the GUI | |
| 104 | * | |
| 105 | * @author jimp | |
| 106 | * | |
| 107 | * @param <AlignmentPanelT> | |
| 108 | * implementation of the AlignmentViewPanel used by the class | |
| 109 | */ | |
| 110 | public abstract class AlignmentViewport<AlignmentPanelT extends AlignmentViewPanel> | |
| 111 | implements AlignViewportI, CommandListener, VamsasSource | |
| 112 | { | |
| 113 | public static final String PROPERTY_ALIGNMENT = "alignment"; | |
| 114 | public static final String PROPERTY_SEQUENCE = "sequence"; | |
| 115 | protected ViewportRanges ranges; | |
| 116 | ||
| 117 | protected ViewStyleI viewStyle = new ViewStyle(); | |
| 118 | ||
| 119 | /** | |
| 120 | * A viewport that hosts the cDna view of this (protein), or vice versa (if | |
| 121 | * set). | |
| 122 | */ | |
| 123 | AlignViewportI codingComplement = null; | |
| 124 | ||
| 125 | FeaturesDisplayedI featuresDisplayed = null; | |
| 126 | ||
| 127 | protected Deque<CommandI> historyList = new ArrayDeque<>(); | |
| 128 | ||
| 129 | protected Deque<CommandI> redoList = new ArrayDeque<>(); | |
| 130 | ||
| 131 | /** | |
| 132 | * used to determine if quit should be confirmed | |
| 133 | */ | |
| 134 | private boolean savedUpToDate = false; | |
| 135 | ||
| 136 | /** | |
| 137 | * alignment displayed in the viewport. Please use get/setter | |
| 138 | */ | |
| 139 | protected AlignmentI alignment; | |
| 140 | ||
| 141 | /* | |
| 142 | * probably unused indicator that view is of a dataset rather than an | |
| 143 | * alignment | |
| 144 | */ | |
| 145 | ||
| 146 | protected boolean ignoreBelowBackGroundFrequencyCalculation = false; | |
| 147 | ||
| 148 | protected boolean infoLetterHeight = false; | |
| 149 | ||
| 150 | protected AlignmentAnnotation occupancy; | |
| 151 | ||
| 152 | /** | |
| 153 | * results of alignment consensus analysis for visible portion of view | |
| 154 | */ | |
| 155 | protected ProfilesI consensusProfiles; | |
| 156 | ||
| 157 | /** | |
| 158 | * HMM profile for the alignment | |
| 159 | */ | |
| 160 | protected ProfilesI hmmProfiles; | |
| 161 | ||
| 162 | 595 |  public AlignmentViewport(AlignmentI al) |
| 163 | { | |
| 164 | 595 | setAlignment(al); |
| 165 | 595 | ranges = new ViewportRanges(al); |
| 166 | } | |
| 167 | ||
| 168 | protected AlignmentPanelT alignPanel = null; | |
| 169 | ||
| 170 | 513 | public void setAlignPanel(AlignmentPanelT ap) |
| 171 | { | |
| 172 | 513 | alignPanel = ap; |
| 173 | } | |
| 174 | ||
| 175 | /** | |
| 176 | * return the AlignmentViewPanel containing the given viewport. Use this to | |
| 177 | * get the components currently handling the given viewport. | |
| 178 | * | |
| 179 | * @param av | |
| 180 | * @return null or an alignPanel guaranteed to have non-null alignFrame | |
| 181 | * reference | |
| 182 | */ | |
| 183 | 10442 | public AlignmentPanelT getAlignPanel() |
| 184 | { | |
| 185 | 10442 | return alignPanel; |
| 186 | } | |
| 187 | ||
| 188 | /** | |
| 189 | * @param name | |
| 190 | * @see jalview.api.ViewStyleI#setFontName(java.lang.String) | |
| 191 | */ | |
| 192 | 0 | @Override |
| 193 | public void setFontName(String name) | |
| 194 | { | |
| 195 | 0 | viewStyle.setFontName(name); |
| 196 | } | |
| 197 | ||
| 198 | /** | |
| 199 | * @param style | |
| 200 | * @see jalview.api.ViewStyleI#setFontStyle(int) | |
| 201 | */ | |
| 202 | 0 | @Override |
| 203 | public void setFontStyle(int style) | |
| 204 | { | |
| 205 | 0 | viewStyle.setFontStyle(style); |
| 206 | } | |
| 207 | ||
| 208 | /** | |
| 209 | * @param size | |
| 210 | * @see jalview.api.ViewStyleI#setFontSize(int) | |
| 211 | */ | |
| 212 | 0 | @Override |
| 213 | public void setFontSize(int size) | |
| 214 | { | |
| 215 | 0 | viewStyle.setFontSize(size); |
| 216 | } | |
| 217 | ||
| 218 | /** | |
| 219 | * @return | |
| 220 | * @see jalview.api.ViewStyleI#getFontStyle() | |
| 221 | */ | |
| 222 | 0 | @Override |
| 223 | public int getFontStyle() | |
| 224 | { | |
| 225 | 0 | return viewStyle.getFontStyle(); |
| 226 | } | |
| 227 | ||
| 228 | /** | |
| 229 | * @return | |
| 230 | * @see jalview.api.ViewStyleI#getFontName() | |
| 231 | */ | |
| 232 | 0 | @Override |
| 233 | public String getFontName() | |
| 234 | { | |
| 235 | 0 | return viewStyle.getFontName(); |
| 236 | } | |
| 237 | ||
| 238 | /** | |
| 239 | * @return | |
| 240 | * @see jalview.api.ViewStyleI#getFontSize() | |
| 241 | */ | |
| 242 | 0 | @Override |
| 243 | public int getFontSize() | |
| 244 | { | |
| 245 | 0 | return viewStyle.getFontSize(); |
| 246 | } | |
| 247 | ||
| 248 | /** | |
| 249 | * @param upperCasebold | |
| 250 | * @see jalview.api.ViewStyleI#setUpperCasebold(boolean) | |
| 251 | */ | |
| 252 | 0 | @Override |
| 253 | public void setUpperCasebold(boolean upperCasebold) | |
| 254 | { | |
| 255 | 0 | viewStyle.setUpperCasebold(upperCasebold); |
| 256 | } | |
| 257 | ||
| 258 | /** | |
| 259 | * @return | |
| 260 | * @see jalview.api.ViewStyleI#isUpperCasebold() | |
| 261 | */ | |
| 262 | 0 | @Override |
| 263 | public boolean isUpperCasebold() | |
| 264 | { | |
| 265 | 0 | return viewStyle.isUpperCasebold(); |
| 266 | } | |
| 267 | ||
| 268 | /** | |
| 269 | * @return | |
| 270 | * @see jalview.api.ViewStyleI#isSeqNameItalics() | |
| 271 | */ | |
| 272 | 2487 | @Override |
| 273 | public boolean isSeqNameItalics() | |
| 274 | { | |
| 275 | 2487 | return viewStyle.isSeqNameItalics(); |
| 276 | } | |
| 277 | ||
| 278 | /** | |
| 279 | * @param colourByReferenceSeq | |
| 280 | * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean) | |
| 281 | */ | |
| 282 | 10 | @Override |
| 283 | public void setColourByReferenceSeq(boolean colourByReferenceSeq) | |
| 284 | { | |
| 285 | 10 | viewStyle.setColourByReferenceSeq(colourByReferenceSeq); |
| 286 | } | |
| 287 | ||
| 288 | /** | |
| 289 | * @param b | |
| 290 | * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean) | |
| 291 | */ | |
| 292 | 802 | @Override |
| 293 | public void setColourAppliesToAllGroups(boolean b) | |
| 294 | { | |
| 295 | 802 | viewStyle.setColourAppliesToAllGroups(b); |
| 296 | } | |
| 297 | ||
| 298 | /** | |
| 299 | * @return | |
| 300 | * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups() | |
| 301 | */ | |
| 302 | 1027 | @Override |
| 303 | public boolean getColourAppliesToAllGroups() | |
| 304 | { | |
| 305 | 1027 | return viewStyle.getColourAppliesToAllGroups(); |
| 306 | } | |
| 307 | ||
| 308 | /** | |
| 309 | * @return | |
| 310 | * @see jalview.api.ViewStyleI#getAbovePIDThreshold() | |
| 311 | */ | |
| 312 | 939 | @Override |
| 313 | public boolean getAbovePIDThreshold() | |
| 314 | { | |
| 315 | 939 | return viewStyle.getAbovePIDThreshold(); |
| 316 | } | |
| 317 | ||
| 318 | 939 | @Override |
| 319 | public boolean getByConsensusSecondaryStructureSelected() | |
| 320 | { | |
| 321 | 939 | return viewStyle.getByConsensusSecondaryStructureSelected(); |
| 322 | } | |
| 323 | ||
| 324 | 96 | public void setShowStructureProvider(boolean b) |
| 325 | { | |
| 326 | 96 | viewStyle.setShowStructureProvider(b); |
| 327 | } | |
| 328 | ||
| 329 | 5911 | public boolean isShowStructureProvider() |
| 330 | { | |
| 331 | 5911 | return viewStyle.isShowStructureProvider(); |
| 332 | } | |
| 333 | ||
| 334 | /** | |
| 335 | * @param inc | |
| 336 | * @see jalview.api.ViewStyleI#setIncrement(int) | |
| 337 | */ | |
| 338 | 96 | @Override |
| 339 | public void setIncrement(int inc) | |
| 340 | { | |
| 341 | 96 | viewStyle.setIncrement(inc); |
| 342 | } | |
| 343 | ||
| 344 | /** | |
| 345 | * @return | |
| 346 | * @see jalview.api.ViewStyleI#getIncrement() | |
| 347 | */ | |
| 348 | 0 | @Override |
| 349 | public int getIncrement() | |
| 350 | { | |
| 351 | 0 | return viewStyle.getIncrement(); |
| 352 | } | |
| 353 | ||
| 354 | /** | |
| 355 | * @param inc | |
| 356 | * @see jalview.api.ViewStyleI#setConsensusSecondaryStructureThreshold(int) | |
| 357 | */ | |
| 358 | 96 | @Override |
| 359 | public void setConsensusSecondaryStructureThreshold(int val) | |
| 360 | { | |
| 361 | 96 | viewStyle.setConsensusSecondaryStructureThreshold(val); |
| 362 | } | |
| 363 | ||
| 364 | /** | |
| 365 | * @return | |
| 366 | * @see jalview.api.ViewStyleI#getConsensusSecondaryStructureThreshold() | |
| 367 | */ | |
| 368 | 0 | @Override |
| 369 | public int getConsensusSecondaryStructureThreshold() | |
| 370 | { | |
| 371 | 0 | return viewStyle.getConsensusSecondaryStructureThreshold(); |
| 372 | } | |
| 373 | ||
| 374 | /** | |
| 375 | * @param b | |
| 376 | * @see jalview.api.ViewStyleI#setConservationSelected(boolean) | |
| 377 | */ | |
| 378 | 104 | @Override |
| 379 | public void setConservationSelected(boolean b) | |
| 380 | { | |
| 381 | 104 | viewStyle.setConservationSelected(b); |
| 382 | } | |
| 383 | ||
| 384 | /** | |
| 385 | * @param show | |
| 386 | * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean) | |
| 387 | */ | |
| 388 | 0 | @Override |
| 389 | public void setShowHiddenMarkers(boolean show) | |
| 390 | { | |
| 391 | 0 | viewStyle.setShowHiddenMarkers(show); |
| 392 | } | |
| 393 | ||
| 394 | /** | |
| 395 | * @return | |
| 396 | * @see jalview.api.ViewStyleI#getShowHiddenMarkers() | |
| 397 | */ | |
| 398 | 1473 | @Override |
| 399 | public boolean getShowHiddenMarkers() | |
| 400 | { | |
| 401 | 1473 | return viewStyle.getShowHiddenMarkers(); |
| 402 | } | |
| 403 | ||
| 404 | /** | |
| 405 | * @param b | |
| 406 | * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean) | |
| 407 | */ | |
| 408 | 9 | @Override |
| 409 | public void setScaleRightWrapped(boolean b) | |
| 410 | { | |
| 411 | 9 | viewStyle.setScaleRightWrapped(b); |
| 412 | } | |
| 413 | ||
| 414 | /** | |
| 415 | * @param b | |
| 416 | * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean) | |
| 417 | */ | |
| 418 | 11 | @Override |
| 419 | public void setScaleLeftWrapped(boolean b) | |
| 420 | { | |
| 421 | 11 | viewStyle.setScaleLeftWrapped(b); |
| 422 | } | |
| 423 | ||
| 424 | /** | |
| 425 | * @param b | |
| 426 | * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean) | |
| 427 | */ | |
| 428 | 14 | @Override |
| 429 | public void setScaleAboveWrapped(boolean b) | |
| 430 | { | |
| 431 | 14 | viewStyle.setScaleAboveWrapped(b); |
| 432 | } | |
| 433 | ||
| 434 | /** | |
| 435 | * @return | |
| 436 | * @see jalview.api.ViewStyleI#getScaleLeftWrapped() | |
| 437 | */ | |
| 438 | 2690 | @Override |
| 439 | public boolean getScaleLeftWrapped() | |
| 440 | { | |
| 441 | 2690 | return viewStyle.getScaleLeftWrapped(); |
| 442 | } | |
| 443 | ||
| 444 | /** | |
| 445 | * @return | |
| 446 | * @see jalview.api.ViewStyleI#getScaleAboveWrapped() | |
| 447 | */ | |
| 448 | 2172 | @Override |
| 449 | public boolean getScaleAboveWrapped() | |
| 450 | { | |
| 451 | 2172 | return viewStyle.getScaleAboveWrapped(); |
| 452 | } | |
| 453 | ||
| 454 | /** | |
| 455 | * @return | |
| 456 | * @see jalview.api.ViewStyleI#getScaleRightWrapped() | |
| 457 | */ | |
| 458 | 3572 | @Override |
| 459 | public boolean getScaleRightWrapped() | |
| 460 | { | |
| 461 | 3572 | return viewStyle.getScaleRightWrapped(); |
| 462 | } | |
| 463 | ||
| 464 | /** | |
| 465 | * @param b | |
| 466 | * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean) | |
| 467 | */ | |
| 468 | 105 | @Override |
| 469 | public void setAbovePIDThreshold(boolean b) | |
| 470 | { | |
| 471 | 105 | viewStyle.setAbovePIDThreshold(b); |
| 472 | } | |
| 473 | ||
| 474 | 96 | @Override |
| 475 | public void setByConsensusSecondaryStructureSelected(boolean b) | |
| 476 | { | |
| 477 | 96 | viewStyle.setByConsensusSecondaryStructureSelected(b); |
| 478 | } | |
| 479 | ||
| 480 | /** | |
| 481 | * @param thresh | |
| 482 | * @see jalview.api.ViewStyleI#setThreshold(int) | |
| 483 | */ | |
| 484 | 117 | @Override |
| 485 | public void setThreshold(int thresh) | |
| 486 | { | |
| 487 | 117 | viewStyle.setThreshold(thresh); |
| 488 | } | |
| 489 | ||
| 490 | /** | |
| 491 | * @return | |
| 492 | * @see jalview.api.ViewStyleI#getThreshold() | |
| 493 | */ | |
| 494 | 0 | @Override |
| 495 | public int getThreshold() | |
| 496 | { | |
| 497 | 0 | return viewStyle.getThreshold(); |
| 498 | } | |
| 499 | ||
| 500 | /** | |
| 501 | * @return | |
| 502 | * @see jalview.api.ViewStyleI#getShowJVSuffix() | |
| 503 | */ | |
| 504 | 19415 | @Override |
| 505 | public boolean getShowJVSuffix() | |
| 506 | { | |
| 507 | 19415 | return viewStyle.getShowJVSuffix(); |
| 508 | } | |
| 509 | ||
| 510 | /** | |
| 511 | * @param b | |
| 512 | * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean) | |
| 513 | */ | |
| 514 | 97 | @Override |
| 515 | public void setShowJVSuffix(boolean b) | |
| 516 | { | |
| 517 | 97 | viewStyle.setShowJVSuffix(b); |
| 518 | } | |
| 519 | ||
| 520 | /** | |
| 521 | * @param state | |
| 522 | * @see jalview.api.ViewStyleI#setWrapAlignment(boolean) | |
| 523 | */ | |
| 524 | 113 | @Override |
| 525 | public void setWrapAlignment(boolean state) | |
| 526 | { | |
| 527 | 113 | viewStyle.setWrapAlignment(state); |
| 528 | 113 | ranges.setWrappedMode(state); |
| 529 | } | |
| 530 | ||
| 531 | /** | |
| 532 | * @param state | |
| 533 | * @see jalview.api.ViewStyleI#setShowText(boolean) | |
| 534 | */ | |
| 535 | 96 | @Override |
| 536 | public void setShowText(boolean state) | |
| 537 | { | |
| 538 | 96 | viewStyle.setShowText(state); |
| 539 | } | |
| 540 | ||
| 541 | /** | |
| 542 | * @param state | |
| 543 | * @see jalview.api.ViewStyleI#setRenderGaps(boolean) | |
| 544 | */ | |
| 545 | 96 | @Override |
| 546 | public void setRenderGaps(boolean state) | |
| 547 | { | |
| 548 | 96 | viewStyle.setRenderGaps(state); |
| 549 | } | |
| 550 | ||
| 551 | /** | |
| 552 | * @return | |
| 553 | * @see jalview.api.ViewStyleI#getColourText() | |
| 554 | */ | |
| 555 | 789457 | @Override |
| 556 | public boolean getColourText() | |
| 557 | { | |
| 558 | 789458 | return viewStyle.getColourText(); |
| 559 | } | |
| 560 | ||
| 561 | /** | |
| 562 | * @param state | |
| 563 | * @see jalview.api.ViewStyleI#setColourText(boolean) | |
| 564 | */ | |
| 565 | 96 | @Override |
| 566 | public void setColourText(boolean state) | |
| 567 | { | |
| 568 | 96 | viewStyle.setColourText(state); |
| 569 | } | |
| 570 | ||
| 571 | /** | |
| 572 | * @return | |
| 573 | * @see jalview.api.ViewStyleI#getWrapAlignment() | |
| 574 | */ | |
| 575 | 26336 | @Override |
| 576 | public boolean getWrapAlignment() | |
| 577 | { | |
| 578 | 26336 | return viewStyle.getWrapAlignment(); |
| 579 | } | |
| 580 | ||
| 581 | /** | |
| 582 | * @return | |
| 583 | * @see jalview.api.ViewStyleI#getShowText() | |
| 584 | */ | |
| 585 | 790194 | @Override |
| 586 | public boolean getShowText() | |
| 587 | { | |
| 588 | 790194 | return viewStyle.getShowText(); |
| 589 | } | |
| 590 | ||
| 591 | /** | |
| 592 | * @return | |
| 593 | * @see jalview.api.ViewStyleI#getWrappedWidth() | |
| 594 | */ | |
| 595 | 3 | @Override |
| 596 | public int getWrappedWidth() | |
| 597 | { | |
| 598 | 3 | return viewStyle.getWrappedWidth(); |
| 599 | } | |
| 600 | ||
| 601 | /** | |
| 602 | * @param w | |
| 603 | * @see jalview.api.ViewStyleI#setWrappedWidth(int) | |
| 604 | */ | |
| 605 | 702 | @Override |
| 606 | public void setWrappedWidth(int w) | |
| 607 | { | |
| 608 | 702 | viewStyle.setWrappedWidth(w); |
| 609 | } | |
| 610 | ||
| 611 | /** | |
| 612 | * @return | |
| 613 | * @see jalview.api.ViewStyleI#getCharHeight() | |
| 614 | */ | |
| 615 | 103221 | @Override |
| 616 | public int getCharHeight() | |
| 617 | { | |
| 618 | 103221 | return viewStyle.getCharHeight(); |
| 619 | } | |
| 620 | ||
| 621 | /** | |
| 622 | * @param h | |
| 623 | * @see jalview.api.ViewStyleI#setCharHeight(int) | |
| 624 | */ | |
| 625 | 699 | @Override |
