Coverage Report
File AlignmentViewport.java
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21% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignmentViewport | 92 | 811 | 486 |
Contributing tests
This file is covered by 312 tests.
.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.viewmodel; | |
| 22 | ||
| 23 | import java.awt.Color; | |
| 24 | import java.beans.PropertyChangeSupport; | |
| 25 | import java.util.ArrayDeque; | |
| 26 | import java.util.ArrayList; | |
| 27 | import java.util.BitSet; | |
| 28 | import java.util.Deque; | |
| 29 | import java.util.HashMap; | |
| 30 | import java.util.Hashtable; | |
| 31 | import java.util.Iterator; | |
| 32 | import java.util.List; | |
| 33 | import java.util.Map; | |
| 34 | ||
| 35 | import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; | |
| 36 | import jalview.analysis.AlignmentUtils; | |
| 37 | import jalview.analysis.Conservation; | |
| 38 | import jalview.analysis.TreeModel; | |
| 39 | import jalview.api.AlignCalcManagerI; | |
| 40 | import jalview.api.AlignCalcWorkerI; | |
| 41 | import jalview.api.AlignExportSettingsI; | |
| 42 | import jalview.api.AlignViewportI; | |
| 43 | import jalview.api.AlignmentViewPanel; | |
| 44 | import jalview.api.FeaturesDisplayedI; | |
| 45 | import jalview.api.ViewStyleI; | |
| 46 | import jalview.bin.Console; | |
| 47 | import jalview.commands.CommandI; | |
| 48 | import jalview.datamodel.AlignedCodonFrame; | |
| 49 | import jalview.datamodel.AlignmentAnnotation; | |
| 50 | import jalview.datamodel.AlignmentExportData; | |
| 51 | import jalview.datamodel.AlignmentI; | |
| 52 | import jalview.datamodel.AlignmentView; | |
| 53 | import jalview.datamodel.Annotation; | |
| 54 | import jalview.datamodel.ColumnSelection; | |
| 55 | import jalview.datamodel.ContactListI; | |
| 56 | import jalview.datamodel.ContactMatrixI; | |
| 57 | import jalview.datamodel.HiddenColumns; | |
| 58 | import jalview.datamodel.HiddenSequences; | |
| 59 | import jalview.datamodel.ProfilesI; | |
| 60 | import jalview.datamodel.SearchResultsI; | |
| 61 | import jalview.datamodel.Sequence; | |
| 62 | import jalview.datamodel.SequenceCollectionI; | |
| 63 | import jalview.datamodel.SequenceGroup; | |
| 64 | import jalview.datamodel.SequenceI; | |
| 65 | import jalview.gui.QuitHandler; | |
| 66 | import jalview.project.Jalview2XML; | |
| 67 | import jalview.renderer.ResidueShader; | |
| 68 | import jalview.renderer.ResidueShaderI; | |
| 69 | import jalview.schemes.ColourSchemeI; | |
| 70 | import jalview.structure.CommandListener; | |
| 71 | import jalview.structure.StructureSelectionManager; | |
| 72 | import jalview.structure.VamsasSource; | |
| 73 | import jalview.util.Comparison; | |
| 74 | import jalview.util.Constants; | |
| 75 | import jalview.util.MapList; | |
| 76 | import jalview.util.MappingUtils; | |
| 77 | import jalview.util.MessageManager; | |
| 78 | import jalview.viewmodel.styles.ViewStyle; | |
| 79 | import jalview.workers.AlignCalcManager; | |
| 80 | import jalview.workers.ComplementConsensusThread; | |
| 81 | import jalview.workers.ConsensusThread; | |
| 82 | import jalview.workers.SecondaryStructureConsensusThread; | |
| 83 | import jalview.workers.StrucConsensusThread; | |
| 84 | ||
| 85 | /** | |
| 86 | * base class holding visualization and analysis attributes and common logic for | |
| 87 | * an active alignment view displayed in the GUI | |
| 88 | * | |
| 89 | * @author jimp | |
| 90 | * | |
| 91 | */ | |
| 92 | public abstract class AlignmentViewport | |
| 93 | implements AlignViewportI, CommandListener, VamsasSource | |
| 94 | { | |
| 95 | protected ViewportRanges ranges; | |
| 96 | ||
| 97 | protected ViewStyleI viewStyle = new ViewStyle(); | |
| 98 | ||
| 99 | /** | |
| 100 | * A viewport that hosts the cDna view of this (protein), or vice versa (if | |
| 101 | * set). | |
| 102 | */ | |
| 103 | AlignViewportI codingComplement = null; | |
| 104 | ||
| 105 | FeaturesDisplayedI featuresDisplayed = null; | |
| 106 | ||
| 107 | protected Deque<CommandI> historyList = new ArrayDeque<>(); | |
| 108 | ||
| 109 | protected Deque<CommandI> redoList = new ArrayDeque<>(); | |
| 110 | ||
| 111 | /** | |
| 112 | * used to determine if quit should be confirmed | |
| 113 | */ | |
| 114 | private boolean savedUpToDate = false; | |
| 115 | ||
| 116 | /** | |
| 117 | * alignment displayed in the viewport. Please use get/setter | |
| 118 | */ | |
| 119 | protected AlignmentI alignment; | |
| 120 | ||
| 121 | 531 |  public AlignmentViewport(AlignmentI al) |
| 122 | { | |
| 123 | 531 | setAlignment(al); |
| 124 | 531 | ranges = new ViewportRanges(al); |
| 125 | } | |
| 126 | ||
| 127 | /** | |
| 128 | * @param name | |
| 129 | * @see jalview.api.ViewStyleI#setFontName(java.lang.String) | |
| 130 | */ | |
| 131 | 0 | @Override |
| 132 | public void setFontName(String name) | |
| 133 | { | |
| 134 | 0 | viewStyle.setFontName(name); |
| 135 | } | |
| 136 | ||
| 137 | /** | |
| 138 | * @param style | |
| 139 | * @see jalview.api.ViewStyleI#setFontStyle(int) | |
| 140 | */ | |
| 141 | 0 | @Override |
| 142 | public void setFontStyle(int style) | |
| 143 | { | |
| 144 | 0 | viewStyle.setFontStyle(style); |
| 145 | } | |
| 146 | ||
| 147 | /** | |
| 148 | * @param size | |
| 149 | * @see jalview.api.ViewStyleI#setFontSize(int) | |
| 150 | */ | |
| 151 | 0 | @Override |
| 152 | public void setFontSize(int size) | |
| 153 | { | |
| 154 | 0 | viewStyle.setFontSize(size); |
| 155 | } | |
| 156 | ||
| 157 | /** | |
| 158 | * @return | |
| 159 | * @see jalview.api.ViewStyleI#getFontStyle() | |
| 160 | */ | |
| 161 | 0 | @Override |
| 162 | public int getFontStyle() | |
| 163 | { | |
| 164 | 0 | return viewStyle.getFontStyle(); |
| 165 | } | |
| 166 | ||
| 167 | /** | |
| 168 | * @return | |
| 169 | * @see jalview.api.ViewStyleI#getFontName() | |
| 170 | */ | |
| 171 | 0 | @Override |
| 172 | public String getFontName() | |
| 173 | { | |
| 174 | 0 | return viewStyle.getFontName(); |
| 175 | } | |
| 176 | ||
| 177 | /** | |
| 178 | * @return | |
| 179 | * @see jalview.api.ViewStyleI#getFontSize() | |
| 180 | */ | |
| 181 | 0 | @Override |
| 182 | public int getFontSize() | |
| 183 | { | |
| 184 | 0 | return viewStyle.getFontSize(); |
| 185 | } | |
| 186 | ||
| 187 | /** | |
| 188 | * @param upperCasebold | |
| 189 | * @see jalview.api.ViewStyleI#setUpperCasebold(boolean) | |
| 190 | */ | |
| 191 | 0 | @Override |
| 192 | public void setUpperCasebold(boolean upperCasebold) | |
| 193 | { | |
| 194 | 0 | viewStyle.setUpperCasebold(upperCasebold); |
| 195 | } | |
| 196 | ||
| 197 | /** | |
| 198 | * @return | |
| 199 | * @see jalview.api.ViewStyleI#isUpperCasebold() | |
| 200 | */ | |
| 201 | 0 | @Override |
| 202 | public boolean isUpperCasebold() | |
| 203 | { | |
| 204 | 0 | return viewStyle.isUpperCasebold(); |
| 205 | } | |
| 206 | ||
| 207 | /** | |
| 208 | * @return | |
| 209 | * @see jalview.api.ViewStyleI#isSeqNameItalics() | |
| 210 | */ | |
| 211 | 3109 | @Override |
| 212 | public boolean isSeqNameItalics() | |
| 213 | { | |
| 214 | 3109 | return viewStyle.isSeqNameItalics(); |
| 215 | } | |
| 216 | ||
| 217 | /** | |
| 218 | * @param colourByReferenceSeq | |
| 219 | * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean) | |
