Coverage Report
File AlignmentViewport.java
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22% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignmentViewport | 89 | 745 | 460 |
Contributing tests
This file is covered by 317 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.Conservation; | |
| 37 | import jalview.analysis.TreeModel; | |
| 38 | import jalview.api.AlignCalcManagerI; | |
| 39 | import jalview.api.AlignExportSettingsI; | |
| 40 | import jalview.api.AlignViewportI; | |
| 41 | import jalview.api.AlignmentViewPanel; | |
| 42 | import jalview.api.FeaturesDisplayedI; | |
| 43 | import jalview.api.ViewStyleI; | |
| 44 | import jalview.bin.Console; | |
| 45 | import jalview.commands.CommandI; | |
| 46 | import jalview.datamodel.AlignedCodonFrame; | |
| 47 | import jalview.datamodel.AlignmentAnnotation; | |
| 48 | import jalview.datamodel.AlignmentExportData; | |
| 49 | import jalview.datamodel.AlignmentI; | |
| 50 | import jalview.datamodel.AlignmentView; | |
| 51 | import jalview.datamodel.Annotation; | |
| 52 | import jalview.datamodel.ColumnSelection; | |
| 53 | import jalview.datamodel.ContactListI; | |
| 54 | import jalview.datamodel.ContactMatrixI; | |
| 55 | import jalview.datamodel.HiddenColumns; | |
| 56 | import jalview.datamodel.HiddenSequences; | |
| 57 | import jalview.datamodel.ProfilesI; | |
| 58 | import jalview.datamodel.SearchResultsI; | |
| 59 | import jalview.datamodel.Sequence; | |
| 60 | import jalview.datamodel.SequenceCollectionI; | |
| 61 | import jalview.datamodel.SequenceGroup; | |
| 62 | import jalview.datamodel.SequenceI; | |
| 63 | import jalview.gui.QuitHandler; | |
| 64 | import jalview.project.Jalview2XML; | |
| 65 | import jalview.renderer.ResidueShader; | |
| 66 | import jalview.renderer.ResidueShaderI; | |
| 67 | import jalview.schemes.ColourSchemeI; | |
| 68 | import jalview.structure.CommandListener; | |
| 69 | import jalview.structure.StructureSelectionManager; | |
| 70 | import jalview.structure.VamsasSource; | |
| 71 | import jalview.util.Comparison; | |
| 72 | import jalview.util.MapList; | |
| 73 | import jalview.util.MappingUtils; | |
| 74 | import jalview.util.MessageManager; | |
| 75 | import jalview.viewmodel.styles.ViewStyle; | |
| 76 | import jalview.workers.AlignCalcManager; | |
| 77 | import jalview.workers.ComplementConsensusThread; | |
| 78 | import jalview.workers.ConsensusThread; | |
| 79 | import jalview.workers.SecondaryStructureConsensusThread; | |
| 80 | import jalview.workers.StrucConsensusThread; | |
| 81 | ||
| 82 | /** | |
| 83 | * base class holding visualization and analysis attributes and common logic for | |
| 84 | * an active alignment view displayed in the GUI | |
| 85 | * | |
| 86 | * @author jimp | |
| 87 | * | |
| 88 | */ | |
| 89 | public abstract class AlignmentViewport | |
| 90 | implements AlignViewportI, CommandListener, VamsasSource | |
| 91 | { | |
| 92 | protected ViewportRanges ranges; | |
| 93 | ||
| 94 | protected ViewStyleI viewStyle = new ViewStyle(); | |
| 95 | ||
| 96 | /** | |
| 97 | * A viewport that hosts the cDna view of this (protein), or vice versa (if | |
| 98 | * set). | |
| 99 | */ | |
| 100 | AlignViewportI codingComplement = null; | |
| 101 | ||
| 102 | FeaturesDisplayedI featuresDisplayed = null; | |
| 103 | ||
| 104 | protected Deque<CommandI> historyList = new ArrayDeque<>(); | |
| 105 | ||
| 106 | protected Deque<CommandI> redoList = new ArrayDeque<>(); | |
| 107 | ||
| 108 | /** | |
| 109 | * used to determine if quit should be confirmed | |
| 110 | */ | |
| 111 | private boolean savedUpToDate = false; | |
| 112 | ||
| 113 | /** | |
| 114 | * alignment displayed in the viewport. Please use get/setter | |
| 115 | */ | |
| 116 | protected AlignmentI alignment; | |
| 117 | ||
| 118 | 508 |  public AlignmentViewport(AlignmentI al) |
| 119 | { | |
| 120 | 508 | setAlignment(al); |
| 121 | 508 | ranges = new ViewportRanges(al); |
| 122 | } | |
| 123 | ||
| 124 | /** | |
| 125 | * @param name | |
| 126 | * @see jalview.api.ViewStyleI#setFontName(java.lang.String) | |
| 127 | */ | |
| 128 | 0 | @Override |
| 129 | public void setFontName(String name) | |
| 130 | { | |
| 131 | 0 | viewStyle.setFontName(name); |
| 132 | } | |
| 133 | ||
| 134 | /** | |
| 135 | * @param style | |
| 136 | * @see jalview.api.ViewStyleI#setFontStyle(int) | |
| 137 | */ | |
| 138 | 0 | @Override |
| 139 | public void setFontStyle(int style) | |
| 140 | { | |
| 141 | 0 | viewStyle.setFontStyle(style); |
| 142 | } | |
| 143 | ||
| 144 | /** | |
| 145 | * @param size | |
| 146 | * @see jalview.api.ViewStyleI#setFontSize(int) | |
| 147 | */ | |
| 148 | 0 | @Override |
| 149 | public void setFontSize(int size) | |
| 150 | { | |
| 151 | 0 | viewStyle.setFontSize(size); |
| 152 | } | |
| 153 | ||
| 154 | /** | |
| 155 | * @return | |
| 156 | * @see jalview.api.ViewStyleI#getFontStyle() | |
| 157 | */ | |
| 158 | 0 | @Override |
| 159 | public int getFontStyle() | |
| 160 | { | |
| 161 | 0 | return viewStyle.getFontStyle(); |
| 162 | } | |
| 163 | ||
| 164 | /** | |
| 165 | * @return | |
| 166 | * @see jalview.api.ViewStyleI#getFontName() | |
| 167 | */ | |
| 168 | 0 | @Override |
| 169 | public String getFontName() | |
| 170 | { | |
| 171 | 0 | return viewStyle.getFontName(); |
| 172 | } | |
| 173 | ||
| 174 | /** | |
| 175 | * @return | |
| 176 | * @see jalview.api.ViewStyleI#getFontSize() | |
| 177 | */ | |
| 178 | 0 | @Override |
| 179 | public int getFontSize() | |
| 180 | { | |
| 181 | 0 | return viewStyle.getFontSize(); |
| 182 | } | |
| 183 | ||
| 184 | /** | |
| 185 | * @param upperCasebold | |
| 186 | * @see jalview.api.ViewStyleI#setUpperCasebold(boolean) | |
| 187 | */ | |
| 188 | 0 | @Override |
| 189 | public void setUpperCasebold(boolean upperCasebold) | |
| 190 | { | |
| 191 | 0 | viewStyle.setUpperCasebold(upperCasebold); |
| 192 | } | |
| 193 | ||
| 194 | /** | |
| 195 | * @return | |
| 196 | * @see jalview.api.ViewStyleI#isUpperCasebold() | |
| 197 | */ | |
| 198 | 0 | @Override |
| 199 | public boolean isUpperCasebold() | |
| 200 | { | |
| 201 | 0 | return viewStyle.isUpperCasebold(); |
| 202 | } | |
| 203 | ||
| 204 | /** | |
| 205 | * @return | |
| 206 | * @see jalview.api.ViewStyleI#isSeqNameItalics() | |
| 207 | */ | |
| 208 | 2160 | @Override |
| 209 | public boolean isSeqNameItalics() | |
| 210 | { | |
| 211 | 2160 | return viewStyle.isSeqNameItalics(); |
| 212 | } | |
| 213 | ||
| 214 | /** | |
| 215 | * @param colourByReferenceSeq | |
| 216 | * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean) | |
| 217 | */ | |
| 218 | 10 | @Override |
| 219 | public void setColourByReferenceSeq(boolean colourByReferenceSeq) | |
| 220 | { | |
| 221 | 10 | viewStyle.setColourByReferenceSeq(colourByReferenceSeq); |
| 222 | } | |
| 223 | ||
| 224 | /** | |
| 225 | * @param b | |
| 226 | * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean) | |
| 227 | */ | |
| 228 | 693 | @Override |
| 229 | public void setColourAppliesToAllGroups(boolean b) | |
| 230 | { | |
| 231 | 693 | viewStyle.setColourAppliesToAllGroups(b); |
| 232 | } | |
| 233 | ||
| 234 | /** | |
| 235 | * @return | |
| 236 | * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups() | |
| 237 | */ | |
| 238 | 962 | @Override |
| 239 | public boolean getColourAppliesToAllGroups() | |
| 240 | { | |
| 241 | 962 | return viewStyle.getColourAppliesToAllGroups(); |
| 242 | } | |
| 243 | ||
| 244 | /** | |
| 245 | * @return | |
| 246 | * @see jalview.api.ViewStyleI#getAbovePIDThreshold() | |
| 247 | */ | |
| 248 | 878 | @Override |
| 249 | public boolean getAbovePIDThreshold() | |
| 250 | { | |
| 251 | 878 | return viewStyle.getAbovePIDThreshold(); |
| 252 | } | |
| 253 | ||
| 254 | /** | |
| 255 | * @param inc | |
| 256 | * @see jalview.api.ViewStyleI#setIncrement(int) | |
| 257 | */ | |
| 258 | 85 | @Override |
| 259 | public void setIncrement(int inc) | |
| 260 | { | |
| 261 | 85 | viewStyle.setIncrement(inc); |
| 262 | } | |
| 263 | ||
| 264 | /** | |
| 265 | * @return | |
| 266 | * @see jalview.api.ViewStyleI#getIncrement() | |
| 267 | */ | |
| 268 | 0 | @Override |
| 269 | public int getIncrement() | |
| 270 | { | |
| 271 | 0 | return viewStyle.getIncrement(); |
| 272 | } | |
| 273 | ||
| 274 | /** | |
| 275 | * @param b | |
| 276 | * @see jalview.api.ViewStyleI#setConservationSelected(boolean) | |
| 277 | */ | |
| 278 | 93 | @Override |
| 279 | public void setConservationSelected(boolean b) | |
| 280 | { | |
| 281 | 93 | viewStyle.setConservationSelected(b); |
| 282 | } | |
| 283 | ||
| 284 | /** | |
| 285 | * @param show | |
| 286 | * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean) | |
| 287 | */ | |
| 288 | 0 | @Override |
| 289 | public void setShowHiddenMarkers(boolean show) | |
| 290 | { | |
| 291 | 0 | viewStyle.setShowHiddenMarkers(show); |
| 292 | } | |
| 293 | ||
| 294 | /** | |
| 295 | * @return | |
| 296 | * @see jalview.api.ViewStyleI#getShowHiddenMarkers() | |
| 297 | */ | |
| 298 | 4745 | @Override |
| 299 | public boolean getShowHiddenMarkers() | |
| 300 | { | |
| 301 | 4745 | return viewStyle.getShowHiddenMarkers(); |
| 302 | } | |
| 303 | ||
| 304 | /** | |
| 305 | * @param b | |
| 306 | * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean) | |
| 307 | */ | |
| 308 | 9 | @Override |
| 309 | public void setScaleRightWrapped(boolean b) | |
| 310 | { | |
| 311 | 9 | viewStyle.setScaleRightWrapped(b); |
| 312 | } | |
| 313 | ||
| 314 | /** | |
| 315 | * @param b | |
| 316 | * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean) | |
| 317 | */ | |
| 318 | 11 | @Override |
| 319 | public void setScaleLeftWrapped(boolean b) | |
| 320 | { | |
| 321 | 11 | viewStyle.setScaleLeftWrapped(b); |
| 322 | } | |
| 323 | ||
| 324 | /** | |
| 325 | * @param b | |
| 326 | * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean) | |
| 327 | */ | |
| 328 | 9 | @Override |
| 329 | public void setScaleAboveWrapped(boolean b) | |
| 330 | { | |
| 331 | 9 | viewStyle.setScaleAboveWrapped(b); |
| 332 | } | |
| 333 | ||
| 334 | /** | |
| 335 | * @return | |
| 336 | * @see jalview.api.ViewStyleI#getScaleLeftWrapped() | |
| 337 | */ | |
| 338 | 1070 | @Override |
| 339 | public boolean getScaleLeftWrapped() | |
| 340 | { | |
| 341 | 1070 | return viewStyle.getScaleLeftWrapped(); |
| 342 | } | |
| 343 | ||
| 344 | /** | |
| 345 | * @return | |
| 346 | * @see jalview.api.ViewStyleI#getScaleAboveWrapped() | |
| 347 | */ | |
| 348 | 727 | @Override |
| 349 | public boolean getScaleAboveWrapped() | |
| 350 | { | |
| 351 | 727 | return viewStyle.getScaleAboveWrapped(); |
| 352 | } | |
| 353 | ||
| 354 | /** | |
| 355 | * @return | |
| 356 | * @see jalview.api.ViewStyleI#getScaleRightWrapped() | |
| 357 | */ | |
| 358 | 1708 | @Override |
| 359 | public boolean getScaleRightWrapped() | |
| 360 | { | |
| 361 | 1708 | return viewStyle.getScaleRightWrapped(); |
| 362 | } | |
| 363 | ||
| 364 | /** | |
| 365 | * @param b | |
| 366 | * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean) | |
| 367 | */ | |
| 368 | 94 | @Override |
| 369 | public void setAbovePIDThreshold(boolean b) | |
| 370 | { | |
| 371 | 94 | viewStyle.setAbovePIDThreshold(b); |
| 372 | } | |
| 373 | ||
| 374 | /** | |
| 375 | * @param thresh | |
| 376 | * @see jalview.api.ViewStyleI#setThreshold(int) | |
| 377 | */ | |
| 378 | 106 | @Override |
| 379 | public void setThreshold(int thresh) | |
| 380 | { | |
| 381 | 106 | viewStyle.setThreshold(thresh); |
| 382 | } | |
| 383 | ||
| 384 | /** | |
| 385 | * @return | |
| 386 | * @see jalview.api.ViewStyleI#getThreshold() | |
| 387 | */ | |
| 388 | 0 | @Override |
| 389 | public int getThreshold() | |
| 390 | { | |
| 391 | 0 | return viewStyle.getThreshold(); |
| 392 | } | |
| 393 | ||
| 394 | /** | |
| 395 | * @return | |
| 396 | * @see jalview.api.ViewStyleI#getShowJVSuffix() | |
| 397 | */ | |
| 398 | 33785 | @Override |
| 399 | public boolean getShowJVSuffix() | |
| 400 | { | |
| 401 | 33785 | return viewStyle.getShowJVSuffix(); |
| 402 | } | |
| 403 | ||
| 404 | /** | |
| 405 | * @param b | |
| 406 | * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean) | |
| 407 | */ | |
| 408 | 86 | @Override |
| 409 | public void setShowJVSuffix(boolean b) | |
| 410 | { | |
| 411 | 86 | viewStyle.setShowJVSuffix(b); |
| 412 | } | |
| 413 | ||
| 414 | /** | |
| 415 | * @param state | |
| 416 | * @see jalview.api.ViewStyleI#setWrapAlignment(boolean) | |
| 417 | */ | |
| 418 | 97 | @Override |
| 419 | public void setWrapAlignment(boolean state) | |
| 420 | { | |
| 421 | 97 | viewStyle.setWrapAlignment(state); |
| 422 | 97 | ranges.setWrappedMode(state); |
| 423 | } | |
| 424 | ||
| 425 | /** | |
| 426 | * @param state | |
| 427 | * @see jalview.api.ViewStyleI#setShowText(boolean) | |
| 428 | */ | |
| 429 | 85 | @Override |
| 430 | public void setShowText(boolean state) | |
| 431 | { | |
| 432 | 85 | viewStyle.setShowText(state); |
| 433 | } | |
| 434 | ||
| 435 | /** | |
| 436 | * @param state | |
| 437 | * @see jalview.api.ViewStyleI#setRenderGaps(boolean) | |
| 438 | */ | |
| 439 | 85 | @Override |
| 440 | public void setRenderGaps(boolean state) | |
| 441 | { | |
| 442 | 85 | viewStyle.setRenderGaps(state); |
| 443 | } | |
| 444 | ||
| 445 | /** | |
| 446 | * @return | |
| 447 | * @see jalview.api.ViewStyleI#getColourText() | |
| 448 | */ | |
| 449 | 355412 | @Override |
| 450 | public boolean getColourText() | |
| 451 | { | |
| 452 | 355412 | return viewStyle.getColourText(); |
| 453 | } | |
| 454 | ||
| 455 | /** | |
| 456 | * @param state | |
| 457 | * @see jalview.api.ViewStyleI#setColourText(boolean) | |
| 458 | */ | |
| 459 | 85 | @Override |
| 460 | public void setColourText(boolean state) | |