| 626 | public void setCharHeight(int h) | |
| 627 | { | |
| 628 | 699 | viewStyle.setCharHeight(h); |
| 629 | } | |
| 630 | ||
| 631 | /** | |
| 632 | * @return | |
| 633 | * @see jalview.api.ViewStyleI#getCharWidth() | |
| 634 | */ | |
| 635 | 1713463 | @Override |
| 636 | public int getCharWidth() | |
| 637 | { | |
| 638 | 1713465 | return viewStyle.getCharWidth(); |
| 639 | } | |
| 640 | ||
| 641 | /** | |
| 642 | * @param w | |
| 643 | * @see jalview.api.ViewStyleI#setCharWidth(int) | |
| 644 | */ | |
| 645 | 702 | @Override |
| 646 | public void setCharWidth(int w) | |
| 647 | { | |
| 648 | 702 | viewStyle.setCharWidth(w); |
| 649 | } | |
| 650 | ||
| 651 | /** | |
| 652 | * @return | |
| 653 | * @see jalview.api.ViewStyleI#getShowBoxes() | |
| 654 | */ | |
| 655 | 922646 | @Override |
| 656 | public boolean getShowBoxes() | |
| 657 | { | |
| 658 | 922649 | return viewStyle.getShowBoxes(); |
| 659 | } | |
| 660 | ||
| 661 | /** | |
| 662 | * @return | |
| 663 | * @see jalview.api.ViewStyleI#getShowUnconserved() | |
| 664 | */ | |
| 665 | 788608 | @Override |
| 666 | public boolean getShowUnconserved() | |
| 667 | { | |
| 668 | 788610 | return viewStyle.getShowUnconserved(); |
| 669 | } | |
| 670 | ||
| 671 | /** | |
| 672 | * @param showunconserved | |
| 673 | * @see jalview.api.ViewStyleI#setShowUnconserved(boolean) | |
| 674 | */ | |
| 675 | 96 | @Override |
| 676 | public void setShowUnconserved(boolean showunconserved) | |
| 677 | { | |
| 678 | 96 | viewStyle.setShowUnconserved(showunconserved); |
| 679 | } | |
| 680 | ||
| 681 | /** | |
| 682 | * @param default1 | |
| 683 | * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean) | |
| 684 | */ | |
| 685 | 0 | @Override |
| 686 | public void setSeqNameItalics(boolean default1) | |
| 687 | { | |
| 688 | 0 | viewStyle.setSeqNameItalics(default1); |
| 689 | } | |
| 690 | ||
| 691 | 378988 | @Override |
| 692 | public AlignmentI getAlignment() | |
| 693 | { | |
| 694 | 378992 | return alignment; |
| 695 | } | |
| 696 | ||
| 697 | 0 | @Override |
| 698 | public char getGapCharacter() | |
| 699 | { | |
| 700 | 0 | return alignment.getGapCharacter(); |
| 701 | } | |
| 702 | ||
| 703 | protected String sequenceSetID; | |
| 704 | ||
| 705 | /** | |
| 706 | * probably unused indicator that view is of a dataset rather than an | |
| 707 | * alignment | |
| 708 | */ | |
| 709 | protected boolean isDataset = false; | |
| 710 | ||
| 711 | ||
| 712 | 0 | public void setDataset(boolean b) |
| 713 | { | |
| 714 | 0 | isDataset = b; |
| 715 | } | |
| 716 | ||
| 717 | 513 | public boolean isDataset() |
| 718 | { | |
| 719 | 513 | return isDataset; |
| 720 | } | |
| 721 | ||
| 722 | private Map<SequenceI, SequenceCollectionI> hiddenRepSequences; | |
| 723 | ||
| 724 | protected ColumnSelection colSel = new ColumnSelection(); | |
| 725 | ||
| 726 | protected boolean autoCalculateConsensusAndConservation = true; | |
| 727 | ||
| 728 | 729 | public boolean getAutoCalculateConsensusAndConservation() |
| 729 | { // BH 2019.07.24 | |
| 730 | 729 | return autoCalculateConsensusAndConservation; |
| 731 | } | |
| 732 | ||
| 733 | 0 | public void setAutoCalculateConsensusAndConservation(boolean b) |
| 734 | { | |
| 735 | 0 | autoCalculateConsensusAndConservation = b; |
| 736 | } | |
| 737 | ||
| 738 | protected boolean autoCalculateStrucConsensus = true; | |
| 739 | ||
| 740 | 0 | public boolean getAutoCalculateStrucConsensus() |
| 741 | { // BH 2019.07.24 | |
| 742 | 0 | return autoCalculateStrucConsensus; |
| 743 | } | |
| 744 | ||
| 745 | 0 | public void setAutoCalculateStrucConsensus(boolean b) |
| 746 | { | |
| 747 | 0 | autoCalculateStrucConsensus = b; |
| 748 | } | |
| 749 | protected boolean ignoreGapsInConsensusCalculation = false; | |
| 750 | ||
| 751 | protected ResidueShaderI residueShading = new ResidueShader(); | |
| 752 | ||
| 753 | ||
| 754 | 282 | @Override |
| 755 | public void setGlobalColourScheme(ColourSchemeI cs) | |
| 756 | { | |
| 757 | // TODO: logic refactored from AlignFrame changeColour - | |
| 758 | // TODO: autorecalc stuff should be changed to rely on the worker system | |
| 759 | // check to see if we should implement a changeColour(cs) method rather than | |
| 760 | // put the logic in here | |
| 761 | // - means that caller decides if they want to just modify state and defer | |
| 762 | // calculation till later or to do all calculations in thread. | |
| 763 | // via changecolour | |
| 764 | ||
| 765 | /* | |
| 766 | * only instantiate alignment colouring once, thereafter update it; | |
| 767 | * this means that any conservation or PID threshold settings | |
| 768 | * persist when the alignment colour scheme is changed | |
| 769 | */ | |
| 770 | 282 | if (residueShading == null) |
| 771 | { | |
| 772 | 0 | residueShading = new ResidueShader(viewStyle); |
| 773 | } | |
| 774 | 282 | residueShading.setColourScheme(cs); |
| 775 | ||
| 776 | // TODO: do threshold and increment belong in ViewStyle or ResidueShader? | |
| 777 | // ...problem: groups need these, but do not currently have a ViewStyle | |
| 778 | ||
| 779 | 282 | if (cs != null) |
| 780 | { | |
| 781 | 88 | if (getConservationSelected()) |
| 782 | { | |
| 783 | 15 | residueShading.setConservation(hconservation); |
| 784 | } | |
| 785 | /* | |
| 786 | * reset conservation flag in case just set to false if | |
| 787 | * Conservation was null (calculation still in progress) | |
| 788 | */ | |
| 789 | 88 | residueShading.setConservationApplied(getConservationSelected()); |
| 790 | 88 | residueShading.alignmentChanged(alignment, hiddenRepSequences); |
| 791 | } | |
| 792 | ||
| 793 | /* | |
| 794 | * if 'apply colour to all groups' is selected... do so | |
| 795 | * (but don't transfer any colour threshold settings to groups) | |
| 796 | */ | |
| 797 | 282 | if (getColourAppliesToAllGroups()) |
| 798 | { | |
| 799 | 72 | for (SequenceGroup sg : getAlignment().getGroups()) |
| 800 | { | |
| 801 | /* | |
| 802 | * retain any colour thresholds per group while | |
| 803 | * changing choice of colour scheme (JAL-2386) | |
| 804 | */ | |
| 805 | 9 | sg.setColourScheme( |
| 806 | 9 | cs == null ? null : cs.getInstance(this, sg)); |
| 807 | 9 | if (cs != null) |
| 808 | { | |
| 809 | 8 | sg.getGroupColourScheme().alignmentChanged(sg, |
| 810 | hiddenRepSequences); | |
| 811 | } | |
| 812 | } | |
| 813 | } | |
| 814 | } | |
| 815 | ||
| 816 | 1492 | @Override |
| 817 | public ColourSchemeI getGlobalColourScheme() | |
| 818 | { | |
| 819 | 1492 | return residueShading == null ? null : residueShading.getColourScheme(); |
| 820 | } | |
| 821 | ||
| 822 | 927855 | @Override |
| 823 | public ResidueShaderI getResidueShading() | |
| 824 | { | |
| 825 | 927856 | return residueShading; |
| 826 | } | |
| 827 | ||
| 828 | ||
| 829 | protected AlignmentAnnotation consensus; | |
| 830 | ||
| 831 | protected List<AlignmentAnnotation> secondaryStructureConsensus; | |
| 832 | ||
| 833 | protected AlignmentAnnotation complementConsensus; | |
| 834 | ||
| 835 | protected AlignmentAnnotation gapcounts; | |
| 836 | ||
| 837 | protected AlignmentAnnotation strucConsensus; | |
| 838 | ||
| 839 | protected AlignmentAnnotation conservation; | |
| 840 | ||
| 841 | protected AlignmentAnnotation quality; | |
| 842 | ||
| 843 | protected AlignmentAnnotation[] groupConsensus; | |
| 844 | ||
| 845 | protected AlignmentAnnotation[] groupSSConsensus; | |
| 846 | ||
| 847 | protected AlignmentAnnotation[] groupConservation; | |
| 848 | ||
| 849 | /** | |
| 850 | * results of alignment consensus analysis for visible portion of view | |
| 851 | */ | |
| 852 | protected ProfilesI hconsensus = null; | |
| 853 | ||
| 854 | protected Map<String, ProfilesI> hSSConsensusProfileMap = null; | |
| 855 | ||
| 856 | ||
| 857 | /** | |
| 858 | * results of cDNA complement consensus visible portion of view | |
| 859 | */ | |
| 860 | protected Hashtable<String, Object>[] hcomplementConsensus = null; | |
| 861 | ||
| 862 | /** | |
| 863 | * results of secondary structure base pair consensus for visible portion of | |
| 864 | * view | |
| 865 | */ | |
| 866 | protected Hashtable<String, Object>[] hStrucConsensus = null; | |
| 867 | ||
| 868 | protected Conservation hconservation = null; | |
| 869 | ||
| 870 | ||
| 871 | 855 | @Override |
| 872 | public void setConservation(Conservation cons) | |
| 873 | { | |
| 874 | 855 | hconservation = cons; |
| 875 | } | |
| 876 | ||
| 877 | 1768 | @Override |
| 878 | public List<String> getSecondaryStructureSources() | |
| 879 | { | |
| 880 | 1768 | return viewStyle.getSecondaryStructureSources(); |
| 881 | } | |
| 882 | ||
| 883 | 3046 | @Override |
| 884 | public void setSecondaryStructureSources( | |
| 885 | List<String> secondaryStructureSources) | |
| 886 | { | |
| 887 | 3046 | viewStyle.setSecondaryStructureSources(secondaryStructureSources); |
| 888 | } | |
| 889 | ||
| 890 | 595 | protected void setSecondaryStructureSources(AlignmentAnnotation[] aa) |
| 891 | { | |
| 892 | 595 | List<String> sources = null; |
| 893 | ||
| 894 | 595 | if (aa != null) |
| 895 | { | |
| 896 | 494 | sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa); |
| 897 | 494 | if (sources != null) |
| 898 | { | |
| 899 | 494 | sources.add(0, Constants.SS_ALL_PROVIDERS); |
| 900 | 494 | viewStyle.setSecondaryStructureSources(sources); |
| 901 | } | |
| 902 | } | |
| 903 | } | |
| 904 | ||
| 905 | /** | |
| 906 | * percentage gaps allowed in a column before all amino acid properties should | |
| 907 | * be considered unconserved | |
| 908 | */ | |
| 909 | int ConsPercGaps = 25; // JBPNote : This should be a scalable property! | |
| 910 | ||
| 911 | 1738 | @Override |
| 912 | public int getConsPercGaps() | |
| 913 | { | |
| 914 | 1738 | return ConsPercGaps; |
| 915 | } | |
| 916 | ||
| 917 | 922 | @Override |
| 918 | public void setSequenceConsensusHash(ProfilesI hconsensus) | |
| 919 | { | |
| 920 | 922 | this.hconsensus = hconsensus; |
| 921 | } | |
| 922 | ||
| 923 | 1173 | @Override |
| 924 | public void setSequenceSSConsensusHash( | |
| 925 | Map<String, ProfilesI> hSSConsensusProfileMap) | |
| 926 | { | |
| 927 | 1173 | this.hSSConsensusProfileMap = hSSConsensusProfileMap; |
| 928 | } | |
| 929 | ||
| 930 | 3 | @Override |
| 931 | public void setComplementConsensusHash( | |
| 932 | Hashtable<String, Object>[] hconsensus) | |
| 933 | { | |
| 934 | 3 | this.hcomplementConsensus = hconsensus; |
| 935 | } | |
| 936 | ||
| 937 | 4240 | @Override |
| 938 | public ProfilesI getSequenceConsensusHash() | |
| 939 | { | |
| 940 | 4240 | return hconsensus; |
| 941 | } | |
| 942 | ||
| 943 | 4491 | @Override |
| 944 | public Map<String, ProfilesI> getSequenceSSConsensusHash() | |
| 945 | { | |
| 946 | 4491 | return hSSConsensusProfileMap; |
| 947 | } | |
| 948 | ||
| 949 | 3 | @Override |
| 950 | public void setHmmProfiles(ProfilesI info) | |
| 951 | { | |
| 952 | 3 | hmmProfiles = info; |
| 953 | } | |
| 954 | ||
| 955 | 3 | @Override |
| 956 | public ProfilesI getHmmProfiles() | |
| 957 | { | |
| 958 | 3 | return hmmProfiles; |
| 959 | } | |
| 960 | ||
| 961 | 3205 | @Override |
| 962 | public Hashtable<String, Object>[] getComplementConsensusHash() | |
| 963 | { | |
| 964 | 3205 | return hcomplementConsensus; |
| 965 | } | |
| 966 | ||
| 967 | 3204 | @Override |
| 968 | public Hashtable<String, Object>[] getRnaStructureConsensusHash() | |
| 969 | { | |
| 970 | 3204 | return hStrucConsensus; |
| 971 | } | |
| 972 | ||
| 973 | 2 | @Override |
| 974 | public void setRnaStructureConsensusHash( | |
| 975 | Hashtable<String, Object>[] hStrucConsensus) | |
| 976 | { | |
| 977 | 2 | this.hStrucConsensus = hStrucConsensus; |
| 978 | ||
| 979 | } | |
| 980 | ||
| 981 | 1611 | @Override |
| 982 | public AlignmentAnnotation getAlignmentQualityAnnot() | |
| 983 | { | |
| 984 | 1611 | return quality; |
| 985 | } | |
| 986 | ||
| 987 | 2467 | @Override |
| 988 | public AlignmentAnnotation getAlignmentConservationAnnotation() | |
| 989 | { | |
| 990 | 2467 | return conservation; |
| 991 | } | |
| 992 | ||
| 993 | 6647 | @Override |
| 994 | public AlignmentAnnotation getAlignmentConsensusAnnotation() | |
| 995 | { | |
| 996 | 6647 | return consensus; |
| 997 | } | |
| 998 | ||
| 999 | 6741 | @Override |
| 1000 | public List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation() | |
| 1001 | { | |
| 1002 | 6741 | return secondaryStructureConsensus; |
| 1003 | } | |
| 1004 | ||
| 1005 | 2776 | @Override |
| 1006 | public AlignmentAnnotation getAlignmentGapAnnotation() | |
| 1007 | { | |
| 1008 | 2776 | return gapcounts; |
| 1009 | } | |
| 1010 | ||
| 1011 | 3211 | @Override |
| 1012 | public AlignmentAnnotation getComplementConsensusAnnotation() | |
| 1013 | { | |
| 1014 | 3211 | return complementConsensus; |
| 1015 | } | |
| 1016 | ||
| 1017 | 3204 | @Override |
| 1018 | public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() | |
| 1019 | { | |
| 1020 | 3204 | return strucConsensus; |
| 1021 | } | |
| 1022 | ||
| 1023 | protected AlignCalcManagerI2 calculator = new AlignCalcManager2(); | |
| 1024 | ||
| 1025 | /** | |
| 1026 | * trigger update of conservation annotation | |
| 1027 | */ | |
| 1028 | 1065 | public void updateConservation(final AlignmentViewPanel ap) |
| 1029 | { | |
| 1030 | // see note in mantis : issue number 8585 | |
| 1031 | 1065 | if (alignment.isNucleotide() |
| 1032 | || (conservation == null && quality == null) | |
| 1033 | || !autoCalculateConsensusAndConservation) | |
| 1034 | { | |
| 1035 | 286 | return; |
| 1036 | } | |
| 1037 | 779 | if (calculator.getWorkersOfClass( |
| 1038 | jalview.workers.ConservationThread.class).isEmpty()) | |
| 1039 | { | |
| 1040 | 401 | calculator.registerWorker( |
| 1041 | new jalview.workers.ConservationThread(this, ap)); | |
| 1042 | } | |
| 1043 | } | |
| 1044 | ||
| 1045 | /** | |
| 1046 | * trigger update of consensus annotation | |
| 1047 | */ | |
| 1048 | 1424 | public void updateConsensus(final AlignmentViewPanel ap) |
| 1049 | { | |
| 1050 | // see note in mantis : issue number 8585 | |
| 1051 | 1424 | if (consensus == null || !autoCalculateConsensusAndConservation) |
| 1052 | { | |
| 1053 | 0 | return; |
| 1054 | } | |
| 1055 | 1424 | if (calculator.getWorkersOfClass(ConsensusThread.class).isEmpty()) |
| 1056 | { | |
| 1057 | 482 | calculator.registerWorker(new ConsensusThread(this, ap)); |
| 1058 | } | |
| 1059 | ||
| 1060 | /* | |
| 1061 | * A separate thread to compute cDNA consensus for a protein alignment | |
| 1062 | * which has mapping to cDNA | |
| 1063 | */ | |
| 1064 | 1424 | final AlignmentI al = this.getAlignment(); |
| 1065 | 1424 | if (!al.isNucleotide() && al.getCodonFrames() != null |
| 1066 | && !al.getCodonFrames().isEmpty()) | |
| 1067 | { | |
| 1068 | /* | |
| 1069 | * fudge - check first for protein-to-nucleotide mappings | |
| 1070 | * (we don't want to do this for protein-to-protein) | |
| 1071 | */ | |
| 1072 | 5 | boolean doConsensus = false; |
| 1073 | 5 | for (AlignedCodonFrame mapping : al.getCodonFrames()) |
| 1074 | { | |
| 1075 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 1076 | 5 | MapList[] mapLists = mapping.getdnaToProt(); |
| 1077 | // mapLists can be empty if project load has not finished resolving seqs | |
| 1078 | 5 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 1079 | { | |
| 1080 | 5 | doConsensus = true; |
| 1081 | 5 | break; |
| 1082 | } | |
| 1083 | } | |
| 1084 | 5 | if (doConsensus) |
| 1085 | { | |
| 1086 | 5 | if (calculator.getWorkersOfClass(ComplementConsensusThread.class).isEmpty()) |
| 1087 | { | |
| 1088 | 4 | calculator.registerWorker(new ComplementConsensusThread(this, ap)); |
| 1089 | } | |
| 1090 | } | |
| 1091 | } | |
| 1092 | } | |
| 1093 | ||