| 220 | */ | |
| 221 | 10 | @Override |
| 222 | public void setColourByReferenceSeq(boolean colourByReferenceSeq) | |
| 223 | { | |
| 224 | 10 | viewStyle.setColourByReferenceSeq(colourByReferenceSeq); |
| 225 | } | |
| 226 | ||
| 227 | /** | |
| 228 | * @param b | |
| 229 | * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean) | |
| 230 | */ | |
| 231 | 724 | @Override |
| 232 | public void setColourAppliesToAllGroups(boolean b) | |
| 233 | { | |
| 234 | 724 | viewStyle.setColourAppliesToAllGroups(b); |
| 235 | } | |
| 236 | ||
| 237 | /** | |
| 238 | * @return | |
| 239 | * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups() | |
| 240 | */ | |
| 241 | 1004 | @Override |
| 242 | public boolean getColourAppliesToAllGroups() | |
| 243 | { | |
| 244 | 1004 | return viewStyle.getColourAppliesToAllGroups(); |
| 245 | } | |
| 246 | ||
| 247 | /** | |
| 248 | * @return | |
| 249 | * @see jalview.api.ViewStyleI#getAbovePIDThreshold() | |
| 250 | */ | |
| 251 | 911 | @Override |
| 252 | public boolean getAbovePIDThreshold() | |
| 253 | { | |
| 254 | 911 | return viewStyle.getAbovePIDThreshold(); |
| 255 | } | |
| 256 | ||
| 257 | 911 | @Override |
| 258 | public boolean getByConsensusSecondaryStructureSelected() | |
| 259 | { | |
| 260 | 911 | return viewStyle.getByConsensusSecondaryStructureSelected(); |
| 261 | } | |
| 262 | ||
| 263 | 89 | public void setShowStructureProvider(boolean b) |
| 264 | { | |
| 265 | 89 | viewStyle.setShowStructureProvider(b); |
| 266 | } | |
| 267 | ||
| 268 | 6641 | public boolean isShowStructureProvider() |
| 269 | { | |
| 270 | 6641 | return viewStyle.isShowStructureProvider(); |
| 271 | } | |
| 272 | ||
| 273 | /** | |
| 274 | * @param inc | |
| 275 | * @see jalview.api.ViewStyleI#setIncrement(int) | |
| 276 | */ | |
| 277 | 89 | @Override |
| 278 | public void setIncrement(int inc) | |
| 279 | { | |
| 280 | 89 | viewStyle.setIncrement(inc); |
| 281 | } | |
| 282 | ||
| 283 | /** | |
| 284 | * @return | |
| 285 | * @see jalview.api.ViewStyleI#getIncrement() | |
| 286 | */ | |
| 287 | 0 | @Override |
| 288 | public int getIncrement() | |
| 289 | { | |
| 290 | 0 | return viewStyle.getIncrement(); |
| 291 | } | |
| 292 | ||
| 293 | /** | |
| 294 | * @param inc | |
| 295 | * @see jalview.api.ViewStyleI#setConsensusSecondaryStructureThreshold(int) | |
| 296 | */ | |
| 297 | 89 | @Override |
| 298 | public void setConsensusSecondaryStructureThreshold(int val) | |
| 299 | { | |
| 300 | 89 | viewStyle.setConsensusSecondaryStructureThreshold(val); |
| 301 | } | |
| 302 | ||
| 303 | /** | |
| 304 | * @return | |
| 305 | * @see jalview.api.ViewStyleI#getConsensusSecondaryStructureThreshold() | |
| 306 | */ | |
| 307 | 0 | @Override |
| 308 | public int getConsensusSecondaryStructureThreshold() | |
| 309 | { | |
| 310 | 0 | return viewStyle.getConsensusSecondaryStructureThreshold(); |
| 311 | } | |
| 312 | ||
| 313 | /** | |
| 314 | * @param b | |
| 315 | * @see jalview.api.ViewStyleI#setConservationSelected(boolean) | |
| 316 | */ | |
| 317 | 97 | @Override |
| 318 | public void setConservationSelected(boolean b) | |
| 319 | { | |
| 320 | 97 | viewStyle.setConservationSelected(b); |
| 321 | } | |
| 322 | ||
| 323 | /** | |
| 324 | * @param show | |
| 325 | * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean) | |
| 326 | */ | |
| 327 | 0 | @Override |
| 328 | public void setShowHiddenMarkers(boolean show) | |
| 329 | { | |
| 330 | 0 | viewStyle.setShowHiddenMarkers(show); |
| 331 | } | |
| 332 | ||
| 333 | /** | |
| 334 | * @return | |
| 335 | * @see jalview.api.ViewStyleI#getShowHiddenMarkers() | |
| 336 | */ | |
| 337 | 5515 | @Override |
| 338 | public boolean getShowHiddenMarkers() | |
| 339 | { | |
| 340 | 5515 | return viewStyle.getShowHiddenMarkers(); |
| 341 | } | |
| 342 | ||
| 343 | /** | |
| 344 | * @param b | |
| 345 | * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean) | |
| 346 | */ | |
| 347 | 9 | @Override |
| 348 | public void setScaleRightWrapped(boolean b) | |
| 349 | { | |
| 350 | 9 | viewStyle.setScaleRightWrapped(b); |
| 351 | } | |
| 352 | ||
| 353 | /** | |
| 354 | * @param b | |
| 355 | * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean) | |
| 356 | */ | |
| 357 | 11 | @Override |
| 358 | public void setScaleLeftWrapped(boolean b) | |
| 359 | { | |
| 360 | 11 | viewStyle.setScaleLeftWrapped(b); |
| 361 | } | |
| 362 | ||
| 363 | /** | |
| 364 | * @param b | |
| 365 | * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean) | |
| 366 | */ | |
| 367 | 9 | @Override |
| 368 | public void setScaleAboveWrapped(boolean b) | |
| 369 | { | |
| 370 | 9 | viewStyle.setScaleAboveWrapped(b); |
| 371 | } | |
| 372 | ||
| 373 | /** | |
| 374 | * @return | |
| 375 | * @see jalview.api.ViewStyleI#getScaleLeftWrapped() | |
| 376 | */ | |
| 377 | 1273 | @Override |
| 378 | public boolean getScaleLeftWrapped() | |
| 379 | { | |
| 380 | 1273 | return viewStyle.getScaleLeftWrapped(); |
| 381 | } | |
| 382 | ||
| 383 | /** | |
| 384 | * @return | |
| 385 | * @see jalview.api.ViewStyleI#getScaleAboveWrapped() | |
| 386 | */ | |
| 387 | 877 | @Override |
| 388 | public boolean getScaleAboveWrapped() | |
| 389 | { | |
| 390 | 877 | return viewStyle.getScaleAboveWrapped(); |
| 391 | } | |
| 392 | ||
| 393 | /** | |
| 394 | * @return | |
| 395 | * @see jalview.api.ViewStyleI#getScaleRightWrapped() | |
| 396 | */ | |
| 397 | 2064 | @Override |
| 398 | public boolean getScaleRightWrapped() | |
| 399 | { | |
| 400 | 2064 | return viewStyle.getScaleRightWrapped(); |
| 401 | } | |
| 402 | ||
| 403 | /** | |
| 404 | * @param b | |
| 405 | * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean) | |
| 406 | */ | |
| 407 | 98 | @Override |
| 408 | public void setAbovePIDThreshold(boolean b) | |
| 409 | { | |
| 410 | 98 | viewStyle.setAbovePIDThreshold(b); |
| 411 | } | |
| 412 | ||
| 413 | 89 | @Override |
| 414 | public void setByConsensusSecondaryStructureSelected(boolean b) | |
| 415 | { | |
| 416 | 89 | viewStyle.setByConsensusSecondaryStructureSelected(b); |
| 417 | } | |
| 418 | ||
| 419 | /** | |
| 420 | * @param thresh | |
| 421 | * @see jalview.api.ViewStyleI#setThreshold(int) | |
| 422 | */ | |
| 423 | 110 | @Override |
| 424 | public void setThreshold(int thresh) | |
| 425 | { | |
| 426 | 110 | viewStyle.setThreshold(thresh); |
| 427 | } | |
| 428 | ||
| 429 | /** | |
| 430 | * @return | |
| 431 | * @see jalview.api.ViewStyleI#getThreshold() | |
| 432 | */ | |
| 433 | 0 | @Override |
| 434 | public int getThreshold() | |
| 435 | { | |
| 436 | 0 | return viewStyle.getThreshold(); |
| 437 | } | |
| 438 | ||
| 439 | /** | |
| 440 | * @return | |
| 441 | * @see jalview.api.ViewStyleI#getShowJVSuffix() | |
| 442 | */ | |
| 443 | 45878 | @Override |
| 444 | public boolean getShowJVSuffix() | |
| 445 | { | |
| 446 | 45878 | return viewStyle.getShowJVSuffix(); |
| 447 | } | |
| 448 | ||
| 449 | /** | |
| 450 | * @param b | |
| 451 | * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean) | |
| 452 | */ | |
| 453 | 90 | @Override |
| 454 | public void setShowJVSuffix(boolean b) | |
| 455 | { | |
| 456 | 90 | viewStyle.setShowJVSuffix(b); |
| 457 | } | |
| 458 | ||
| 459 | /** | |
| 460 | * @param state | |