| 461 | { | |
| 462 | 85 | viewStyle.setColourText(state); |
| 463 | } | |
| 464 | ||
| 465 | /** | |
| 466 | * @return | |
| 467 | * @see jalview.api.ViewStyleI#getWrapAlignment() | |
| 468 | */ | |
| 469 | 23697 | @Override |
| 470 | public boolean getWrapAlignment() | |
| 471 | { | |
| 472 | 23697 | return viewStyle.getWrapAlignment(); |
| 473 | } | |
| 474 | ||
| 475 | /** | |
| 476 | * @return | |
| 477 | * @see jalview.api.ViewStyleI#getShowText() | |
| 478 | */ | |
| 479 | 356084 | @Override |
| 480 | public boolean getShowText() | |
| 481 | { | |
| 482 | 356084 | return viewStyle.getShowText(); |
| 483 | } | |
| 484 | ||
| 485 | /** | |
| 486 | * @return | |
| 487 | * @see jalview.api.ViewStyleI#getWrappedWidth() | |
| 488 | */ | |
| 489 | 2 | @Override |
| 490 | public int getWrappedWidth() | |
| 491 | { | |
| 492 | 2 | return viewStyle.getWrappedWidth(); |
| 493 | } | |
| 494 | ||
| 495 | /** | |
| 496 | * @param w | |
| 497 | * @see jalview.api.ViewStyleI#setWrappedWidth(int) | |
| 498 | */ | |
| 499 | 656 | @Override |
| 500 | public void setWrappedWidth(int w) | |
| 501 | { | |
| 502 | 656 | viewStyle.setWrappedWidth(w); |
| 503 | } | |
| 504 | ||
| 505 | /** | |
| 506 | * @return | |
| 507 | * @see jalview.api.ViewStyleI#getCharHeight() | |
| 508 | */ | |
| 509 | 80919 | @Override |
| 510 | public int getCharHeight() | |
| 511 | { | |
| 512 | 80919 | return viewStyle.getCharHeight(); |
| 513 | } | |
| 514 | ||
| 515 | /** | |
| 516 | * @param h | |
| 517 | * @see jalview.api.ViewStyleI#setCharHeight(int) | |
| 518 | */ | |
| 519 | 596 | @Override |
| 520 | public void setCharHeight(int h) | |
| 521 | { | |
| 522 | 596 | viewStyle.setCharHeight(h); |
| 523 | } | |
| 524 | ||
| 525 | /** | |
| 526 | * @return | |
| 527 | * @see jalview.api.ViewStyleI#getCharWidth() | |
| 528 | */ | |
| 529 | 1115962 | @Override |
| 530 | public int getCharWidth() | |
| 531 | { | |
| 532 | 1115963 | return viewStyle.getCharWidth(); |
| 533 | } | |
| 534 | ||
| 535 | /** | |
| 536 | * @param w | |
| 537 | * @see jalview.api.ViewStyleI#setCharWidth(int) | |
| 538 | */ | |
| 539 | 599 | @Override |
| 540 | public void setCharWidth(int w) | |
| 541 | { | |
| 542 | 599 | viewStyle.setCharWidth(w); |
| 543 | } | |
| 544 | ||
| 545 | /** | |
| 546 | * @return | |
| 547 | * @see jalview.api.ViewStyleI#getShowBoxes() | |
| 548 | */ | |
| 549 | 389105 | @Override |
| 550 | public boolean getShowBoxes() | |
| 551 | { | |
| 552 | 389107 | return viewStyle.getShowBoxes(); |
| 553 | } | |
| 554 | ||
| 555 | /** | |
| 556 | * @return | |
| 557 | * @see jalview.api.ViewStyleI#getShowUnconserved() | |
| 558 | */ | |
| 559 | 353740 | @Override |
| 560 | public boolean getShowUnconserved() | |
| 561 | { | |
| 562 | 353740 | return viewStyle.getShowUnconserved(); |
| 563 | } | |
| 564 | ||
| 565 | /** | |
| 566 | * @param showunconserved | |
| 567 | * @see jalview.api.ViewStyleI#setShowUnconserved(boolean) | |
| 568 | */ | |
| 569 | 85 | @Override |
| 570 | public void setShowUnconserved(boolean showunconserved) | |
| 571 | { | |
| 572 | 85 | viewStyle.setShowUnconserved(showunconserved); |
| 573 | } | |
| 574 | ||
| 575 | /** | |
| 576 | * @param default1 | |
| 577 | * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean) | |
| 578 | */ | |
| 579 | 0 | @Override |
| 580 | public void setSeqNameItalics(boolean default1) | |
| 581 | { | |
| 582 | 0 | viewStyle.setSeqNameItalics(default1); |
| 583 | } | |
| 584 | ||
| 585 | 152589 | @Override |
| 586 | public AlignmentI getAlignment() | |
| 587 | { | |
| 588 | 152590 | return alignment; |
| 589 | } | |
| 590 | ||
| 591 | 0 | @Override |
| 592 | public char getGapCharacter() | |
| 593 | { | |
| 594 | 0 | return alignment.getGapCharacter(); |
| 595 | } | |
| 596 | ||
| 597 | protected String sequenceSetID; | |
| 598 | ||
| 599 | /** | |
| 600 | * probably unused indicator that view is of a dataset rather than an | |
| 601 | * alignment | |
| 602 | */ | |
| 603 | protected boolean isDataset = false; | |
| 604 | ||
| 605 | 0 | public void setDataset(boolean b) |
| 606 | { | |
| 607 | 0 | isDataset = b; |
| 608 | } | |
| 609 | ||
| 610 | 478 | public boolean isDataset() |
| 611 | { | |
| 612 | 478 | return isDataset; |
| 613 | } | |
| 614 | ||
| 615 | private Map<SequenceI, SequenceCollectionI> hiddenRepSequences; | |
| 616 | ||
| 617 | protected ColumnSelection colSel = new ColumnSelection(); | |
| 618 | ||
| 619 | public boolean autoCalculateConsensus = true; | |
| 620 | ||
| 621 | protected boolean autoCalculateStrucConsensus = true; | |
| 622 | ||
| 623 | protected boolean ignoreGapsInConsensusCalculation = false; | |
| 624 | ||
| 625 | protected ResidueShaderI residueShading = new ResidueShader(); | |
| 626 | ||
| 627 | 274 | @Override |
| 628 | public void setGlobalColourScheme(ColourSchemeI cs) | |
| 629 | { | |
| 630 | // TODO: logic refactored from AlignFrame changeColour - | |
| 631 | // TODO: autorecalc stuff should be changed to rely on the worker system | |
| 632 | // check to see if we should implement a changeColour(cs) method rather than | |
| 633 | // put the logic in here | |
| 634 | // - means that caller decides if they want to just modify state and defer | |
| 635 | // calculation till later or to do all calculations in thread. | |
| 636 | // via changecolour | |
| 637 | ||
| 638 | /* | |
| 639 | * only instantiate alignment colouring once, thereafter update it; | |
| 640 | * this means that any conservation or PID threshold settings | |
| 641 | * persist when the alignment colour scheme is changed | |
| 642 | */ | |
| 643 | 274 | if (residueShading == null) |
| 644 | { | |
| 645 | 0 | residueShading = new ResidueShader(viewStyle); |
| 646 | } | |
| 647 | 274 | residueShading.setColourScheme(cs); |
| 648 | ||
| 649 | // TODO: do threshold and increment belong in ViewStyle or ResidueShader? | |
| 650 | // ...problem: groups need these, but do not currently have a ViewStyle | |
| 651 | ||
| 652 | 274 | if (cs != null) |
| 653 | { | |
| 654 | 81 | if (getConservationSelected()) |
| 655 | { | |
| 656 | 15 | residueShading.setConservation(hconservation); |
| 657 | } | |
| 658 | /* | |
| 659 | * reset conservation flag in case just set to false if | |
| 660 | * Conservation was null (calculation still in progress) | |
| 661 | */ | |
| 662 | 81 | residueShading.setConservationApplied(getConservationSelected()); |
| 663 | 81 | residueShading.alignmentChanged(alignment, hiddenRepSequences); |
| 664 | } | |
| 665 | ||
| 666 | /* | |
| 667 | * if 'apply colour to all groups' is selected... do so | |
| 668 | * (but don't transfer any colour threshold settings to groups) | |
| 669 | */ | |
| 670 | 274 | if (getColourAppliesToAllGroups()) |
| 671 | { | |
| 672 | 86 | for (SequenceGroup sg : getAlignment().getGroups()) |
| 673 | { | |
| 674 | /* | |
| 675 | * retain any colour thresholds per group while | |
| 676 | * changing choice of colour scheme (JAL-2386) | |
| 677 | */ | |
| 678 | 9 | sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg)); |
| 679 | 9 | if (cs != null) |
| 680 | { | |
| 681 | 8 | sg.getGroupColourScheme().alignmentChanged(sg, |
| 682 | hiddenRepSequences); | |
| 683 | } | |
| 684 | } | |
| 685 | } | |
| 686 | } | |
| 687 | ||
| 688 | 1399 | @Override |
| 689 | public ColourSchemeI getGlobalColourScheme() | |
| 690 | { | |
| 691 | 1399 | return residueShading == null ? null : residueShading.getColourScheme(); |
| 692 | } | |
| 693 | ||
| 694 | 391846 | @Override |
| 695 | public ResidueShaderI getResidueShading() | |
| 696 | { | |
| 697 | 391845 | return residueShading; |
| 698 | } | |
| 699 | ||
| 700 | protected AlignmentAnnotation consensus; | |
| 701 | ||
| 702 | protected AlignmentAnnotation secondaryStructureConsensus; | |
| 703 | ||
| 704 | protected AlignmentAnnotation complementConsensus; | |
| 705 | ||
| 706 | protected AlignmentAnnotation gapcounts; | |
| 707 | ||
| 708 | protected AlignmentAnnotation strucConsensus; | |
| 709 | ||
| 710 | protected AlignmentAnnotation conservation; | |
| 711 | ||
| 712 | protected AlignmentAnnotation quality; | |
| 713 | ||
| 714 | protected AlignmentAnnotation[] groupConsensus; | |
| 715 | ||
| 716 | protected AlignmentAnnotation[] groupSSConsensus; | |
| 717 | ||
| 718 | protected AlignmentAnnotation[] groupConservation; | |
| 719 | ||
| 720 | /** | |
| 721 | * results of alignment consensus analysis for visible portion of view | |
| 722 | */ | |
| 723 | protected ProfilesI hconsensus = null; | |
| 724 | ||
| 725 | protected ProfilesI hSSConsensus = null; | |
| 726 | ||
| 727 | /** | |
| 728 | * results of cDNA complement consensus visible portion of view | |
| 729 | */ | |
| 730 | protected Hashtable<String, Object>[] hcomplementConsensus = null; | |
| 731 | ||
| 732 | /** | |
| 733 | * results of secondary structure base pair consensus for visible portion of | |
| 734 | * view | |
| 735 | */ | |
| 736 | protected Hashtable<String, Object>[] hStrucConsensus = null; | |
| 737 | ||
| 738 | protected Conservation hconservation = null; | |
| 739 | ||
| 740 | 990 | @Override |
| 741 | public void setConservation(Conservation cons) | |
| 742 | { | |
| 743 | 990 | hconservation = cons; |
| 744 | } | |
| 745 | ||
| 746 | /** | |
| 747 | * percentage gaps allowed in a column before all amino acid properties should | |
| 748 | * be considered unconserved | |
| 749 | */ | |
| 750 | int ConsPercGaps = 25; // JBPNote : This should be a scalable property! | |
| 751 | ||
| 752 | 1833 | @Override |
| 753 | public int getConsPercGaps() | |
| 754 | { | |
| 755 | 1833 | return ConsPercGaps; |
| 756 | } | |
| 757 | ||
| 758 | 971 | @Override |
| 759 | public void setSequenceConsensusHash(ProfilesI hconsensus) | |
| 760 | { | |
| 761 | 971 | this.hconsensus = hconsensus; |
| 762 | } | |
| 763 | ||
| 764 | 0 | @Override |
| 765 | public void setSequenceSSConsensusHash(ProfilesI hSSConsensus) | |
| 766 | { | |
| 767 | 0 | this.hSSConsensus = hSSConsensus; |
| 768 | } | |
| 769 | ||
| 770 | 4 | @Override |
| 771 | public void setComplementConsensusHash( | |
| 772 | Hashtable<String, Object>[] hconsensus) | |
| 773 | { | |
| 774 | 4 | this.hcomplementConsensus = hconsensus; |
| 775 | } | |
| 776 | ||
| 777 | 2907 | @Override |
| 778 | public ProfilesI getSequenceConsensusHash() | |
| 779 | { | |
| 780 | 2907 | return hconsensus; |
| 781 | } | |
| 782 | ||
| 783 | 1917 | @Override |
| 784 | public ProfilesI getSequenceSSConsensusHash() | |
| 785 | { | |
| 786 | 1917 | return hSSConsensus; |
| 787 | } | |
| 788 | ||
| 789 | 1836 | @Override |
| 790 | public Hashtable<String, Object>[] getComplementConsensusHash() | |
| 791 | { | |
| 792 | 1836 | return hcomplementConsensus; |
| 793 | } | |
| 794 | ||
| 795 | 1836 | @Override |
| 796 | public Hashtable<String, Object>[] getRnaStructureConsensusHash() | |
| 797 | { | |
| 798 | 1836 | return hStrucConsensus; |
| 799 | } | |
| 800 | ||
| 801 | 4 | @Override |
| 802 | public void setRnaStructureConsensusHash( | |
| 803 | Hashtable<String, Object>[] hStrucConsensus) | |
| 804 | { | |
| 805 | 4 | this.hStrucConsensus = hStrucConsensus; |
| 806 | ||
| 807 | } | |
| 808 | ||
| 809 | 1431 | @Override |
| 810 | public AlignmentAnnotation getAlignmentQualityAnnot() | |
| 811 | { | |
| 812 | 1431 | return quality; |
| 813 | } | |
| 814 | ||
| 815 | 2255 | @Override |
| 816 | public AlignmentAnnotation getAlignmentConservationAnnotation() | |
| 817 | { | |
| 818 | 2255 | return conservation; |
| 819 | } | |
| 820 | ||
| 821 | 5197 | @Override |
| 822 | public AlignmentAnnotation getAlignmentConsensusAnnotation() | |
| 823 | { | |
| 824 | 5197 | return consensus; |
| 825 | } | |
| 826 | ||
| 827 | 1832 | @Override |
| 828 | public AlignmentAnnotation getAlignmentSecondaryStructureConsensusAnnotation() | |
| 829 | { | |
| 830 | 1832 | return secondaryStructureConsensus; |
| 831 | } | |
| 832 | ||
| 833 | 3020 | @Override |
| 834 | public AlignmentAnnotation getAlignmentGapAnnotation() | |
| 835 | { | |
| 836 | 3020 | return gapcounts; |
| 837 | } | |
| 838 | ||
| 839 | 1844 | @Override |
| 840 | public AlignmentAnnotation getComplementConsensusAnnotation() | |
| 841 | { | |
| 842 | 1844 | return complementConsensus; |
| 843 | } | |
| 844 | ||
| 845 | 1836 | @Override |
| 846 | public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() | |
| 847 | { | |
| 848 | 1836 | return strucConsensus; |
| 849 | } | |
| 850 | ||
| 851 | protected AlignCalcManagerI calculator = new AlignCalcManager(); | |
| 852 | ||
| 853 | /** | |
| 854 | * trigger update of conservation annotation | |
| 855 | */ | |
| 856 | 995 | public void updateConservation(final AlignmentViewPanel ap) |
| 857 | { | |
| 858 | // see note in mantis : issue number 8585 | |
| 859 | 995 | if (alignment.isNucleotide() |
| 860 | || (conservation == null && quality == null) | |
| 861 | || !autoCalculateConsensus) | |
| 862 | { | |
| 863 | 216 | return; |
| 864 | } | |
| 865 | 779 | if (calculator.getRegisteredWorkersOfClass( |
| 866 | jalview.workers.ConservationThread.class) == null) | |
| 867 | { | |
| 868 | 441 | calculator.registerWorker( |
| 869 | new jalview.workers.ConservationThread(this, ap)); | |
| 870 | } | |
| 871 | } | |
| 872 | ||
| 873 | /** | |
| 874 | * trigger update of consensus annotation | |
| 875 | */ | |
| 876 | 1009 | public void updateConsensus(final AlignmentViewPanel ap) |
| 877 | { | |
| 878 | // see note in mantis : issue number 8585 | |
| 879 | 1009 | if (consensus == null || !autoCalculateConsensus) |
| 880 | { | |
| 881 | 0 | return; |
| 882 | } | |
| 883 | 1009 | if (calculator |
| 884 | .getRegisteredWorkersOfClass(ConsensusThread.class) == null) | |
| 885 | { | |