| 1094 | /** | |
| 1095 | * trigger update of Secondary Structure consensus annotation | |
| 1096 | */ | |
| 1097 | 1873 | public void updateSecondaryStructureConsensus(final AlignmentViewPanel ap) |
| 1098 | { | |
| 1099 | // see note in mantis : issue number 8585 | |
| 1100 | 1873 | if (secondaryStructureConsensus == null || !autoCalculateConsensusAndConservation) |
| 1101 | { | |
| 1102 | 0 | return; |
| 1103 | } | |
| 1104 | 1873 | setSecondaryStructureSources(); |
| 1105 | 1873 | List<String> ssSources = viewStyle.getSecondaryStructureSources(); |
| 1106 | 1873 | if (secondaryStructureConsensus.size() != ssSources.size()) |
| 1107 | { | |
| 1108 | ||
| 1109 | 93 | for (String source : ssSources) |
| 1110 | { | |
| 1111 | 108 | boolean ssConsensusForSourcePresent = false; |
| 1112 | 108 | for (AlignmentAnnotation aa : secondaryStructureConsensus) |
| 1113 | { | |
| 1114 | 30 | if (aa.description.startsWith(source)) |
| 1115 | { | |
| 1116 | 15 | ssConsensusForSourcePresent = true; |
| 1117 | 15 | break; |
| 1118 | } | |
| 1119 | } | |
| 1120 | ||
| 1121 | 108 | if (!ssConsensusForSourcePresent) |
| 1122 | { | |
| 1123 | 93 | AlignmentAnnotation ssConsensus = new AlignmentAnnotation( |
| 1124 | MessageManager.getString("label.ssconsensus_label") + " " | |
| 1125 | + source, | |
| 1126 | source + " " | |
| 1127 | + MessageManager | |
| 1128 | .getString("label.ssconsensus_descr"), | |
| 1129 | new Annotation[1], 0f, 100f, | |
| 1130 | AlignmentAnnotation.BAR_GRAPH); | |
| 1131 | ||
| 1132 | 93 | ssConsensus.hasText = true; |
| 1133 | 93 | ssConsensus.autoCalculated = true; |
| 1134 | 93 | secondaryStructureConsensus.add(ssConsensus); |
| 1135 | 93 | if (showSSConsensus) |
| 1136 | { | |
| 1137 | 0 | alignment.addAnnotation(ssConsensus); |
| 1138 | ||
| 1139 | } | |
| 1140 | } | |
| 1141 | } | |
| 1142 | } | |
| 1143 | 1873 | List<AlignCalcWorkerI> ssworkers = calculator.getWorkersOfClass( |
| 1144 | SecondaryStructureConsensusThread.class); | |
| 1145 | 1873 | if (ssworkers == null || ssworkers.isEmpty()) |
| 1146 | { | |
| 1147 | 482 | calculator.registerWorker( |
| 1148 | new SecondaryStructureConsensusThread(this, ap)); | |
| 1149 | } else { | |
| 1150 | 1391 | calculator.startWorker(ssworkers.get(0)); |
| 1151 | } | |
| 1152 | 1873 | ap.adjustAnnotationHeight(); |
| 1153 | ||
| 1154 | } | |
| 1155 | ||
| 1156 | 492 | @Override |
| 1157 | public void initInformationWorker(final AlignmentViewPanel ap) | |
| 1158 | { | |
| 1159 | 492 | if (calculator.getWorkersOfClass(InformationThread.class).isEmpty()) |
| 1160 | { | |
| 1161 | 482 | calculator.registerWorker(new InformationThread(this, ap)); |
| 1162 | } | |
| 1163 | } | |
| 1164 | // --------START Structure Conservation | |
| 1165 | 1421 | public void updateStrucConsensus(final AlignmentViewPanel ap) |
| 1166 | { | |
| 1167 | 1421 | if (autoCalculateStrucConsensus && strucConsensus == null |
| 1168 | && alignment.isNucleotide() && alignment.hasRNAStructure()) | |
| 1169 | { | |
| 1170 | // secondary structure has been added - so init the consensus line | |
| 1171 | 0 | initRNAStructure(); |
| 1172 | } | |
| 1173 | ||
| 1174 | // see note in mantis : issue number 8585 | |
| 1175 | 1421 | if (strucConsensus == null || !autoCalculateStrucConsensus) |
| 1176 | { | |
| 1177 | 1417 | return; |
| 1178 | } | |
| 1179 | 4 | if (calculator.getWorkersOfClass(StrucConsensusThread.class).isEmpty()) |
| 1180 | { | |
| 1181 | 2 | calculator.registerWorker(new StrucConsensusThread(this, ap)); |
| 1182 | } | |
| 1183 | } | |
| 1184 | ||
| 1185 | 3579 | public boolean isCalcInProgress() |
| 1186 | { | |
| 1187 | 3579 | return calculator.isWorking(); |
| 1188 | } | |
| 1189 | ||
| 1190 | 11616 | @Override |
| 1191 | public boolean isCalculationInProgress( | |
| 1192 | AlignmentAnnotation alignmentAnnotation) | |
| 1193 | { | |
| 1194 | 11616 | if (!alignmentAnnotation.autoCalculated) |
| 1195 | { | |
| 1196 | 0 | return false; |
| 1197 | } | |
| 1198 | 11616 | if (calculator.isWorkingWithAnnotation(alignmentAnnotation)) |
| 1199 | { | |
| 1200 | // jalview.bin.Console.errPrintln("grey out | |
| 1201 | // ("+alignmentAnnotation.label+")"); | |
| 1202 | 321 | return true; |
| 1203 | } | |
| 1204 | 11295 | return false; |
| 1205 | } | |
| 1206 | ||
| 1207 | private ScheduledExecutorService serviceExecutor = Executors.newSingleThreadScheduledExecutor(); | |
| 1208 | ||
| 1209 | /** | |
| 1210 | * Get a default scheduled executor service which can be used by | |
| 1211 | * services and calculators to run parallel jobs associated with this | |
| 1212 | * viewport. | |
| 1213 | * | |
| 1214 | * @return default service executor of that viewport | |
| 1215 | */ | |
| 1216 | 26 | public ScheduledExecutorService getServiceExecutor() |
| 1217 | { | |
| 1218 | 26 | return serviceExecutor; |
| 1219 | } | |
| 1220 | ||
| 1221 | 907 | public void setAlignment(AlignmentI align) |
| 1222 | { | |
| 1223 | 907 | this.alignment = align; |
| 1224 | } | |
| 1225 | ||
| 1226 | /** | |
| 1227 | * Clean up references when this viewport is closed | |
| 1228 | */ | |
| 1229 | 312 | @Override |
| 1230 | public void dispose() | |
| 1231 | { | |
| 1232 | /* | |
| 1233 | * defensively null out references to large objects in case | |
| 1234 | * this object is not garbage collected (as if!) | |
| 1235 | */ | |
| 1236 | 312 | alignPanel=null; |
| 1237 | 312 | consensus = null; |
| 1238 | 312 | complementConsensus = null; |
| 1239 | 312 | strucConsensus = null; |
| 1240 | 312 | secondaryStructureConsensus = null; |
| 1241 | 312 | conservation = null; |
| 1242 | 312 | quality = null; |
| 1243 | 312 | consensusProfiles = null; |
| 1244 | 312 | groupConsensus = null; |
| 1245 | 312 | groupConservation = null; |
| 1246 | 312 | hconsensus = null; |
| 1247 | 312 | hconservation = null; |
| 1248 | 312 | hcomplementConsensus = null; |
| 1249 | 312 | gapcounts = null; |
| 1250 | 312 | calculator.shutdown(); |
| 1251 | 312 | calculator = null; |
| 1252 | 312 | serviceExecutor.shutdown(); |
| 1253 | 312 | serviceExecutor = null; |
| 1254 | 312 | residueShading = null; // may hold a reference to Consensus |
| 1255 | 312 | changeSupport = null; |
| 1256 | 312 | ranges = null; |
| 1257 | 312 | currentTree = null; |
| 1258 | 312 | selectionGroup = null; |
| 1259 | 312 | colSel = null; |
| 1260 | 312 | setAlignment(null); |
| 1261 | } | |
| 1262 | ||
| 1263 | 3813 | @Override |
| 1264 | public boolean isClosed() | |
| 1265 | { | |
| 1266 | // TODO: check that this isClosed is only true after panel is closed, not | |
| 1267 | // before it is fully constructed. | |
| 1268 | 3813 | return alignment == null; |
| 1269 | } | |
| 1270 | ||
| 1271 | 3805 | @Override |
| 1272 | public AlignCalcManagerI2 getCalcManager() | |
| 1273 | { | |
| 1274 | 3805 | return calculator; |
| 1275 | } | |
| 1276 | ||
| 1277 | /** | |
| 1278 | * should conservation rows be shown for groups | |
| 1279 | */ | |
| 1280 | protected boolean showGroupConservation = false; | |
| 1281 | ||
| 1282 | /** | |
| 1283 | * should consensus rows be shown for groups | |
| 1284 | */ | |
| 1285 | protected boolean showGroupConsensus = false; | |
| 1286 | ||
| 1287 | protected boolean showGroupSSConsensus = false; | |
| 1288 | ||
| 1289 | /** | |
| 1290 | * should consensus profile be rendered by default | |
| 1291 | */ | |
| 1292 | protected boolean showSequenceLogo = false; | |
| 1293 | ||
| 1294 | /** | |
| 1295 | * should consensus profile be rendered normalised to row height | |
| 1296 | */ | |
| 1297 | protected boolean normaliseSequenceLogo = false; | |
| 1298 | ||
| 1299 | /** | |
| 1300 | * should consensus histograms be rendered by default | |
| 1301 | */ | |
| 1302 | protected boolean showConsensusHistogram = true; | |
| 1303 | ||
| 1304 | /** | |
| 1305 | * should hmm profile be rendered by default | |
| 1306 | */ | |
| 1307 | protected boolean hmmShowSequenceLogo = false; | |
| 1308 | ||
| 1309 | /** | |
| 1310 | * should hmm profile be rendered normalised to row height | |
| 1311 | */ | |
| 1312 | protected boolean hmmNormaliseSequenceLogo = false; | |
| 1313 | ||
| 1314 | /** | |
| 1315 | * should information histograms be rendered by default | |
| 1316 | */ | |
| 1317 | protected boolean hmmShowHistogram = true; | |
| 1318 | ||
| 1319 | /** | |
| 1320 | * @return the showConsensusProfile | |
| 1321 | */ | |
| 1322 | 6600 | @Override |
| 1323 | public boolean isShowSequenceLogo() | |
| 1324 | { | |
| 1325 | 6600 | return showSequenceLogo; |
| 1326 | } | |
| 1327 | ||
| 1328 | /** | |
| 1329 | * @return the showInformationProfile | |
| 1330 | */ | |
| 1331 | 1183 | @Override |
| 1332 | public boolean isShowHMMSequenceLogo() | |
| 1333 | { | |
| 1334 | 1183 | return hmmShowSequenceLogo; |
| 1335 | } | |
| 1336 | ||
| 1337 | /** | |
| 1338 | * @param showSequenceLogo | |
| 1339 | * the new value | |
| 1340 | */ | |
| 1341 | 96 | public void setShowSequenceLogo(boolean showSequenceLogo) |
| 1342 | { | |
| 1343 | 96 | if (showSequenceLogo != this.showSequenceLogo) |
| 1344 | { | |
| 1345 | // TODO: decouple settings setting from calculation when refactoring | |
| 1346 | // annotation update method from alignframe to viewport | |
| 1347 | 20 | this.showSequenceLogo = showSequenceLogo; |
| 1348 | 20 | for (AlignCalcWorkerI worker : calculator.getWorkers()) |
| 1349 | { | |
| 1350 | 80 | if (worker.getClass().equals(ConsensusThread.class) || |
| 1351 | worker.getClass().equals(ComplementConsensusThread.class) || | |
| 1352 | worker.getClass().equals(StrucConsensusThread.class) || | |
| 1353 | worker.getClass().equals(SecondaryStructureConsensusThread.class)) | |
| 1354 | { | |
| 1355 | 40 | worker.updateAnnotation(); |
| 1356 | } | |
| 1357 | } | |
| 1358 | } | |
| 1359 | 96 | this.showSequenceLogo = showSequenceLogo; |
| 1360 | } | |
| 1361 | ||
| 1362 | 595 | public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo) |
| 1363 | { | |
| 1364 | 595 | if (showHMMSequenceLogo != this.hmmShowSequenceLogo) |
| 1365 | { | |
| 1366 | 225 | this.hmmShowSequenceLogo = showHMMSequenceLogo; |
| 1367 | // TODO: updateAnnotation if description (tooltip) will show | |
| 1368 | // profile in place of information content? | |
| 1369 | // calculator.updateAnnotationFor(InformationThread.class); | |
| 1370 | } | |
| 1371 | 595 | this.hmmShowSequenceLogo = showHMMSequenceLogo; |
| 1372 | } | |
| 1373 | /** | |
| 1374 | * @param showConsensusHistogram | |
| 1375 | * the showConsensusHistogram to set | |
| 1376 | */ | |
| 1377 | 96 | public void setShowConsensusHistogram(boolean showConsensusHistogram) |
| 1378 | { | |
| 1379 | 96 | this.showConsensusHistogram = showConsensusHistogram; |
| 1380 | } | |
| 1381 | ||
| 1382 | /** | |
| 1383 | * @param showInformationHistogram | |
| 1384 | */ | |
| 1385 | 595 | public void setShowInformationHistogram(boolean showInformationHistogram) |
| 1386 | { | |
| 1387 | 595 | this.hmmShowHistogram = showInformationHistogram; |
| 1388 | } | |
| 1389 | ||
| 1390 | /** | |
| 1391 | * @return the showGroupConservation | |
| 1392 | */ | |
| 1393 | 1219 | public boolean isShowGroupConservation() |
| 1394 | { | |
| 1395 | 1219 | return showGroupConservation; |
| 1396 | } | |
| 1397 | ||
| 1398 | /** | |
| 1399 | * @param showGroupConservation | |
| 1400 | * the showGroupConservation to set | |
| 1401 | */ | |
| 1402 | 96 | public void setShowGroupConservation(boolean showGroupConservation) |
| 1403 | { | |
| 1404 | 96 | this.showGroupConservation = showGroupConservation; |
| 1405 | } | |
| 1406 | ||
| 1407 | /** | |
| 1408 | * @return the showGroupConsensus | |
| 1409 | */ | |
| 1410 | 1219 | public boolean isShowGroupConsensus() |
| 1411 | { | |
| 1412 | 1219 | return showGroupConsensus; |
| 1413 | } | |
| 1414 | ||
| 1415 | 1219 | public boolean isShowGroupSSConsensus() |
| 1416 | { | |
| 1417 | 1219 | return showGroupSSConsensus; |
| 1418 | } | |
| 1419 | ||
| 1420 | /** | |
| 1421 | * @param showGroupConsensus | |
| 1422 | * the showGroupConsensus to set | |
| 1423 | */ | |
| 1424 | 96 | public void setShowGroupConsensus(boolean showGroupConsensus) |
| 1425 | { | |
| 1426 | 96 | this.showGroupConsensus = showGroupConsensus; |
| 1427 | } | |
| 1428 | ||
| 1429 | 96 | public void setShowGroupSSConsensus(boolean showGroupSSConsensus) |
| 1430 | { | |
| 1431 | 96 | this.showGroupSSConsensus = showGroupSSConsensus; |
| 1432 | } | |
| 1433 | ||
| 1434 | /** | |
| 1435 | * @param showSSConsensus | |
| 1436 | * the showSSConsensus to set | |
| 1437 | */ | |
| 1438 | 0 | public void setShowSSConsensus(boolean showSSConsensus) |
| 1439 | { | |
| 1440 | 0 | this.showSSConsensus = showSSConsensus; |
| 1441 | } | |
| 1442 | ||
| 1443 | /** | |
| 1444 | * | |
| 1445 | * @return flag to indicate if the consensus histogram should be rendered by | |
| 1446 | * default | |
| 1447 | */ | |
| 1448 | 4421 | @Override |
| 1449 | public boolean isShowConsensusHistogram() | |
| 1450 | { | |
| 1451 | 4421 | return this.showConsensusHistogram; |
| 1452 | } | |
| 1453 | ||
| 1454 | /** | |
| 1455 | * | |
| 1456 | * @return flag to indicate if the information content histogram should be | |
| 1457 | * rendered by default | |
| 1458 | */ | |
| 1459 | 1183 | @Override |
| 1460 | public boolean isShowInformationHistogram() | |
| 1461 | { | |
| 1462 | 1183 | return this.hmmShowHistogram; |
| 1463 | } | |
| 1464 | ||
| 1465 | /** | |
| 1466 | * when set, updateAlignment will always ensure sequences are of equal length | |
| 1467 | */ | |
| 1468 | private boolean padGaps = false; | |
| 1469 | ||
| 1470 | /** | |
| 1471 | * when set, alignment should be reordered according to a newly opened tree | |
| 1472 | */ | |
| 1473 | public boolean sortByTree = false; | |
| 1474 | ||
| 1475 | /** | |
| 1476 | * | |
| 1477 | * | |
| 1478 | * @return null or the currently selected sequence region | |
| 1479 | */ | |
| 1480 | 29259 | @Override |
| 1481 | public SequenceGroup getSelectionGroup() | |
| 1482 | { | |
| 1483 | 29259 | return selectionGroup; |
| 1484 | } | |
| 1485 | ||
| 1486 | /** | |
| 1487 | * Set the selection group for this window. Also sets the current alignment as | |
| 1488 | * the context for the group, if it does not already have one. | |
| 1489 | * @param sg | |
| 1490 | * - group holding references to sequences in this alignment view | |
| 1491 | * | |
| 1492 | */ | |
| 1493 | 235 | @Override |
| 1494 | public void setSelectionGroup(SequenceGroup sg) | |
| 1495 | { | |
| 1496 | 235 | selectionGroup = sg; |
| 1497 | 235 | if (sg != null && sg.getContext() == null) |
| 1498 | { | |
| 1499 | 37 | sg.setContext(alignment); |
| 1500 | } | |
| 1501 | } | |
| 1502 | ||
| 1503 | 1 | public void setHiddenColumns(HiddenColumns hidden) |
| 1504 | { | |
| 1505 | 1 | this.alignment.setHiddenColumns(hidden); |
| 1506 | } | |
| 1507 | ||
| 1508 | 5815 | @Override |
| 1509 | public ColumnSelection getColumnSelection() | |
| 1510 | { | |
| 1511 | 5815 | return colSel; |
| 1512 | } | |
| 1513 | ||
| 1514 | 13 | @Override |
| 1515 | public void setColumnSelection(ColumnSelection colSel) | |
| 1516 | { | |
| 1517 | 13 | this.colSel = colSel; |
| 1518 | 13 | if (colSel != null) |
| 1519 | { | |
| 1520 | 13 | updateHiddenColumns(); |
| 1521 | } | |
| 1522 | 13 | isColSelChanged(true); |
| 1523 | } | |
| 1524 | ||
| 1525 | /** | |
| 1526 | * | |
| 1527 | * @return | |
| 1528 | */ | |
| 1529 | 32 | @Override |
| 1530 | public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences() | |
| 1531 | { | |
| 1532 | 32 | return hiddenRepSequences; |
| 1533 | } | |
| 1534 | ||
| 1535 | 0 | @Override |
| 1536 | public void setHiddenRepSequences( | |
| 1537 | Map<SequenceI, SequenceCollectionI> hiddenRepSequences) | |
| 1538 | { | |