| 461 | * @see jalview.api.ViewStyleI#setWrapAlignment(boolean) | |
| 462 | */ | |
| 463 | 101 | @Override |
| 464 | public void setWrapAlignment(boolean state) | |
| 465 | { | |
| 466 | 101 | viewStyle.setWrapAlignment(state); |
| 467 | 101 | ranges.setWrappedMode(state); |
| 468 | } | |
| 469 | ||
| 470 | /** | |
| 471 | * @param state | |
| 472 | * @see jalview.api.ViewStyleI#setShowText(boolean) | |
| 473 | */ | |
| 474 | 89 | @Override |
| 475 | public void setShowText(boolean state) | |
| 476 | { | |
| 477 | 89 | viewStyle.setShowText(state); |
| 478 | } | |
| 479 | ||
| 480 | /** | |
| 481 | * @param state | |
| 482 | * @see jalview.api.ViewStyleI#setRenderGaps(boolean) | |
| 483 | */ | |
| 484 | 89 | @Override |
| 485 | public void setRenderGaps(boolean state) | |
| 486 | { | |
| 487 | 89 | viewStyle.setRenderGaps(state); |
| 488 | } | |
| 489 | ||
| 490 | /** | |
| 491 | * @return | |
| 492 | * @see jalview.api.ViewStyleI#getColourText() | |
| 493 | */ | |
| 494 | 468903 | @Override |
| 495 | public boolean getColourText() | |
| 496 | { | |
| 497 | 468903 | return viewStyle.getColourText(); |
| 498 | } | |
| 499 | ||
| 500 | /** | |
| 501 | * @param state | |
| 502 | * @see jalview.api.ViewStyleI#setColourText(boolean) | |
| 503 | */ | |
| 504 | 89 | @Override |
| 505 | public void setColourText(boolean state) | |
| 506 | { | |
| 507 | 89 | viewStyle.setColourText(state); |
| 508 | } | |
| 509 | ||
| 510 | /** | |
| 511 | * @return | |
| 512 | * @see jalview.api.ViewStyleI#getWrapAlignment() | |
| 513 | */ | |
| 514 | 32319 | @Override |
| 515 | public boolean getWrapAlignment() | |
| 516 | { | |
| 517 | 32319 | return viewStyle.getWrapAlignment(); |
| 518 | } | |
| 519 | ||
| 520 | /** | |
| 521 | * @return | |
| 522 | * @see jalview.api.ViewStyleI#getShowText() | |
| 523 | */ | |
| 524 | 469606 | @Override |
| 525 | public boolean getShowText() | |
| 526 | { | |
| 527 | 469606 | return viewStyle.getShowText(); |
| 528 | } | |
| 529 | ||
| 530 | /** | |
| 531 | * @return | |
| 532 | * @see jalview.api.ViewStyleI#getWrappedWidth() | |
| 533 | */ | |
| 534 | 2 | @Override |
| 535 | public int getWrappedWidth() | |
| 536 | { | |
| 537 | 2 | return viewStyle.getWrappedWidth(); |
| 538 | } | |
| 539 | ||
| 540 | /** | |
| 541 | * @param w | |
| 542 | * @see jalview.api.ViewStyleI#setWrappedWidth(int) | |
| 543 | */ | |
| 544 | 806 | @Override |
| 545 | public void setWrappedWidth(int w) | |
| 546 | { | |
| 547 | 806 | viewStyle.setWrappedWidth(w); |
| 548 | } | |
| 549 | ||
| 550 | /** | |
| 551 | * @return | |
| 552 | * @see jalview.api.ViewStyleI#getCharHeight() | |
| 553 | */ | |
| 554 | 112562 | @Override |
| 555 | public int getCharHeight() | |
| 556 | { | |
| 557 | 112562 | return viewStyle.getCharHeight(); |
| 558 | } | |
| 559 | ||
| 560 | /** | |
| 561 | * @param h | |
| 562 | * @see jalview.api.ViewStyleI#setCharHeight(int) | |
| 563 | */ | |
| 564 | 623 | @Override |
| 565 | public void setCharHeight(int h) | |
| 566 | { | |
| 567 | 623 | viewStyle.setCharHeight(h); |
| 568 | } | |
| 569 | ||
| 570 | /** | |
| 571 | * @return | |
| 572 | * @see jalview.api.ViewStyleI#getCharWidth() | |
| 573 | */ | |
| 574 | 1463142 | @Override |
| 575 | public int getCharWidth() | |
| 576 | { | |
| 577 | 1463142 | return viewStyle.getCharWidth(); |
| 578 | } | |
| 579 | ||
| 580 | /** | |
| 581 | * @param w | |
| 582 | * @see jalview.api.ViewStyleI#setCharWidth(int) | |
| 583 | */ | |
| 584 | 626 | @Override |
| 585 | public void setCharWidth(int w) | |
| 586 | { | |
| 587 | 626 | viewStyle.setCharWidth(w); |
| 588 | } | |
| 589 | ||
| 590 | /** | |
| 591 | * @return | |
| 592 | * @see jalview.api.ViewStyleI#getShowBoxes() | |
| 593 | */ | |
| 594 | 530349 | @Override |
| 595 | public boolean getShowBoxes() | |
| 596 | { | |
| 597 | 530353 | return viewStyle.getShowBoxes(); |
| 598 | } | |
| 599 | ||
| 600 | /** | |
| 601 | * @return | |
| 602 | * @see jalview.api.ViewStyleI#getShowUnconserved() | |
| 603 | */ | |
| 604 | 467479 | @Override |
| 605 | public boolean getShowUnconserved() | |
| 606 | { | |
| 607 | 467479 | return viewStyle.getShowUnconserved(); |
| 608 | } | |
| 609 | ||
| 610 | /** | |
| 611 | * @param showunconserved | |
| 612 | * @see jalview.api.ViewStyleI#setShowUnconserved(boolean) | |
| 613 | */ | |
| 614 | 89 | @Override |
| 615 | public void setShowUnconserved(boolean showunconserved) | |
| 616 | { | |
| 617 | 89 | viewStyle.setShowUnconserved(showunconserved); |
| 618 | } | |
| 619 | ||
| 620 | /** | |
| 621 | * @param default1 | |
| 622 | * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean) | |
| 623 | */ | |
| 624 | 0 | @Override |
| 625 | public void setSeqNameItalics(boolean default1) | |
| 626 | { | |
| 627 | 0 | viewStyle.setSeqNameItalics(default1); |
| 628 | } | |
| 629 | ||
| 630 | 243447 | @Override |
| 631 | public AlignmentI getAlignment() | |
| 632 | { | |
| 633 | 243450 | return alignment; |
| 634 | } | |
| 635 | ||
| 636 | 0 | @Override |
| 637 | public char getGapCharacter() | |
| 638 | { | |
| 639 | 0 | return alignment.getGapCharacter(); |
| 640 | } | |
| 641 | ||
| 642 | protected String sequenceSetID; | |
| 643 | ||
| 644 | /** | |
| 645 | * probably unused indicator that view is of a dataset rather than an | |
| 646 | * alignment | |
| 647 | */ | |
| 648 | protected boolean isDataset = false; | |
| 649 | ||
| 650 | 0 | public void setDataset(boolean b) |
| 651 | { | |
| 652 | 0 | isDataset = b; |
| 653 | } | |
| 654 | ||
| 655 | 501 | public boolean isDataset() |
| 656 | { | |
| 657 | 501 | return isDataset; |
| 658 | } | |
| 659 | ||
| 660 | private Map<SequenceI, SequenceCollectionI> hiddenRepSequences; | |
| 661 | ||
| 662 | protected ColumnSelection colSel = new ColumnSelection(); | |
| 663 | ||
| 664 | public boolean autoCalculateConsensus = true; | |
| 665 | ||
| 666 | protected boolean autoCalculateStrucConsensus = true; | |
| 667 | ||
| 668 | protected boolean ignoreGapsInConsensusCalculation = false; | |
| 669 | ||
| 670 | protected ResidueShaderI residueShading = new ResidueShader(); | |
| 671 | ||
| 672 | 285 | @Override |
| 673 | public void setGlobalColourScheme(ColourSchemeI cs) | |
| 674 | { | |
| 675 | // TODO: logic refactored from AlignFrame changeColour - | |
| 676 | // TODO: autorecalc stuff should be changed to rely on the worker system | |
| 677 | // check to see if we should implement a changeColour(cs) method rather than | |
| 678 | // put the logic in here | |
| 679 | // - means that caller decides if they want to just modify state and defer | |
| 680 | // calculation till later or to do all calculations in thread. | |
| 681 | // via changecolour | |
| 682 | ||
| 683 | /* | |
| 684 | * only instantiate alignment colouring once, thereafter update it; | |
| 685 | * this means that any conservation or PID threshold settings | |
| 686 | * persist when the alignment colour scheme is changed | |
| 687 | */ | |
| 688 | 285 | if (residueShading == null) |
| 689 | { | |
| 690 | 0 | residueShading = new ResidueShader(viewStyle); |
| 691 | } | |
| 692 | 285 | residueShading.setColourScheme(cs); |
| 693 | ||
| 694 | // TODO: do threshold and increment belong in ViewStyle or ResidueShader? | |