| 886 | 467 | calculator.registerWorker(new ConsensusThread(this, ap)); |
| 887 | } | |
| 888 | ||
| 889 | /* | |
| 890 | * A separate thread to compute cDNA consensus for a protein alignment | |
| 891 | * which has mapping to cDNA | |
| 892 | */ | |
| 893 | 1009 | final AlignmentI al = this.getAlignment(); |
| 894 | 1009 | if (!al.isNucleotide() && al.getCodonFrames() != null |
| 895 | && !al.getCodonFrames().isEmpty()) | |
| 896 | { | |
| 897 | /* | |
| 898 | * fudge - check first for protein-to-nucleotide mappings | |
| 899 | * (we don't want to do this for protein-to-protein) | |
| 900 | */ | |
| 901 | 4 | boolean doConsensus = false; |
| 902 | 4 | for (AlignedCodonFrame mapping : al.getCodonFrames()) |
| 903 | { | |
| 904 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 905 | 4 | MapList[] mapLists = mapping.getdnaToProt(); |
| 906 | // mapLists can be empty if project load has not finished resolving seqs | |
| 907 | 4 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 908 | { | |
| 909 | 4 | doConsensus = true; |
| 910 | 4 | break; |
| 911 | } | |
| 912 | } | |
| 913 | 4 | if (doConsensus) |
| 914 | { | |
| 915 | 4 | if (calculator.getRegisteredWorkersOfClass( |
| 916 | ComplementConsensusThread.class) == null) | |
| 917 | { | |
| 918 | 4 | calculator |
| 919 | .registerWorker(new ComplementConsensusThread(this, ap)); | |
| 920 | } | |
| 921 | } | |
| 922 | } | |
| 923 | } | |
| 924 | ||
| 925 | /** | |
| 926 | * trigger update of consensus annotation | |
| 927 | */ | |
| 928 | 1009 | public void updateSecondaryStructureConsensus(final AlignmentViewPanel ap) |
| 929 | { | |
| 930 | // see note in mantis : issue number 8585 | |
| 931 | 1009 | if (secondaryStructureConsensus == null || !autoCalculateConsensus) |
| 932 | { | |
| 933 | 1009 | return; |
| 934 | } | |
| 935 | 0 | if (calculator.getRegisteredWorkersOfClass( |
| 936 | SecondaryStructureConsensusThread.class) == null) | |
| 937 | { | |
| 938 | 0 | calculator.registerWorker( |
| 939 | new SecondaryStructureConsensusThread(this, ap)); | |
| 940 | } | |
| 941 | } | |
| 942 | ||
| 943 | // --------START Structure Conservation | |
| 944 | 1006 | public void updateStrucConsensus(final AlignmentViewPanel ap) |
| 945 | { | |
| 946 | 1006 | if (autoCalculateStrucConsensus && strucConsensus == null |
| 947 | && alignment.isNucleotide() && alignment.hasRNAStructure()) | |
| 948 | { | |
| 949 | // secondary structure has been added - so init the consensus line | |
| 950 | 0 | initRNAStructure(); |
| 951 | } | |
| 952 | ||
| 953 | // see note in mantis : issue number 8585 | |
| 954 | 1006 | if (strucConsensus == null || !autoCalculateStrucConsensus) |
| 955 | { | |
| 956 | 1003 | return; |
| 957 | } | |
| 958 | 3 | if (calculator.getRegisteredWorkersOfClass( |
| 959 | StrucConsensusThread.class) == null) | |
| 960 | { | |
| 961 | 3 | calculator.registerWorker(new StrucConsensusThread(this, ap)); |
| 962 | } | |
| 963 | } | |
| 964 | ||
| 965 | 2324 | public boolean isCalcInProgress() |
| 966 | { | |
| 967 | 2324 | return calculator.isWorking(); |
| 968 | } | |
| 969 | ||
| 970 | 7003 | @Override |
| 971 | public boolean isCalculationInProgress( | |
| 972 | AlignmentAnnotation alignmentAnnotation) | |
| 973 | { | |
| 974 | 7003 | if (!alignmentAnnotation.autoCalculated) |
| 975 | { | |
| 976 | 0 | return false; |
| 977 | } | |
| 978 | 7003 | if (calculator.workingInvolvedWith(alignmentAnnotation)) |
| 979 | { | |
| 980 | // jalview.bin.Console.errPrintln("grey out | |
| 981 | // ("+alignmentAnnotation.label+")"); | |
| 982 | 244 | return true; |
| 983 | } | |
| 984 | 6759 | return false; |
| 985 | } | |
| 986 | ||
| 987 | 761 | public void setAlignment(AlignmentI align) |
| 988 | { | |
| 989 | 761 | this.alignment = align; |
| 990 | } | |
| 991 | ||
| 992 | /** | |
| 993 | * Clean up references when this viewport is closed | |
| 994 | */ | |
| 995 | 253 | @Override |
| 996 | public void dispose() | |
| 997 | { | |
| 998 | /* | |
| 999 | * defensively null out references to large objects in case | |
| 1000 | * this object is not garbage collected (as if!) | |
| 1001 | */ | |
| 1002 | 253 | consensus = null; |
| 1003 | 253 | complementConsensus = null; |
| 1004 | 253 | strucConsensus = null; |
| 1005 | 253 | secondaryStructureConsensus = null; |
| 1006 | 253 | conservation = null; |
| 1007 | 253 | quality = null; |
| 1008 | 253 | groupConsensus = null; |
| 1009 | 253 | groupConservation = null; |
| 1010 | 253 | hconsensus = null; |
| 1011 | 253 | hconservation = null; |
| 1012 | 253 | hcomplementConsensus = null; |
| 1013 | 253 | gapcounts = null; |
| 1014 | 253 | calculator = null; |
| 1015 | 253 | residueShading = null; // may hold a reference to Consensus |
| 1016 | 253 | changeSupport = null; |
| 1017 | 253 | ranges = null; |
| 1018 | 253 | currentTree = null; |
| 1019 | 253 | selectionGroup = null; |
| 1020 | 253 | colSel = null; |
| 1021 | 253 | setAlignment(null); |
| 1022 | } | |
| 1023 | ||
| 1024 | 2980 | @Override |
| 1025 | public boolean isClosed() | |
| 1026 | { | |
| 1027 | // TODO: check that this isClosed is only true after panel is closed, not | |
| 1028 | // before it is fully constructed. | |
| 1029 | 2980 | return alignment == null; |
| 1030 | } | |
| 1031 | ||
| 1032 | 3060 | @Override |
| 1033 | public AlignCalcManagerI getCalcManager() | |
| 1034 | { | |
| 1035 | 3060 | return calculator; |
| 1036 | } | |
| 1037 | ||
| 1038 | /** | |
| 1039 | * should conservation rows be shown for groups | |
| 1040 | */ | |
| 1041 | protected boolean showGroupConservation = false; | |
| 1042 | ||
| 1043 | /** | |
| 1044 | * should consensus rows be shown for groups | |
| 1045 | */ | |
| 1046 | protected boolean showGroupConsensus = false; | |
| 1047 | ||
| 1048 | protected boolean showGroupSSConsensus = false; | |
| 1049 | ||
| 1050 | /** | |
| 1051 | * should consensus profile be rendered by default | |
| 1052 | */ | |
| 1053 | protected boolean showSequenceLogo = false; | |
| 1054 | ||
| 1055 | protected boolean showSequenceSSLogo = false; | |
| 1056 | ||
| 1057 | /** | |
| 1058 | * should consensus profile be rendered normalised to row height | |
| 1059 | */ | |
| 1060 | protected boolean normaliseSequenceLogo = false; | |
| 1061 | ||
| 1062 | /** | |
| 1063 | * should consensus histograms be rendered by default | |
| 1064 | */ | |
| 1065 | protected boolean showConsensusHistogram = true; | |
| 1066 | ||
| 1067 | protected boolean showSSConsensusHistogram = true; | |
| 1068 | ||
| 1069 | 0 | public void setShowSSConsensusHistogram(boolean showSSConsensusHistogram) |
| 1070 | { | |
| 1071 | 0 | this.showSSConsensusHistogram = showSSConsensusHistogram; |
| 1072 | } | |
| 1073 | ||
| 1074 | /** | |
| 1075 | * @return the showConsensusProfile | |
| 1076 | */ | |
| 1077 | 3675 | @Override |
| 1078 | public boolean isShowSequenceLogo() | |
| 1079 | { | |
| 1080 | 3675 | return showSequenceLogo; |
| 1081 | } | |
| 1082 | ||
| 1083 | 130 | @Override |
| 1084 | public boolean isShowSequenceSSLogo() | |
| 1085 | { | |
| 1086 | 130 | return showSequenceSSLogo; |
| 1087 | } | |
| 1088 | ||
| 1089 | /** | |
| 1090 | * @param showSequenceLogo | |
| 1091 | * the new value | |
| 1092 | */ | |
| 1093 | 85 | public void setShowSequenceLogo(boolean showSequenceLogo) |
| 1094 | { | |
| 1095 | 85 | if (showSequenceLogo != this.showSequenceLogo) |
| 1096 | { | |
| 1097 | // TODO: decouple settings setting from calculation when refactoring | |
| 1098 | // annotation update method from alignframe to viewport | |
| 1099 | 16 | this.showSequenceLogo = showSequenceLogo; |
| 1100 | 16 | calculator.updateAnnotationFor(ConsensusThread.class); |
| 1101 | 16 | calculator.updateAnnotationFor(ComplementConsensusThread.class); |
| 1102 | 16 | calculator.updateAnnotationFor(StrucConsensusThread.class); |
| 1103 | } | |
| 1104 | 85 | this.showSequenceLogo = showSequenceLogo; |
| 1105 | } | |
| 1106 | ||
| 1107 | 0 | public void setShowSequenceSSLogo(boolean showSequenceSSLogo) |
| 1108 | { | |
| 1109 | 0 | if (showSequenceSSLogo != this.showSequenceSSLogo) |
| 1110 | { | |
| 1111 | // TODO: decouple settings setting from calculation when refactoring | |
| 1112 | // annotation update method from alignframe to viewport | |
| 1113 | 0 | this.showSequenceSSLogo = showSequenceSSLogo; |
| 1114 | 0 | calculator |
| 1115 | .updateAnnotationFor(SecondaryStructureConsensusThread.class); | |
| 1116 | } | |
| 1117 | 0 | this.showSequenceSSLogo = showSequenceSSLogo; |
| 1118 | } | |
| 1119 | ||
| 1120 | /** | |
| 1121 | * @param showConsensusHistogram | |
| 1122 | * the showConsensusHistogram to set | |
| 1123 | */ | |
| 1124 | 85 | public void setShowConsensusHistogram(boolean showConsensusHistogram) |
| 1125 | { | |
| 1126 | 85 | this.showConsensusHistogram = showConsensusHistogram; |
| 1127 | } | |
| 1128 | ||
| 1129 | /** | |
| 1130 | * @return the showGroupConservation | |
| 1131 | */ | |
| 1132 | 848 | public boolean isShowGroupConservation() |
| 1133 | { | |
| 1134 | 848 | return showGroupConservation; |
| 1135 | } | |
| 1136 | ||
| 1137 | /** | |
| 1138 | * @param showGroupConservation | |
| 1139 | * the showGroupConservation to set | |
| 1140 | */ | |
| 1141 | 85 | public void setShowGroupConservation(boolean showGroupConservation) |
| 1142 | { | |
| 1143 | 85 | this.showGroupConservation = showGroupConservation; |
| 1144 | } | |
| 1145 | ||
| 1146 | /** | |
| 1147 | * @return the showGroupConsensus | |
| 1148 | */ | |
| 1149 | 848 | public boolean isShowGroupConsensus() |
| 1150 | { | |
| 1151 | 848 | return showGroupConsensus; |
| 1152 | } | |
| 1153 | ||
| 1154 | 130 | public boolean isShowGroupSSConsensus() |
| 1155 | { | |
| 1156 | 130 | return showGroupSSConsensus; |
| 1157 | } | |
| 1158 | ||
| 1159 | /** | |
| 1160 | * @param showGroupConsensus | |
| 1161 | * the showGroupConsensus to set | |
| 1162 | */ | |
| 1163 | 85 | public void setShowGroupConsensus(boolean showGroupConsensus) |
| 1164 | { | |
| 1165 | 85 | this.showGroupConsensus = showGroupConsensus; |
| 1166 | } | |
| 1167 | ||
| 1168 | 0 | public void setShowGroupSSConsensus(boolean showGroupSSConsensus) |
| 1169 | { | |
| 1170 | 0 | this.showGroupSSConsensus = showGroupSSConsensus; |
| 1171 | } | |
| 1172 | ||
| 1173 | /** | |
| 1174 | * @param showSSConsensus | |
| 1175 | * the showSSConsensus to set | |
| 1176 | */ | |
| 1177 | 0 | public void setShowSSConsensus(boolean showSSConsensus) |
| 1178 | { | |
| 1179 | 0 | this.showSSConsensus = showSSConsensus; |
| 1180 | } | |
| 1181 | ||
| 1182 | /** | |
| 1183 | * | |
| 1184 | * @return flag to indicate if the consensus histogram should be rendered by | |
| 1185 | * default | |
| 1186 | */ | |
| 1187 | 2680 | @Override |
| 1188 | public boolean isShowConsensusHistogram() | |
| 1189 | { | |
| 1190 | 2680 | return this.showConsensusHistogram; |
| 1191 | } | |
| 1192 | ||
| 1193 | 130 | @Override |
| 1194 | public boolean isShowSSConsensusHistogram() | |
| 1195 | { | |
| 1196 | 130 | return this.showSSConsensusHistogram; |
| 1197 | } | |
| 1198 | ||
| 1199 | /** | |
| 1200 | * when set, updateAlignment will always ensure sequences are of equal length | |
| 1201 | */ | |
| 1202 | private boolean padGaps = false; | |
| 1203 | ||
| 1204 | /** | |
| 1205 | * when set, alignment should be reordered according to a newly opened tree | |
| 1206 | */ | |
| 1207 | public boolean sortByTree = false; | |
| 1208 | ||
| 1209 | /** | |
| 1210 | * | |
| 1211 | * | |
| 1212 | * @return null or the currently selected sequence region | |
| 1213 | */ | |
| 1214 | 14908 | @Override |
| 1215 | public SequenceGroup getSelectionGroup() | |
| 1216 | { | |
| 1217 | 14908 | return selectionGroup; |
| 1218 | } | |
| 1219 | ||
| 1220 | /** | |
| 1221 | * Set the selection group for this window. Also sets the current alignment as | |
| 1222 | * the context for the group, if it does not already have one. | |
| 1223 | * | |
| 1224 | * @param sg | |
| 1225 | * - group holding references to sequences in this alignment view | |
| 1226 | * | |
| 1227 | */ | |
| 1228 | 146 | @Override |
| 1229 | public void setSelectionGroup(SequenceGroup sg) | |
| 1230 | { | |
| 1231 | 146 | selectionGroup = sg; |
| 1232 | 146 | if (sg != null && sg.getContext() == null) |
| 1233 | { | |
| 1234 | 36 | sg.setContext(alignment); |
| 1235 | } | |
| 1236 | } | |
| 1237 | ||
| 1238 | 1 | public void setHiddenColumns(HiddenColumns hidden) |
| 1239 | { | |
| 1240 | 1 | this.alignment.setHiddenColumns(hidden); |
| 1241 | } | |
| 1242 | ||
| 1243 | 3664 | @Override |
| 1244 | public ColumnSelection getColumnSelection() | |
| 1245 | { | |
| 1246 | 3664 | return colSel; |
| 1247 | } | |
| 1248 | ||
| 1249 | 13 | @Override |
| 1250 | public void setColumnSelection(ColumnSelection colSel) | |
| 1251 | { | |
| 1252 | 13 | this.colSel = colSel; |
| 1253 | 13 | if (colSel != null) |
| 1254 | { | |
| 1255 | 13 | updateHiddenColumns(); |
| 1256 | } | |
| 1257 | 13 | isColSelChanged(true); |
| 1258 | } | |
| 1259 | ||
| 1260 | /** | |
| 1261 | * | |
| 1262 | * @return | |
| 1263 | */ | |
| 1264 | 32 | @Override |
| 1265 | public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences() | |
| 1266 | { | |
| 1267 | 32 | return hiddenRepSequences; |
| 1268 | } | |
| 1269 | ||
| 1270 | 0 | @Override |
| 1271 | public void setHiddenRepSequences( | |
| 1272 | Map<SequenceI, SequenceCollectionI> hiddenRepSequences) | |
| 1273 | { | |
| 1274 | 0 | this.hiddenRepSequences = hiddenRepSequences; |
| 1275 | } | |
| 1276 | ||
| 1277 | 0 | @Override |
| 1278 | public boolean hasSelectedColumns() | |
| 1279 | { | |
| 1280 | 0 | ColumnSelection columnSelection = getColumnSelection(); |