| 1539 | 0 | this.hiddenRepSequences = hiddenRepSequences; |
| 1540 | } | |
| 1541 | ||
| 1542 | 0 | @Override |
| 1543 | public boolean hasSelectedColumns() | |
| 1544 | { | |
| 1545 | 0 | ColumnSelection columnSelection = getColumnSelection(); |
| 1546 | 0 | return columnSelection != null && columnSelection.hasSelectedColumns(); |
| 1547 | } | |
| 1548 | ||
| 1549 | 15006 | @Override |
| 1550 | public boolean hasHiddenColumns() | |
| 1551 | { | |
| 1552 | 15006 | return alignment.getHiddenColumns() != null |
| 1553 | && alignment.getHiddenColumns().hasHiddenColumns(); | |
| 1554 | } | |
| 1555 | ||
| 1556 | 14 | public void updateHiddenColumns() |
| 1557 | { | |
| 1558 | // this method doesn't really do anything now. But - it could, since a | |
| 1559 | // column Selection could be in the process of modification | |
| 1560 | // hasHiddenColumns = colSel.hasHiddenColumns(); | |
| 1561 | } | |
| 1562 | ||
| 1563 | 3747 | @Override |
| 1564 | public boolean hasHiddenRows() | |
| 1565 | { | |
| 1566 | 3747 | return alignment.getHiddenSequences().getSize() > 0; |
| 1567 | } | |
| 1568 | ||
| 1569 | protected SequenceGroup selectionGroup; | |
| 1570 | ||
| 1571 | 96 | public void setSequenceSetId(String newid) |
| 1572 | { | |
| 1573 | 96 | if (sequenceSetID != null) |
| 1574 | { | |
| 1575 | 96 | jalview.bin.Console.errPrintln( |
| 1576 | "Warning - overwriting a sequenceSetId for a viewport!"); | |
| 1577 | } | |
| 1578 | 96 | sequenceSetID = new String(newid); |
| 1579 | } | |
| 1580 | ||
| 1581 | 5279 | @Override |
| 1582 | public String getSequenceSetId() | |
| 1583 | { | |
| 1584 | 5279 | if (sequenceSetID == null) |
| 1585 | { | |
| 1586 | 389 | sequenceSetID = alignment.hashCode() + ""; |
| 1587 | } | |
| 1588 | ||
| 1589 | 5279 | return sequenceSetID; |
| 1590 | } | |
| 1591 | ||
| 1592 | /** | |
| 1593 | * unique viewId for synchronizing state (e.g. with stored Jalview Project) | |
| 1594 | * | |
| 1595 | */ | |
| 1596 | protected String viewId = null; | |
| 1597 | ||
| 1598 | 615 | @Override |
| 1599 | public String getViewId() | |
| 1600 | { | |
| 1601 | 615 | if (viewId == null) |
| 1602 | { | |
| 1603 | 303 | viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; |
| 1604 | } | |
| 1605 | 615 | return viewId; |
| 1606 | } | |
| 1607 | ||
| 1608 | 99 | public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) |
| 1609 | { | |
| 1610 | 99 | ignoreGapsInConsensusCalculation = b; |
| 1611 | 99 | if (ap != null) |
| 1612 | { | |
| 1613 | 3 | updateConsensus(ap); |
| 1614 | 3 | updateSecondaryStructureConsensus(ap); |
| 1615 | 3 | if (residueShading != null) |
| 1616 | { | |
| 1617 | 3 | residueShading.setThreshold(residueShading.getThreshold(), |
| 1618 | ignoreGapsInConsensusCalculation); | |
| 1619 | } | |
| 1620 | } | |
| 1621 | } | |
| 1622 | ||
| 1623 | 0 | public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap) |
| 1624 | { | |
| 1625 | 0 | ignoreBelowBackGroundFrequencyCalculation = b; |
| 1626 | } | |
| 1627 | ||
| 1628 | 0 | public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap) |
| 1629 | { | |
| 1630 | 0 | infoLetterHeight = b; |
| 1631 | } | |
| 1632 | ||
| 1633 | private long sgrouphash = -1, colselhash = -1; | |
| 1634 | ||
| 1635 | /** | |
| 1636 | * checks current SelectionGroup against record of last hash value, and | |
| 1637 | * updates record. | |
| 1638 | * | |
| 1639 | * @param b | |
| 1640 | * update the record of last hash value | |
| 1641 | * | |
| 1642 | * @return true if SelectionGroup changed since last call (when b is true) | |
| 1643 | */ | |
| 1644 | 443 | public boolean isSelectionGroupChanged(boolean b) |
| 1645 | { | |
| 1646 | 443 | int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1 |
| 1647 | : selectionGroup.hashCode(); | |
| 1648 | 443 | if (hc != -1 && hc != sgrouphash) |
| 1649 | { | |
| 1650 | 105 | if (b) |
| 1651 | { | |
| 1652 | 9 | sgrouphash = hc; |
| 1653 | } | |
| 1654 | 105 | return true; |
| 1655 | } | |
| 1656 | 338 | return false; |
| 1657 | } | |
| 1658 | ||
| 1659 | /** | |
| 1660 | * checks current colsel against record of last hash value, and optionally | |
| 1661 | * updates record. | |
| 1662 | * | |
| 1663 | * @param updateHash | |
| 1664 | * update the record of last hash value | |
| 1665 | * @return true if colsel changed since last call (when b is true) | |
| 1666 | */ | |
| 1667 | 266 | public boolean isColSelChanged(boolean updateHash) |
| 1668 | { | |
| 1669 | 266 | int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode(); |
| 1670 | 266 | if (hc != -1 && hc != colselhash) |
| 1671 | { | |
| 1672 | 17 | if (updateHash) |
| 1673 | { | |
| 1674 | 17 | colselhash = hc; |
| 1675 | } | |
| 1676 | 17 | return true; |
| 1677 | } | |
| 1678 | 249 | notifySequence(); |
| 1679 | 249 | return false; |
| 1680 | } | |
| 1681 | ||
| 1682 | 5455 | @Override |
| 1683 | public boolean isIgnoreGapsConsensus() | |
| 1684 | { | |
| 1685 | 5455 | return ignoreGapsInConsensusCalculation; |
| 1686 | } | |
| 1687 | ||
| 1688 | 3205 | @Override |
| 1689 | public boolean isIgnoreBelowBackground() | |
| 1690 | { | |
| 1691 | 3205 | return ignoreBelowBackGroundFrequencyCalculation; |
| 1692 | } | |
| 1693 | ||
| 1694 | 3205 | @Override |
| 1695 | public boolean isInfoLetterHeight() | |
| 1696 | { | |
| 1697 | 3205 | return infoLetterHeight; |
| 1698 | } | |
| 1699 | // property change stuff | |
| 1700 | // JBPNote Prolly only need this in the applet version. | |
| 1701 | private PropertyChangeSupport changeSupport = new PropertyChangeSupport( | |
| 1702 | this); | |
| 1703 | ||
| 1704 | protected boolean showConservation = true; | |
| 1705 | ||
| 1706 | protected boolean showQuality = true; | |
| 1707 | ||
| 1708 | protected boolean showConsensus = true; | |
| 1709 | ||
| 1710 | protected boolean showSSConsensus = true; | |
| 1711 | ||
| 1712 | protected boolean showOccupancy = true; | |
| 1713 | ||
| 1714 | private Map<SequenceI, Color> sequenceColours = new HashMap<>(); | |
| 1715 | ||
| 1716 | private Map<AlignmentAnnotation, Color> annotationColours = new HashMap<>(); | |
| 1717 | ||
| 1718 | protected SequenceAnnotationOrder sortAnnotationsBy = null; | |
| 1719 | ||
| 1720 | protected boolean showAutocalculatedAbove; | |
| 1721 | ||
| 1722 | /** | |
| 1723 | * when set, view will scroll to show the highlighted position | |
| 1724 | */ | |
| 1725 | private boolean followHighlight = true; | |
| 1726 | ||
| 1727 | /** | |
| 1728 | * Property change listener for changes in alignment | |
| 1729 | * | |
| 1730 | * @param listener | |
| 1731 | * DOCUMENT ME! | |
| 1732 | */ | |
| 1733 | 529 | public void addPropertyChangeListener( |
| 1734 | java.beans.PropertyChangeListener listener) | |
| 1735 | { | |
| 1736 | 529 | changeSupport.addPropertyChangeListener(listener); |
| 1737 | } | |
| 1738 | ||
| 1739 | /** | |
| 1740 | * DOCUMENT ME! | |
| 1741 | * | |
| 1742 | * @param listener | |
| 1743 | * DOCUMENT ME! | |
| 1744 | */ | |
| 1745 | 331 | public void removePropertyChangeListener( |
| 1746 | java.beans.PropertyChangeListener listener) | |
| 1747 | { | |
| 1748 | 331 | if (changeSupport != null) |
| 1749 | { | |
| 1750 | 330 | changeSupport.removePropertyChangeListener(listener); |
| 1751 | } | |
| 1752 | } | |
| 1753 | ||
| 1754 | /** | |
| 1755 | * Property change listener for changes in alignment | |
| 1756 | * | |
| 1757 | * @param prop | |
| 1758 | * DOCUMENT ME! | |
| 1759 | * @param oldvalue | |
| 1760 | * DOCUMENT ME! | |
| 1761 | * @param newvalue | |
| 1762 | * DOCUMENT ME! | |
| 1763 | */ | |
| 1764 | 0 | public void firePropertyChange(String prop, Object oldvalue, |
| 1765 | Object newvalue) | |
| 1766 | { | |
| 1767 | 0 | changeSupport.firePropertyChange(prop, oldvalue, newvalue); |
| 1768 | } | |
| 1769 | ||
| 1770 | ||
| 1771 | /** | |
| 1772 | * Notify TreePanel and AlignmentPanel of some sort of alignment change. | |
| 1773 | */ | |
| 1774 | 75 | public void notifyAlignment() |
| 1775 | { | |
| 1776 | 75 | changeSupport.firePropertyChange(PROPERTY_ALIGNMENT, null, alignment.getSequences()); |
| 1777 | } | |
| 1778 | ||
| 1779 | /** | |
| 1780 | * Notify AlignmentPanel of a sequence column selection or visibility changes. | |
| 1781 | */ | |
| 1782 | 250 | public void notifySequence() |
| 1783 | { | |
| 1784 | 250 | changeSupport.firePropertyChange(PROPERTY_SEQUENCE, null, null); |
| 1785 | } | |
| 1786 | ||
| 1787 | 0 | @Override |
| 1788 | public void notifyAlignmentChanged() | |
| 1789 | { | |
| 1790 | 0 | firePropertyChange("alignment", null, alignment); |
| 1791 | } | |
| 1792 | ||
| 1793 | // common hide/show column stuff | |
| 1794 | ||
| 1795 | 6 | public void hideSelectedColumns() |
| 1796 | { | |
| 1797 | 6 | if (colSel.isEmpty()) |
| 1798 | { | |
| 1799 | 2 | return; |
| 1800 | } | |
| 1801 | ||
| 1802 | 4 | colSel.hideSelectedColumns(alignment); |
| 1803 | 4 | setSelectionGroup(null); |
| 1804 | 4 | isColSelChanged(true); |
| 1805 | } | |
| 1806 | ||
| 1807 | 71 | public void hideColumns(int start, int end) |
| 1808 | { | |
| 1809 | 71 | if (start == end) |
| 1810 | { | |
| 1811 | 2 | colSel.hideSelectedColumns(start, alignment.getHiddenColumns()); |
| 1812 | } | |
| 1813 | else | |
| 1814 | { | |
| 1815 | 69 | alignment.getHiddenColumns().hideColumns(start, end); |
| 1816 | } | |
| 1817 | 71 | isColSelChanged(true); |
| 1818 | } | |
| 1819 | ||
| 1820 | 1 | public void showColumn(int col) |
| 1821 | { | |
| 1822 | 1 | alignment.getHiddenColumns().revealHiddenColumns(col, colSel); |
| 1823 | 1 | isColSelChanged(true); |
| 1824 | } | |
| 1825 | ||
| 1826 | 5 | public void showAllHiddenColumns() |
| 1827 | { | |
| 1828 | 5 | alignment.getHiddenColumns().revealAllHiddenColumns(colSel); |
| 1829 | 5 | isColSelChanged(true); |
| 1830 | } | |
| 1831 | ||
| 1832 | // common hide/show seq stuff | |
| 1833 | 1 | public void showAllHiddenSeqs() |
| 1834 | { | |
| 1835 | 1 | int startSeq = ranges.getStartSeq(); |
| 1836 | 1 | int endSeq = ranges.getEndSeq(); |
| 1837 | ||
| 1838 | 1 | if (alignment.getHiddenSequences().getSize() > 0) |
| 1839 | { | |
| 1840 | 1 | if (selectionGroup == null) |
| 1841 | { | |
| 1842 | 0 | selectionGroup = new SequenceGroup(); |
| 1843 | 0 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1844 | } | |
| 1845 | 1 | List<SequenceI> tmp = alignment.getHiddenSequences() |
| 1846 | .showAll(hiddenRepSequences); | |
| 1847 | 1 | for (SequenceI seq : tmp) |
| 1848 | { | |
| 1849 | 2 | selectionGroup.addSequence(seq, false); |
| 1850 | 2 | setSequenceAnnotationsVisible(seq, true); |
| 1851 | } | |
| 1852 | ||
| 1853 | 1 | hiddenRepSequences = null; |
| 1854 | ||
| 1855 | 1 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1856 | ||
| 1857 | // used to set hasHiddenRows/hiddenRepSequences here, after the property | |
| 1858 | // changed event | |
| 1859 | 1 | notifySequence(); |
| 1860 | 1 | sendSelection(); |
| 1861 | } | |
| 1862 | } | |
| 1863 | ||
| 1864 | 2 | public void showSequence(int index) |
| 1865 | { | |
| 1866 | 2 | int startSeq = ranges.getStartSeq(); |
| 1867 | 2 | int endSeq = ranges.getEndSeq(); |
| 1868 | ||
| 1869 | 2 | List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index, |
| 1870 | hiddenRepSequences); | |
| 1871 | 2 | if (tmp.size() > 0) |
| 1872 | { | |
| 1873 | 2 | if (selectionGroup == null) |
| 1874 | { | |
| 1875 | 2 | selectionGroup = new SequenceGroup(); |
| 1876 | 2 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1877 | } | |
| 1878 | ||
| 1879 | 2 | for (SequenceI seq : tmp) |
| 1880 | { | |
| 1881 | 3 | selectionGroup.addSequence(seq, false); |
| 1882 | 3 | setSequenceAnnotationsVisible(seq, true); |
| 1883 | } | |
| 1884 | ||
| 1885 | 2 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1886 | ||
| 1887 | 2 | notifyAlignment(); |
| 1888 | 2 | sendSelection(); |
| 1889 | } | |
| 1890 | } | |
| 1891 | ||
| 1892 | 0 | public void hideAllSelectedSeqs() |
| 1893 | { | |
| 1894 | 0 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1895 | { | |
| 1896 | 0 | return; |
| 1897 | } | |
| 1898 | ||
| 1899 | 0 | SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); |
| 1900 | ||
| 1901 | 0 | hideSequence(seqs); |
| 1902 | ||
| 1903 | 0 | setSelectionGroup(null); |
| 1904 | } | |
| 1905 | ||
| 1906 | 54 | public void hideSequence(SequenceI[] seq) |
| 1907 | { | |
| 1908 | /* | |
| 1909 | * cache offset to first visible sequence | |
| 1910 | */ | |
| 1911 | 54 | int startSeq = ranges.getStartSeq(); |
| 1912 | ||
| 1913 | 54 | if (seq != null) |
| 1914 | { | |
| 1915 | 252 | for (int i = 0; i < seq.length; i++) |
| 1916 | { | |
| 1917 | 198 | alignment.getHiddenSequences().hideSequence(seq[i]); |
| 1918 | 198 | setSequenceAnnotationsVisible(seq[i], false); |
| 1919 | } | |
| 1920 | 54 | ranges.setStartSeq(startSeq); |
| 1921 | 54 | notifyAlignment(); |
| 1922 | } | |
| 1923 | } | |
| 1924 | ||
| 1925 | /** | |
| 1926 | * Hides the specified sequence, or the sequences it represents | |
| 1927 | * | |
| 1928 | * @param sequence | |
| 1929 | * the sequence to hide, or keep as representative | |
| 1930 | * @param representGroup | |
| 1931 | * if true, hide the current selection group except for the | |
| 1932 | * representative sequence | |
| 1933 | */ | |
| 1934 | 3 | public void hideSequences(SequenceI sequence, boolean representGroup) |
| 1935 | { | |
| 1936 | 3 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1937 | { | |
| 1938 | 0 | hideSequence(new SequenceI[] { sequence }); |
| 1939 | 0 | return; |
| 1940 | } | |
| 1941 | ||
| 1942 | 3 | if (representGroup) |
| 1943 | { | |
| 1944 | 3 | hideRepSequences(sequence, selectionGroup); |
| 1945 | 3 | setSelectionGroup(null); |
| 1946 | 3 | return; |
| 1947 | } | |
| 1948 | ||
| 1949 | 0 | int gsize = selectionGroup.getSize(); |
| 1950 | 0 | SequenceI[] hseqs = selectionGroup.getSequences() |
| 1951 | .toArray(new SequenceI[gsize]); | |
| 1952 | ||
| 1953 | 0 | hideSequence(hseqs); |
| 1954 | 0 | setSelectionGroup(null); |
| 1955 | 0 | sendSelection(); |
| 1956 | } | |
| 1957 | ||
| 1958 | /** | |
| 1959 | * Set visibility for any annotations for the given sequence. | |
| 1960 | * | |
| 1961 | * @param sequenceI | |
| 1962 | */ | |
| 1963 | 203 | protected void setSequenceAnnotationsVisible(SequenceI sequenceI, |
| 1964 | boolean visible) | |
| 1965 | { | |
| 1966 | 203 | AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation(); |
| 1967 | 203 | if (anns != null) |
| 1968 | { | |
| 1969 | 203 | for (AlignmentAnnotation ann : anns) |
| 1970 | { | |
| 1971 | 1033 | if (ann.sequenceRef == sequenceI) |
| 1972 | { | |
| 1973 | 0 | ann.visible = visible; |
| 1974 | } | |
| 1975 | } | |
| 1976 | } | |
| 1977 | } | |
| 1978 | ||
| 1979 | 5 | public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) |
| 1980 | { | |
| 1981 | 5 | int sSize = sg.getSize(); |
| 1982 | 5 | if (sSize < 2) |
| 1983 | { | |
| 1984 | 0 | return; |
| 1985 | } | |
| 1986 | ||
| 1987 | 5 | if (hiddenRepSequences == null) |
| 1988 | { | |
| 1989 | 5 | hiddenRepSequences = new Hashtable<>(); |
| 1990 | } | |
| 1991 | ||
| 1992 | 5 | hiddenRepSequences.put(repSequence, sg); |
| 1993 | ||
| 1994 | // Hide all sequences except the repSequence | |
| 1995 | 5 | SequenceI[] seqs = new SequenceI[sSize - 1]; |
| 1996 | 5 | int index = 0; |
| 1997 | 16 | for (int i = 0; i < sSize; i++) |
| 1998 | { | |
| 1999 | 11 | if (sg.getSequenceAt(i) != repSequence) |
| 2000 | { | |
| 2001 | 6 | if (index == sSize - 1) |
| 2002 | { | |
| 2003 | 0 | return; |
| 2004 | } | |
| 2005 | ||
| 2006 | 6 | seqs[index++] = sg.getSequenceAt(i); |
| 2007 | } | |
| 2008 | } | |
| 2009 | 5 | sg.setSeqrep(repSequence); // note: not done in 2.7applet |
| 2010 | 5 | sg.setHidereps(true); // note: not done in 2.7applet |