| 695 | // ...problem: groups need these, but do not currently have a ViewStyle | |
| 696 | ||
| 697 | 285 | if (cs != null) |
| 698 | { | |
| 699 | 88 | if (getConservationSelected()) |
| 700 | { | |
| 701 | 15 | residueShading.setConservation(hconservation); |
| 702 | } | |
| 703 | /* | |
| 704 | * reset conservation flag in case just set to false if | |
| 705 | * Conservation was null (calculation still in progress) | |
| 706 | */ | |
| 707 | 88 | residueShading.setConservationApplied(getConservationSelected()); |
| 708 | 88 | residueShading.alignmentChanged(alignment, hiddenRepSequences); |
| 709 | } | |
| 710 | ||
| 711 | /* | |
| 712 | * if 'apply colour to all groups' is selected... do so | |
| 713 | * (but don't transfer any colour threshold settings to groups) | |
| 714 | */ | |
| 715 | 285 | if (getColourAppliesToAllGroups()) |
| 716 | { | |
| 717 | 89 | for (SequenceGroup sg : getAlignment().getGroups()) |
| 718 | { | |
| 719 | /* | |
| 720 | * retain any colour thresholds per group while | |
| 721 | * changing choice of colour scheme (JAL-2386) | |
| 722 | */ | |
| 723 | 9 | sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg)); |
| 724 | 9 | if (cs != null) |
| 725 | { | |
| 726 | 8 | sg.getGroupColourScheme().alignmentChanged(sg, |
| 727 | hiddenRepSequences); | |
| 728 | } | |
| 729 | } | |
| 730 | } | |
| 731 | } | |
| 732 | ||
| 733 | 1463 | @Override |
| 734 | public ColourSchemeI getGlobalColourScheme() | |
| 735 | { | |
| 736 | 1463 | return residueShading == null ? null : residueShading.getColourScheme(); |
| 737 | } | |
| 738 | ||
| 739 | 536646 | @Override |
| 740 | public ResidueShaderI getResidueShading() | |
| 741 | { | |
| 742 | 536648 | return residueShading; |
| 743 | } | |
| 744 | ||
| 745 | protected AlignmentAnnotation consensus; | |
| 746 | ||
| 747 | protected List<AlignmentAnnotation> secondaryStructureConsensus; | |
| 748 | ||
| 749 | protected AlignmentAnnotation complementConsensus; | |
| 750 | ||
| 751 | protected AlignmentAnnotation gapcounts; | |
| 752 | ||
| 753 | protected AlignmentAnnotation strucConsensus; | |
| 754 | ||
| 755 | protected AlignmentAnnotation conservation; | |
| 756 | ||
| 757 | protected AlignmentAnnotation quality; | |
| 758 | ||
| 759 | protected AlignmentAnnotation[] groupConsensus; | |
| 760 | ||
| 761 | protected AlignmentAnnotation[] groupSSConsensus; | |
| 762 | ||
| 763 | protected AlignmentAnnotation[] groupConservation; | |
| 764 | ||
| 765 | /** | |
| 766 | * results of alignment consensus analysis for visible portion of view | |
| 767 | */ | |
| 768 | protected ProfilesI hconsensus = null; | |
| 769 | ||
| 770 | protected Map<String, ProfilesI> hSSConsensusProfileMap = null; | |
| 771 | ||
| 772 | ||
| 773 | /** | |
| 774 | * results of cDNA complement consensus visible portion of view | |
| 775 | */ | |
| 776 | protected Hashtable<String, Object>[] hcomplementConsensus = null; | |
| 777 | ||
| 778 | /** | |
| 779 | * results of secondary structure base pair consensus for visible portion of | |
| 780 | * view | |
| 781 | */ | |
| 782 | protected Hashtable<String, Object>[] hStrucConsensus = null; | |
| 783 | ||
| 784 | protected Conservation hconservation = null; | |
| 785 | ||
| 786 | 1388 | @Override |
| 787 | public void setConservation(Conservation cons) | |
| 788 | { | |
| 789 | 1388 | hconservation = cons; |
| 790 | } | |
| 791 | ||
| 792 | 2645 | @Override |
| 793 | public List<String> getSecondaryStructureSources() | |
| 794 | { | |
| 795 | 2645 | return viewStyle.getSecondaryStructureSources(); |
| 796 | } | |
| 797 | ||
| 798 | 3508 | @Override |
| 799 | public void setSecondaryStructureSources( | |
| 800 | List<String> secondaryStructureSources) | |
| 801 | { | |
| 802 | 3508 | viewStyle.setSecondaryStructureSources(secondaryStructureSources); |
| 803 | } | |
| 804 | ||
| 805 | 531 | protected void setSecondaryStructureSources(AlignmentAnnotation[] aa) |
| 806 | { | |
| 807 | 531 | List<String> sources = null; |
| 808 | ||
| 809 | 531 | if (aa != null) |
| 810 | { | |
| 811 | 439 | sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa); |
| 812 | 439 | if (sources != null) |
| 813 | { | |
| 814 | 439 | sources.add(0, Constants.SS_ALL_PROVIDERS); |
| 815 | 439 | viewStyle.setSecondaryStructureSources(sources); |
| 816 | } | |
| 817 | } | |
| 818 | } | |
| 819 | ||
| 820 | /** | |
| 821 | * percentage gaps allowed in a column before all amino acid properties should | |
| 822 | * be considered unconserved | |
| 823 | */ | |
| 824 | int ConsPercGaps = 25; // JBPNote : This should be a scalable property! | |
| 825 | ||
| 826 | 2315 | @Override |
| 827 | public int getConsPercGaps() | |
| 828 | { | |
| 829 | 2315 | return ConsPercGaps; |
| 830 | } | |
| 831 | ||
| 832 | 1376 | @Override |
| 833 | public void setSequenceConsensusHash(ProfilesI hconsensus) | |
| 834 | { | |
| 835 | 1376 | this.hconsensus = hconsensus; |
| 836 | } | |
| 837 | ||
| 838 | 2114 | @Override |
| 839 | public void setSequenceSSConsensusHash( | |
| 840 | Map<String, ProfilesI> hSSConsensusProfileMap) | |
| 841 | { | |
| 842 | 2114 | this.hSSConsensusProfileMap = hSSConsensusProfileMap; |
| 843 | } | |
| 844 | ||
| 845 | 5 | @Override |
| 846 | public void setComplementConsensusHash( | |
| 847 | Hashtable<String, Object>[] hconsensus) | |
| 848 | { | |
| 849 | 5 | this.hcomplementConsensus = hconsensus; |
| 850 | } | |
| 851 | ||
| 852 | 4285 | @Override |
| 853 | public ProfilesI getSequenceConsensusHash() | |
| 854 | { | |
| 855 | 4285 | return hconsensus; |
| 856 | } | |
| 857 | ||
| 858 | 5019 | @Override |
| 859 | public Map<String, ProfilesI> getSequenceSSConsensusHash() | |
| 860 | { | |
| 861 | 5019 | return hSSConsensusProfileMap; |
| 862 | } | |
| 863 | ||
| 864 | 2805 | @Override |
| 865 | public Hashtable<String, Object>[] getComplementConsensusHash() | |
| 866 | { | |
| 867 | 2805 | return hcomplementConsensus; |
| 868 | } | |
| 869 | ||
| 870 | 2807 | @Override |
| 871 | public Hashtable<String, Object>[] getRnaStructureConsensusHash() | |
| 872 | { | |
| 873 | 2807 | return hStrucConsensus; |
| 874 | } | |
| 875 | ||
| 876 | 7 | @Override |
| 877 | public void setRnaStructureConsensusHash( | |
| 878 | Hashtable<String, Object>[] hStrucConsensus) | |
| 879 | { | |
| 880 | 7 | this.hStrucConsensus = hStrucConsensus; |
| 881 | ||
| 882 | } | |
| 883 | ||
| 884 | 2133 | @Override |
| 885 | public AlignmentAnnotation getAlignmentQualityAnnot() | |
| 886 | { | |
| 887 | 2133 | return quality; |
| 888 | } | |
| 889 | ||
| 890 | 3095 | @Override |
| 891 | public AlignmentAnnotation getAlignmentConservationAnnotation() | |
| 892 | { | |
| 893 | 3095 | return conservation; |
| 894 | } | |
| 895 | ||
| 896 | 7709 | @Override |
| 897 | public AlignmentAnnotation getAlignmentConsensusAnnotation() | |
| 898 | { | |
| 899 | 7709 | return consensus; |
| 900 | } | |
| 901 | ||
| 902 | 9476 | @Override |
| 903 | public List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation() | |
| 904 | { | |
| 905 | 9476 | return secondaryStructureConsensus; |
| 906 | } | |
| 907 | ||
| 908 | 4261 | @Override |
| 909 | public AlignmentAnnotation getAlignmentGapAnnotation() | |
| 910 | { | |
| 911 | 4261 | return gapcounts; |
| 912 | } | |