| 1281 | 0 | return columnSelection != null && columnSelection.hasSelectedColumns(); |
| 1282 | } | |
| 1283 | ||
| 1284 | 6668 | @Override |
| 1285 | public boolean hasHiddenColumns() | |
| 1286 | { | |
| 1287 | 6668 | return alignment.getHiddenColumns() != null |
| 1288 | && alignment.getHiddenColumns().hasHiddenColumns(); | |
| 1289 | } | |
| 1290 | ||
| 1291 | 14 | public void updateHiddenColumns() |
| 1292 | { | |
| 1293 | // this method doesn't really do anything now. But - it could, since a | |
| 1294 | // column Selection could be in the process of modification | |
| 1295 | // hasHiddenColumns = colSel.hasHiddenColumns(); | |
| 1296 | } | |
| 1297 | ||
| 1298 | 3445 | @Override |
| 1299 | public boolean hasHiddenRows() | |
| 1300 | { | |
| 1301 | 3445 | return alignment.getHiddenSequences().getSize() > 0; |
| 1302 | } | |
| 1303 | ||
| 1304 | protected SequenceGroup selectionGroup; | |
| 1305 | ||
| 1306 | 85 | public void setSequenceSetId(String newid) |
| 1307 | { | |
| 1308 | 85 | if (sequenceSetID != null) |
| 1309 | { | |
| 1310 | 85 | jalview.bin.Console.errPrintln( |
| 1311 | "Warning - overwriting a sequenceSetId for a viewport!"); | |
| 1312 | } | |
| 1313 | 85 | sequenceSetID = new String(newid); |
| 1314 | } | |
| 1315 | ||
| 1316 | 4892 | @Override |
| 1317 | public String getSequenceSetId() | |
| 1318 | { | |
| 1319 | 4892 | if (sequenceSetID == null) |
| 1320 | { | |
| 1321 | 364 | sequenceSetID = alignment.hashCode() + ""; |
| 1322 | } | |
| 1323 | ||
| 1324 | 4892 | return sequenceSetID; |
| 1325 | } | |
| 1326 | ||
| 1327 | /** | |
| 1328 | * unique viewId for synchronizing state (e.g. with stored Jalview Project) | |
| 1329 | * | |
| 1330 | */ | |
| 1331 | protected String viewId = null; | |
| 1332 | ||
| 1333 | 598 | @Override |
| 1334 | public String getViewId() | |
| 1335 | { | |
| 1336 | 598 | if (viewId == null) |
| 1337 | { | |
| 1338 | 300 | viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; |
| 1339 | } | |
| 1340 | 598 | return viewId; |
| 1341 | } | |
| 1342 | ||
| 1343 | 88 | public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) |
| 1344 | { | |
| 1345 | 88 | ignoreGapsInConsensusCalculation = b; |
| 1346 | 88 | if (ap != null) |
| 1347 | { | |
| 1348 | 3 | updateConsensus(ap); |
| 1349 | 3 | updateSecondaryStructureConsensus(ap); |
| 1350 | 3 | if (residueShading != null) |
| 1351 | { | |
| 1352 | 3 | residueShading.setThreshold(residueShading.getThreshold(), |
| 1353 | ignoreGapsInConsensusCalculation); | |
| 1354 | } | |
| 1355 | } | |
| 1356 | ||
| 1357 | } | |
| 1358 | ||
| 1359 | private long sgrouphash = -1, colselhash = -1; | |
| 1360 | ||
| 1361 | /** | |
| 1362 | * checks current SelectionGroup against record of last hash value, and | |
| 1363 | * updates record. | |
| 1364 | * | |
| 1365 | * @param b | |
| 1366 | * update the record of last hash value | |
| 1367 | * | |
| 1368 | * @return true if SelectionGroup changed since last call (when b is true) | |
| 1369 | */ | |
| 1370 | 173 | public boolean isSelectionGroupChanged(boolean b) |
| 1371 | { | |
| 1372 | 173 | int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1 |
| 1373 | : selectionGroup.hashCode(); | |
| 1374 | 173 | if (hc != -1 && hc != sgrouphash) |
| 1375 | { | |
| 1376 | 9 | if (b) |
| 1377 | { | |
| 1378 | 9 | sgrouphash = hc; |
| 1379 | } | |
| 1380 | 9 | return true; |
| 1381 | } | |
| 1382 | 164 | return false; |
| 1383 | } | |
| 1384 | ||
| 1385 | /** | |
| 1386 | * checks current colsel against record of last hash value, and optionally | |
| 1387 | * updates record. | |
| 1388 | * | |
| 1389 | * @param b | |
| 1390 | * update the record of last hash value | |
| 1391 | * @return true if colsel changed since last call (when b is true) | |
| 1392 | */ | |
| 1393 | 179 | public boolean isColSelChanged(boolean b) |
| 1394 | { | |
| 1395 | 179 | int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode(); |
| 1396 | 179 | if (hc != -1 && hc != colselhash) |
| 1397 | { | |
| 1398 | 17 | if (b) |
| 1399 | { | |
| 1400 | 17 | colselhash = hc; |
| 1401 | } | |
| 1402 | 17 | return true; |
| 1403 | } | |
| 1404 | 162 | return false; |
| 1405 | } | |
| 1406 | ||
| 1407 | 2896 | @Override |
| 1408 | public boolean isIgnoreGapsConsensus() | |
| 1409 | { | |
| 1410 | 2896 | return ignoreGapsInConsensusCalculation; |
| 1411 | } | |
| 1412 | ||
| 1413 | // property change stuff | |
| 1414 | // JBPNote Prolly only need this in the applet version. | |
| 1415 | private PropertyChangeSupport changeSupport = new PropertyChangeSupport( | |
| 1416 | this); | |
| 1417 | ||
| 1418 | protected boolean showConservation = true; | |
| 1419 | ||
| 1420 | protected boolean showQuality = true; | |
| 1421 | ||
| 1422 | protected boolean showConsensus = true; | |
| 1423 | ||
| 1424 | protected boolean showSSConsensus = false; | |
| 1425 | ||
| 1426 | protected boolean showOccupancy = true; | |
| 1427 | ||
| 1428 | private Map<SequenceI, Color> sequenceColours = new HashMap<>(); | |
| 1429 | ||
| 1430 | protected SequenceAnnotationOrder sortAnnotationsBy = null; | |
| 1431 | ||
| 1432 | protected boolean showAutocalculatedAbove; | |
| 1433 | ||
| 1434 | /** | |
| 1435 | * when set, view will scroll to show the highlighted position | |
| 1436 | */ | |
| 1437 | private boolean followHighlight = true; | |
| 1438 | ||
| 1439 | /** | |
| 1440 | * Property change listener for changes in alignment | |
| 1441 | * | |
| 1442 | * @param listener | |
| 1443 | * DOCUMENT ME! | |
| 1444 | */ | |
| 1445 | 492 | public void addPropertyChangeListener( |
| 1446 | java.beans.PropertyChangeListener listener) | |
| 1447 | { | |
| 1448 | 492 | changeSupport.addPropertyChangeListener(listener); |
| 1449 | } | |
| 1450 | ||
| 1451 | /** | |
| 1452 | * DOCUMENT ME! | |
| 1453 | * | |
| 1454 | * @param listener | |
| 1455 | * DOCUMENT ME! | |
| 1456 | */ | |
| 1457 | 265 | public void removePropertyChangeListener( |
| 1458 | java.beans.PropertyChangeListener listener) | |
| 1459 | { | |
| 1460 | 265 | if (changeSupport != null) |
| 1461 | { | |
| 1462 | 264 | changeSupport.removePropertyChangeListener(listener); |
| 1463 | } | |
| 1464 | } | |
| 1465 | ||
| 1466 | /** | |
| 1467 | * Property change listener for changes in alignment | |
| 1468 | * | |
| 1469 | * @param prop | |
| 1470 | * DOCUMENT ME! | |
| 1471 | * @param oldvalue | |
| 1472 | * DOCUMENT ME! | |
| 1473 | * @param newvalue | |
| 1474 | * DOCUMENT ME! | |
| 1475 | */ | |
| 1476 | 78 | public void firePropertyChange(String prop, Object oldvalue, |
| 1477 | Object newvalue) | |
| 1478 | { | |
| 1479 | 78 | changeSupport.firePropertyChange(prop, oldvalue, newvalue); |
| 1480 | } | |
| 1481 | ||
| 1482 | 0 | @Override |
| 1483 | public void notifyAlignmentChanged() | |
| 1484 | { | |
| 1485 | 0 | firePropertyChange("alignment", null, alignment); |
| 1486 | } | |
| 1487 | ||
| 1488 | // common hide/show column stuff | |
| 1489 | ||
| 1490 | 6 | public void hideSelectedColumns() |
| 1491 | { | |
| 1492 | 6 | if (colSel.isEmpty()) |
| 1493 | { | |
| 1494 | 2 | return; |
| 1495 | } | |
| 1496 | ||
| 1497 | 4 | colSel.hideSelectedColumns(alignment); |
| 1498 | 4 | setSelectionGroup(null); |
| 1499 | 4 | isColSelChanged(true); |
| 1500 | } | |
| 1501 | ||
| 1502 | 71 | public void hideColumns(int start, int end) |
| 1503 | { | |
| 1504 | 71 | if (start == end) |
| 1505 | { | |
| 1506 | 2 | colSel.hideSelectedColumns(start, alignment.getHiddenColumns()); |
| 1507 | } | |
| 1508 | else | |
| 1509 | { | |
| 1510 | 69 | alignment.getHiddenColumns().hideColumns(start, end); |
| 1511 | } | |
| 1512 | 71 | isColSelChanged(true); |
| 1513 | } | |
| 1514 | ||
| 1515 | 1 | public void showColumn(int col) |
| 1516 | { | |
| 1517 | 1 | alignment.getHiddenColumns().revealHiddenColumns(col, colSel); |
| 1518 | 1 | isColSelChanged(true); |
| 1519 | } | |
| 1520 | ||
| 1521 | 5 | public void showAllHiddenColumns() |
| 1522 | { | |
| 1523 | 5 | alignment.getHiddenColumns().revealAllHiddenColumns(colSel); |
| 1524 | 5 | isColSelChanged(true); |
| 1525 | } | |
| 1526 | ||
| 1527 | // common hide/show seq stuff | |
| 1528 | 1 | public void showAllHiddenSeqs() |
| 1529 | { | |
| 1530 | 1 | int startSeq = ranges.getStartSeq(); |
| 1531 | 1 | int endSeq = ranges.getEndSeq(); |
| 1532 | ||
| 1533 | 1 | if (alignment.getHiddenSequences().getSize() > 0) |
| 1534 | { | |
| 1535 | 1 | if (selectionGroup == null) |
| 1536 | { | |
| 1537 | 0 | selectionGroup = new SequenceGroup(); |
| 1538 | 0 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1539 | } | |
| 1540 | 1 | List<SequenceI> tmp = alignment.getHiddenSequences() |
| 1541 | .showAll(hiddenRepSequences); | |
| 1542 | 1 | for (SequenceI seq : tmp) |
| 1543 | { | |
| 1544 | 2 | selectionGroup.addSequence(seq, false); |
| 1545 | 2 | setSequenceAnnotationsVisible(seq, true); |
| 1546 | } | |
| 1547 | ||
| 1548 | 1 | hiddenRepSequences = null; |
| 1549 | ||
| 1550 | 1 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1551 | ||
| 1552 | 1 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1553 | // used to set hasHiddenRows/hiddenRepSequences here, after the property | |
| 1554 | // changed event | |
| 1555 | 1 | sendSelection(); |
| 1556 | } | |
| 1557 | } | |
| 1558 | ||
| 1559 | 2 | public void showSequence(int index) |
| 1560 | { | |
| 1561 | 2 | int startSeq = ranges.getStartSeq(); |
| 1562 | 2 | int endSeq = ranges.getEndSeq(); |
| 1563 | ||
| 1564 | 2 | List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index, |
| 1565 | hiddenRepSequences); | |
| 1566 | 2 | if (tmp.size() > 0) |
| 1567 | { | |
| 1568 | 2 | if (selectionGroup == null) |
| 1569 | { | |
| 1570 | 2 | selectionGroup = new SequenceGroup(); |
| 1571 | 2 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1572 | } | |
| 1573 | ||
| 1574 | 2 | for (SequenceI seq : tmp) |
| 1575 | { | |
| 1576 | 3 | selectionGroup.addSequence(seq, false); |
| 1577 | 3 | setSequenceAnnotationsVisible(seq, true); |
| 1578 | } | |
| 1579 | ||
| 1580 | 2 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1581 | ||
| 1582 | 2 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1583 | 2 | sendSelection(); |
| 1584 | } | |
| 1585 | } | |
| 1586 | ||
| 1587 | 0 | public void hideAllSelectedSeqs() |
| 1588 | { | |
| 1589 | 0 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1590 | { | |
| 1591 | 0 | return; |
| 1592 | } | |
| 1593 | ||
| 1594 | 0 | SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); |
| 1595 | ||
| 1596 | 0 | hideSequence(seqs); |
| 1597 | ||
| 1598 | 0 | setSelectionGroup(null); |
| 1599 | } | |
| 1600 | ||
| 1601 | 54 | public void hideSequence(SequenceI[] seq) |
| 1602 | { | |
| 1603 | /* | |
| 1604 | * cache offset to first visible sequence | |
| 1605 | */ | |
| 1606 | 54 | int startSeq = ranges.getStartSeq(); |
| 1607 | ||
| 1608 | 54 | if (seq != null) |
| 1609 | { | |
| 1610 | 252 | for (int i = 0; i < seq.length; i++) |
| 1611 | { | |
| 1612 | 198 | alignment.getHiddenSequences().hideSequence(seq[i]); |
| 1613 | 198 | setSequenceAnnotationsVisible(seq[i], false); |
| 1614 | } | |
| 1615 | 54 | ranges.setStartSeq(startSeq); |
| 1616 | 54 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1617 | } | |
| 1618 | } | |
| 1619 | ||
| 1620 | /** | |
| 1621 | * Hides the specified sequence, or the sequences it represents | |
| 1622 | * | |
| 1623 | * @param sequence | |
| 1624 | * the sequence to hide, or keep as representative | |
| 1625 | * @param representGroup | |
| 1626 | * if true, hide the current selection group except for the | |
| 1627 | * representative sequence | |
| 1628 | */ | |
| 1629 | 3 | public void hideSequences(SequenceI sequence, boolean representGroup) |
| 1630 | { | |
| 1631 | 3 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1632 | { | |
| 1633 | 0 | hideSequence(new SequenceI[] { sequence }); |
| 1634 | 0 | return; |
| 1635 | } | |
| 1636 | ||
| 1637 | 3 | if (representGroup) |
| 1638 | { | |
| 1639 | 3 | hideRepSequences(sequence, selectionGroup); |
| 1640 | 3 | setSelectionGroup(null); |
| 1641 | 3 | return; |
| 1642 | } | |
| 1643 | ||
| 1644 | 0 | int gsize = selectionGroup.getSize(); |
| 1645 | 0 | SequenceI[] hseqs = selectionGroup.getSequences() |
| 1646 | .toArray(new SequenceI[gsize]); | |
| 1647 | ||
| 1648 | 0 | hideSequence(hseqs); |
| 1649 | 0 | setSelectionGroup(null); |
| 1650 | 0 | sendSelection(); |
| 1651 | } | |
| 1652 | ||
| 1653 | /** | |
| 1654 | * Set visibility for any annotations for the given sequence. | |
| 1655 | * | |
| 1656 | * @param sequenceI | |
| 1657 | */ | |
| 1658 | 203 | protected void setSequenceAnnotationsVisible(SequenceI sequenceI, |
| 1659 | boolean visible) | |
| 1660 | { | |
| 1661 | 203 | AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation(); |
| 1662 | 203 | if (anns != null) |
| 1663 | { | |
| 1664 | 203 | for (AlignmentAnnotation ann : anns) |
| 1665 | { | |
| 1666 | 1033 | if (ann.sequenceRef == sequenceI) |
| 1667 | { | |
| 1668 | 0 | ann.visible = visible; |
| 1669 | } | |
| 1670 | } | |
| 1671 | } | |
| 1672 | } | |
| 1673 | ||
| 1674 | 5 | public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) |
| 1675 | { | |
| 1676 | 5 | int sSize = sg.getSize(); |
| 1677 | 5 | if (sSize < 2) |
| 1678 | { | |
| 1679 | 0 | return; |
| 1680 | } | |
| 1681 | ||
| 1682 | 5 | if (hiddenRepSequences == null) |
| 1683 | { | |
| 1684 | 5 | hiddenRepSequences = new Hashtable<>(); |
| 1685 | } | |
| 1686 | ||
| 1687 | 5 | hiddenRepSequences.put(repSequence, sg); |
| 1688 | ||
| 1689 | // Hide all sequences except the repSequence | |
| 1690 | 5 | SequenceI[] seqs = new SequenceI[sSize - 1]; |
| 1691 | 5 | int index = 0; |
| 1692 | 16 | for (int i = 0; i < sSize; i++) |
| 1693 | { | |