| 2011 | 5 | hideSequence(seqs); |
| 2012 | ||
| 2013 | } | |
| 2014 | ||
| 2015 | /** | |
| 2016 | * | |
| 2017 | * @return null or the current reference sequence | |
| 2018 | */ | |
| 2019 | 0 | public SequenceI getReferenceSeq() |
| 2020 | { | |
| 2021 | 0 | return alignment.getSeqrep(); |
| 2022 | } | |
| 2023 | ||
| 2024 | /** | |
| 2025 | * @param seq | |
| 2026 | * @return true iff seq is the reference for the alignment | |
| 2027 | */ | |
| 2028 | 411 | public boolean isReferenceSeq(SequenceI seq) |
| 2029 | { | |
| 2030 | 411 | return alignment.getSeqrep() == seq; |
| 2031 | } | |
| 2032 | ||
| 2033 | /** | |
| 2034 | * | |
| 2035 | * @param seq | |
| 2036 | * @return true if there are sequences represented by this sequence that are | |
| 2037 | * currently hidden | |
| 2038 | */ | |
| 2039 | 598 | public boolean isHiddenRepSequence(SequenceI seq) |
| 2040 | { | |
| 2041 | 598 | return (hiddenRepSequences != null |
| 2042 | && hiddenRepSequences.containsKey(seq)); | |
| 2043 | } | |
| 2044 | ||
| 2045 | /** | |
| 2046 | * | |
| 2047 | * @param seq | |
| 2048 | * @return null or a sequence group containing the sequences that seq | |
| 2049 | * represents | |
| 2050 | */ | |
| 2051 | 2 | public SequenceGroup getRepresentedSequences(SequenceI seq) |
| 2052 | { | |
| 2053 | 2 | return (SequenceGroup) (hiddenRepSequences == null ? null |
| 2054 | : hiddenRepSequences.get(seq)); | |
| 2055 | } | |
| 2056 | ||
| 2057 | 0 | @Override |
| 2058 | public int adjustForHiddenSeqs(int alignmentIndex) | |
| 2059 | { | |
| 2060 | 0 | return alignment.getHiddenSequences() |
| 2061 | .adjustForHiddenSeqs(alignmentIndex); | |
| 2062 | } | |
| 2063 | ||
| 2064 | 0 | @Override |
| 2065 | public void invertColumnSelection() | |
| 2066 | { | |
| 2067 | 0 | colSel.invertColumnSelection(0, alignment.getWidth(), alignment); |
| 2068 | 0 | isColSelChanged(true); |
| 2069 | } | |
| 2070 | ||
| 2071 | 4 | @Override |
| 2072 | public SequenceI[] getSelectionAsNewSequence() | |
| 2073 | { | |
| 2074 | 4 | SequenceI[] sequences; |
| 2075 | // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - | |
| 2076 | // this was the only caller in the applet for this method | |
| 2077 | // JBPNote: in applet, this method returned references to the alignment | |
| 2078 | // sequences, and it did not honour the presence/absence of annotation | |
| 2079 | // attached to the alignment (probably!) | |
| 2080 | 4 | if (selectionGroup == null || selectionGroup.getSize() == 0) |
| 2081 | { | |
| 2082 | 2 | sequences = alignment.getSequencesArray(); |
| 2083 | 2 | AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); |
| 2084 | 4 | for (int i = 0; i < sequences.length; i++) |
| 2085 | { | |
| 2086 | // construct new sequence with subset of visible annotation | |
| 2087 | 2 | sequences[i] = new Sequence(sequences[i], annots); |
| 2088 | } | |
| 2089 | } | |
| 2090 | else | |
| 2091 | { | |
| 2092 | 2 | sequences = selectionGroup.getSelectionAsNewSequences(alignment); |
| 2093 | } | |
| 2094 | ||
| 2095 | 4 | return sequences; |
| 2096 | } | |
| 2097 | ||
| 2098 | 28 | @Override |
| 2099 | public SequenceI[] getSequenceSelection() | |
| 2100 | { | |
| 2101 | 28 | SequenceI[] sequences = null; |
| 2102 | 28 | if (selectionGroup != null) |
| 2103 | { | |
| 2104 | 4 | sequences = selectionGroup.getSequencesInOrder(alignment); |
| 2105 | } | |
| 2106 | 28 | if (sequences == null) |
| 2107 | { | |
| 2108 | 24 | sequences = alignment.getSequencesArray(); |
| 2109 | } | |
| 2110 | 28 | return sequences; |
| 2111 | } | |
| 2112 | ||
| 2113 | 73 | @Override |
| 2114 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 2115 | boolean selectedOnly) | |
| 2116 | { | |
| 2117 | 73 | return getAlignmentView(selectedOnly, false); |
| 2118 | } | |
| 2119 | ||
| 2120 | 74 | @Override |
| 2121 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 2122 | boolean selectedOnly, boolean markGroups) | |
| 2123 | { | |
| 2124 | 74 | return new AlignmentView(alignment, alignment.getHiddenColumns(), |
| 2125 | selectionGroup, | |
| 2126 | alignment.getHiddenColumns() != null | |
| 2127 | && alignment.getHiddenColumns().hasHiddenColumns(), | |
| 2128 | selectedOnly, markGroups); | |
| 2129 | } | |
| 2130 | ||
| 2131 | 24 | @Override |
| 2132 | public String[] getViewAsString(boolean selectedRegionOnly) | |
| 2133 | { | |
| 2134 | 24 | return getViewAsString(selectedRegionOnly, true); |
| 2135 | } | |
| 2136 | ||
| 2137 | 24 | @Override |
| 2138 | public String[] getViewAsString(boolean selectedRegionOnly, | |
| 2139 | boolean exportHiddenSeqs) | |
| 2140 | { | |
| 2141 | 24 | String[] selection = null; |
| 2142 | 24 | SequenceI[] seqs = null; |
| 2143 | 24 | int i, iSize; |
| 2144 | 24 | int start = 0, end = 0; |
| 2145 | 24 | if (selectedRegionOnly && selectionGroup != null) |
| 2146 | { | |
| 2147 | 0 | iSize = selectionGroup.getSize(); |
| 2148 | 0 | seqs = selectionGroup.getSequencesInOrder(alignment); |
| 2149 | 0 | start = selectionGroup.getStartRes(); |
| 2150 | 0 | end = selectionGroup.getEndRes() + 1; |
| 2151 | } | |
| 2152 | else | |
| 2153 | { | |
| 2154 | 24 | if (hasHiddenRows() && exportHiddenSeqs) |
| 2155 | { | |
| 2156 | 0 | AlignmentI fullAlignment = alignment.getHiddenSequences() |
| 2157 | .getFullAlignment(); | |
| 2158 | 0 | iSize = fullAlignment.getHeight(); |
| 2159 | 0 | seqs = fullAlignment.getSequencesArray(); |
| 2160 | 0 | end = fullAlignment.getWidth(); |
| 2161 | } | |
| 2162 | else | |
| 2163 | { | |
| 2164 | 24 | iSize = alignment.getHeight(); |
| 2165 | 24 | seqs = alignment.getSequencesArray(); |
| 2166 | 24 | end = alignment.getWidth(); |
| 2167 | } | |
| 2168 | } | |
| 2169 | ||
| 2170 | 24 | selection = new String[iSize]; |
| 2171 | 24 | if (alignment.getHiddenColumns() != null |
| 2172 | && alignment.getHiddenColumns().hasHiddenColumns()) | |
| 2173 | { | |
| 2174 | 206 | for (i = 0; i < iSize; i++) |
| 2175 | { | |
| 2176 | 188 | Iterator<int[]> blocks = alignment.getHiddenColumns() |
| 2177 | .getVisContigsIterator(start, end + 1, false); | |
| 2178 | 188 | selection[i] = seqs[i].getSequenceStringFromIterator(blocks); |
| 2179 | } | |
| 2180 | } | |
| 2181 | else | |
| 2182 | { | |
| 2183 | 36 | for (i = 0; i < iSize; i++) |
| 2184 | { | |
| 2185 | 30 | selection[i] = seqs[i].getSequenceAsString(start, end); |
| 2186 | } | |
| 2187 | ||
| 2188 | } | |
| 2189 | 24 | return selection; |
| 2190 | } | |
| 2191 | ||
| 2192 | 0 | @Override |
| 2193 | public List<int[]> getVisibleRegionBoundaries(int min, int max) | |
| 2194 | { | |
| 2195 | 0 | ArrayList<int[]> regions = new ArrayList<>(); |
| 2196 | 0 | int start = min; |
| 2197 | 0 | int end = max; |
| 2198 | ||
| 2199 | 0 | do |
| 2200 | { | |
| 2201 | 0 | HiddenColumns hidden = alignment.getHiddenColumns(); |
| 2202 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 2203 | { | |
| 2204 | 0 | if (start == 0) |
| 2205 | { | |
| 2206 | 0 | start = hidden.visibleToAbsoluteColumn(start); |
| 2207 | } | |
| 2208 | ||
| 2209 | 0 | end = hidden.getNextHiddenBoundary(false, start); |
| 2210 | 0 | if (start == end) |
| 2211 | { | |
| 2212 | 0 | end = max; |
| 2213 | } | |
| 2214 | 0 | if (end > max) |
| 2215 | { | |
| 2216 | 0 | end = max; |
| 2217 | } | |
| 2218 | } | |
| 2219 | ||
| 2220 | 0 | regions.add(new int[] { start, end }); |
| 2221 | ||
| 2222 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 2223 | { | |
| 2224 | 0 | start = hidden.visibleToAbsoluteColumn(end); |
| 2225 | 0 | start = hidden.getNextHiddenBoundary(true, start) + 1; |
| 2226 | } | |
| 2227 | 0 | } while (end < max); |
| 2228 | ||
| 2229 | // int[][] startEnd = new int[regions.size()][2]; | |
| 2230 | ||
| 2231 | 0 | return regions; |
| 2232 | } | |
| 2233 | ||
| 2234 | 1 | @Override |
| 2235 | public List<AlignmentAnnotation> getVisibleAlignmentAnnotation( | |
| 2236 | boolean selectedOnly) | |
| 2237 | { | |
| 2238 | 1 | ArrayList<AlignmentAnnotation> ala = new ArrayList<>(); |
| 2239 | 1 | AlignmentAnnotation[] aa; |
| 2240 | ? | if ((aa = alignment.getAlignmentAnnotation()) != null) |
| 2241 | { | |
| 2242 | 1 | for (AlignmentAnnotation annot : aa) |
| 2243 | { | |
| 2244 | 4 | AlignmentAnnotation clone = new AlignmentAnnotation(annot); |
| 2245 | 4 | if (selectedOnly && selectionGroup != null) |
| 2246 | { | |
| 2247 | 4 | clone.makeVisibleAnnotation( |
| 2248 | selectionGroup.getStartRes(), selectionGroup.getEndRes(), | |
| 2249 | alignment.getHiddenColumns()); | |
| 2250 | } | |
| 2251 | else | |
| 2252 | { | |
| 2253 | 0 | clone.makeVisibleAnnotation(alignment.getHiddenColumns()); |
| 2254 | } | |
| 2255 | 4 | ala.add(clone); |
| 2256 | } | |
| 2257 | } | |
| 2258 | 1 | return ala; |
| 2259 | } | |
| 2260 | ||
| 2261 | 2150 | @Override |
| 2262 | public boolean isPadGaps() | |
| 2263 | { | |
| 2264 | 2150 | return padGaps; |
| 2265 | } | |
| 2266 | ||
| 2267 | 595 | @Override |
| 2268 | public void setPadGaps(boolean padGaps) | |
| 2269 | { | |
| 2270 | 595 | this.padGaps = padGaps; |
| 2271 | } | |
| 2272 | ||
| 2273 | /** | |
| 2274 | * apply any post-edit constraints and trigger any calculations needed after | |
| 2275 | * an edit has been performed on the alignment | |
| 2276 | * | |
| 2277 | * @param ap | |
| 2278 | */ | |
| 2279 | 929 | @Override |
| 2280 | public void alignmentChanged(AlignmentViewPanel ap) | |
| 2281 | { | |
| 2282 | 929 | if (isPadGaps()) |
| 2283 | { | |
| 2284 | 470 | alignment.padGaps(); |
| 2285 | } | |
| 2286 | 929 | if (autoCalculateConsensusAndConservation) |
| 2287 | { | |
| 2288 | 929 | updateConsensus(ap); |
| 2289 | 929 | updateSecondaryStructureConsensus(ap); |
| 2290 | } | |
| 2291 | 929 | if (hconsensus != null && autoCalculateConsensusAndConservation) |
| 2292 | { | |
| 2293 | 573 | updateConservation(ap); |
| 2294 | } | |
| 2295 | 929 | if (autoCalculateStrucConsensus) |
| 2296 | { | |
| 2297 | 929 | updateStrucConsensus(ap); |
| 2298 | } | |
| 2299 | ||
| 2300 | // Reset endRes of groups if beyond alignment width | |
| 2301 | 929 | int alWidth = alignment.getWidth(); |
| 2302 | 929 | List<SequenceGroup> groups = alignment.getGroups(); |
| 2303 | 929 | if (groups != null) |
| 2304 | { | |
| 2305 | 929 | for (SequenceGroup sg : groups) |
| 2306 | { | |
| 2307 | 237 | if (sg.getEndRes() > alWidth) |
| 2308 | { | |
| 2309 | 0 | sg.setEndRes(alWidth - 1); |
| 2310 | } | |
| 2311 | } | |
| 2312 | } | |
| 2313 | ||
| 2314 | 929 | if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) |
| 2315 | { | |
| 2316 | 0 | selectionGroup.setEndRes(alWidth - 1); |
| 2317 | } | |
| 2318 | ||
| 2319 | 929 | updateAllColourSchemes(); |
| 2320 | 929 | calculator.restartWorkers(); |
| 2321 | } | |
| 2322 | ||
| 2323 | /** | |
| 2324 | * reset scope and do calculations for all applied colourschemes on alignment | |
| 2325 | */ | |
| 2326 | 929 | void updateAllColourSchemes() |
| 2327 | { | |
| 2328 | 929 | ResidueShaderI rs = residueShading; |
| 2329 | 929 | if (rs != null) |
| 2330 | { | |
| 2331 | 929 | rs.alignmentChanged(alignment, hiddenRepSequences); |
| 2332 | ||
| 2333 | 929 | rs.setConsensus(hconsensus); |
| 2334 | 929 | if (rs.conservationApplied()) |
| 2335 | { | |
| 2336 | 3 | rs.setConservation(Conservation.calculateConservation("All", |
| 2337 | alignment.getSequences(), 0, alignment.getWidth(), false, | |
| 2338 | getConsPercGaps(), false)); | |
| 2339 | } | |
| 2340 | } | |
| 2341 | ||
| 2342 | 929 | for (SequenceGroup sg : alignment.getGroups()) |
| 2343 | { | |
| 2344 | 237 | if (sg.cs != null) |
| 2345 | { | |
| 2346 | 237 | sg.cs.alignmentChanged(sg, hiddenRepSequences); |
| 2347 | } | |
| 2348 | 237 | sg.recalcConservation(); |
| 2349 | } | |
| 2350 | } | |
| 2351 | ||
| 2352 | 595 | protected void initAutoAnnotation() |
| 2353 | { | |
| 2354 | // TODO: add menu option action that nulls or creates consensus object | |
| 2355 | // depending on if the user wants to see the annotation or not in a | |
| 2356 | // specific alignment | |
| 2357 | ||
| 2358 | 595 | if (hconsensus == null && !isDataset) |
| 2359 | { | |
| 2360 | 595 | if (!alignment.isNucleotide()) |
| 2361 | { | |
| 2362 | 475 | initConservation(); |
| 2363 | 475 | initQuality(); |
| 2364 | } | |
| 2365 | else | |
| 2366 | { | |
| 2367 | 120 | initRNAStructure(); |
| 2368 | } | |
| 2369 | 595 | consensus = new AlignmentAnnotation("Consensus", |
| 2370 | MessageManager.getString("label.consensus_descr"), | |
| 2371 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2372 | 595 | setSecondaryStructureSources(alignment.getAlignmentAnnotation()); |
| 2373 | ||
| 2374 | 595 | List<String> secondaryStructureSources = getSecondaryStructureSources(); |
| 2375 | 595 | boolean singleProvider = false; |
| 2376 | ||
| 2377 | 595 | if (secondaryStructureSources != null) |
| 2378 | { | |
| 2379 | 595 | if(secondaryStructureSources.size() == 2) |
| 2380 | { | |
| 2381 | 16 | singleProvider = true; //Single provider if size is 2 (All, Provider 1) |
| 2382 | } | |
| 2383 | ||
| 2384 | 595 | AlignmentUtils.assignColorsForSecondaryStructureProviders(secondaryStructureSources); |
| 2385 | ||
| 2386 | 595 | secondaryStructureConsensus = new ArrayList<AlignmentAnnotation>(); |
| 2387 | 595 | for (String ssSource : secondaryStructureSources) |
| 2388 | { | |
| 2389 | ||
| 2390 | 526 | AlignmentAnnotation ssConsensus = new AlignmentAnnotation( |
| 2391 | MessageManager.getString("label.ssconsensus_label") + " " | |
| 2392 | + ssSource, | |
| 2393 | ssSource + " " | |
| 2394 | + MessageManager | |
| 2395 | .getString("label.ssconsensus_descr"), | |
| 2396 | new Annotation[1], 0f, 100f, | |
| 2397 | AlignmentAnnotation.BAR_GRAPH); | |
| 2398 | 526 | ssConsensus.autoCalculated=true; |
| 2399 | 526 | ssConsensus.hasData=false; |
| 2400 | 526 | ssConsensus.hasText=true; |
| 2401 | // Hide global ss consensus for all providers if only one provider is present | |
| 2402 | 526 | ssConsensus.visible = ssSource.equals(Constants.SS_ALL_PROVIDERS) && singleProvider ? false : true; |
| 2403 | ||
| 2404 | 526 | secondaryStructureConsensus.add(ssConsensus); |
| 2405 | } | |
| 2406 | ||
| 2407 | } | |
| 2408 | ||
| 2409 | 595 | initConsensus(consensus); |
| 2410 | 595 | initSSConsensus(secondaryStructureConsensus); |
| 2411 | 595 | initGapCounts(); |
| 2412 | 595 | initComplementConsensus(); |
| 2413 | } | |
| 2414 | } | |
| 2415 | /** | |
| 2416 | * set Secondary structure annotation providers for current set of annotation | |
| 2417 | */ | |
| 2418 | 3046 | @Override |
| 2419 | public void setSecondaryStructureSources() | |
| 2420 | { | |
| 2421 | 3046 | List<String> sources = null; |
| 2422 | 3046 | AlignmentAnnotation[] aa = getAlignment() |
| 2423 | .getAlignmentAnnotation(); | |
| 2424 | 3046 | if (aa != null) |
| 2425 | { | |
| 2426 | 3046 | sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa); |
| 2427 | 3046 | if (sources != null) |
| 2428 | { | |
| 2429 | 3046 | sources.add(0, Constants.SS_ALL_PROVIDERS); |
| 2430 | 3046 | setSecondaryStructureSources(sources); |
| 2431 | } | |
| 2432 | } | |
| 2433 | } | |
| 2434 | ||
| 2435 | /** | |
| 2436 | * If this is a protein alignment and there are mappings to cDNA, adds the | |
| 2437 | * cDNA consensus annotation and returns true, else returns false. | |
| 2438 | */ | |
| 2439 | 605 | public boolean initComplementConsensus() |
| 2440 | { | |
| 2441 | 605 | if (!alignment.isNucleotide()) |
| 2442 | { | |
| 2443 | 484 | final List<AlignedCodonFrame> codonMappings = alignment |
| 2444 | .getCodonFrames(); | |
| 2445 | 484 | if (codonMappings != null && !codonMappings.isEmpty()) |
| 2446 | { | |
| 2447 | 4 | boolean doConsensus = false; |
| 2448 | 4 | for (AlignedCodonFrame mapping : codonMappings) |