| 913 | ||
| 914 | 2815 | @Override |
| 915 | public AlignmentAnnotation getComplementConsensusAnnotation() | |
| 916 | { | |
| 917 | 2815 | return complementConsensus; |
| 918 | } | |
| 919 | ||
| 920 | 2807 | @Override |
| 921 | public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() | |
| 922 | { | |
| 923 | 2807 | return strucConsensus; |
| 924 | } | |
| 925 | ||
| 926 | protected AlignCalcManagerI calculator = new AlignCalcManager(); | |
| 927 | ||
| 928 | /** | |
| 929 | * trigger update of conservation annotation | |
| 930 | */ | |
| 931 | 1363 | public void updateConservation(final AlignmentViewPanel ap) |
| 932 | { | |
| 933 | // see note in mantis : issue number 8585 | |
| 934 | 1363 | if (alignment.isNucleotide() |
| 935 | || (conservation == null && quality == null) | |
| 936 | || !autoCalculateConsensus) | |
| 937 | { | |
| 938 | 283 | return; |
| 939 | } | |
| 940 | 1080 | if (calculator.getRegisteredWorkersOfClass( |
| 941 | jalview.workers.ConservationThread.class) == null) | |
| 942 | { | |
| 943 | 502 | calculator.registerWorker( |
| 944 | new jalview.workers.ConservationThread(this, ap)); | |
| 945 | } | |
| 946 | } | |
| 947 | ||
| 948 | /** | |
| 949 | * trigger update of consensus annotation | |
| 950 | */ | |
| 951 | 1384 | public void updateConsensus(final AlignmentViewPanel ap) |
| 952 | { | |
| 953 | // see note in mantis : issue number 8585 | |
| 954 | 1384 | if (consensus == null || !autoCalculateConsensus) |
| 955 | { | |
| 956 | 0 | return; |
| 957 | } | |
| 958 | 1384 | if (calculator |
| 959 | .getRegisteredWorkersOfClass(ConsensusThread.class) == null) | |
| 960 | { | |
| 961 | 518 | calculator.registerWorker(new ConsensusThread(this, ap)); |
| 962 | } | |
| 963 | ||
| 964 | /* | |
| 965 | * A separate thread to compute cDNA consensus for a protein alignment | |
| 966 | * which has mapping to cDNA | |
| 967 | */ | |
| 968 | 1384 | final AlignmentI al = this.getAlignment(); |
| 969 | 1384 | if (!al.isNucleotide() && al.getCodonFrames() != null |
| 970 | && !al.getCodonFrames().isEmpty()) | |
| 971 | { | |
| 972 | /* | |
| 973 | * fudge - check first for protein-to-nucleotide mappings | |
| 974 | * (we don't want to do this for protein-to-protein) | |
| 975 | */ | |
| 976 | 5 | boolean doConsensus = false; |
| 977 | 5 | for (AlignedCodonFrame mapping : al.getCodonFrames()) |
| 978 | { | |
| 979 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 980 | 5 | MapList[] mapLists = mapping.getdnaToProt(); |
| 981 | // mapLists can be empty if project load has not finished resolving seqs | |
| 982 | 5 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 983 | { | |
| 984 | 5 | doConsensus = true; |
| 985 | 5 | break; |
| 986 | } | |
| 987 | } | |
| 988 | 5 | if (doConsensus) |
| 989 | { | |
| 990 | 5 | if (calculator.getRegisteredWorkersOfClass( |
| 991 | ComplementConsensusThread.class) == null) | |
| 992 | { | |
| 993 | 4 | calculator |
| 994 | .registerWorker(new ComplementConsensusThread(this, ap)); | |
| 995 | } | |
| 996 | } | |
| 997 | } | |
| 998 | } | |
| 999 | ||
| 1000 | /** | |
| 1001 | * trigger update of Secondary Structure consensus annotation | |
| 1002 | */ | |
| 1003 | 1393 | public void updateSecondaryStructureConsensus(final AlignmentViewPanel ap) |
| 1004 | { | |
| 1005 | // see note in mantis : issue number 8585 | |
| 1006 | 1393 | if (secondaryStructureConsensus == null || !autoCalculateConsensus) |
| 1007 | { | |
| 1008 | 0 | return; |
| 1009 | } | |
| 1010 | 1393 | setSecondaryStructureSources(); |
| 1011 | 1393 | List<String> ssSources = viewStyle.getSecondaryStructureSources(); |
| 1012 | 1393 | if (secondaryStructureConsensus.size() != ssSources.size()) |
| 1013 | { | |
| 1014 | ||
| 1015 | 103 | for (String source : ssSources) |
| 1016 | { | |
| 1017 | 128 | boolean ssConsensusForSourcePresent = false; |
| 1018 | 128 | for (AlignmentAnnotation aa : secondaryStructureConsensus) |
| 1019 | { | |
| 1020 | 50 | if (aa.description.startsWith(source)) |
| 1021 | { | |
| 1022 | 25 | ssConsensusForSourcePresent = true; |
| 1023 | 25 | break; |
| 1024 | } | |
| 1025 | } | |
| 1026 | ||
| 1027 | 128 | if (!ssConsensusForSourcePresent) |
| 1028 | { | |
| 1029 | 103 | AlignmentAnnotation ssConsensus = new AlignmentAnnotation( |
| 1030 | MessageManager.getString("label.ssconsensus_label") + " " | |
| 1031 | + source, | |
| 1032 | source + " " | |
| 1033 | + MessageManager | |
| 1034 | .getString("label.ssconsensus_descr"), | |
| 1035 | new Annotation[1], 0f, 100f, | |
| 1036 | AlignmentAnnotation.BAR_GRAPH); | |
| 1037 | ||
| 1038 | 103 | ssConsensus.hasText = true; |
| 1039 | 103 | ssConsensus.autoCalculated = true; |
| 1040 | 103 | secondaryStructureConsensus.add(ssConsensus); |
| 1041 | 103 | if (showSSConsensus) |
| 1042 | { | |
| 1043 | 0 | alignment.addAnnotation(ssConsensus); |
| 1044 | ||
| 1045 | } | |
| 1046 | } | |
| 1047 | } | |
| 1048 | } | |
| 1049 | 1393 | List<AlignCalcWorkerI> ssworkers = calculator.getRegisteredWorkersOfClass( |
| 1050 | SecondaryStructureConsensusThread.class); | |
| 1051 | 1393 | if (ssworkers == null) |
| 1052 | { | |
| 1053 | 563 | calculator.registerWorker( |
| 1054 | new SecondaryStructureConsensusThread(this, ap)); | |
| 1055 | } else { | |
| 1056 | 830 | calculator.startWorker(ssworkers.get(0)); |
| 1057 | } | |
| 1058 | 1393 | ap.adjustAnnotationHeight(); |
| 1059 | ||
| 1060 | } | |
| 1061 | ||
| 1062 | // --------START Structure Conservation | |
| 1063 | 1381 | public void updateStrucConsensus(final AlignmentViewPanel ap) |
| 1064 | { | |
| 1065 | 1381 | if (autoCalculateStrucConsensus && strucConsensus == null |
| 1066 | && alignment.isNucleotide() && alignment.hasRNAStructure()) | |
| 1067 | { | |
| 1068 | // secondary structure has been added - so init the consensus line | |
| 1069 | 0 | initRNAStructure(); |
| 1070 | } | |
| 1071 | ||
| 1072 | // see note in mantis : issue number 8585 | |
| 1073 | 1381 | if (strucConsensus == null || !autoCalculateStrucConsensus) |
| 1074 | { | |
| 1075 | 1377 | return; |
| 1076 | } | |
| 1077 | 4 | if (calculator.getRegisteredWorkersOfClass( |
| 1078 | StrucConsensusThread.class) == null) | |
| 1079 | { | |
| 1080 | 4 | calculator.registerWorker(new StrucConsensusThread(this, ap)); |
| 1081 | } | |
| 1082 | } | |
| 1083 | ||
| 1084 | 3089 | public boolean isCalcInProgress() |
| 1085 | { | |
| 1086 | 3089 | return calculator.isWorking(); |
| 1087 | } | |
| 1088 | ||
| 1089 | 10528 | @Override |
| 1090 | public boolean isCalculationInProgress( | |
| 1091 | AlignmentAnnotation alignmentAnnotation) | |
| 1092 | { | |
| 1093 | 10528 | if (!alignmentAnnotation.autoCalculated) |
| 1094 | { | |
| 1095 | 0 | return false; |
| 1096 | } | |
| 1097 | 10528 | if (calculator.workingInvolvedWith(alignmentAnnotation)) |
| 1098 | { | |
| 1099 | // jalview.bin.Console.errPrintln("grey out | |
| 1100 | // ("+alignmentAnnotation.label+")"); | |
| 1101 | 293 | return true; |
| 1102 | } | |
| 1103 | 10235 | return false; |
| 1104 | } | |
| 1105 | ||
| 1106 | 800 | public void setAlignment(AlignmentI align) |
| 1107 | { | |
| 1108 | 800 | this.alignment = align; |
| 1109 | } | |
| 1110 | ||
| 1111 | /** | |
| 1112 | * Clean up references when this viewport is closed | |