| 1694 | 11 | if (sg.getSequenceAt(i) != repSequence) |
| 1695 | { | |
| 1696 | 6 | if (index == sSize - 1) |
| 1697 | { | |
| 1698 | 0 | return; |
| 1699 | } | |
| 1700 | ||
| 1701 | 6 | seqs[index++] = sg.getSequenceAt(i); |
| 1702 | } | |
| 1703 | } | |
| 1704 | 5 | sg.setSeqrep(repSequence); // note: not done in 2.7applet |
| 1705 | 5 | sg.setHidereps(true); // note: not done in 2.7applet |
| 1706 | 5 | hideSequence(seqs); |
| 1707 | ||
| 1708 | } | |
| 1709 | ||
| 1710 | /** | |
| 1711 | * | |
| 1712 | * @return null or the current reference sequence | |
| 1713 | */ | |
| 1714 | 0 | public SequenceI getReferenceSeq() |
| 1715 | { | |
| 1716 | 0 | return alignment.getSeqrep(); |
| 1717 | } | |
| 1718 | ||
| 1719 | /** | |
| 1720 | * @param seq | |
| 1721 | * @return true iff seq is the reference for the alignment | |
| 1722 | */ | |
| 1723 | 3245 | public boolean isReferenceSeq(SequenceI seq) |
| 1724 | { | |
| 1725 | 3245 | return alignment.getSeqrep() == seq; |
| 1726 | } | |
| 1727 | ||
| 1728 | /** | |
| 1729 | * | |
| 1730 | * @param seq | |
| 1731 | * @return true if there are sequences represented by this sequence that are | |
| 1732 | * currently hidden | |
| 1733 | */ | |
| 1734 | 3331 | public boolean isHiddenRepSequence(SequenceI seq) |
| 1735 | { | |
| 1736 | 3331 | return (hiddenRepSequences != null |
| 1737 | && hiddenRepSequences.containsKey(seq)); | |
| 1738 | } | |
| 1739 | ||
| 1740 | /** | |
| 1741 | * | |
| 1742 | * @param seq | |
| 1743 | * @return null or a sequence group containing the sequences that seq | |
| 1744 | * represents | |
| 1745 | */ | |
| 1746 | 2 | public SequenceGroup getRepresentedSequences(SequenceI seq) |
| 1747 | { | |
| 1748 | 2 | return (SequenceGroup) (hiddenRepSequences == null ? null |
| 1749 | : hiddenRepSequences.get(seq)); | |
| 1750 | } | |
| 1751 | ||
| 1752 | 0 | @Override |
| 1753 | public int adjustForHiddenSeqs(int alignmentIndex) | |
| 1754 | { | |
| 1755 | 0 | return alignment.getHiddenSequences() |
| 1756 | .adjustForHiddenSeqs(alignmentIndex); | |
| 1757 | } | |
| 1758 | ||
| 1759 | 0 | @Override |
| 1760 | public void invertColumnSelection() | |
| 1761 | { | |
| 1762 | 0 | colSel.invertColumnSelection(0, alignment.getWidth(), alignment); |
| 1763 | 0 | isColSelChanged(true); |
| 1764 | } | |
| 1765 | ||
| 1766 | 4 | @Override |
| 1767 | public SequenceI[] getSelectionAsNewSequence() | |
| 1768 | { | |
| 1769 | 4 | SequenceI[] sequences; |
| 1770 | // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - | |
| 1771 | // this was the only caller in the applet for this method | |
| 1772 | // JBPNote: in applet, this method returned references to the alignment | |
| 1773 | // sequences, and it did not honour the presence/absence of annotation | |
| 1774 | // attached to the alignment (probably!) | |
| 1775 | 4 | if (selectionGroup == null || selectionGroup.getSize() == 0) |
| 1776 | { | |
| 1777 | 2 | sequences = alignment.getSequencesArray(); |
| 1778 | 2 | AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); |
| 1779 | 4 | for (int i = 0; i < sequences.length; i++) |
| 1780 | { | |
| 1781 | // construct new sequence with subset of visible annotation | |
| 1782 | 2 | sequences[i] = new Sequence(sequences[i], annots); |
| 1783 | } | |
| 1784 | } | |
| 1785 | else | |
| 1786 | { | |
| 1787 | 2 | sequences = selectionGroup.getSelectionAsNewSequences(alignment); |
| 1788 | } | |
| 1789 | ||
| 1790 | 4 | return sequences; |
| 1791 | } | |
| 1792 | ||
| 1793 | 28 | @Override |
| 1794 | public SequenceI[] getSequenceSelection() | |
| 1795 | { | |
| 1796 | 28 | SequenceI[] sequences = null; |
| 1797 | 28 | if (selectionGroup != null) |
| 1798 | { | |
| 1799 | 4 | sequences = selectionGroup.getSequencesInOrder(alignment); |
| 1800 | } | |
| 1801 | 28 | if (sequences == null) |
| 1802 | { | |
| 1803 | 24 | sequences = alignment.getSequencesArray(); |
| 1804 | } | |
| 1805 | 28 | return sequences; |
| 1806 | } | |
| 1807 | ||
| 1808 | 20 | @Override |
| 1809 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 1810 | boolean selectedOnly) | |
| 1811 | { | |
| 1812 | 20 | return getAlignmentView(selectedOnly, false); |
| 1813 | } | |
| 1814 | ||
| 1815 | 21 | @Override |
| 1816 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 1817 | boolean selectedOnly, boolean markGroups) | |
| 1818 | { | |
| 1819 | 21 | return new AlignmentView(alignment, alignment.getHiddenColumns(), |
| 1820 | selectionGroup, | |
| 1821 | alignment.getHiddenColumns() != null | |
| 1822 | && alignment.getHiddenColumns().hasHiddenColumns(), | |
| 1823 | selectedOnly, markGroups); | |
| 1824 | } | |
| 1825 | ||
| 1826 | 24 | @Override |
| 1827 | public String[] getViewAsString(boolean selectedRegionOnly) | |
| 1828 | { | |
| 1829 | 24 | return getViewAsString(selectedRegionOnly, true); |
| 1830 | } | |
| 1831 | ||
| 1832 | 24 | @Override |
| 1833 | public String[] getViewAsString(boolean selectedRegionOnly, | |
| 1834 | boolean exportHiddenSeqs) | |
| 1835 | { | |
| 1836 | 24 | String[] selection = null; |
| 1837 | 24 | SequenceI[] seqs = null; |
| 1838 | 24 | int i, iSize; |
| 1839 | 24 | int start = 0, end = 0; |
| 1840 | 24 | if (selectedRegionOnly && selectionGroup != null) |
| 1841 | { | |
| 1842 | 0 | iSize = selectionGroup.getSize(); |
| 1843 | 0 | seqs = selectionGroup.getSequencesInOrder(alignment); |
| 1844 | 0 | start = selectionGroup.getStartRes(); |
| 1845 | 0 | end = selectionGroup.getEndRes() + 1; |
| 1846 | } | |
| 1847 | else | |
| 1848 | { | |
| 1849 | 24 | if (hasHiddenRows() && exportHiddenSeqs) |
| 1850 | { | |
| 1851 | 0 | AlignmentI fullAlignment = alignment.getHiddenSequences() |
| 1852 | .getFullAlignment(); | |
| 1853 | 0 | iSize = fullAlignment.getHeight(); |
| 1854 | 0 | seqs = fullAlignment.getSequencesArray(); |
| 1855 | 0 | end = fullAlignment.getWidth(); |
| 1856 | } | |
| 1857 | else | |
| 1858 | { | |
| 1859 | 24 | iSize = alignment.getHeight(); |
| 1860 | 24 | seqs = alignment.getSequencesArray(); |
| 1861 | 24 | end = alignment.getWidth(); |
| 1862 | } | |
| 1863 | } | |
| 1864 | ||
| 1865 | 24 | selection = new String[iSize]; |
| 1866 | 24 | if (alignment.getHiddenColumns() != null |
| 1867 | && alignment.getHiddenColumns().hasHiddenColumns()) | |
| 1868 | { | |
| 1869 | 206 | for (i = 0; i < iSize; i++) |
| 1870 | { | |
| 1871 | 188 | Iterator<int[]> blocks = alignment.getHiddenColumns() |
| 1872 | .getVisContigsIterator(start, end + 1, false); | |
| 1873 | 188 | selection[i] = seqs[i].getSequenceStringFromIterator(blocks); |
| 1874 | } | |
| 1875 | } | |
| 1876 | else | |
| 1877 | { | |
| 1878 | 36 | for (i = 0; i < iSize; i++) |
| 1879 | { | |
| 1880 | 30 | selection[i] = seqs[i].getSequenceAsString(start, end); |
| 1881 | } | |
| 1882 | ||
| 1883 | } | |
| 1884 | 24 | return selection; |
| 1885 | } | |
| 1886 | ||
| 1887 | 0 | @Override |
| 1888 | public List<int[]> getVisibleRegionBoundaries(int min, int max) | |
| 1889 | { | |
| 1890 | 0 | ArrayList<int[]> regions = new ArrayList<>(); |
| 1891 | 0 | int start = min; |
| 1892 | 0 | int end = max; |
| 1893 | ||
| 1894 | 0 | do |
| 1895 | { | |
| 1896 | 0 | HiddenColumns hidden = alignment.getHiddenColumns(); |
| 1897 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 1898 | { | |
| 1899 | 0 | if (start == 0) |
| 1900 | { | |
| 1901 | 0 | start = hidden.visibleToAbsoluteColumn(start); |
| 1902 | } | |
| 1903 | ||
| 1904 | 0 | end = hidden.getNextHiddenBoundary(false, start); |
| 1905 | 0 | if (start == end) |
| 1906 | { | |
| 1907 | 0 | end = max; |
| 1908 | } | |
| 1909 | 0 | if (end > max) |
| 1910 | { | |
| 1911 | 0 | end = max; |
| 1912 | } | |
| 1913 | } | |
| 1914 | ||
| 1915 | 0 | regions.add(new int[] { start, end }); |
| 1916 | ||
| 1917 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 1918 | { | |
| 1919 | 0 | start = hidden.visibleToAbsoluteColumn(end); |
| 1920 | 0 | start = hidden.getNextHiddenBoundary(true, start) + 1; |
| 1921 | } | |
| 1922 | 0 | } while (end < max); |
| 1923 | ||
| 1924 | // int[][] startEnd = new int[regions.size()][2]; | |
| 1925 | ||
| 1926 | 0 | return regions; |
| 1927 | } | |
| 1928 | ||
| 1929 | 1 | @Override |
| 1930 | public List<AlignmentAnnotation> getVisibleAlignmentAnnotation( | |
| 1931 | boolean selectedOnly) | |
| 1932 | { | |
| 1933 | 1 | ArrayList<AlignmentAnnotation> ala = new ArrayList<>(); |
| 1934 | 1 | AlignmentAnnotation[] aa; |
| 1935 | ? | if ((aa = alignment.getAlignmentAnnotation()) != null) |
| 1936 | { | |
| 1937 | 1 | for (AlignmentAnnotation annot : aa) |
| 1938 | { | |
| 1939 | 4 | AlignmentAnnotation clone = new AlignmentAnnotation(annot); |
| 1940 | 4 | if (selectedOnly && selectionGroup != null) |
| 1941 | { | |
| 1942 | 4 | clone.makeVisibleAnnotation(selectionGroup.getStartRes(), |
| 1943 | selectionGroup.getEndRes(), alignment.getHiddenColumns()); | |
| 1944 | } | |
| 1945 | else | |
| 1946 | { | |
| 1947 | 0 | clone.makeVisibleAnnotation(alignment.getHiddenColumns()); |
| 1948 | } | |
| 1949 | 4 | ala.add(clone); |
| 1950 | } | |
| 1951 | } | |
| 1952 | 1 | return ala; |
| 1953 | } | |
| 1954 | ||
| 1955 | 1678 | @Override |
| 1956 | public boolean isPadGaps() | |
| 1957 | { | |
| 1958 | 1678 | return padGaps; |
| 1959 | } | |
| 1960 | ||
| 1961 | 508 | @Override |
| 1962 | public void setPadGaps(boolean padGaps) | |
| 1963 | { | |
| 1964 | 508 | this.padGaps = padGaps; |
| 1965 | } | |
| 1966 | ||
| 1967 | /** | |
| 1968 | * apply any post-edit constraints and trigger any calculations needed after | |
| 1969 | * an edit has been performed on the alignment | |
| 1970 | * | |
| 1971 | * @param ap | |
| 1972 | */ | |
| 1973 | 549 | @Override |
| 1974 | public void alignmentChanged(AlignmentViewPanel ap) | |
| 1975 | { | |
| 1976 | 549 | if (isPadGaps()) |
| 1977 | { | |
| 1978 | 310 | alignment.padGaps(); |
| 1979 | } | |
| 1980 | 549 | if (autoCalculateConsensus) |
| 1981 | { | |
| 1982 | 549 | updateConsensus(ap); |
| 1983 | 549 | updateSecondaryStructureConsensus(ap); |
| 1984 | } | |
| 1985 | 549 | if (hconsensus != null && autoCalculateConsensus) |
| 1986 | { | |
| 1987 | 538 | updateConservation(ap); |
| 1988 | } | |
| 1989 | 549 | if (autoCalculateStrucConsensus) |
| 1990 | { | |
| 1991 | 549 | updateStrucConsensus(ap); |
| 1992 | } | |
| 1993 | ||
| 1994 | // Reset endRes of groups if beyond alignment width | |
| 1995 | 549 | int alWidth = alignment.getWidth(); |
| 1996 | 549 | List<SequenceGroup> groups = alignment.getGroups(); |
| 1997 | 549 | if (groups != null) |
| 1998 | { | |
| 1999 | 549 | for (SequenceGroup sg : groups) |
| 2000 | { | |
| 2001 | 175 | if (sg.getEndRes() > alWidth) |
| 2002 | { | |
| 2003 | 0 | sg.setEndRes(alWidth - 1); |
| 2004 | } | |
| 2005 | } | |
| 2006 | } | |
| 2007 | ||
| 2008 | 549 | if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) |
| 2009 | { | |
| 2010 | 0 | selectionGroup.setEndRes(alWidth - 1); |
| 2011 | } | |
| 2012 | ||
| 2013 | 549 | updateAllColourSchemes(); |
| 2014 | 549 | calculator.restartWorkers(); |
| 2015 | // alignment.adjustSequenceAnnotations(); | |
| 2016 | } | |
| 2017 | ||
| 2018 | /** | |
| 2019 | * reset scope and do calculations for all applied colourschemes on alignment | |
| 2020 | */ | |
| 2021 | 549 | void updateAllColourSchemes() |
| 2022 | { | |
| 2023 | 549 | ResidueShaderI rs = residueShading; |
| 2024 | 549 | if (rs != null) |
| 2025 | { | |
| 2026 | 549 | rs.alignmentChanged(alignment, hiddenRepSequences); |
| 2027 | ||
| 2028 | 549 | rs.setConsensus(hconsensus); |
| 2029 | 549 | if (rs.conservationApplied()) |
| 2030 | { | |
| 2031 | 3 | rs.setConservation(Conservation.calculateConservation("All", |
| 2032 | alignment.getSequences(), 0, alignment.getWidth(), false, | |
| 2033 | getConsPercGaps(), false)); | |
| 2034 | } | |
| 2035 | } | |
| 2036 | ||
| 2037 | 549 | for (SequenceGroup sg : alignment.getGroups()) |
| 2038 | { | |
| 2039 | 175 | if (sg.cs != null) |
| 2040 | { | |
| 2041 | 175 | sg.cs.alignmentChanged(sg, hiddenRepSequences); |
| 2042 | } | |
| 2043 | 175 | sg.recalcConservation(); |
| 2044 | } | |
| 2045 | } | |
| 2046 | ||
| 2047 | 508 | protected void initAutoAnnotation() |
| 2048 | { | |
| 2049 | // TODO: add menu option action that nulls or creates consensus object | |
| 2050 | // depending on if the user wants to see the annotation or not in a | |
| 2051 | // specific alignment | |
| 2052 | ||
| 2053 | 508 | if (hconsensus == null && !isDataset) |
| 2054 | { | |
| 2055 | 508 | if (!alignment.isNucleotide()) |
| 2056 | { | |
| 2057 | 397 | initConservation(); |
| 2058 | 397 | initQuality(); |
| 2059 | 397 | initSSConsensus(); |
| 2060 | } | |
| 2061 | else | |
| 2062 | { | |
| 2063 | 111 | initRNAStructure(); |
| 2064 | } | |
| 2065 | 508 | consensus = new AlignmentAnnotation("Consensus", |
| 2066 | MessageManager.getString("label.consensus_descr"), | |
| 2067 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2068 | ||
| 2069 | ||
| 2070 | 508 | initConsensus(consensus); |
| 2071 | 508 | initGapCounts(); |
| 2072 | 508 | initComplementConsensus(); |
| 2073 | } | |
| 2074 | } | |
| 2075 | ||
| 2076 | /** | |
| 2077 | * If this is a protein alignment and there are mappings to cDNA, adds the | |
| 2078 | * cDNA consensus annotation and returns true, else returns false. | |
| 2079 | */ | |
| 2080 | 518 | public boolean initComplementConsensus() |
| 2081 | { | |
| 2082 | 518 | if (!alignment.isNucleotide()) |
| 2083 | { | |
| 2084 | 406 | final List<AlignedCodonFrame> codonMappings = alignment |
| 2085 | .getCodonFrames(); | |
| 2086 | 406 | if (codonMappings != null && !codonMappings.isEmpty()) |
| 2087 | { | |
| 2088 | 4 | boolean doConsensus = false; |