| 2449 | { | |
| 2450 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 2451 | 4 | MapList[] mapLists = mapping.getdnaToProt(); |
| 2452 | // mapLists can be empty if project load has not finished resolving | |
| 2453 | // seqs | |
| 2454 | 4 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 2455 | { | |
| 2456 | 4 | doConsensus = true; |
| 2457 | 4 | break; |
| 2458 | } | |
| 2459 | } | |
| 2460 | 4 | if (doConsensus) |
| 2461 | { | |
| 2462 | 4 | Iterable<AlignmentAnnotation> annots = alignment |
| 2463 | .findAnnotations(null, null, "cDNA Consensus"); | |
| 2464 | 4 | if (annots != null && (complementConsensus == null)) |
| 2465 | { | |
| 2466 | 4 | for (AlignmentAnnotation ann : annots) |
| 2467 | { | |
| 2468 | 0 | if (ann.autoCalculated) |
| 2469 | { | |
| 2470 | 0 | complementConsensus = ann; |
| 2471 | } | |
| 2472 | } | |
| 2473 | } | |
| 2474 | 4 | if (complementConsensus == null) |
| 2475 | { | |
| 2476 | 4 | complementConsensus = new AlignmentAnnotation("cDNA Consensus", |
| 2477 | MessageManager | |
| 2478 | .getString("label.complement_consensus_descr"), | |
| 2479 | new Annotation[1], 0f, 100f, | |
| 2480 | AlignmentAnnotation.BAR_GRAPH); | |
| 2481 | 4 | initConsensus(complementConsensus); |
| 2482 | } | |
| 2483 | 4 | return true; |
| 2484 | } | |
| 2485 | } | |
| 2486 | } | |
| 2487 | 601 | return false; |
| 2488 | } | |
| 2489 | ||
| 2490 | 599 | private void initConsensus(AlignmentAnnotation aa) |
| 2491 | { | |
| 2492 | 599 | aa.hasText = true; |
| 2493 | 599 | aa.autoCalculated = true; |
| 2494 | ||
| 2495 | 599 | if (showConsensus) |
| 2496 | { | |
| 2497 | 598 | alignment.addAnnotation(aa); |
| 2498 | } | |
| 2499 | } | |
| 2500 | ||
| 2501 | 595 | private void initSSConsensus( |
| 2502 | List<AlignmentAnnotation> secondaryStructureConsensuses) | |
| 2503 | { | |
| 2504 | 595 | if (secondaryStructureConsensuses == null) |
| 2505 | { | |
| 2506 | 0 | return; |
| 2507 | } | |
| 2508 | 595 | for (AlignmentAnnotation aa : secondaryStructureConsensuses) |
| 2509 | { | |
| 2510 | 526 | aa.hasText = true; |
| 2511 | 526 | aa.autoCalculated = true; |
| 2512 | ||
| 2513 | 526 | if (showSSConsensus) |
| 2514 | { | |
| 2515 | 0 | alignment.addAnnotation(aa); |
| 2516 | } | |
| 2517 | ||
| 2518 | } | |
| 2519 | } | |
| 2520 | ||
| 2521 | // these should be extracted from the view model - style and settings for | |
| 2522 | // derived annotation | |
| 2523 | 595 | private void initGapCounts() |
| 2524 | { | |
| 2525 | 595 | if (showOccupancy) |
| 2526 | { | |
| 2527 | 591 | gapcounts = new AlignmentAnnotation("Occupancy", |
| 2528 | MessageManager.getString("label.occupancy_descr"), | |
| 2529 | new Annotation[1], 0f, alignment.getHeight(), | |
| 2530 | AlignmentAnnotation.BAR_GRAPH); | |
| 2531 | 591 | gapcounts.hasText = true; |
| 2532 | 591 | gapcounts.autoCalculated = true; |
| 2533 | 591 | gapcounts.scaleColLabel = true; |
| 2534 | 591 | gapcounts.graph = AlignmentAnnotation.BAR_GRAPH; |
| 2535 | ||
| 2536 | 591 | alignment.addAnnotation(gapcounts); |
| 2537 | } | |
| 2538 | } | |
| 2539 | ||
| 2540 | 475 | private void initConservation() |
| 2541 | { | |
| 2542 | 475 | if (showConservation) |
| 2543 | { | |
| 2544 | 474 | if (conservation == null) |
| 2545 | { | |
| 2546 | 474 | conservation = new AlignmentAnnotation("Conservation", |
| 2547 | MessageManager.formatMessage("label.conservation_descr", | |
| 2548 | getConsPercGaps()), | |
| 2549 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2550 | 474 | conservation.hasText = true; |
| 2551 | 474 | conservation.autoCalculated = true; |
| 2552 | 474 | alignment.addAnnotation(conservation); |
| 2553 | } | |
| 2554 | } | |
| 2555 | } | |
| 2556 | ||
| 2557 | 475 | private void initQuality() |
| 2558 | { | |
| 2559 | 475 | if (showQuality) |
| 2560 | { | |
| 2561 | 475 | if (quality == null) |
| 2562 | { | |
| 2563 | 475 | quality = new AlignmentAnnotation("Quality", |
| 2564 | MessageManager.getString("label.quality_descr"), | |
| 2565 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2566 | 475 | quality.hasText = true; |
| 2567 | 475 | quality.autoCalculated = true; |
| 2568 | 475 | alignment.addAnnotation(quality); |
| 2569 | } | |
| 2570 | } | |
| 2571 | } | |
| 2572 | ||
| 2573 | 120 | private void initRNAStructure() |
| 2574 | { | |
| 2575 | 120 | if (alignment.hasRNAStructure() && strucConsensus == null) |
| 2576 | { | |
| 2577 | 2 | strucConsensus = new AlignmentAnnotation("StrucConsensus", |
| 2578 | MessageManager.getString("label.strucconsensus_descr"), | |
| 2579 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2580 | 2 | strucConsensus.hasText = true; |
| 2581 | 2 | strucConsensus.autoCalculated = true; |
| 2582 | ||
| 2583 | 2 | if (showConsensus) |
| 2584 | { | |
| 2585 | 2 | alignment.addAnnotation(strucConsensus); |
| 2586 | } | |
| 2587 | } | |
| 2588 | } | |
| 2589 | ||
| 2590 | /* | |
| 2591 | * (non-Javadoc) | |
| 2592 | * | |
| 2593 | * @see jalview.api.AlignViewportI#calcPanelHeight() | |
| 2594 | */ | |
| 2595 | 6921 | @Override |
| 2596 | public int calcPanelHeight() | |
| 2597 | { | |
| 2598 | // setHeight of panels | |
| 2599 | 6921 | AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation(); |
| 2600 | 6921 | int height = 0; |
| 2601 | 6921 | int charHeight = getCharHeight(); |
| 2602 | 6921 | if (anns != null) |
| 2603 | { | |
| 2604 | 6921 | BitSet graphgrp = new BitSet(); |
| 2605 | 6921 | for (AlignmentAnnotation aa : anns) |
| 2606 | { | |
| 2607 | 35276 | if (aa == null) |
| 2608 | { | |
| 2609 | 0 | jalview.bin.Console.errPrintln("Null annotation row: ignoring."); |
| 2610 | 0 | continue; |
| 2611 | } | |
| 2612 | 35276 | if (!aa.isForDisplay()) |
| 2613 | { | |
| 2614 | 5514 | continue; |
| 2615 | } | |
| 2616 | 29762 | if (aa.graphGroup > -1) |
| 2617 | { | |
| 2618 | 300 | if (graphgrp.get(aa.graphGroup)) |
| 2619 | { | |
| 2620 | 15 | continue; |
| 2621 | } | |
| 2622 | else | |
| 2623 | { | |
| 2624 | 285 | graphgrp.set(aa.graphGroup); |
| 2625 | } | |
| 2626 | } | |
| 2627 | 29747 | aa.height = 0; |
| 2628 | ||
| 2629 | 29747 | if (aa.hasText) |
| 2630 | { | |
| 2631 | 26176 | aa.height += charHeight; |
| 2632 | } | |
| 2633 | ||
| 2634 | 29747 | if (aa.hasIcons) |
| 2635 | { | |
| 2636 | 2246 | aa.height += 16; |
| 2637 | } | |
| 2638 | ||
| 2639 | 29747 | if (aa.graph > 0) |
| 2640 | { | |
| 2641 | 26339 | aa.height += aa.graphHeight + 20; |
| 2642 | } | |
| 2643 | ||
| 2644 | 29747 | if (aa.height == 0) |
| 2645 | { | |
| 2646 | 432 | aa.height = 20; |
| 2647 | } | |
| 2648 | ||
| 2649 | 29747 | height += aa.height; |
| 2650 | } | |
| 2651 | } | |
| 2652 | 6921 | if (height == 0) |
| 2653 | { | |
| 2654 | // set minimum | |
| 2655 | 28 | height = 20; |
| 2656 | } | |
| 2657 | 6921 | return height; |
| 2658 | } | |
| 2659 | ||
| 2660 | 440 | @Override |
| 2661 | public void updateGroupAnnotationSettings(boolean applyGlobalSettings, | |
| 2662 | boolean preserveNewGroupSettings) | |
| 2663 | { | |
| 2664 | 440 | boolean updateCalcs = false; |
| 2665 | 440 | boolean conv = isShowGroupConservation(); |
| 2666 | 440 | boolean cons = isShowGroupConsensus(); |
| 2667 | 440 | boolean sscons = isShowGroupSSConsensus(); |
| 2668 | 440 | boolean showprf = isShowSequenceLogo(); |
| 2669 | 440 | boolean showConsHist = isShowConsensusHistogram(); |
| 2670 | 440 | boolean normLogo = isNormaliseSequenceLogo(); |
| 2671 | 440 | boolean showHMMPrf = isShowHMMSequenceLogo(); |
| 2672 | 440 | boolean showInfoHist = isShowInformationHistogram(); |
| 2673 | 440 | boolean normHMMLogo = isNormaliseHMMSequenceLogo(); |
| 2674 | ||
| 2675 | /** | |
| 2676 | * TODO reorder the annotation rows according to group/sequence ordering on | |
| 2677 | * alignment | |
| 2678 | */ | |
| 2679 | // boolean sortg = true; | |
| 2680 | ||
| 2681 | // remove old automatic annotation | |
| 2682 | // add any new annotation | |
| 2683 | ||
| 2684 | // intersect alignment annotation with alignment groups | |
| 2685 | ||
| 2686 | 440 | AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation(); |
| 2687 | ||
| 2688 | 440 | List<SequenceGroup> oldrfs = new ArrayList<>(); |
| 2689 | 440 | if (aan != null) |
| 2690 | { | |
| 2691 | 2847 | for (int an = 0; an < aan.length; an++) |
| 2692 | { | |
| 2693 | 2407 | if (aan[an].autoCalculated && aan[an].groupRef != null) |
| 2694 | { | |
| 2695 | 0 | oldrfs.add(aan[an].groupRef); |
| 2696 | 0 | alignment.deleteAnnotation(aan[an], false); |
| 2697 | } | |
| 2698 | } | |
| 2699 | } | |
| 2700 | 440 | if (alignment.getGroups() != null) |
| 2701 | { | |
| 2702 | 440 | for (SequenceGroup sg : alignment.getGroups()) |
| 2703 | { | |
| 2704 | 70 | updateCalcs = false; |
| 2705 | 70 | if (applyGlobalSettings |
| 2706 | || (!preserveNewGroupSettings && !oldrfs.contains(sg))) | |
| 2707 | { | |
| 2708 | // set defaults for this group's conservation/consensus | |
| 2709 | 11 | sg.setshowSequenceLogo(showprf); |
| 2710 | 11 | sg.setShowConsensusHistogram(showConsHist); |
| 2711 | 11 | sg.setNormaliseSequenceLogo(normLogo); |
| 2712 | 11 | sg.setShowHMMSequenceLogo(showHMMPrf); |
| 2713 | 11 | sg.setShowInformationHistogram(showInfoHist); |
| 2714 | 11 | sg.setNormaliseHMMSequenceLogo(normHMMLogo); |
| 2715 | } | |
| 2716 | 70 | if (conv) |
| 2717 | { | |
| 2718 | 0 | updateCalcs = true; |
| 2719 | 0 | alignment.addAnnotation(sg.getConservationRow(), 0); |
| 2720 | } | |
| 2721 | 70 | if (cons) |
| 2722 | { | |
| 2723 | 24 | updateCalcs = true; |
| 2724 | 24 | alignment.addAnnotation(sg.getConsensus(), 0); |
| 2725 | } | |
| 2726 | 70 | if (sscons) |
| 2727 | { | |
| 2728 | 0 | updateCalcs = true; |
| 2729 | 0 | List<String> secondaryStructureSources = getSecondaryStructureSources(); |
| 2730 | 0 | if (secondaryStructureSources != null) |
| 2731 | { | |
| 2732 | 0 | List<AlignmentAnnotation> ssAa = sg |
| 2733 | .getSSConsensus(secondaryStructureSources); | |
| 2734 | 0 | if (ssAa != null) |
| 2735 | { | |
| 2736 | 0 | for (AlignmentAnnotation aa : ssAa) |
| 2737 | { | |
| 2738 | // Setting annotation visibility to true for the secondary | |
| 2739 | // structure consensus for all providers | |
| 2740 | 0 | if (aa.label.contains(Constants.SS_ALL_PROVIDERS)) |
| 2741 | { | |
| 2742 | 0 | aa.visible = true; |
| 2743 | } | |
| 2744 | 0 | alignment.addAnnotation(aa, 0); |
| 2745 | } | |
| 2746 | } | |
| 2747 | } | |
| 2748 | } | |
| 2749 | // refresh the annotation rows | |
| 2750 | 70 | if (updateCalcs) |
| 2751 | { | |
| 2752 | 24 | sg.recalcConservation(); |
| 2753 | } | |
| 2754 | } | |
| 2755 | } | |
| 2756 | 440 | oldrfs.clear(); |
| 2757 | } | |
| 2758 | ||
| 2759 | 26657 | @Override |
| 2760 | public boolean isDisplayReferenceSeq() | |
| 2761 | { | |
| 2762 | 26657 | return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq(); |
| 2763 | } | |
| 2764 | ||
| 2765 | 10 | @Override |
| 2766 | public void setDisplayReferenceSeq(boolean displayReferenceSeq) | |
| 2767 | { | |
| 2768 | 10 | viewStyle.setDisplayReferenceSeq(displayReferenceSeq); |
| 2769 | } | |
| 2770 | ||
| 2771 | 5 | @Override |
| 2772 | public boolean isColourByReferenceSeq() | |
| 2773 | { | |
| 2774 | 5 | return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq(); |
| 2775 | } | |
| 2776 | ||
| 2777 | 30051 | @Override |
| 2778 | public Color getSequenceColour(SequenceI seq) | |
| 2779 | { | |
| 2780 | 30051 | Color sqc = sequenceColours.get(seq); |
| 2781 | 30051 | return (sqc == null ? Color.white : sqc); |
| 2782 | } | |
| 2783 | ||
| 2784 | 1325 | @Override |
| 2785 | public void setSequenceColour(SequenceI seq, Color col) | |
| 2786 | { | |
| 2787 | 1325 | if (col == null) |
| 2788 | { | |
| 2789 | 0 | sequenceColours.remove(seq); |
| 2790 | } | |
| 2791 | else | |
| 2792 | { | |
| 2793 | 1325 | sequenceColours.put(seq, col); |
| 2794 | } | |
| 2795 | } | |
| 2796 | ||
| 2797 | 9 | @Override |
| 2798 | public void updateSequenceIdColours() | |
| 2799 | { | |
| 2800 | 9 | for (SequenceGroup sg : alignment.getGroups()) |
| 2801 | { | |
| 2802 | 5 | if (sg.idColour != null) |
| 2803 | { | |
| 2804 | 0 | for (SequenceI s : sg.getSequences(getHiddenRepSequences())) |
| 2805 | { | |
| 2806 | 0 | sequenceColours.put(s, sg.idColour); |
| 2807 | } | |
| 2808 | } | |
| 2809 | } | |
| 2810 | } | |
| 2811 | ||
| 2812 | 1 | @Override |
| 2813 | public void clearSequenceColours() | |
| 2814 | { | |
| 2815 | 1 | sequenceColours.clear(); |
| 2816 | } | |
| 2817 | ||
| 2818 | ||
| 2819 | 188 | @Override |
| 2820 | public Color getAnnotationColour(AlignmentAnnotation annot) | |
| 2821 | { | |
| 2822 | 188 | Color annotColor = annotationColours.get(annot); |
| 2823 | 188 | return (annotColor == null ? Color.white : annotColor); |
| 2824 | } | |
| 2825 | ||
| 2826 | 12 | @Override |
| 2827 | public void setAnnotationColour(AlignmentAnnotation annot, Color col) | |
| 2828 | { | |
| 2829 | 12 | if (col == null) |
| 2830 | { | |
| 2831 | 0 | annotationColours.remove(annot); |
| 2832 | 0 | annot.setAnnotationGroupColour(Color.WHITE); |
| 2833 | } | |
| 2834 | else | |
| 2835 | { | |
| 2836 | 12 | annotationColours.put(annot, col); |
| 2837 | 12 | annot.setAnnotationGroupColour(col); |
| 2838 | } | |
| 2839 | } | |
| 2840 | ||
| 2841 | 1283 | @Override |
| 2842 | public void updateAnnotationColours() | |
| 2843 | { | |
| 2844 | 1283 | for (SequenceGroup sg : alignment.getGroups()) |
| 2845 | { | |
| 2846 | 930 | if (sg.idColour != null) |
| 2847 | { | |
| 2848 | 925 | for (AlignmentAnnotation annot : sg.getAlignmentAnnotation()) |
| 2849 | { | |
| 2850 | 384 | annotationColours.put(annot, sg.idColour); |
| 2851 | 384 | annot.setAnnotationGroupColour(sg.idColour); |
| 2852 | } | |
| 2853 | } | |
| 2854 | } | |
| 2855 | } | |
| 2856 | ||
| 2857 | 1 | @Override |
| 2858 | public void clearAnnotationColours() | |
| 2859 | { | |
| 2860 | 1 | for (AlignmentAnnotation annot : annotationColours.keySet()) |
| 2861 | { | |
| 2862 | 4 | annot.setAnnotationGroupColour(Color.WHITE); |
| 2863 | } | |
| 2864 | 1 | annotationColours.clear(); |
| 2865 | } | |
| 2866 | ||
| 2867 | 0 | @Override |
| 2868 | public Map<AlignmentAnnotation, Color> getAnnotationColours() | |
| 2869 | { | |
| 2870 | 0 | return annotationColours; |
| 2871 | } | |
| 2872 | ||
| 2873 | 0 | @Override |
| 2874 | public void setAnnotationColours( | |
| 2875 | Map<AlignmentAnnotation, Color> annotationColours) | |
| 2876 | { | |
| 2877 | 0 | this.annotationColours = annotationColours; |
| 2878 | } | |
| 2879 | ||
| 2880 | 1273 | @Override |
| 2881 | public AlignViewportI getCodingComplement() | |
| 2882 | { | |
| 2883 | 1273 | return this.codingComplement; |
| 2884 | } | |
| 2885 | ||
| 2886 | /** | |
| 2887 | * Set this as the (cDna/protein) complement of the given viewport. Also | |
| 2888 | * ensures the reverse relationship is set on the given viewport. | |
| 2889 | */ | |
| 2890 | 6 | @Override |
| 2891 | public void setCodingComplement(AlignViewportI av) | |
| 2892 | { | |
| 2893 | 6 | if (this == av) |
| 2894 | { | |
| 2895 | 0 | jalview.bin.Console |
| 2896 | .errPrintln("Ignoring recursive setCodingComplement request"); | |
| 2897 | } | |
| 2898 | else | |
| 2899 | { | |
| 2900 | 6 | this.codingComplement = av; |
| 2901 | // avoid infinite recursion! | |
| 2902 | 6 | if (av.getCodingComplement() != this) |
| 2903 | { | |
| 2904 | 3 | av.setCodingComplement(this); |
| 2905 | } | |
| 2906 | } | |
| 2907 | } | |
| 2908 | ||
| 2909 | 25 | @Override |
| 2910 | public boolean isNucleotide() | |
| 2911 | { | |
| 2912 | 25 | return getAlignment() == null ? false : getAlignment().isNucleotide(); |
| 2913 | } | |
| 2914 | ||
| 2915 | 1142962 | @Override |
| 2916 | public FeaturesDisplayedI getFeaturesDisplayed() | |