| 1113 | */ | |
| 1114 | 269 | @Override |
| 1115 | public void dispose() | |
| 1116 | { | |
| 1117 | /* | |
| 1118 | * defensively null out references to large objects in case | |
| 1119 | * this object is not garbage collected (as if!) | |
| 1120 | */ | |
| 1121 | 269 | consensus = null; |
| 1122 | 269 | complementConsensus = null; |
| 1123 | 269 | strucConsensus = null; |
| 1124 | 269 | secondaryStructureConsensus = null; |
| 1125 | 269 | conservation = null; |
| 1126 | 269 | quality = null; |
| 1127 | 269 | groupConsensus = null; |
| 1128 | 269 | groupConservation = null; |
| 1129 | 269 | hconsensus = null; |
| 1130 | 269 | hconservation = null; |
| 1131 | 269 | hcomplementConsensus = null; |
| 1132 | 269 | gapcounts = null; |
| 1133 | 269 | calculator = null; |
| 1134 | 269 | residueShading = null; // may hold a reference to Consensus |
| 1135 | 269 | changeSupport = null; |
| 1136 | 269 | ranges = null; |
| 1137 | 269 | currentTree = null; |
| 1138 | 269 | selectionGroup = null; |
| 1139 | 269 | colSel = null; |
| 1140 | 269 | setAlignment(null); |
| 1141 | } | |
| 1142 | ||
| 1143 | 6294 | @Override |
| 1144 | public boolean isClosed() | |
| 1145 | { | |
| 1146 | // TODO: check that this isClosed is only true after panel is closed, not | |
| 1147 | // before it is fully constructed. | |
| 1148 | 6294 | return alignment == null; |
| 1149 | } | |
| 1150 | ||
| 1151 | 2113 | @Override |
| 1152 | public AlignCalcManagerI getCalcManager() | |
| 1153 | { | |
| 1154 | 2113 | return calculator; |
| 1155 | } | |
| 1156 | ||
| 1157 | /** | |
| 1158 | * should conservation rows be shown for groups | |
| 1159 | */ | |
| 1160 | protected boolean showGroupConservation = false; | |
| 1161 | ||
| 1162 | /** | |
| 1163 | * should consensus rows be shown for groups | |
| 1164 | */ | |
| 1165 | protected boolean showGroupConsensus = false; | |
| 1166 | ||
| 1167 | protected boolean showGroupSSConsensus = false; | |
| 1168 | ||
| 1169 | /** | |
| 1170 | * should consensus profile be rendered by default | |
| 1171 | */ | |
| 1172 | protected boolean showSequenceLogo = false; | |
| 1173 | ||
| 1174 | /** | |
| 1175 | * should consensus profile be rendered normalised to row height | |
| 1176 | */ | |
| 1177 | protected boolean normaliseSequenceLogo = false; | |
| 1178 | ||
| 1179 | /** | |
| 1180 | * should consensus histograms be rendered by default | |
| 1181 | */ | |
| 1182 | protected boolean showConsensusHistogram = true; | |
| 1183 | ||
| 1184 | /** | |
| 1185 | * @return the showConsensusProfile | |
| 1186 | */ | |
| 1187 | 7412 | @Override |
| 1188 | public boolean isShowSequenceLogo() | |
| 1189 | { | |
| 1190 | 7412 | return showSequenceLogo; |
| 1191 | } | |
| 1192 | ||
| 1193 | /** | |
| 1194 | * @param showSequenceLogo | |
| 1195 | * the new value | |
| 1196 | */ | |
| 1197 | 89 | public void setShowSequenceLogo(boolean showSequenceLogo) |
| 1198 | { | |
| 1199 | 89 | if (showSequenceLogo != this.showSequenceLogo) |
| 1200 | { | |
| 1201 | // TODO: decouple settings setting from calculation when refactoring | |
| 1202 | // annotation update method from alignframe to viewport | |
| 1203 | 20 | this.showSequenceLogo = showSequenceLogo; |
| 1204 | 20 | calculator.updateAnnotationFor(ConsensusThread.class); |
| 1205 | 20 | calculator.updateAnnotationFor(ComplementConsensusThread.class); |
| 1206 | 20 | calculator.updateAnnotationFor(StrucConsensusThread.class); |
| 1207 | ||
| 1208 | // to do | |
| 1209 | ||
| 1210 | 20 | calculator |
| 1211 | .updateAnnotationFor(SecondaryStructureConsensusThread.class); | |
| 1212 | } | |
| 1213 | 89 | this.showSequenceLogo = showSequenceLogo; |
| 1214 | } | |
| 1215 | ||
| 1216 | /** | |
| 1217 | * @param showConsensusHistogram | |
| 1218 | * the showConsensusHistogram to set | |
| 1219 | */ | |
| 1220 | 89 | public void setShowConsensusHistogram(boolean showConsensusHistogram) |
| 1221 | { | |
| 1222 | 89 | this.showConsensusHistogram = showConsensusHistogram; |
| 1223 | } | |
| 1224 | ||
| 1225 | /** | |
| 1226 | * @return the showGroupConservation | |
| 1227 | */ | |
| 1228 | 886 | public boolean isShowGroupConservation() |
| 1229 | { | |
| 1230 | 886 | return showGroupConservation; |
| 1231 | } | |
| 1232 | ||
| 1233 | /** | |
| 1234 | * @param showGroupConservation | |
| 1235 | * the showGroupConservation to set | |
| 1236 | */ | |
| 1237 | 89 | public void setShowGroupConservation(boolean showGroupConservation) |
| 1238 | { | |
| 1239 | 89 | this.showGroupConservation = showGroupConservation; |
| 1240 | } | |
| 1241 | ||
| 1242 | /** | |
| 1243 | * @return the showGroupConsensus | |
| 1244 | */ | |
| 1245 | 886 | public boolean isShowGroupConsensus() |
| 1246 | { | |
| 1247 | 886 | return showGroupConsensus; |
| 1248 | } | |
| 1249 | ||
| 1250 | 886 | public boolean isShowGroupSSConsensus() |
| 1251 | { | |
| 1252 | 886 | return showGroupSSConsensus; |
| 1253 | } | |
| 1254 | ||
| 1255 | /** | |
| 1256 | * @param showGroupConsensus | |
| 1257 | * the showGroupConsensus to set | |
| 1258 | */ | |
| 1259 | 89 | public void setShowGroupConsensus(boolean showGroupConsensus) |
| 1260 | { | |
| 1261 | 89 | this.showGroupConsensus = showGroupConsensus; |
| 1262 | } | |
| 1263 | ||
| 1264 | 89 | public void setShowGroupSSConsensus(boolean showGroupSSConsensus) |
| 1265 | { | |
| 1266 | 89 | this.showGroupSSConsensus = showGroupSSConsensus; |
| 1267 | } | |
| 1268 | ||
| 1269 | /** | |
| 1270 | * @param showSSConsensus | |
| 1271 | * the showSSConsensus to set | |
| 1272 | */ | |
| 1273 | 0 | public void setShowSSConsensus(boolean showSSConsensus) |
| 1274 | { | |
| 1275 | 0 | this.showSSConsensus = showSSConsensus; |
| 1276 | } | |
| 1277 | ||
| 1278 | /** | |
| 1279 | * | |
| 1280 | * @return flag to indicate if the consensus histogram should be rendered by | |
| 1281 | * default | |
| 1282 | */ | |
| 1283 | 3686 | @Override |
| 1284 | public boolean isShowConsensusHistogram() | |
| 1285 | { | |
| 1286 | 3686 | return this.showConsensusHistogram; |
| 1287 | } | |
| 1288 | ||
| 1289 | /** | |
| 1290 | * when set, updateAlignment will always ensure sequences are of equal length | |
| 1291 | */ | |
| 1292 | private boolean padGaps = false; | |
| 1293 | ||
| 1294 | /** | |
| 1295 | * when set, alignment should be reordered according to a newly opened tree | |
| 1296 | */ | |
| 1297 | public boolean sortByTree = false; | |
| 1298 | ||
| 1299 | /** | |
| 1300 | * | |
| 1301 | * | |
| 1302 | * @return null or the currently selected sequence region | |
| 1303 | */ | |
| 1304 | 26006 | @Override |
| 1305 | public SequenceGroup getSelectionGroup() | |
| 1306 | { | |
| 1307 | 26006 | return selectionGroup; |
| 1308 | } | |
| 1309 | ||
| 1310 | /** | |
| 1311 | * Set the selection group for this window. Also sets the current alignment as | |
| 1312 | * the context for the group, if it does not already have one. | |
| 1313 | * @param sg | |
| 1314 | * - group holding references to sequences in this alignment view | |
| 1315 | * | |
| 1316 | */ | |
| 1317 | 150 | @Override |
| 1318 | public void setSelectionGroup(SequenceGroup sg) | |
| 1319 | { | |
| 1320 | 150 | selectionGroup = sg; |
| 1321 | 150 | if (sg != null && sg.getContext() == null) |