| 2089 | 4 | for (AlignedCodonFrame mapping : codonMappings) |
| 2090 | { | |
| 2091 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 2092 | 4 | MapList[] mapLists = mapping.getdnaToProt(); |
| 2093 | // mapLists can be empty if project load has not finished resolving | |
| 2094 | // seqs | |
| 2095 | 4 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 2096 | { | |
| 2097 | 4 | doConsensus = true; |
| 2098 | 4 | break; |
| 2099 | } | |
| 2100 | } | |
| 2101 | 4 | if (doConsensus) |
| 2102 | { | |
| 2103 | 4 | complementConsensus = new AlignmentAnnotation("cDNA Consensus", |
| 2104 | MessageManager | |
| 2105 | .getString("label.complement_consensus_descr"), | |
| 2106 | new Annotation[1], 0f, 100f, | |
| 2107 | AlignmentAnnotation.BAR_GRAPH); | |
| 2108 | 4 | initConsensus(complementConsensus); |
| 2109 | 4 | return true; |
| 2110 | } | |
| 2111 | } | |
| 2112 | } | |
| 2113 | 514 | return false; |
| 2114 | } | |
| 2115 | ||
| 2116 | 512 | private void initConsensus(AlignmentAnnotation aa) |
| 2117 | { | |
| 2118 | 512 | aa.hasText = true; |
| 2119 | 512 | aa.autoCalculated = true; |
| 2120 | ||
| 2121 | 512 | if (showConsensus) |
| 2122 | { | |
| 2123 | 511 | alignment.addAnnotation(aa); |
| 2124 | } | |
| 2125 | } | |
| 2126 | ||
| 2127 | 397 | private void initSSConsensus() |
| 2128 | { | |
| 2129 | 397 | if (!alignment.isNucleotide() && showSSConsensus) |
| 2130 | { | |
| 2131 | 0 | if (secondaryStructureConsensus == null) |
| 2132 | { | |
| 2133 | 0 | secondaryStructureConsensus = new AlignmentAnnotation( |
| 2134 | MessageManager.getString("label.ssconsensus_label"), | |
| 2135 | MessageManager.getString("label.ssconsensus_descr"), | |
| 2136 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2137 | ||
| 2138 | 0 | secondaryStructureConsensus.hasText = true; |
| 2139 | 0 | secondaryStructureConsensus.autoCalculated = true; |
| 2140 | } | |
| 2141 | 0 | alignment.addAnnotation(secondaryStructureConsensus); |
| 2142 | } | |
| 2143 | } | |
| 2144 | ||
| 2145 | // these should be extracted from the view model - style and settings for | |
| 2146 | // derived annotation | |
| 2147 | 508 | private void initGapCounts() |
| 2148 | { | |
| 2149 | 508 | if (showOccupancy) |
| 2150 | { | |
| 2151 | 504 | gapcounts = new AlignmentAnnotation("Occupancy", |
| 2152 | MessageManager.getString("label.occupancy_descr"), | |
| 2153 | new Annotation[1], 0f, alignment.getHeight(), | |
| 2154 | AlignmentAnnotation.BAR_GRAPH); | |
| 2155 | 504 | gapcounts.hasText = true; |
| 2156 | 504 | gapcounts.autoCalculated = true; |
| 2157 | 504 | gapcounts.scaleColLabel = true; |
| 2158 | 504 | gapcounts.graph = AlignmentAnnotation.BAR_GRAPH; |
| 2159 | ||
| 2160 | 504 | alignment.addAnnotation(gapcounts); |
| 2161 | } | |
| 2162 | } | |
| 2163 | ||
| 2164 | 397 | private void initConservation() |
| 2165 | { | |
| 2166 | 397 | if (showConservation) |
| 2167 | { | |
| 2168 | 396 | if (conservation == null) |
| 2169 | { | |
| 2170 | 396 | conservation = new AlignmentAnnotation("Conservation", |
| 2171 | MessageManager.formatMessage("label.conservation_descr", | |
| 2172 | getConsPercGaps()), | |
| 2173 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2174 | 396 | conservation.hasText = true; |
| 2175 | 396 | conservation.autoCalculated = true; |
| 2176 | 396 | alignment.addAnnotation(conservation); |
| 2177 | } | |
| 2178 | } | |
| 2179 | } | |
| 2180 | ||
| 2181 | 397 | private void initQuality() |
| 2182 | { | |
| 2183 | 397 | if (showQuality) |
| 2184 | { | |
| 2185 | 397 | if (quality == null) |
| 2186 | { | |
| 2187 | 397 | quality = new AlignmentAnnotation("Quality", |
| 2188 | MessageManager.getString("label.quality_descr"), | |
| 2189 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2190 | 397 | quality.hasText = true; |
| 2191 | 397 | quality.autoCalculated = true; |
| 2192 | 397 | alignment.addAnnotation(quality); |
| 2193 | } | |
| 2194 | } | |
| 2195 | } | |
| 2196 | ||
| 2197 | 111 | private void initRNAStructure() |
| 2198 | { | |
| 2199 | 111 | if (alignment.hasRNAStructure() && strucConsensus == null) |
| 2200 | { | |
| 2201 | 2 | strucConsensus = new AlignmentAnnotation("StrucConsensus", |
| 2202 | MessageManager.getString("label.strucconsensus_descr"), | |
| 2203 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2204 | 2 | strucConsensus.hasText = true; |
| 2205 | 2 | strucConsensus.autoCalculated = true; |
| 2206 | ||
| 2207 | 2 | if (showConsensus) |
| 2208 | { | |
| 2209 | 2 | alignment.addAnnotation(strucConsensus); |
| 2210 | } | |
| 2211 | } | |
| 2212 | } | |
| 2213 | ||
| 2214 | /* | |
| 2215 | * (non-Javadoc) | |
| 2216 | * | |
| 2217 | * @see jalview.api.AlignViewportI#calcPanelHeight() | |
| 2218 | */ | |
| 2219 | 3691 | @Override |
| 2220 | public int calcPanelHeight() | |
| 2221 | { | |
| 2222 | // setHeight of panels | |
| 2223 | 3691 | AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation(); |
| 2224 | 3691 | int height = 0; |
| 2225 | 3691 | int charHeight = getCharHeight(); |
| 2226 | 3691 | if (anns != null) |
| 2227 | { | |
| 2228 | 3691 | BitSet graphgrp = new BitSet(); |
| 2229 | 3691 | for (AlignmentAnnotation aa : anns) |
| 2230 | { | |
| 2231 | 17229 | if (aa == null) |
| 2232 | { | |
| 2233 | 0 | jalview.bin.Console.errPrintln("Null annotation row: ignoring."); |
| 2234 | 0 | continue; |
| 2235 | } | |
| 2236 | 17229 | if (!aa.isForDisplay()) |
| 2237 | { | |
| 2238 | 1377 | continue; |
| 2239 | } | |
| 2240 | 15852 | if (aa.graphGroup > -1) |
| 2241 | { | |
| 2242 | 300 | if (graphgrp.get(aa.graphGroup)) |
| 2243 | { | |
| 2244 | 150 | continue; |
| 2245 | } | |
| 2246 | else | |
| 2247 | { | |
| 2248 | 150 | graphgrp.set(aa.graphGroup); |
| 2249 | } | |
| 2250 | } | |
| 2251 | 15702 | aa.height = 0; |
| 2252 | ||
| 2253 | 15702 | if (aa.hasText) |
| 2254 | { | |
| 2255 | 13938 | aa.height += charHeight; |
| 2256 | } | |
| 2257 | ||
| 2258 | 15702 | if (aa.hasIcons) |
| 2259 | { | |
| 2260 | 671 | aa.height += 16; |
| 2261 | } | |
| 2262 | ||
| 2263 | 15702 | if (aa.graph > 0) |
| 2264 | { | |
| 2265 | 14642 | aa.height += aa.graphHeight + 20; |
| 2266 | } | |
| 2267 | ||
| 2268 | 15702 | if (aa.height == 0) |
| 2269 | { | |
| 2270 | 156 | aa.height = 20; |
| 2271 | } | |
| 2272 | ||
| 2273 | 15702 | height += aa.height; |
| 2274 | } | |
| 2275 | } | |
| 2276 | 3691 | if (height == 0) |
| 2277 | { | |
| 2278 | // set minimum | |
| 2279 | 18 | height = 20; |
| 2280 | } | |
| 2281 | 3691 | return height; |
| 2282 | } | |
| 2283 | ||
| 2284 | 130 | @Override |
| 2285 | public void updateGroupAnnotationSettings(boolean applyGlobalSettings, | |
| 2286 | boolean preserveNewGroupSettings) | |
| 2287 | { | |
| 2288 | 130 | boolean updateCalcs = false; |
| 2289 | 130 | boolean conv = isShowGroupConservation(); |
| 2290 | 130 | boolean cons = isShowGroupConsensus(); |
| 2291 | 130 | boolean sscons = isShowGroupSSConsensus(); |
| 2292 | 130 | boolean showprf = isShowSequenceLogo(); |
| 2293 | 130 | boolean showSSprf = isShowSequenceSSLogo(); |
| 2294 | 130 | boolean showConsHist = isShowConsensusHistogram(); |
| 2295 | 130 | boolean showSSConsHist = isShowSSConsensusHistogram(); |
| 2296 | 130 | boolean normLogo = isNormaliseSequenceLogo(); |
| 2297 | ||
| 2298 | /** | |
| 2299 | * TODO reorder the annotation rows according to group/sequence ordering on | |
| 2300 | * alignment | |
| 2301 | */ | |
| 2302 | // boolean sortg = true; | |
| 2303 | ||
| 2304 | // remove old automatic annotation | |
| 2305 | // add any new annotation | |
| 2306 | ||
| 2307 | // intersect alignment annotation with alignment groups | |
| 2308 | ||
| 2309 | 130 | AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation(); |
| 2310 | 130 | List<SequenceGroup> oldrfs = new ArrayList<>(); |
| 2311 | 130 | if (aan != null) |
| 2312 | { | |
| 2313 | 1021 | for (int an = 0; an < aan.length; an++) |
| 2314 | { | |
| 2315 | 891 | if (aan[an].autoCalculated && aan[an].groupRef != null) |
| 2316 | { | |
| 2317 | 0 | oldrfs.add(aan[an].groupRef); |
| 2318 | 0 | alignment.deleteAnnotation(aan[an], false); |
| 2319 | } | |
| 2320 | } | |
| 2321 | } | |
| 2322 | 130 | if (alignment.getGroups() != null) |
| 2323 | { | |
| 2324 | 130 | for (SequenceGroup sg : alignment.getGroups()) |
| 2325 | { | |
| 2326 | 56 | updateCalcs = false; |
| 2327 | 56 | if (applyGlobalSettings |
| 2328 | || (!preserveNewGroupSettings && !oldrfs.contains(sg))) | |
| 2329 | { | |
| 2330 | // set defaults for this group's conservation/consensus | |
| 2331 | 9 | sg.setshowSequenceLogo(showprf); |
| 2332 | 9 | sg.setshowSequenceSSLogo(showSSprf); |
| 2333 | 9 | sg.setShowConsensusHistogram(showConsHist); |
| 2334 | 9 | sg.setShowSSConsensusHistogram(showSSConsHist); |
| 2335 | 9 | sg.setNormaliseSequenceLogo(normLogo); |
| 2336 | } | |
| 2337 | 56 | if (conv) |
| 2338 | { | |
| 2339 | 0 | updateCalcs = true; |
| 2340 | 0 | alignment.addAnnotation(sg.getConservationRow(), 0); |
| 2341 | } | |
| 2342 | 56 | if (cons) |
| 2343 | { | |
| 2344 | 24 | updateCalcs = true; |
| 2345 | 24 | alignment.addAnnotation(sg.getConsensus(), 0); |
| 2346 | } | |
| 2347 | 56 | if (sscons) |
| 2348 | { | |
| 2349 | 0 | updateCalcs = true; |
| 2350 | 0 | alignment.addAnnotation(sg.getSSConsensus(), 0); |
| 2351 | } | |
| 2352 | // refresh the annotation rows | |
| 2353 | 56 | if (updateCalcs) |
| 2354 | { | |
| 2355 | 24 | sg.recalcConservation(); |
| 2356 | } | |
| 2357 | } | |
| 2358 | } | |
| 2359 | 130 | oldrfs.clear(); |
| 2360 | } | |
| 2361 | ||
| 2362 | 16352 | @Override |
| 2363 | public boolean isDisplayReferenceSeq() | |
| 2364 | { | |
| 2365 | 16352 | return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq(); |
| 2366 | } | |
| 2367 | ||
| 2368 | 10 | @Override |
| 2369 | public void setDisplayReferenceSeq(boolean displayReferenceSeq) | |
| 2370 | { | |
| 2371 | 10 | viewStyle.setDisplayReferenceSeq(displayReferenceSeq); |
| 2372 | } | |
| 2373 | ||
| 2374 | 5 | @Override |
| 2375 | public boolean isColourByReferenceSeq() | |
| 2376 | { | |
| 2377 | 5 | return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq(); |
| 2378 | } | |
| 2379 | ||
| 2380 | 11042 | @Override |
| 2381 | public Color getSequenceColour(SequenceI seq) | |
| 2382 | { | |
| 2383 | 11042 | Color sqc = sequenceColours.get(seq); |
| 2384 | 11042 | return (sqc == null ? Color.white : sqc); |
| 2385 | } | |
| 2386 | ||
| 2387 | 1192 | @Override |
| 2388 | public void setSequenceColour(SequenceI seq, Color col) | |
| 2389 | { | |
| 2390 | 1192 | if (col == null) |
| 2391 | { | |
| 2392 | 0 | sequenceColours.remove(seq); |
| 2393 | } | |
| 2394 | else | |
| 2395 | { | |
| 2396 | 1192 | sequenceColours.put(seq, col); |
| 2397 | } | |
| 2398 | } | |
| 2399 | ||
| 2400 | 5 | @Override |
| 2401 | public void updateSequenceIdColours() | |
| 2402 | { | |
| 2403 | 5 | for (SequenceGroup sg : alignment.getGroups()) |
| 2404 | { | |
| 2405 | 5 | if (sg.idColour != null) |
| 2406 | { | |
| 2407 | 0 | for (SequenceI s : sg.getSequences(getHiddenRepSequences())) |
| 2408 | { | |
| 2409 | 0 | sequenceColours.put(s, sg.idColour); |
| 2410 | } | |
| 2411 | } | |
| 2412 | } | |
| 2413 | } | |
| 2414 | ||
| 2415 | 0 | @Override |
| 2416 | public void clearSequenceColours() | |
| 2417 | { | |
| 2418 | 0 | sequenceColours.clear(); |
| 2419 | } | |
| 2420 | ||
| 2421 | 1050 | @Override |
| 2422 | public AlignViewportI getCodingComplement() | |
| 2423 | { | |
| 2424 | 1050 | return this.codingComplement; |
| 2425 | } | |
| 2426 | ||
| 2427 | /** | |
| 2428 | * Set this as the (cDna/protein) complement of the given viewport. Also | |
| 2429 | * ensures the reverse relationship is set on the given viewport. | |
| 2430 | */ | |
| 2431 | 6 | @Override |
| 2432 | public void setCodingComplement(AlignViewportI av) | |
| 2433 | { | |
| 2434 | 6 | if (this == av) |
| 2435 | { | |
| 2436 | 0 | jalview.bin.Console |
| 2437 | .errPrintln("Ignoring recursive setCodingComplement request"); | |
| 2438 | } | |
| 2439 | else | |
| 2440 | { | |
| 2441 | 6 | this.codingComplement = av; |
| 2442 | // avoid infinite recursion! | |
| 2443 | 6 | if (av.getCodingComplement() != this) |
| 2444 | { | |
| 2445 | 3 | av.setCodingComplement(this); |
| 2446 | } | |
| 2447 | } | |
| 2448 | } | |
| 2449 | ||
| 2450 | 25 | @Override |
| 2451 | public boolean isNucleotide() | |
| 2452 | { | |
| 2453 | 25 | return getAlignment() == null ? false : getAlignment().isNucleotide(); |
| 2454 | } | |
| 2455 | ||
| 2456 | 1231274 | @Override |
| 2457 | public FeaturesDisplayedI getFeaturesDisplayed() | |
| 2458 | { | |
| 2459 | 1231290 | return featuresDisplayed; |
| 2460 | } | |
| 2461 | ||
| 2462 | 112 | @Override |
| 2463 | public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) | |
| 2464 | { | |
| 2465 | 112 | featuresDisplayed = featuresDisplayedI; |
| 2466 | } | |
| 2467 | ||
| 2468 | 83 | @Override |
| 2469 | public boolean areFeaturesDisplayed() | |
| 2470 | { | |
| 2471 | 83 | return featuresDisplayed != null |
| 2472 | && featuresDisplayed.getRegisteredFeaturesCount() > 0; | |
| 2473 | } | |
| 2474 | ||
| 2475 | /** | |
| 2476 | * set the flag | |
| 2477 | * | |
| 2478 | * @param b | |
| 2479 | * features are displayed if true | |
| 2480 | */ | |
| 2481 | 141 | @Override |
| 2482 | public void setShowSequenceFeatures(boolean b) | |
| 2483 | { | |
| 2484 | 141 | viewStyle.setShowSequenceFeatures(b); |
| 2485 | } | |
| 2486 | ||
| 2487 | 398845 | @Override |
| 2488 | public boolean isShowSequenceFeatures() | |
| 2489 | { | |
| 2490 | 398898 | return viewStyle.isShowSequenceFeatures(); |
| 2491 | } | |
| 2492 | ||
| 2493 | 0 | @Override |
| 2494 | public void setShowSequenceFeaturesHeight(boolean selected) | |