| 2917 | { | |
| 2918 | 1142962 | return featuresDisplayed; |
| 2919 | } | |
| 2920 | ||
| 2921 | 119 | @Override |
| 2922 | public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) | |
| 2923 | { | |
| 2924 | 119 | featuresDisplayed = featuresDisplayedI; |
| 2925 | } | |
| 2926 | ||
| 2927 | 83 | @Override |
| 2928 | public boolean areFeaturesDisplayed() | |
| 2929 | { | |
| 2930 | 83 | return featuresDisplayed != null |
| 2931 | && featuresDisplayed.getRegisteredFeaturesCount() > 0; | |
| 2932 | } | |
| 2933 | ||
| 2934 | /** | |
| 2935 | * set the flag | |
| 2936 | * | |
| 2937 | * @param b | |
| 2938 | * features are displayed if true | |
| 2939 | */ | |
| 2940 | 156 | @Override |
| 2941 | public void setShowSequenceFeatures(boolean b) | |
| 2942 | { | |
| 2943 | 156 | viewStyle.setShowSequenceFeatures(b); |
| 2944 | } | |
| 2945 | ||
| 2946 | 419456 | @Override |
| 2947 | public boolean isShowSequenceFeatures() | |
| 2948 | { | |
| 2949 | 419464 | return viewStyle.isShowSequenceFeatures(); |
| 2950 | } | |
| 2951 | ||
| 2952 | 0 | @Override |
| 2953 | public void setShowSequenceFeaturesHeight(boolean selected) | |
| 2954 | { | |
| 2955 | 0 | viewStyle.setShowSequenceFeaturesHeight(selected); |
| 2956 | } | |
| 2957 | ||
| 2958 | 0 | @Override |
| 2959 | public boolean isShowSequenceFeaturesHeight() | |
| 2960 | { | |
| 2961 | 0 | return viewStyle.isShowSequenceFeaturesHeight(); |
| 2962 | } | |
| 2963 | ||
| 2964 | 799 | @Override |
| 2965 | public void setShowAnnotation(boolean b) | |
| 2966 | { | |
| 2967 | 799 | viewStyle.setShowAnnotation(b); |
| 2968 | } | |
| 2969 | ||
| 2970 | 5540 | @Override |
| 2971 | public boolean isShowAnnotation() | |
| 2972 | { | |
| 2973 | 5540 | return viewStyle.isShowAnnotation(); |
| 2974 | } | |
| 2975 | ||
| 2976 | 16305 | @Override |
| 2977 | public boolean isRightAlignIds() | |
| 2978 | { | |
| 2979 | 16305 | return viewStyle.isRightAlignIds(); |
| 2980 | } | |
| 2981 | ||
| 2982 | 691 | @Override |
| 2983 | public void setRightAlignIds(boolean rightAlignIds) | |
| 2984 | { | |
| 2985 | 691 | viewStyle.setRightAlignIds(rightAlignIds); |
| 2986 | } | |
| 2987 | ||
| 2988 | 1115 | @Override |
| 2989 | public boolean getConservationSelected() | |
| 2990 | { | |
| 2991 | 1115 | return viewStyle.getConservationSelected(); |
| 2992 | } | |
| 2993 | ||
| 2994 | 96 | @Override |
| 2995 | public void setShowBoxes(boolean state) | |
| 2996 | { | |
| 2997 | 96 | viewStyle.setShowBoxes(state); |
| 2998 | } | |
| 2999 | ||
| 3000 | /** | |
| 3001 | * @return | |
| 3002 | * @see jalview.api.ViewStyleI#getTextColour() | |
| 3003 | */ | |
| 3004 | 834786 | @Override |
| 3005 | public Color getTextColour() | |
| 3006 | { | |
| 3007 | 834787 | return viewStyle.getTextColour(); |
| 3008 | } | |
| 3009 | ||
| 3010 | /** | |
| 3011 | * @return | |
| 3012 | * @see jalview.api.ViewStyleI#getTextColour2() | |
| 3013 | */ | |
| 3014 | 50 | @Override |
| 3015 | public Color getTextColour2() | |
| 3016 | { | |
| 3017 | 50 | return viewStyle.getTextColour2(); |
| 3018 | } | |
| 3019 | ||
| 3020 | /** | |
| 3021 | * @return | |
| 3022 | * @see jalview.api.ViewStyleI#getThresholdTextColour() | |
| 3023 | */ | |
| 3024 | 789451 | @Override |
| 3025 | public int getThresholdTextColour() | |
| 3026 | { | |
| 3027 | 789452 | return viewStyle.getThresholdTextColour(); |
| 3028 | } | |
| 3029 | ||
| 3030 | /** | |
| 3031 | * @return | |
| 3032 | * @see jalview.api.ViewStyleI#isConservationColourSelected() | |
| 3033 | */ | |
| 3034 | 0 | @Override |
| 3035 | public boolean isConservationColourSelected() | |
| 3036 | { | |
| 3037 | 0 | return viewStyle.isConservationColourSelected(); |
| 3038 | } | |
| 3039 | ||
| 3040 | /** | |
| 3041 | * @return | |
| 3042 | * @see jalview.api.ViewStyleI#isRenderGaps() | |
| 3043 | */ | |
| 3044 | 5949 | @Override |
| 3045 | public boolean isRenderGaps() | |
| 3046 | { | |
| 3047 | 5949 | return viewStyle.isRenderGaps(); |
| 3048 | } | |
| 3049 | ||
| 3050 | /** | |
| 3051 | * @return | |
| 3052 | * @see jalview.api.ViewStyleI#isShowColourText() | |
| 3053 | */ | |
| 3054 | 729 | @Override |
| 3055 | public boolean isShowColourText() | |
| 3056 | { | |
| 3057 | 729 | return viewStyle.isShowColourText(); |
| 3058 | } | |
| 3059 | ||
| 3060 | /** | |
| 3061 | * @param conservationColourSelected | |
| 3062 | * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean) | |
| 3063 | */ | |
| 3064 | 0 | @Override |
| 3065 | public void setConservationColourSelected( | |
| 3066 | boolean conservationColourSelected) | |
| 3067 | { | |
| 3068 | 0 | viewStyle.setConservationColourSelected(conservationColourSelected); |
| 3069 | } | |
| 3070 | ||
| 3071 | /** | |
| 3072 | * @param showColourText | |
| 3073 | * @see jalview.api.ViewStyleI#setShowColourText(boolean) | |
| 3074 | */ | |
| 3075 | 0 | @Override |
| 3076 | public void setShowColourText(boolean showColourText) | |
| 3077 | { | |
| 3078 | 0 | viewStyle.setShowColourText(showColourText); |
| 3079 | } | |
| 3080 | ||
| 3081 | /** | |
| 3082 | * @param textColour | |
| 3083 | * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color) | |
| 3084 | */ | |
| 3085 | 96 | @Override |
| 3086 | public void setTextColour(Color textColour) | |
| 3087 | { | |
| 3088 | 96 | viewStyle.setTextColour(textColour); |
| 3089 | } | |
| 3090 | ||
| 3091 | /** | |
| 3092 | * @param thresholdTextColour | |
| 3093 | * @see jalview.api.ViewStyleI#setThresholdTextColour(int) | |
| 3094 | */ | |
| 3095 | 96 | @Override |
| 3096 | public void setThresholdTextColour(int thresholdTextColour) | |
| 3097 | { | |
| 3098 | 96 | viewStyle.setThresholdTextColour(thresholdTextColour); |
| 3099 | } | |
| 3100 | ||
| 3101 | /** | |
| 3102 | * @param textColour2 | |
| 3103 | * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color) | |
| 3104 | */ | |
| 3105 | 96 | @Override |
| 3106 | public void setTextColour2(Color textColour2) | |
| 3107 | { | |
| 3108 | 96 | viewStyle.setTextColour2(textColour2); |
| 3109 | } | |
| 3110 | ||
| 3111 | 158 | @Override |
| 3112 | public ViewStyleI getViewStyle() | |
| 3113 | { | |
| 3114 | 158 | return new ViewStyle(viewStyle); |
| 3115 | } | |
| 3116 | ||
| 3117 | 97 | @Override |
| 3118 | public void setViewStyle(ViewStyleI settingsForView) | |
| 3119 | { | |
| 3120 | 97 | viewStyle = new ViewStyle(settingsForView); |
| 3121 | 97 | if (residueShading != null) |
| 3122 | { | |
| 3123 | 97 | residueShading.setConservationApplied( |
| 3124 | settingsForView.isConservationColourSelected()); | |
| 3125 | } | |
| 3126 | } | |
| 3127 | ||
| 3128 | 0 | @Override |
| 3129 | public boolean sameStyle(ViewStyleI them) | |
| 3130 | { | |
| 3131 | 0 | return viewStyle.sameStyle(them); |
| 3132 | } | |
| 3133 | ||
| 3134 | /** | |
| 3135 | * @return | |
| 3136 | * @see jalview.api.ViewStyleI#getIdWidth() | |
| 3137 | */ | |
| 3138 | 8821 | @Override |
| 3139 | public int getIdWidth() | |
| 3140 | { | |
| 3141 | 8821 | return viewStyle.getIdWidth(); |
| 3142 | } | |
| 3143 | ||
| 3144 | /** | |
| 3145 | * @param i | |
| 3146 | * @see jalview.api.ViewStyleI#setIdWidth(int) | |
| 3147 | */ | |
| 3148 | 737 | @Override |
| 3149 | public void setIdWidth(int i) | |
| 3150 | { | |
| 3151 | 737 | viewStyle.setIdWidth(i); |
| 3152 | } | |
| 3153 | ||
| 3154 | /** | |
| 3155 | * @return | |
| 3156 | * @see jalview.api.ViewStyleI#isCentreColumnLabels() | |
| 3157 | */ | |
| 3158 | 729 | @Override |
| 3159 | public boolean isCentreColumnLabels() | |
| 3160 | { | |
| 3161 | 729 | return viewStyle.isCentreColumnLabels(); |
| 3162 | } | |
| 3163 | ||
| 3164 | /** | |
| 3165 | * @param centreColumnLabels | |
| 3166 | * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean) | |
| 3167 | */ | |
| 3168 | 691 | @Override |
| 3169 | public void setCentreColumnLabels(boolean centreColumnLabels) | |
| 3170 | { | |
| 3171 | 691 | viewStyle.setCentreColumnLabels(centreColumnLabels); |
| 3172 | } | |
| 3173 | ||
| 3174 | /** | |
| 3175 | * @param showdbrefs | |
| 3176 | * @see jalview.api.ViewStyleI#setShowDBRefs(boolean) | |
| 3177 | */ | |
| 3178 | 691 | @Override |
| 3179 | public void setShowDBRefs(boolean showdbrefs) | |
| 3180 | { | |
| 3181 | 691 | viewStyle.setShowDBRefs(showdbrefs); |
| 3182 | } | |
| 3183 | ||
| 3184 | /** | |
| 3185 | * @return | |
| 3186 | * @see jalview.api.ViewStyleI#isShowDBRefs() | |
| 3187 | */ | |
| 3188 | 779 | @Override |
| 3189 | public boolean isShowDBRefs() | |
| 3190 | { | |
| 3191 | 779 | return viewStyle.isShowDBRefs(); |
| 3192 | } | |
| 3193 | ||
| 3194 | /** | |
| 3195 | * @return | |
| 3196 | * @see jalview.api.ViewStyleI#isShowNPFeats() | |
| 3197 | */ | |
| 3198 | 779 | @Override |
| 3199 | public boolean isShowNPFeats() | |
| 3200 | { | |
| 3201 | 779 | return viewStyle.isShowNPFeats(); |
| 3202 | } | |
| 3203 | ||
| 3204 | /** | |
| 3205 | * @param shownpfeats | |
| 3206 | * @see jalview.api.ViewStyleI#setShowNPFeats(boolean) | |
| 3207 | */ | |
| 3208 | 691 | @Override |
| 3209 | public void setShowNPFeats(boolean shownpfeats) | |
| 3210 | { | |
| 3211 | 691 | viewStyle.setShowNPFeats(shownpfeats); |
| 3212 | } | |
| 3213 | ||
| 3214 | public abstract StructureSelectionManager getStructureSelectionManager(); | |
| 3215 | ||
| 3216 | /** | |
| 3217 | * Add one command to the command history list. | |
| 3218 | * | |
| 3219 | * @param command | |
| 3220 | */ | |
| 3221 | 1 | public void addToHistoryList(CommandI command) |
| 3222 | { | |
| 3223 | 1 | if (this.historyList != null) |
| 3224 | { | |
| 3225 | 1 | this.historyList.push(command); |
| 3226 | 1 | broadcastCommand(command, false); |
| 3227 | 1 | setSavedUpToDate(false); |
| 3228 | 1 | Jalview2XML.setStateSavedUpToDate(false); |
| 3229 | } | |
| 3230 | } | |
| 3231 | ||
| 3232 | 1 | protected void broadcastCommand(CommandI command, boolean undo) |
| 3233 | { | |
| 3234 | 1 | getStructureSelectionManager().commandPerformed(command, undo, |
| 3235 | getVamsasSource()); | |
| 3236 | } | |
| 3237 | ||
| 3238 | /** | |
| 3239 | * Add one command to the command redo list. | |
| 3240 | * | |
| 3241 | * @param command | |
| 3242 | */ | |
| 3243 | 0 | public void addToRedoList(CommandI command) |
| 3244 | { | |
| 3245 | 0 | if (this.redoList != null) |
| 3246 | { | |
| 3247 | 0 | this.redoList.push(command); |
| 3248 | } | |
| 3249 | 0 | broadcastCommand(command, true); |
| 3250 | } | |
| 3251 | ||
| 3252 | /** | |
| 3253 | * Clear the command redo list. | |
| 3254 | */ | |
| 3255 | 1 | public void clearRedoList() |
| 3256 | { | |
| 3257 | 1 | if (this.redoList != null) |
| 3258 | { | |
| 3259 | 1 | this.redoList.clear(); |
| 3260 | } | |
| 3261 | } | |
| 3262 | ||
| 3263 | 53 | public void setHistoryList(Deque<CommandI> list) |
| 3264 | { | |
| 3265 | 53 | this.historyList = list; |
| 3266 | } | |
| 3267 | ||
| 3268 | 1705 | public Deque<CommandI> getHistoryList() |
| 3269 | { | |
| 3270 | 1705 | return this.historyList; |
| 3271 | } | |
| 3272 | ||
| 3273 | 53 | public void setRedoList(Deque<CommandI> list) |
| 3274 | { | |
| 3275 | 53 | this.redoList = list; |
| 3276 | } | |
| 3277 | ||
| 3278 | 1703 | public Deque<CommandI> getRedoList() |
| 3279 | { | |
| 3280 | 1703 | return this.redoList; |
| 3281 | } | |
| 3282 | ||
| 3283 | 1 | @Override |
| 3284 | public VamsasSource getVamsasSource() | |
| 3285 | { | |
| 3286 | 1 | return this; |
| 3287 | } | |
| 3288 | ||
| 3289 | 7209 | public SequenceAnnotationOrder getSortAnnotationsBy() |
| 3290 | { | |
| 3291 | 7209 | return sortAnnotationsBy; |
| 3292 | } | |
| 3293 | ||
| 3294 | 0 | public void setSortAnnotationsBy( |
| 3295 | SequenceAnnotationOrder sortAnnotationsBy) | |
| 3296 | { | |
| 3297 | 0 | this.sortAnnotationsBy = sortAnnotationsBy; |
| 3298 | } | |
| 3299 | ||
| 3300 | 7209 | public boolean isShowAutocalculatedAbove() |
| 3301 | { | |
| 3302 | 7209 | return showAutocalculatedAbove; |
| 3303 | } | |
| 3304 | ||
| 3305 | 487 | public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) |
| 3306 | { | |
| 3307 | 487 | this.showAutocalculatedAbove = showAutocalculatedAbove; |
| 3308 | } | |
| 3309 | ||
| 3310 | 3 | @Override |
| 3311 | public boolean isScaleProteinAsCdna() | |
| 3312 | { | |
| 3313 | 3 | return viewStyle.isScaleProteinAsCdna(); |
| 3314 | } | |
| 3315 | ||
| 3316 | 0 | @Override |
| 3317 | public void setScaleProteinAsCdna(boolean b) | |
| 3318 | { | |
| 3319 | 0 | viewStyle.setScaleProteinAsCdna(b); |
| 3320 | } | |
| 3321 | ||
| 3322 | 0 | @Override |
| 3323 | public boolean isProteinFontAsCdna() | |
| 3324 | { | |
| 3325 | 0 | return viewStyle.isProteinFontAsCdna(); |
| 3326 | } | |
| 3327 | ||
| 3328 | 0 | @Override |
| 3329 | public void setProteinFontAsCdna(boolean b) | |
| 3330 | { | |
| 3331 | 0 | viewStyle.setProteinFontAsCdna(b); |
| 3332 | } | |
| 3333 | ||
| 3334 | 96 | @Override |
| 3335 | public void setShowComplementFeatures(boolean b) | |
| 3336 | { | |
| 3337 | 96 | viewStyle.setShowComplementFeatures(b); |
| 3338 | } | |
| 3339 | ||
| 3340 | 416968 | @Override |
| 3341 | public boolean isShowComplementFeatures() | |
| 3342 | { | |
| 3343 | 416996 | return viewStyle.isShowComplementFeatures(); |
| 3344 | } | |
| 3345 | ||
| 3346 | 96 | @Override |
| 3347 | public void setShowComplementFeaturesOnTop(boolean b) | |
| 3348 | { | |
| 3349 | 96 | viewStyle.setShowComplementFeaturesOnTop(b); |
| 3350 | } | |
| 3351 | ||
| 3352 | 51 | @Override |
| 3353 | public boolean isShowComplementFeaturesOnTop() | |
| 3354 | { | |
| 3355 | 51 | return viewStyle.isShowComplementFeaturesOnTop(); |
| 3356 | } | |
| 3357 | ||
| 3358 | /** | |
| 3359 | * @return true if view should scroll to show the highlighted region of a | |
| 3360 | * sequence | |
| 3361 | * @return | |
| 3362 | */ | |
| 3363 | 60 | @Override |
| 3364 | public final boolean isFollowHighlight() | |
| 3365 | { | |
| 3366 | 60 | return followHighlight; |
| 3367 | } | |
| 3368 | ||
| 3369 | 96 | @Override |
| 3370 | public final void setFollowHighlight(boolean b) | |
| 3371 | { | |
| 3372 | 96 | this.followHighlight = b; |
| 3373 | } | |
| 3374 | ||
| 3375 | 51999 | @Override |
| 3376 | public ViewportRanges getRanges() | |
| 3377 | { | |
| 3378 | 51999 | return ranges; |
| 3379 | } | |
| 3380 | ||
| 3381 | /** | |
| 3382 | * Helper method to populate the SearchResults with the location in the | |
| 3383 | * complementary alignment to scroll to, in order to match this one. | |
| 3384 | * | |
| 3385 | * @param sr | |
| 3386 | * the SearchResults to add to | |
| 3387 | * @return the offset (below top of visible region) of the matched sequence | |
| 3388 | */ | |
| 3389 | 654 | protected int findComplementScrollTarget(SearchResultsI sr) |
| 3390 | { | |
| 3391 | 654 | final AlignViewportI complement = getCodingComplement(); |
| 3392 | 654 | if (complement == null || !complement.isFollowHighlight()) |
| 3393 | { | |
| 3394 | 652 | return 0; |
| 3395 | } | |
| 3396 | 2 | boolean iAmProtein = !getAlignment().isNucleotide(); |
| 3397 | 2 | AlignmentI proteinAlignment = iAmProtein ? getAlignment() |
| 3398 | : complement.getAlignment(); | |
| 3399 | 2 | if (proteinAlignment == null) |
| 3400 | { | |
| 3401 | 0 | return 0; |
| 3402 | } | |
| 3403 | 2 | final List<AlignedCodonFrame> mappings = proteinAlignment |
| 3404 | .getCodonFrames(); | |
| 3405 | ||
| 3406 | /* | |
| 3407 | * Heuristic: find the first mapped sequence (if any) with a non-gapped | |
| 3408 | * residue in the middle column of the visible region. Scroll the | |
| 3409 | * complementary alignment to line up the corresponding residue. | |
| 3410 | */ | |
| 3411 | 2 | int seqOffset = 0; |
| 3412 | 2 | SequenceI sequence = null; |
| 3413 | ||
| 3414 | /* | |