| 1322 | { | |
| 1323 | 37 | sg.setContext(alignment); |
| 1324 | } | |
| 1325 | } | |
| 1326 | ||
| 1327 | 1 | public void setHiddenColumns(HiddenColumns hidden) |
| 1328 | { | |
| 1329 | 1 | this.alignment.setHiddenColumns(hidden); |
| 1330 | } | |
| 1331 | ||
| 1332 | 5486 | @Override |
| 1333 | public ColumnSelection getColumnSelection() | |
| 1334 | { | |
| 1335 | 5486 | return colSel; |
| 1336 | } | |
| 1337 | ||
| 1338 | 13 | @Override |
| 1339 | public void setColumnSelection(ColumnSelection colSel) | |
| 1340 | { | |
| 1341 | 13 | this.colSel = colSel; |
| 1342 | 13 | if (colSel != null) |
| 1343 | { | |
| 1344 | 13 | updateHiddenColumns(); |
| 1345 | } | |
| 1346 | 13 | isColSelChanged(true); |
| 1347 | } | |
| 1348 | ||
| 1349 | /** | |
| 1350 | * | |
| 1351 | * @return | |
| 1352 | */ | |
| 1353 | 32 | @Override |
| 1354 | public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences() | |
| 1355 | { | |
| 1356 | 32 | return hiddenRepSequences; |
| 1357 | } | |
| 1358 | ||
| 1359 | 0 | @Override |
| 1360 | public void setHiddenRepSequences( | |
| 1361 | Map<SequenceI, SequenceCollectionI> hiddenRepSequences) | |
| 1362 | { | |
| 1363 | 0 | this.hiddenRepSequences = hiddenRepSequences; |
| 1364 | } | |
| 1365 | ||
| 1366 | 0 | @Override |
| 1367 | public boolean hasSelectedColumns() | |
| 1368 | { | |
| 1369 | 0 | ColumnSelection columnSelection = getColumnSelection(); |
| 1370 | 0 | return columnSelection != null && columnSelection.hasSelectedColumns(); |
| 1371 | } | |
| 1372 | ||
| 1373 | 9500 | @Override |
| 1374 | public boolean hasHiddenColumns() | |
| 1375 | { | |
| 1376 | 9500 | return alignment.getHiddenColumns() != null |
| 1377 | && alignment.getHiddenColumns().hasHiddenColumns(); | |
| 1378 | } | |
| 1379 | ||
| 1380 | 13 | public void updateHiddenColumns() |
| 1381 | { | |
| 1382 | // this method doesn't really do anything now. But - it could, since a | |
| 1383 | // column Selection could be in the process of modification | |
| 1384 | // hasHiddenColumns = colSel.hasHiddenColumns(); | |
| 1385 | } | |
| 1386 | ||
| 1387 | 4482 | @Override |
| 1388 | public boolean hasHiddenRows() | |
| 1389 | { | |
| 1390 | 4482 | return alignment.getHiddenSequences().getSize() > 0; |
| 1391 | } | |
| 1392 | ||
| 1393 | protected SequenceGroup selectionGroup; | |
| 1394 | ||
| 1395 | 89 | public void setSequenceSetId(String newid) |
| 1396 | { | |
| 1397 | 89 | if (sequenceSetID != null) |
| 1398 | { | |
| 1399 | 89 | jalview.bin.Console.errPrintln( |
| 1400 | "Warning - overwriting a sequenceSetId for a viewport!"); | |
| 1401 | } | |
| 1402 | 89 | sequenceSetID = new String(newid); |
| 1403 | } | |
| 1404 | ||
| 1405 | 4367 | @Override |
| 1406 | public String getSequenceSetId() | |
| 1407 | { | |
| 1408 | 4367 | if (sequenceSetID == null) |
| 1409 | { | |
| 1410 | 383 | sequenceSetID = alignment.hashCode() + ""; |
| 1411 | } | |
| 1412 | ||
| 1413 | 4367 | return sequenceSetID; |
| 1414 | } | |
| 1415 | ||
| 1416 | /** | |
| 1417 | * unique viewId for synchronizing state (e.g. with stored Jalview Project) | |
| 1418 | * | |
| 1419 | */ | |
| 1420 | protected String viewId = null; | |
| 1421 | ||
| 1422 | 619 | @Override |
| 1423 | public String getViewId() | |
| 1424 | { | |
| 1425 | 619 | if (viewId == null) |
| 1426 | { | |
| 1427 | 315 | viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; |
| 1428 | } | |
| 1429 | 619 | return viewId; |
| 1430 | } | |
| 1431 | ||
| 1432 | 92 | public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) |
| 1433 | { | |
| 1434 | 92 | ignoreGapsInConsensusCalculation = b; |
| 1435 | 92 | if (ap != null) |
| 1436 | { | |
| 1437 | 3 | updateConsensus(ap); |
| 1438 | 3 | updateSecondaryStructureConsensus(ap); |
| 1439 | 3 | if (residueShading != null) |
| 1440 | { | |
| 1441 | 3 | residueShading.setThreshold(residueShading.getThreshold(), |
| 1442 | ignoreGapsInConsensusCalculation); | |
| 1443 | } | |
| 1444 | } | |
| 1445 | ||
| 1446 | } | |
| 1447 | ||
| 1448 | private long sgrouphash = -1, colselhash = -1; | |
| 1449 | ||
| 1450 | /** | |
| 1451 | * checks current SelectionGroup against record of last hash value, and | |
| 1452 | * updates record. | |
| 1453 | * | |
| 1454 | * @param b | |
| 1455 | * update the record of last hash value | |
| 1456 | * | |
| 1457 | * @return true if SelectionGroup changed since last call (when b is true) | |
| 1458 | */ | |
| 1459 | 177 | public boolean isSelectionGroupChanged(boolean b) |
| 1460 | { | |
| 1461 | 177 | int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1 |
| 1462 | : selectionGroup.hashCode(); | |
| 1463 | 177 | if (hc != -1 && hc != sgrouphash) |
| 1464 | { | |
| 1465 | 9 | if (b) |
| 1466 | { | |
| 1467 | 9 | sgrouphash = hc; |
| 1468 | } | |
| 1469 | 9 | return true; |
| 1470 | } | |
| 1471 | 168 | return false; |
| 1472 | } | |
| 1473 | ||
| 1474 | /** | |
| 1475 | * checks current colsel against record of last hash value, and optionally | |
| 1476 | * updates record. | |
| 1477 | * | |
| 1478 | * @param b | |
| 1479 | * update the record of last hash value | |
| 1480 | * @return true if colsel changed since last call (when b is true) | |
| 1481 | */ | |
| 1482 | 181 | public boolean isColSelChanged(boolean b) |
| 1483 | { | |
| 1484 | 181 | int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode(); |
| 1485 | 181 | if (hc != -1 && hc != colselhash) |
| 1486 | { | |
| 1487 | 17 | if (b) |
| 1488 | { | |
| 1489 | 17 | colselhash = hc; |
| 1490 | } | |
| 1491 | 17 | return true; |
| 1492 | } | |
| 1493 | 164 | return false; |
| 1494 | } | |
| 1495 | ||
| 1496 | 6596 | @Override |
| 1497 | public boolean isIgnoreGapsConsensus() | |
| 1498 | { | |
| 1499 | 6596 | return ignoreGapsInConsensusCalculation; |
| 1500 | } | |
| 1501 | ||
| 1502 | // property change stuff | |
| 1503 | // JBPNote Prolly only need this in the applet version. | |
| 1504 | private PropertyChangeSupport changeSupport = new PropertyChangeSupport( | |
| 1505 | this); | |
| 1506 | ||
| 1507 | protected boolean showConservation = true; | |
| 1508 | ||
| 1509 | protected boolean showQuality = true; | |
| 1510 | ||
| 1511 | protected boolean showConsensus = true; | |
| 1512 | ||
| 1513 | protected boolean showSSConsensus = true; | |
| 1514 | ||
| 1515 | protected boolean showOccupancy = true; | |
| 1516 | ||
| 1517 | private Map<SequenceI, Color> sequenceColours = new HashMap<>(); | |
| 1518 | ||
| 1519 | private Map<AlignmentAnnotation, Color> annotationColours = new HashMap<>(); | |
| 1520 | ||
| 1521 | protected SequenceAnnotationOrder sortAnnotationsBy = null; | |
| 1522 | ||
| 1523 | protected boolean showAutocalculatedAbove; | |
| 1524 | ||
| 1525 | /** | |
| 1526 | * when set, view will scroll to show the highlighted position | |
| 1527 | */ | |
| 1528 | private boolean followHighlight = true; | |
| 1529 | ||
| 1530 | /** | |
| 1531 | * Property change listener for changes in alignment | |
| 1532 | * | |
| 1533 | * @param listener | |
| 1534 | * DOCUMENT ME! | |
| 1535 | */ | |
| 1536 | 519 | public void addPropertyChangeListener( |
| 1537 | java.beans.PropertyChangeListener listener) | |
| 1538 | { | |
| 1539 | 519 | changeSupport.addPropertyChangeListener(listener); |
| 1540 | } | |
| 1541 | ||