| 2495 | { | |
| 2496 | 0 | viewStyle.setShowSequenceFeaturesHeight(selected); |
| 2497 | } | |
| 2498 | ||
| 2499 | 0 | @Override |
| 2500 | public boolean isShowSequenceFeaturesHeight() | |
| 2501 | { | |
| 2502 | 0 | return viewStyle.isShowSequenceFeaturesHeight(); |
| 2503 | } | |
| 2504 | ||
| 2505 | 680 | @Override |
| 2506 | public void setShowAnnotation(boolean b) | |
| 2507 | { | |
| 2508 | 680 | viewStyle.setShowAnnotation(b); |
| 2509 | } | |
| 2510 | ||
| 2511 | 3829 | @Override |
| 2512 | public boolean isShowAnnotation() | |
| 2513 | { | |
| 2514 | 3829 | return viewStyle.isShowAnnotation(); |
| 2515 | } | |
| 2516 | ||
| 2517 | 10836 | @Override |
| 2518 | public boolean isRightAlignIds() | |
| 2519 | { | |
| 2520 | 10836 | return viewStyle.isRightAlignIds(); |
| 2521 | } | |
| 2522 | ||
| 2523 | 593 | @Override |
| 2524 | public void setRightAlignIds(boolean rightAlignIds) | |
| 2525 | { | |
| 2526 | 593 | viewStyle.setRightAlignIds(rightAlignIds); |
| 2527 | } | |
| 2528 | ||
| 2529 | 1040 | @Override |
| 2530 | public boolean getConservationSelected() | |
| 2531 | { | |
| 2532 | 1040 | return viewStyle.getConservationSelected(); |
| 2533 | } | |
| 2534 | ||
| 2535 | 85 | @Override |
| 2536 | public void setShowBoxes(boolean state) | |
| 2537 | { | |
| 2538 | 85 | viewStyle.setShowBoxes(state); |
| 2539 | } | |
| 2540 | ||
| 2541 | /** | |
| 2542 | * @return | |
| 2543 | * @see jalview.api.ViewStyleI#getTextColour() | |
| 2544 | */ | |
| 2545 | 540038 | @Override |
| 2546 | public Color getTextColour() | |
| 2547 | { | |
| 2548 | 540038 | return viewStyle.getTextColour(); |
| 2549 | } | |
| 2550 | ||
| 2551 | /** | |
| 2552 | * @return | |
| 2553 | * @see jalview.api.ViewStyleI#getTextColour2() | |
| 2554 | */ | |
| 2555 | 46 | @Override |
| 2556 | public Color getTextColour2() | |
| 2557 | { | |
| 2558 | 46 | return viewStyle.getTextColour2(); |
| 2559 | } | |
| 2560 | ||
| 2561 | /** | |
| 2562 | * @return | |
| 2563 | * @see jalview.api.ViewStyleI#getThresholdTextColour() | |
| 2564 | */ | |
| 2565 | 355412 | @Override |
| 2566 | public int getThresholdTextColour() | |
| 2567 | { | |
| 2568 | 355412 | return viewStyle.getThresholdTextColour(); |
| 2569 | } | |
| 2570 | ||
| 2571 | /** | |
| 2572 | * @return | |
| 2573 | * @see jalview.api.ViewStyleI#isConservationColourSelected() | |
| 2574 | */ | |
| 2575 | 0 | @Override |
| 2576 | public boolean isConservationColourSelected() | |
| 2577 | { | |
| 2578 | 0 | return viewStyle.isConservationColourSelected(); |
| 2579 | } | |
| 2580 | ||
| 2581 | /** | |
| 2582 | * @return | |
| 2583 | * @see jalview.api.ViewStyleI#isRenderGaps() | |
| 2584 | */ | |
| 2585 | 2721 | @Override |
| 2586 | public boolean isRenderGaps() | |
| 2587 | { | |
| 2588 | 2721 | return viewStyle.isRenderGaps(); |
| 2589 | } | |
| 2590 | ||
| 2591 | /** | |
| 2592 | * @return | |
| 2593 | * @see jalview.api.ViewStyleI#isShowColourText() | |
| 2594 | */ | |
| 2595 | 672 | @Override |
| 2596 | public boolean isShowColourText() | |
| 2597 | { | |
| 2598 | 672 | return viewStyle.isShowColourText(); |
| 2599 | } | |
| 2600 | ||
| 2601 | /** | |
| 2602 | * @param conservationColourSelected | |
| 2603 | * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean) | |
| 2604 | */ | |
| 2605 | 0 | @Override |
| 2606 | public void setConservationColourSelected( | |
| 2607 | boolean conservationColourSelected) | |
| 2608 | { | |
| 2609 | 0 | viewStyle.setConservationColourSelected(conservationColourSelected); |
| 2610 | } | |
| 2611 | ||
| 2612 | /** | |
| 2613 | * @param showColourText | |
| 2614 | * @see jalview.api.ViewStyleI#setShowColourText(boolean) | |
| 2615 | */ | |
| 2616 | 0 | @Override |
| 2617 | public void setShowColourText(boolean showColourText) | |
| 2618 | { | |
| 2619 | 0 | viewStyle.setShowColourText(showColourText); |
| 2620 | } | |
| 2621 | ||
| 2622 | /** | |
| 2623 | * @param textColour | |
| 2624 | * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color) | |
| 2625 | */ | |
| 2626 | 85 | @Override |
| 2627 | public void setTextColour(Color textColour) | |
| 2628 | { | |
| 2629 | 85 | viewStyle.setTextColour(textColour); |
| 2630 | } | |
| 2631 | ||
| 2632 | /** | |
| 2633 | * @param thresholdTextColour | |
| 2634 | * @see jalview.api.ViewStyleI#setThresholdTextColour(int) | |
| 2635 | */ | |
| 2636 | 85 | @Override |
| 2637 | public void setThresholdTextColour(int thresholdTextColour) | |
| 2638 | { | |
| 2639 | 85 | viewStyle.setThresholdTextColour(thresholdTextColour); |
| 2640 | } | |
| 2641 | ||
| 2642 | /** | |
| 2643 | * @param textColour2 | |
| 2644 | * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color) | |
| 2645 | */ | |
| 2646 | 85 | @Override |
| 2647 | public void setTextColour2(Color textColour2) | |
| 2648 | { | |
| 2649 | 85 | viewStyle.setTextColour2(textColour2); |
| 2650 | } | |
| 2651 | ||
| 2652 | 143 | @Override |
| 2653 | public ViewStyleI getViewStyle() | |
| 2654 | { | |
| 2655 | 143 | return new ViewStyle(viewStyle); |
| 2656 | } | |
| 2657 | ||
| 2658 | 86 | @Override |
| 2659 | public void setViewStyle(ViewStyleI settingsForView) | |
| 2660 | { | |
| 2661 | 86 | viewStyle = new ViewStyle(settingsForView); |
| 2662 | 86 | if (residueShading != null) |
| 2663 | { | |
| 2664 | 86 | residueShading.setConservationApplied( |
| 2665 | settingsForView.isConservationColourSelected()); | |
| 2666 | } | |
| 2667 | } | |
| 2668 | ||
| 2669 | 0 | @Override |
| 2670 | public boolean sameStyle(ViewStyleI them) | |
| 2671 | { | |
| 2672 | 0 | return viewStyle.sameStyle(them); |
| 2673 | } | |
| 2674 | ||
| 2675 | /** | |
| 2676 | * @return | |
| 2677 | * @see jalview.api.ViewStyleI#getIdWidth() | |
| 2678 | */ | |
| 2679 | 5821 | @Override |
| 2680 | public int getIdWidth() | |
| 2681 | { | |
| 2682 | 5821 | return viewStyle.getIdWidth(); |
| 2683 | } | |
| 2684 | ||
| 2685 | /** | |
| 2686 | * @param i | |
| 2687 | * @see jalview.api.ViewStyleI#setIdWidth(int) | |
| 2688 | */ | |
| 2689 | 655 | @Override |
| 2690 | public void setIdWidth(int i) | |
| 2691 | { | |
| 2692 | 655 | viewStyle.setIdWidth(i); |
| 2693 | } | |
| 2694 | ||
| 2695 | /** | |
| 2696 | * @return | |
| 2697 | * @see jalview.api.ViewStyleI#isCentreColumnLabels() | |
| 2698 | */ | |
| 2699 | 672 | @Override |
| 2700 | public boolean isCentreColumnLabels() | |
| 2701 | { | |
| 2702 | 672 | return viewStyle.isCentreColumnLabels(); |
| 2703 | } | |
| 2704 | ||
| 2705 | /** | |
| 2706 | * @param centreColumnLabels | |
| 2707 | * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean) | |
| 2708 | */ | |
| 2709 | 593 | @Override |
| 2710 | public void setCentreColumnLabels(boolean centreColumnLabels) | |
| 2711 | { | |
| 2712 | 593 | viewStyle.setCentreColumnLabels(centreColumnLabels); |
| 2713 | } | |
| 2714 | ||
| 2715 | /** | |
| 2716 | * @param showdbrefs | |
| 2717 | * @see jalview.api.ViewStyleI#setShowDBRefs(boolean) | |
| 2718 | */ | |
| 2719 | 593 | @Override |
| 2720 | public void setShowDBRefs(boolean showdbrefs) | |
| 2721 | { | |
| 2722 | 593 | viewStyle.setShowDBRefs(showdbrefs); |
| 2723 | } | |
| 2724 | ||
| 2725 | /** | |
| 2726 | * @return | |
| 2727 | * @see jalview.api.ViewStyleI#isShowDBRefs() | |
| 2728 | */ | |
| 2729 | 718 | @Override |
| 2730 | public boolean isShowDBRefs() | |
| 2731 | { | |
| 2732 | 718 | return viewStyle.isShowDBRefs(); |
| 2733 | } | |
| 2734 | ||
| 2735 | /** | |
| 2736 | * @return | |
| 2737 | * @see jalview.api.ViewStyleI#isShowNPFeats() | |
| 2738 | */ | |
| 2739 | 718 | @Override |
| 2740 | public boolean isShowNPFeats() | |
| 2741 | { | |
| 2742 | 718 | return viewStyle.isShowNPFeats(); |
| 2743 | } | |
| 2744 | ||
| 2745 | /** | |
| 2746 | * @param shownpfeats | |
| 2747 | * @see jalview.api.ViewStyleI#setShowNPFeats(boolean) | |
| 2748 | */ | |
| 2749 | 593 | @Override |
| 2750 | public void setShowNPFeats(boolean shownpfeats) | |
| 2751 | { | |
| 2752 | 593 | viewStyle.setShowNPFeats(shownpfeats); |
| 2753 | } | |
| 2754 | ||
| 2755 | public abstract StructureSelectionManager getStructureSelectionManager(); | |
| 2756 | ||
| 2757 | /** | |
| 2758 | * Add one command to the command history list. | |
| 2759 | * | |
| 2760 | * @param command | |
| 2761 | */ | |
| 2762 | 1 | public void addToHistoryList(CommandI command) |
| 2763 | { | |
| 2764 | 1 | if (this.historyList != null) |
| 2765 | { | |
| 2766 | 1 | this.historyList.push(command); |
| 2767 | 1 | broadcastCommand(command, false); |
| 2768 | 1 | setSavedUpToDate(false); |
| 2769 | 1 | Jalview2XML.setStateSavedUpToDate(false); |
| 2770 | } | |
| 2771 | } | |
| 2772 | ||
| 2773 | 1 | protected void broadcastCommand(CommandI command, boolean undo) |
| 2774 | { | |
| 2775 | 1 | getStructureSelectionManager().commandPerformed(command, undo, |
| 2776 | getVamsasSource()); | |
| 2777 | } | |
| 2778 | ||
| 2779 | /** | |
| 2780 | * Add one command to the command redo list. | |
| 2781 | * | |
| 2782 | * @param command | |
| 2783 | */ | |
| 2784 | 0 | public void addToRedoList(CommandI command) |
| 2785 | { | |
| 2786 | 0 | if (this.redoList != null) |
| 2787 | { | |
| 2788 | 0 | this.redoList.push(command); |
| 2789 | } | |
| 2790 | 0 | broadcastCommand(command, true); |
| 2791 | } | |
| 2792 | ||
| 2793 | /** | |
| 2794 | * Clear the command redo list. | |
| 2795 | */ | |
| 2796 | 1 | public void clearRedoList() |
| 2797 | { | |
| 2798 | 1 | if (this.redoList != null) |
| 2799 | { | |
| 2800 | 1 | this.redoList.clear(); |
| 2801 | } | |
| 2802 | } | |
| 2803 | ||
| 2804 | 53 | public void setHistoryList(Deque<CommandI> list) |
| 2805 | { | |
| 2806 | 53 | this.historyList = list; |
| 2807 | } | |
| 2808 | ||
| 2809 | 1277 | public Deque<CommandI> getHistoryList() |
| 2810 | { | |
| 2811 | 1277 | return this.historyList; |
| 2812 | } | |
| 2813 | ||
| 2814 | 53 | public void setRedoList(Deque<CommandI> list) |
| 2815 | { | |
| 2816 | 53 | this.redoList = list; |
| 2817 | } | |
| 2818 | ||
| 2819 | 1275 | public Deque<CommandI> getRedoList() |
| 2820 | { | |
| 2821 | 1275 | return this.redoList; |
| 2822 | } | |
| 2823 | ||
| 2824 | 1 | @Override |
| 2825 | public VamsasSource getVamsasSource() | |
| 2826 | { | |
| 2827 | 1 | return this; |
| 2828 | } | |
| 2829 | ||
| 2830 | 3595 | public SequenceAnnotationOrder getSortAnnotationsBy() |
| 2831 | { | |
| 2832 | 3595 | return sortAnnotationsBy; |
| 2833 | } | |
| 2834 | ||
| 2835 | 0 | public void setSortAnnotationsBy( |
| 2836 | SequenceAnnotationOrder sortAnnotationsBy) | |
| 2837 | { | |
| 2838 | 0 | this.sortAnnotationsBy = sortAnnotationsBy; |
| 2839 | } | |
| 2840 | ||
| 2841 | 3595 | public boolean isShowAutocalculatedAbove() |
| 2842 | { | |
| 2843 | 3595 | return showAutocalculatedAbove; |
| 2844 | } | |
| 2845 | ||
| 2846 | 452 | public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) |
| 2847 | { | |
| 2848 | 452 | this.showAutocalculatedAbove = showAutocalculatedAbove; |
| 2849 | } | |
| 2850 | ||
| 2851 | 3 | @Override |
| 2852 | public boolean isScaleProteinAsCdna() | |
| 2853 | { | |
| 2854 | 3 | return viewStyle.isScaleProteinAsCdna(); |
| 2855 | } | |
| 2856 | ||
| 2857 | 0 | @Override |
| 2858 | public void setScaleProteinAsCdna(boolean b) | |
| 2859 | { | |
| 2860 | 0 | viewStyle.setScaleProteinAsCdna(b); |
| 2861 | } | |
| 2862 | ||
| 2863 | 0 | @Override |
| 2864 | public boolean isProteinFontAsCdna() | |
| 2865 | { | |
| 2866 | 0 | return viewStyle.isProteinFontAsCdna(); |
| 2867 | } | |
| 2868 | ||
| 2869 | 0 | @Override |
| 2870 | public void setProteinFontAsCdna(boolean b) | |
| 2871 | { | |
| 2872 | 0 | viewStyle.setProteinFontAsCdna(b); |
| 2873 | } | |
| 2874 | ||
| 2875 | 85 | @Override |
| 2876 | public void setShowComplementFeatures(boolean b) | |
| 2877 | { | |
| 2878 | 85 | viewStyle.setShowComplementFeatures(b); |
| 2879 | } | |
| 2880 | ||
| 2881 | 400102 | @Override |
| 2882 | public boolean isShowComplementFeatures() | |
| 2883 | { | |
| 2884 | 400137 | return viewStyle.isShowComplementFeatures(); |
| 2885 | } | |
| 2886 | ||
| 2887 | 85 | @Override |
| 2888 | public void setShowComplementFeaturesOnTop(boolean b) | |
| 2889 | { | |
| 2890 | 85 | viewStyle.setShowComplementFeaturesOnTop(b); |
| 2891 | } | |
| 2892 | ||
| 2893 | 47 | @Override |
| 2894 | public boolean isShowComplementFeaturesOnTop() | |
| 2895 | { | |
| 2896 | 47 | return viewStyle.isShowComplementFeaturesOnTop(); |
| 2897 | } | |
| 2898 | ||
| 2899 | /** | |
| 2900 | * @return true if view should scroll to show the highlighted region of a | |
| 2901 | * sequence | |
| 2902 | * @return | |
| 2903 | */ | |
| 2904 | 52 | @Override |
| 2905 | public final boolean isFollowHighlight() | |
| 2906 | { | |
| 2907 | 52 | return followHighlight; |
| 2908 | } | |
| 2909 | ||
| 2910 | 85 | @Override |
| 2911 | public final void setFollowHighlight(boolean b) | |
| 2912 | { | |
| 2913 | 85 | this.followHighlight = b; |
| 2914 | } | |
| 2915 | ||
| 2916 | 30579 | @Override |
| 2917 | public ViewportRanges getRanges() | |
| 2918 | { | |
| 2919 | 30579 | return ranges; |
| 2920 | } | |
| 2921 | ||
| 2922 | /** | |
| 2923 | * Helper method to populate the SearchResults with the location in the | |
| 2924 | * complementary alignment to scroll to, in order to match this one. | |
| 2925 | * | |
| 2926 | * @param sr | |
| 2927 | * the SearchResults to add to | |
| 2928 | * @return the offset (below top of visible region) of the matched sequence | |
| 2929 | */ | |
| 2930 | 617 | protected int findComplementScrollTarget(SearchResultsI sr) |
| 2931 | { | |
| 2932 | 617 | final AlignViewportI complement = getCodingComplement(); |
| 2933 | 617 | if (complement == null || !complement.isFollowHighlight()) |