| 3415 | * locate 'middle' column (true middle if an odd number visible, left of | |
| 3416 | * middle if an even number visible) | |
| 3417 | */ | |
| 3418 | 2 | int middleColumn = ranges.getStartRes() |
| 3419 | + (ranges.getEndRes() - ranges.getStartRes()) / 2; | |
| 3420 | 2 | final HiddenSequences hiddenSequences = getAlignment() |
| 3421 | .getHiddenSequences(); | |
| 3422 | ||
| 3423 | /* | |
| 3424 | * searching to the bottom of the alignment gives smoother scrolling across | |
| 3425 | * all gapped visible regions | |
| 3426 | */ | |
| 3427 | 2 | int lastSeq = alignment.getHeight() - 1; |
| 3428 | 2 | List<AlignedCodonFrame> seqMappings = null; |
| 3429 | 2 | for (int seqNo = ranges |
| 3430 | 2 | .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) |
| 3431 | { | |
| 3432 | 2 | sequence = getAlignment().getSequenceAt(seqNo); |
| 3433 | 2 | if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) |
| 3434 | { | |
| 3435 | 0 | continue; |
| 3436 | } | |
| 3437 | 2 | if (Comparison.isGap(sequence.getCharAt(middleColumn))) |
| 3438 | { | |
| 3439 | 0 | continue; |
| 3440 | } | |
| 3441 | 2 | seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence, |
| 3442 | mappings, | |
| 3443 | getCodingComplement().getAlignment().getSequences()); | |
| 3444 | 2 | if (!seqMappings.isEmpty()) |
| 3445 | { | |
| 3446 | 2 | break; |
| 3447 | } | |
| 3448 | } | |
| 3449 | ||
| 3450 | 2 | if (sequence == null || seqMappings == null || seqMappings.isEmpty()) |
| 3451 | { | |
| 3452 | /* | |
| 3453 | * No ungapped mapped sequence in middle column - do nothing | |
| 3454 | */ | |
| 3455 | 0 | return 0; |
| 3456 | } | |
| 3457 | 2 | MappingUtils.addSearchResults(sr, sequence, |
| 3458 | sequence.findPosition(middleColumn), seqMappings); | |
| 3459 | 2 | return seqOffset; |
| 3460 | } | |
| 3461 | ||
| 3462 | /** | |
| 3463 | * synthesize a column selection if none exists so it covers the given | |
| 3464 | * selection group. if wholewidth is false, no column selection is made if the | |
| 3465 | * selection group covers the whole alignment width. | |
| 3466 | * | |
| 3467 | * @param sg | |
| 3468 | * @param wholewidth | |
| 3469 | */ | |
| 3470 | 0 | public void expandColSelection(SequenceGroup sg, boolean wholewidth) |
| 3471 | { | |
| 3472 | 0 | int sgs, sge; |
| 3473 | 0 | if (sg != null && (sgs = sg.getStartRes()) >= 0 |
| 3474 | && sg.getStartRes() <= (sge = sg.getEndRes()) | |
| 3475 | && !this.hasSelectedColumns()) | |
| 3476 | { | |
| 3477 | 0 | if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) |
| 3478 | { | |
| 3479 | // do nothing | |
| 3480 | 0 | return; |
| 3481 | } | |
| 3482 | 0 | if (colSel == null) |
| 3483 | { | |
| 3484 | 0 | colSel = new ColumnSelection(); |
| 3485 | } | |
| 3486 | 0 | for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) |
| 3487 | { | |
| 3488 | 0 | colSel.addElement(cspos); |
| 3489 | } | |
| 3490 | } | |
| 3491 | } | |
| 3492 | ||
| 3493 | /** | |
| 3494 | * hold status of current selection group - defined on alignment or not. | |
| 3495 | */ | |
| 3496 | private boolean selectionIsDefinedGroup = false; | |
| 3497 | ||
| 3498 | 0 | @Override |
| 3499 | public boolean isSelectionDefinedGroup() | |
| 3500 | { | |
| 3501 | 0 | if (selectionGroup == null) |
| 3502 | { | |
| 3503 | 0 | return false; |
| 3504 | } | |
| 3505 | 0 | if (isSelectionGroupChanged(true)) |
| 3506 | { | |
| 3507 | 0 | selectionIsDefinedGroup = false; |
| 3508 | 0 | List<SequenceGroup> gps = alignment.getGroups(); |
| 3509 | 0 | if (gps == null || gps.size() == 0) |
| 3510 | { | |
| 3511 | 0 | selectionIsDefinedGroup = false; |
| 3512 | } | |
| 3513 | else | |
| 3514 | { | |
| 3515 | 0 | selectionIsDefinedGroup = gps.contains(selectionGroup); |
| 3516 | } | |
| 3517 | } | |
| 3518 | 0 | return selectionGroup.isDefined() || selectionIsDefinedGroup; |
| 3519 | } | |
| 3520 | ||
| 3521 | /** | |
| 3522 | * null, or currently highlighted results on this view | |
| 3523 | */ | |
| 3524 | private SearchResultsI searchResults = null; | |
| 3525 | ||
| 3526 | protected TreeModel currentTree = null; | |
| 3527 | ||
| 3528 | 13113 | @Override |
| 3529 | public boolean hasSearchResults() | |
| 3530 | { | |
| 3531 | 13113 | return searchResults != null; |
| 3532 | } | |
| 3533 | ||
| 3534 | 14 | @Override |
| 3535 | public void setSearchResults(SearchResultsI results) | |
| 3536 | { | |
| 3537 | 14 | searchResults = results; |
| 3538 | } | |
| 3539 | ||
| 3540 | 102 | @Override |
| 3541 | public SearchResultsI getSearchResults() | |
| 3542 | { | |
| 3543 | 102 | return searchResults; |
| 3544 | } | |
| 3545 | ||
| 3546 | 6029 | @Override |
| 3547 | public ContactListI getContactList(AlignmentAnnotation _aa, int column) | |
| 3548 | { | |
| 3549 | 6029 | return alignment.getContactListFor(_aa, column); |
| 3550 | } | |
| 3551 | ||
| 3552 | 386 | @Override |
| 3553 | public ContactMatrixI getContactMatrix( | |
| 3554 | AlignmentAnnotation alignmentAnnotation) | |
| 3555 | { | |
| 3556 | 386 | return alignment.getContactMatrixFor(alignmentAnnotation); |
| 3557 | } | |
| 3558 | ||
| 3559 | /** | |
| 3560 | * get the consensus sequence as displayed under the PID consensus annotation | |
| 3561 | * row. | |
| 3562 | * | |
| 3563 | * @return consensus sequence as a new sequence object | |
| 3564 | */ | |
| 3565 | 1 | public SequenceI getConsensusSeq() |
| 3566 | { | |
| 3567 | 1 | if (consensus == null) |
| 3568 | { | |
| 3569 | 0 | updateConsensus(null); |
| 3570 | } | |
| 3571 | 1 | if (consensus == null) |
| 3572 | { | |
| 3573 | 0 | return null; |
| 3574 | } | |
| 3575 | 1 | StringBuffer seqs = new StringBuffer(); |
| 3576 | 4 | for (int i = 0; i < consensus.annotations.length; i++) |
| 3577 | { | |
| 3578 | 3 | Annotation annotation = consensus.annotations[i]; |
| 3579 | 3 | if (annotation != null) |
| 3580 | { | |
| 3581 | 3 | String description = annotation.description; |
| 3582 | 3 | if (description != null && description.startsWith("[")) |
| 3583 | { | |
| 3584 | // consensus is a tie - just pick the first one | |
| 3585 | 1 | seqs.append(description.charAt(1)); |
| 3586 | } | |
| 3587 | else | |
| 3588 | { | |
| 3589 | 2 | seqs.append(annotation.displayCharacter); |
| 3590 | } | |
| 3591 | } | |
| 3592 | } | |
| 3593 | ||
| 3594 | 1 | SequenceI sq = new Sequence("Consensus", seqs.toString()); |
| 3595 | 1 | sq.setDescription("Percentage Identity Consensus " |
| 3596 | 1 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3597 | 1 | return sq; |
| 3598 | } | |
| 3599 | ||
| 3600 | // TODO JAL-4386 | |
| 3601 | 0 | public SequenceI getSSConsensusSeq() |
| 3602 | { | |
| 3603 | 0 | if (secondaryStructureConsensus == null) |
| 3604 | { | |
| 3605 | 0 | updateSecondaryStructureConsensus(null); |
| 3606 | } | |
| 3607 | 0 | if (secondaryStructureConsensus == null) |
| 3608 | { | |
| 3609 | 0 | return null; |
| 3610 | } | |
| 3611 | 0 | StringBuffer seqs = new StringBuffer(); |
| 3612 | // for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++) | |
| 3613 | // { | |
| 3614 | // Annotation annotation = secondaryStructureConsensus.annotations[i]; | |
| 3615 | // if (annotation != null) | |
| 3616 | // { | |
| 3617 | // String description = annotation.description; | |
| 3618 | // if (description != null && description.startsWith("[")) | |
| 3619 | // { | |
| 3620 | // // consensus is a tie - just pick the first one | |
| 3621 | // seqs.append(description.charAt(1)); | |
| 3622 | // } | |
| 3623 | // else | |
| 3624 | // { | |
| 3625 | // seqs.append(annotation.displayCharacter); | |
| 3626 | // } | |
| 3627 | // } | |
| 3628 | // } | |
| 3629 | ||
| 3630 | 0 | SequenceI sq = new Sequence("Sec Str Consensus", seqs.toString()); |
| 3631 | 0 | sq.setDescription("Percentage Identity Sec Str Consensus " |
| 3632 | 0 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3633 | 0 | return sq; |
| 3634 | } | |
| 3635 | ||
| 3636 | 0 | public boolean hasReferenceAnnotation() |
| 3637 | { | |
| 3638 | 0 | AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation(); |
| 3639 | 0 | for (AlignmentAnnotation annot : annots) |
| 3640 | { | |
| 3641 | 0 | if ("RF".equals(annot.label) || annot.label.contains("Reference")) |
| 3642 | { | |
| 3643 | 0 | return true; |
| 3644 | } | |
| 3645 | } | |
| 3646 | 0 | return false; |
| 3647 | } | |
| 3648 | 22 | @Override |
| 3649 | public void setCurrentTree(TreeModel tree) | |
| 3650 | { | |
| 3651 | 22 | currentTree = tree; |
| 3652 | } | |
| 3653 | ||
| 3654 | 71 | @Override |
| 3655 | public TreeModel getCurrentTree() | |
| 3656 | { | |
| 3657 | 71 | return currentTree; |
| 3658 | } | |
| 3659 | ||
| 3660 | 121 | @Override |
| 3661 | public AlignmentExportData getAlignExportData(AlignExportSettingsI options) | |
| 3662 | { | |
| 3663 | 121 | AlignmentI alignmentToExport = null; |
| 3664 | 121 | String[] omitHidden = null; |
| 3665 | 121 | alignmentToExport = null; |
| 3666 | ||
| 3667 | 121 | if (hasHiddenColumns() && !options.isExportHiddenColumns()) |
| 3668 | { | |
| 3669 | 0 | omitHidden = getViewAsString(false, |
| 3670 | options.isExportHiddenSequences()); | |
| 3671 | } | |
| 3672 | ||
| 3673 | 121 | int[] alignmentStartEnd = new int[2]; |
| 3674 | 121 | if (hasHiddenRows() && options.isExportHiddenSequences()) |
| 3675 | { | |
| 3676 | 0 | alignmentToExport = getAlignment().getHiddenSequences() |
| 3677 | .getFullAlignment(); | |
| 3678 | } | |
| 3679 | else | |
| 3680 | { | |
| 3681 | 121 | alignmentToExport = getAlignment(); |
| 3682 | } | |
| 3683 | 121 | alignmentStartEnd = getAlignment().getHiddenColumns() |
| 3684 | .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); | |
| 3685 | 121 | AlignmentExportData ed = new AlignmentExportData(alignmentToExport, |
| 3686 | omitHidden, alignmentStartEnd); | |
| 3687 | 121 | return ed; |
| 3688 | } | |
| 3689 | ||
| 3690 | 0 | @Override |
| 3691 | public boolean isNormaliseSequenceLogo() | |
| 3692 | { | |
| 3693 | 0 | return normaliseSequenceLogo; |
| 3694 | } | |
| 3695 | ||
| 3696 | 0 | public void setNormaliseSequenceLogo(boolean state) |
| 3697 | { | |
| 3698 | 0 | normaliseSequenceLogo = state; |
| 3699 | } | |
| 3700 | ||
| 3701 | 1183 | @Override |
| 3702 | public boolean isNormaliseHMMSequenceLogo() | |
| 3703 | { | |
| 3704 | 1183 | return hmmNormaliseSequenceLogo; |
| 3705 | } | |
| 3706 | ||
| 3707 | 595 | public void setNormaliseHMMSequenceLogo(boolean state) |
| 3708 | { | |
| 3709 | 595 | hmmNormaliseSequenceLogo = state; |
| 3710 | } | |
| 3711 | /** | |
| 3712 | * flag set to indicate if structure views might be out of sync with sequences | |
| 3713 | * in the alignment | |
| 3714 | */ | |
| 3715 | ||
| 3716 | private boolean needToUpdateStructureViews = false; | |
| 3717 | ||
| 3718 | 0 | @Override |
| 3719 | public boolean isUpdateStructures() | |
| 3720 | { | |
| 3721 | 0 | return needToUpdateStructureViews; |
| 3722 | } | |
| 3723 | ||
| 3724 | 3 | @Override |
| 3725 | public void setUpdateStructures(boolean update) | |
| 3726 | { | |
| 3727 | 3 | needToUpdateStructureViews = update; |
| 3728 | } | |
| 3729 | ||
| 3730 | 4142 | @Override |
| 3731 | public boolean needToUpdateStructureViews() | |
| 3732 | { | |
| 3733 | 4142 | boolean update = needToUpdateStructureViews; |
| 3734 | 4142 | needToUpdateStructureViews = false; |
| 3735 | 4142 | return update; |
| 3736 | } | |
| 3737 | ||
| 3738 | 2 | @Override |
| 3739 | public void addSequenceGroup(SequenceGroup sequenceGroup) | |
| 3740 | { | |
| 3741 | 2 | alignment.addGroup(sequenceGroup); |
| 3742 | ||
| 3743 | 2 | Color col = sequenceGroup.idColour; |
| 3744 | 2 | if (col != null) |
| 3745 | { | |
| 3746 | 2 | col = col.brighter(); |
| 3747 | ||
| 3748 | 2 | for (SequenceI sq : sequenceGroup.getSequences()) |
| 3749 | { | |
| 3750 | 15 | setSequenceColour(sq, col); |
| 3751 | } | |
| 3752 | ||
| 3753 | 2 | List<AlignmentAnnotation> annotations = sequenceGroup.getAnnotationsFromTree(); |
| 3754 | 2 | if (annotations != null) { |
| 3755 | 2 | for (AlignmentAnnotation annot : annotations) { |
| 3756 | 4 | setAnnotationColour(annot, col); |
| 3757 | } | |
| 3758 | } | |
| 3759 | } | |
| 3760 | ||
| 3761 | 2 | if (codingComplement != null) |
| 3762 | { | |
| 3763 | 0 | SequenceGroup mappedGroup = MappingUtils |
| 3764 | .mapSequenceGroup(sequenceGroup, this, codingComplement); | |
| 3765 | 0 | if (mappedGroup.getSequences().size() > 0) |
| 3766 | { | |
| 3767 | 0 | codingComplement.getAlignment().addGroup(mappedGroup); |
| 3768 | ||
| 3769 | 0 | if (col != null) |
| 3770 | { | |
| 3771 | 0 | for (SequenceI seq : mappedGroup.getSequences()) |
| 3772 | { | |
| 3773 | 0 | codingComplement.setSequenceColour(seq, col); |
| 3774 | } | |
| 3775 | } | |
| 3776 | } | |
| 3777 | // propagate the structure view update flag according to our own setting | |
| 3778 | 0 | codingComplement.setUpdateStructures(needToUpdateStructureViews); |
| 3779 | } | |
| 3780 | } | |
| 3781 | ||
| 3782 | 34 | @Override |
| 3783 | public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly) | |
| 3784 | { | |
| 3785 | 34 | int start = 0; |
| 3786 | 34 | int end = 0; |
| 3787 | 34 | if (selectedRegionOnly && selectionGroup != null) |
| 3788 | { | |
| 3789 | 4 | start = selectionGroup.getStartRes(); |
| 3790 | 4 | end = selectionGroup.getEndRes() + 1; |
| 3791 | } | |
| 3792 | else | |
| 3793 | { | |
| 3794 | 30 | end = alignment.getWidth(); |
| 3795 | } | |
| 3796 | 34 | return (alignment.getHiddenColumns().getVisContigsIterator(start, end, |
| 3797 | false)); | |
| 3798 | } | |
| 3799 | ||
| 3800 | 133 | public void setSavedUpToDate(boolean s) |
| 3801 | { | |
| 3802 | 133 | setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES); |
| 3803 | } | |
| 3804 | ||
| 3805 | 465 | public void setSavedUpToDate(boolean s, QuitHandler.Message m) |
| 3806 | { | |
| 3807 | 465 | Console.debug( |
| 3808 | "Setting " + this.getViewId() + " setSavedUpToDate to " + s); | |
| 3809 | 465 | savedUpToDate = s; |
| 3810 | 465 | QuitHandler.setMessage(m); |
| 3811 | } | |
| 3812 | ||
| 3813 | 4 | public boolean savedUpToDate() |
| 3814 | { | |
| 3815 | 4 | Console.debug("Returning " + this.getViewId() + " savedUpToDate value: " |
| 3816 | + savedUpToDate); | |
| 3817 | 4 | return savedUpToDate; |
| 3818 | } | |
| 3819 | /** | |
| 3820 | * Filters out sequences with an eValue higher than the specified value. The | |
| 3821 | * filtered sequences are hidden or deleted. Sequences with no eValues are also | |
| 3822 | * filtered out. | |
| 3823 | * | |
| 3824 | * @param eValue | |
| 3825 | * @param delete | |
| 3826 | */ | |
| 3827 | 0 | public void filterByEvalue(double eValue) |
| 3828 | { | |
| 3829 | 0 | for (SequenceI seq : alignment.getSequencesArray()) |
| 3830 | { | |
| 3831 | 0 | if ((seq.getAnnotation("Search Scores") == null |
| 3832 | || seq.getAnnotation("Search Scores")[0].getEValue() > eValue) | |
| 3833 | && seq.getHMM() == null) | |
| 3834 | { | |
| 3835 | 0 | hideSequence(new SequenceI[] { seq }); |
| 3836 | } | |
| 3837 | } | |
| 3838 | } | |
| 3839 | ||
| 3840 | /** | |
| 3841 | * Filters out sequences with an score lower than the specified value. The | |
| 3842 | * filtered sequences are hidden or deleted. | |
| 3843 | * | |
| 3844 | * @param score | |
| 3845 | * @param delete | |
| 3846 | */ | |
| 3847 | 0 | public void filterByScore(double score) |
| 3848 | { | |
| 3849 | 0 | for (SequenceI seq : alignment.getSequencesArray()) |
| 3850 | { | |
| 3851 | 0 | if ((seq.getAnnotation("Search Scores") == null |
| 3852 | || seq.getAnnotation("Search Scores")[0] | |
| 3853 | .getBitScore() < score) | |
| 3854 | && seq.getHMM() == null) | |
| 3855 | { | |
| 3856 | 0 | hideSequence(new SequenceI[] { seq }); |
| 3857 | } | |
| 3858 | } | |
| 3859 | } | |
| 3860 | } |