| 2934 | { | |
| 2935 | 613 | return 0; |
| 2936 | } | |
| 2937 | 4 | boolean iAmProtein = !getAlignment().isNucleotide(); |
| 2938 | 4 | AlignmentI proteinAlignment = iAmProtein ? getAlignment() |
| 2939 | : complement.getAlignment(); | |
| 2940 | 4 | if (proteinAlignment == null) |
| 2941 | { | |
| 2942 | 0 | return 0; |
| 2943 | } | |
| 2944 | 4 | final List<AlignedCodonFrame> mappings = proteinAlignment |
| 2945 | .getCodonFrames(); | |
| 2946 | ||
| 2947 | /* | |
| 2948 | * Heuristic: find the first mapped sequence (if any) with a non-gapped | |
| 2949 | * residue in the middle column of the visible region. Scroll the | |
| 2950 | * complementary alignment to line up the corresponding residue. | |
| 2951 | */ | |
| 2952 | 4 | int seqOffset = 0; |
| 2953 | 4 | SequenceI sequence = null; |
| 2954 | ||
| 2955 | /* | |
| 2956 | * locate 'middle' column (true middle if an odd number visible, left of | |
| 2957 | * middle if an even number visible) | |
| 2958 | */ | |
| 2959 | 4 | int middleColumn = ranges.getStartRes() |
| 2960 | + (ranges.getEndRes() - ranges.getStartRes()) / 2; | |
| 2961 | 4 | final HiddenSequences hiddenSequences = getAlignment() |
| 2962 | .getHiddenSequences(); | |
| 2963 | ||
| 2964 | /* | |
| 2965 | * searching to the bottom of the alignment gives smoother scrolling across | |
| 2966 | * all gapped visible regions | |
| 2967 | */ | |
| 2968 | 4 | int lastSeq = alignment.getHeight() - 1; |
| 2969 | 4 | List<AlignedCodonFrame> seqMappings = null; |
| 2970 | 4 | for (int seqNo = ranges |
| 2971 | 4 | .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) |
| 2972 | { | |
| 2973 | 4 | sequence = getAlignment().getSequenceAt(seqNo); |
| 2974 | 4 | if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) |
| 2975 | { | |
| 2976 | 0 | continue; |
| 2977 | } | |
| 2978 | 4 | if (Comparison.isGap(sequence.getCharAt(middleColumn))) |
| 2979 | { | |
| 2980 | 0 | continue; |
| 2981 | } | |
| 2982 | 4 | seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence, |
| 2983 | mappings, | |
| 2984 | getCodingComplement().getAlignment().getSequences()); | |
| 2985 | 4 | if (!seqMappings.isEmpty()) |
| 2986 | { | |
| 2987 | 4 | break; |
| 2988 | } | |
| 2989 | } | |
| 2990 | ||
| 2991 | 4 | if (sequence == null || seqMappings == null || seqMappings.isEmpty()) |
| 2992 | { | |
| 2993 | /* | |
| 2994 | * No ungapped mapped sequence in middle column - do nothing | |
| 2995 | */ | |
| 2996 | 0 | return 0; |
| 2997 | } | |
| 2998 | 4 | MappingUtils.addSearchResults(sr, sequence, |
| 2999 | sequence.findPosition(middleColumn), seqMappings); | |
| 3000 | 4 | return seqOffset; |
| 3001 | } | |
| 3002 | ||
| 3003 | /** | |
| 3004 | * synthesize a column selection if none exists so it covers the given | |
| 3005 | * selection group. if wholewidth is false, no column selection is made if the | |
| 3006 | * selection group covers the whole alignment width. | |
| 3007 | * | |
| 3008 | * @param sg | |
| 3009 | * @param wholewidth | |
| 3010 | */ | |
| 3011 | 0 | public void expandColSelection(SequenceGroup sg, boolean wholewidth) |
| 3012 | { | |
| 3013 | 0 | int sgs, sge; |
| 3014 | 0 | if (sg != null && (sgs = sg.getStartRes()) >= 0 |
| 3015 | && sg.getStartRes() <= (sge = sg.getEndRes()) | |
| 3016 | && !this.hasSelectedColumns()) | |
| 3017 | { | |
| 3018 | 0 | if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) |
| 3019 | { | |
| 3020 | // do nothing | |
| 3021 | 0 | return; |
| 3022 | } | |
| 3023 | 0 | if (colSel == null) |
| 3024 | { | |
| 3025 | 0 | colSel = new ColumnSelection(); |
| 3026 | } | |
| 3027 | 0 | for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) |
| 3028 | { | |
| 3029 | 0 | colSel.addElement(cspos); |
| 3030 | } | |
| 3031 | } | |
| 3032 | } | |
| 3033 | ||
| 3034 | /** | |
| 3035 | * hold status of current selection group - defined on alignment or not. | |
| 3036 | */ | |
| 3037 | private boolean selectionIsDefinedGroup = false; | |
| 3038 | ||
| 3039 | 0 | @Override |
| 3040 | public boolean isSelectionDefinedGroup() | |
| 3041 | { | |
| 3042 | 0 | if (selectionGroup == null) |
| 3043 | { | |
| 3044 | 0 | return false; |
| 3045 | } | |
| 3046 | 0 | if (isSelectionGroupChanged(true)) |
| 3047 | { | |
| 3048 | 0 | selectionIsDefinedGroup = false; |
| 3049 | 0 | List<SequenceGroup> gps = alignment.getGroups(); |
| 3050 | 0 | if (gps == null || gps.size() == 0) |
| 3051 | { | |
| 3052 | 0 | selectionIsDefinedGroup = false; |
| 3053 | } | |
| 3054 | else | |
| 3055 | { | |
| 3056 | 0 | selectionIsDefinedGroup = gps.contains(selectionGroup); |
| 3057 | } | |
| 3058 | } | |
| 3059 | 0 | return selectionGroup.isDefined() || selectionIsDefinedGroup; |
| 3060 | } | |
| 3061 | ||
| 3062 | /** | |
| 3063 | * null, or currently highlighted results on this view | |
| 3064 | */ | |
| 3065 | private SearchResultsI searchResults = null; | |
| 3066 | ||
| 3067 | protected TreeModel currentTree = null; | |
| 3068 | ||
| 3069 | 9478 | @Override |
| 3070 | public boolean hasSearchResults() | |
| 3071 | { | |
| 3072 | 9478 | return searchResults != null; |
| 3073 | } | |
| 3074 | ||
| 3075 | 8 | @Override |
| 3076 | public void setSearchResults(SearchResultsI results) | |
| 3077 | { | |
| 3078 | 8 | searchResults = results; |
| 3079 | } | |
| 3080 | ||
| 3081 | 50 | @Override |
| 3082 | public SearchResultsI getSearchResults() | |
| 3083 | { | |
| 3084 | 50 | return searchResults; |
| 3085 | } | |
| 3086 | ||
| 3087 | 3368 | @Override |
| 3088 | public ContactListI getContactList(AlignmentAnnotation _aa, int column) | |
| 3089 | { | |
| 3090 | 3368 | return alignment.getContactListFor(_aa, column); |
| 3091 | } | |
| 3092 | ||
| 3093 | 127 | @Override |
| 3094 | public ContactMatrixI getContactMatrix( | |
| 3095 | AlignmentAnnotation alignmentAnnotation) | |
| 3096 | { | |
| 3097 | 127 | return alignment.getContactMatrixFor(alignmentAnnotation); |
| 3098 | } | |
| 3099 | ||
| 3100 | /** | |
| 3101 | * get the consensus sequence as displayed under the PID consensus annotation | |
| 3102 | * row. | |
| 3103 | * | |
| 3104 | * @return consensus sequence as a new sequence object | |
| 3105 | */ | |
| 3106 | 1 | public SequenceI getConsensusSeq() |
| 3107 | { | |
| 3108 | 1 | if (consensus == null) |
| 3109 | { | |
| 3110 | 0 | updateConsensus(null); |
| 3111 | } | |
| 3112 | 1 | if (consensus == null) |
| 3113 | { | |
| 3114 | 0 | return null; |
| 3115 | } | |
| 3116 | 1 | StringBuffer seqs = new StringBuffer(); |
| 3117 | 4 | for (int i = 0; i < consensus.annotations.length; i++) |
| 3118 | { | |
| 3119 | 3 | Annotation annotation = consensus.annotations[i]; |
| 3120 | 3 | if (annotation != null) |
| 3121 | { | |
| 3122 | 3 | String description = annotation.description; |
| 3123 | 3 | if (description != null && description.startsWith("[")) |
| 3124 | { | |
| 3125 | // consensus is a tie - just pick the first one | |
| 3126 | 1 | seqs.append(description.charAt(1)); |
| 3127 | } | |
| 3128 | else | |
| 3129 | { | |
| 3130 | 2 | seqs.append(annotation.displayCharacter); |
| 3131 | } | |
| 3132 | } | |
| 3133 | } | |
| 3134 | ||
| 3135 | 1 | SequenceI sq = new Sequence("Consensus", seqs.toString()); |
| 3136 | 1 | sq.setDescription("Percentage Identity Consensus " |
| 3137 | 1 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3138 | 1 | return sq; |
| 3139 | } | |
| 3140 | ||
| 3141 | 0 | public SequenceI getSSConsensusSeq() |
| 3142 | { | |
| 3143 | 0 | if (secondaryStructureConsensus == null) |
| 3144 | { | |
| 3145 | 0 | updateSecondaryStructureConsensus(null); |
| 3146 | } | |
| 3147 | 0 | if (secondaryStructureConsensus == null) |
| 3148 | { | |
| 3149 | 0 | return null; |
| 3150 | } | |
| 3151 | 0 | StringBuffer seqs = new StringBuffer(); |
| 3152 | 0 | for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++) |
| 3153 | { | |
| 3154 | 0 | Annotation annotation = secondaryStructureConsensus.annotations[i]; |
| 3155 | 0 | if (annotation != null) |
| 3156 | { | |
| 3157 | 0 | String description = annotation.description; |
| 3158 | 0 | if (description != null && description.startsWith("[")) |
| 3159 | { | |
| 3160 | // consensus is a tie - just pick the first one | |
| 3161 | 0 | seqs.append(description.charAt(1)); |
| 3162 | } | |
| 3163 | else | |
| 3164 | { | |
| 3165 | 0 | seqs.append(annotation.displayCharacter); |
| 3166 | } | |
| 3167 | } | |
| 3168 | } | |
| 3169 | ||
| 3170 | 0 | SequenceI sq = new Sequence("Sec Str Consensus", seqs.toString()); |
| 3171 | 0 | sq.setDescription("Percentage Identity Sec Str Consensus " |
| 3172 | 0 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3173 | 0 | return sq; |
| 3174 | } | |
| 3175 | ||
| 3176 | 28 | @Override |
| 3177 | public void setCurrentTree(TreeModel tree) | |
| 3178 | { | |
| 3179 | 28 | currentTree = tree; |
| 3180 | } | |
| 3181 | ||
| 3182 | 50 | @Override |
| 3183 | public TreeModel getCurrentTree() | |
| 3184 | { | |
| 3185 | 50 | return currentTree; |
| 3186 | } | |
| 3187 | ||
| 3188 | 121 | @Override |
| 3189 | public AlignmentExportData getAlignExportData( | |
| 3190 | AlignExportSettingsI options) | |
| 3191 | { | |
| 3192 | 121 | AlignmentI alignmentToExport = null; |
| 3193 | 121 | String[] omitHidden = null; |
| 3194 | 121 | alignmentToExport = null; |
| 3195 | ||
| 3196 | 121 | if (hasHiddenColumns() && !options.isExportHiddenColumns()) |
| 3197 | { | |
| 3198 | 0 | omitHidden = getViewAsString(false, |
| 3199 | options.isExportHiddenSequences()); | |
| 3200 | } | |
| 3201 | ||
| 3202 | 121 | int[] alignmentStartEnd = new int[2]; |
| 3203 | 121 | if (hasHiddenRows() && options.isExportHiddenSequences()) |
| 3204 | { | |
| 3205 | 0 | alignmentToExport = getAlignment().getHiddenSequences() |
| 3206 | .getFullAlignment(); | |
| 3207 | } | |
| 3208 | else | |
| 3209 | { | |
| 3210 | 121 | alignmentToExport = getAlignment(); |
| 3211 | } | |
| 3212 | 121 | alignmentStartEnd = getAlignment().getHiddenColumns() |
| 3213 | .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); | |
| 3214 | 121 | AlignmentExportData ed = new AlignmentExportData(alignmentToExport, |
| 3215 | omitHidden, alignmentStartEnd); | |
| 3216 | 121 | return ed; |
| 3217 | } | |
| 3218 | ||
| 3219 | /** | |
| 3220 | * flag set to indicate if structure views might be out of sync with sequences | |
| 3221 | * in the alignment | |
| 3222 | */ | |
| 3223 | ||
| 3224 | private boolean needToUpdateStructureViews = false; | |
| 3225 | ||
| 3226 | 0 | @Override |
| 3227 | public boolean isUpdateStructures() | |
| 3228 | { | |
| 3229 | 0 | return needToUpdateStructureViews; |
| 3230 | } | |
| 3231 | ||
| 3232 | 0 | @Override |
| 3233 | public void setUpdateStructures(boolean update) | |
| 3234 | { | |
| 3235 | 0 | needToUpdateStructureViews = update; |
| 3236 | } | |
| 3237 | ||
| 3238 | 741 | @Override |
| 3239 | public boolean needToUpdateStructureViews() | |
| 3240 | { | |
| 3241 | 741 | boolean update = needToUpdateStructureViews; |
| 3242 | 741 | needToUpdateStructureViews = false; |
| 3243 | 741 | return update; |
| 3244 | } | |
| 3245 | ||
| 3246 | 0 | @Override |
| 3247 | public void addSequenceGroup(SequenceGroup sequenceGroup) | |
| 3248 | { | |
| 3249 | 0 | alignment.addGroup(sequenceGroup); |
| 3250 | ||
| 3251 | 0 | Color col = sequenceGroup.idColour; |
| 3252 | 0 | if (col != null) |
| 3253 | { | |
| 3254 | 0 | col = col.brighter(); |
| 3255 | ||
| 3256 | 0 | for (SequenceI sq : sequenceGroup.getSequences()) |
| 3257 | { | |
| 3258 | 0 | setSequenceColour(sq, col); |
| 3259 | } | |
| 3260 | } | |
| 3261 | ||
| 3262 | 0 | if (codingComplement != null) |
| 3263 | { | |
| 3264 | 0 | SequenceGroup mappedGroup = MappingUtils |
| 3265 | .mapSequenceGroup(sequenceGroup, this, codingComplement); | |
| 3266 | 0 | if (mappedGroup.getSequences().size() > 0) |
| 3267 | { | |
| 3268 | 0 | codingComplement.getAlignment().addGroup(mappedGroup); |
| 3269 | ||
| 3270 | 0 | if (col != null) |
| 3271 | { | |
| 3272 | 0 | for (SequenceI seq : mappedGroup.getSequences()) |
| 3273 | { | |
| 3274 | 0 | codingComplement.setSequenceColour(seq, col); |
| 3275 | } | |
| 3276 | } | |
| 3277 | } | |
| 3278 | // propagate the structure view update flag according to our own setting | |
| 3279 | 0 | codingComplement.setUpdateStructures(needToUpdateStructureViews); |
| 3280 | } | |
| 3281 | } | |
| 3282 | ||
| 3283 | 34 | @Override |
| 3284 | public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly) | |
| 3285 | { | |
| 3286 | 34 | int start = 0; |
| 3287 | 34 | int end = 0; |
| 3288 | 34 | if (selectedRegionOnly && selectionGroup != null) |
| 3289 | { | |
| 3290 | 4 | start = selectionGroup.getStartRes(); |
| 3291 | 4 | end = selectionGroup.getEndRes() + 1; |
| 3292 | } | |
| 3293 | else | |
| 3294 | { | |
| 3295 | 30 | end = alignment.getWidth(); |
| 3296 | } | |
| 3297 | 34 | return (alignment.getHiddenColumns().getVisContigsIterator(start, end, |
| 3298 | false)); | |
| 3299 | } | |
| 3300 | ||
| 3301 | 133 | public void setSavedUpToDate(boolean s) |
| 3302 | { | |
| 3303 | 133 | setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES); |
| 3304 | } | |
| 3305 | ||
| 3306 | 452 | public void setSavedUpToDate(boolean s, QuitHandler.Message m) |
| 3307 | { | |
| 3308 | 452 | Console.debug( |
| 3309 | "Setting " + this.getViewId() + " setSavedUpToDate to " + s); | |
| 3310 | 452 | savedUpToDate = s; |
| 3311 | 452 | QuitHandler.setMessage(m); |
| 3312 | } | |
| 3313 | ||
| 3314 | 4 | public boolean savedUpToDate() |
| 3315 | { | |
| 3316 | 4 | Console.debug("Returning " + this.getViewId() + " savedUpToDate value: " |
| 3317 | + savedUpToDate); | |
| 3318 | 4 | return savedUpToDate; |
| 3319 | } | |
| 3320 | } |