| 1542 | /** | |
| 1543 | * DOCUMENT ME! | |
| 1544 | * | |
| 1545 | * @param listener | |
| 1546 | * DOCUMENT ME! | |
| 1547 | */ | |
| 1548 | 286 | public void removePropertyChangeListener( |
| 1549 | java.beans.PropertyChangeListener listener) | |
| 1550 | { | |
| 1551 | 286 | if (changeSupport != null) |
| 1552 | { | |
| 1553 | 285 | changeSupport.removePropertyChangeListener(listener); |
| 1554 | } | |
| 1555 | } | |
| 1556 | ||
| 1557 | /** | |
| 1558 | * Property change listener for changes in alignment | |
| 1559 | * | |
| 1560 | * @param prop | |
| 1561 | * DOCUMENT ME! | |
| 1562 | * @param oldvalue | |
| 1563 | * DOCUMENT ME! | |
| 1564 | * @param newvalue | |
| 1565 | * DOCUMENT ME! | |
| 1566 | */ | |
| 1567 | 78 | public void firePropertyChange(String prop, Object oldvalue, |
| 1568 | Object newvalue) | |
| 1569 | { | |
| 1570 | 78 | changeSupport.firePropertyChange(prop, oldvalue, newvalue); |
| 1571 | } | |
| 1572 | ||
| 1573 | 0 | @Override |
| 1574 | public void notifyAlignmentChanged() | |
| 1575 | { | |
| 1576 | 0 | firePropertyChange("alignment", null, alignment); |
| 1577 | } | |
| 1578 | ||
| 1579 | // common hide/show column stuff | |
| 1580 | ||
| 1581 | 6 | public void hideSelectedColumns() |
| 1582 | { | |
| 1583 | 6 | if (colSel.isEmpty()) |
| 1584 | { | |
| 1585 | 2 | return; |
| 1586 | } | |
| 1587 | ||
| 1588 | 4 | colSel.hideSelectedColumns(alignment); |
| 1589 | 4 | setSelectionGroup(null); |
| 1590 | 4 | isColSelChanged(true); |
| 1591 | } | |
| 1592 | ||
| 1593 | 71 | public void hideColumns(int start, int end) |
| 1594 | { | |
| 1595 | 71 | if (start == end) |
| 1596 | { | |
| 1597 | 2 | colSel.hideSelectedColumns(start, alignment.getHiddenColumns()); |
| 1598 | } | |
| 1599 | else | |
| 1600 | { | |
| 1601 | 69 | alignment.getHiddenColumns().hideColumns(start, end); |
| 1602 | } | |
| 1603 | 71 | isColSelChanged(true); |
| 1604 | } | |
| 1605 | ||
| 1606 | 1 | public void showColumn(int col) |
| 1607 | { | |
| 1608 | 1 | alignment.getHiddenColumns().revealHiddenColumns(col, colSel); |
| 1609 | 1 | isColSelChanged(true); |
| 1610 | } | |
| 1611 | ||
| 1612 | 5 | public void showAllHiddenColumns() |
| 1613 | { | |
| 1614 | 5 | alignment.getHiddenColumns().revealAllHiddenColumns(colSel); |
| 1615 | 5 | isColSelChanged(true); |
| 1616 | } | |
| 1617 | ||
| 1618 | // common hide/show seq stuff | |
| 1619 | 1 | public void showAllHiddenSeqs() |
| 1620 | { | |
| 1621 | 1 | int startSeq = ranges.getStartSeq(); |
| 1622 | 1 | int endSeq = ranges.getEndSeq(); |
| 1623 | ||
| 1624 | 1 | if (alignment.getHiddenSequences().getSize() > 0) |
| 1625 | { | |
| 1626 | 1 | if (selectionGroup == null) |
| 1627 | { | |
| 1628 | 0 | selectionGroup = new SequenceGroup(); |
| 1629 | 0 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1630 | } | |
| 1631 | 1 | List<SequenceI> tmp = alignment.getHiddenSequences() |
| 1632 | .showAll(hiddenRepSequences); | |
| 1633 | 1 | for (SequenceI seq : tmp) |
| 1634 | { | |
| 1635 | 2 | selectionGroup.addSequence(seq, false); |
| 1636 | 2 | setSequenceAnnotationsVisible(seq, true); |
| 1637 | } | |
| 1638 | ||
| 1639 | 1 | hiddenRepSequences = null; |
| 1640 | ||
| 1641 | 1 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1642 | ||
| 1643 | 1 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1644 | // used to set hasHiddenRows/hiddenRepSequences here, after the property | |
| 1645 | // changed event | |
| 1646 | 1 | sendSelection(); |
| 1647 | } | |
| 1648 | } | |
| 1649 | ||
| 1650 | 2 | public void showSequence(int index) |
| 1651 | { | |
| 1652 | 2 | int startSeq = ranges.getStartSeq(); |
| 1653 | 2 | int endSeq = ranges.getEndSeq(); |
| 1654 | ||
| 1655 | 2 | List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index, |
| 1656 | hiddenRepSequences); | |
| 1657 | 2 | if (tmp.size() > 0) |
| 1658 | { | |
| 1659 | 2 | if (selectionGroup == null) |
| 1660 | { | |
| 1661 | 2 | selectionGroup = new SequenceGroup(); |
| 1662 | 2 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1663 | } | |
| 1664 | ||
| 1665 | 2 | for (SequenceI seq : tmp) |
| 1666 | { | |
| 1667 | 3 | selectionGroup.addSequence(seq, false); |
| 1668 | 3 | setSequenceAnnotationsVisible(seq, true); |
| 1669 | } | |
| 1670 | ||
| 1671 | 2 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1672 | ||
| 1673 | 2 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1674 | 2 | sendSelection(); |
| 1675 | } | |
| 1676 | } | |
| 1677 | ||
| 1678 | 0 | public void hideAllSelectedSeqs() |
| 1679 | { | |
| 1680 | 0 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1681 | { | |
| 1682 | 0 | return; |
| 1683 | } | |
| 1684 | ||
| 1685 | 0 | SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); |
| 1686 | ||
| 1687 | 0 | hideSequence(seqs); |
| 1688 | ||
| 1689 | 0 | setSelectionGroup(null); |
| 1690 | } | |
| 1691 | ||
| 1692 | 54 | public void hideSequence(SequenceI[] seq) |
| 1693 | { | |
| 1694 | /* | |
| 1695 | * cache offset to first visible sequence | |
| 1696 | */ | |
| 1697 | 54 | int startSeq = ranges.getStartSeq(); |
| 1698 | ||
| 1699 | 54 | if (seq != null) |
| 1700 | { | |
| 1701 | 252 | for (int i = 0; i < seq.length; i++) |
| 1702 | { | |
| 1703 | 198 | alignment.getHiddenSequences().hideSequence(seq[i]); |
| 1704 | 198 | setSequenceAnnotationsVisible(seq[i], false); |
| 1705 | } | |
| 1706 | 54 | ranges.setStartSeq(startSeq); |
| 1707 | 54 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1708 | } | |
| 1709 | } | |
| 1710 | ||
| 1711 | /** | |
| 1712 | * Hides the specified sequence, or the sequences it represents | |
| 1713 | * | |
| 1714 | * @param sequence | |
| 1715 | * the sequence to hide, or keep as representative | |
| 1716 | * @param representGroup | |
| 1717 | * if true, hide the current selection group except for the | |
| 1718 | * representative sequence | |
| 1719 | */ | |
| 1720 | 3 | public void hideSequences(SequenceI sequence, boolean representGroup) |
| 1721 | { | |
| 1722 | 3 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1723 | { | |
| 1724 | 0 | hideSequence(new SequenceI[] { sequence }); |
| 1725 | 0 | return; |
| 1726 | } | |
| 1727 | ||
| 1728 | 3 | if (representGroup) |
| 1729 | { | |
| 1730 | 3 | hideRepSequences(sequence, selectionGroup); |
| 1731 | 3 | setSelectionGroup(null); |
| 1732 | 3 | return; |
| 1733 | } | |
| 1734 | ||
| 1735 | 0 | int gsize = selectionGroup.getSize(); |
| 1736 | 0 | SequenceI[] hseqs = selectionGroup.getSequences() |
| 1737 | .toArray(new SequenceI[gsize]); | |
| 1738 | ||
| 1739 | 0 | hideSequence(hseqs); |
| 1740 | 0 | setSelectionGroup(null); |
| 1741 | 0 | sendSelection(); |
| 1742 | } | |
| 1743 | ||
| 1744 | /** | |
| 1745 | * Set visibility for any annotations for the given sequence. | |
| 1746 | * | |
| 1747 | * @param sequenceI | |
| 1748 | */ | |
| 1749 | 203 | protected void setSequenceAnnotationsVisible(SequenceI sequenceI, |
| 1750 | boolean visible) | |
| 1751 | { | |
| 1752 | 203 | AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation(); |
| 1753 | 203 | if (anns != null) |
| 1754 | { | |
| 1755 | 203 | for (AlignmentAnnotation ann : anns) |
| 1756 | { | |
| 1757 | 1033 | if (ann.sequenceRef == sequenceI) |
| 1758 | { | |
| 1759 | 0 | ann.visible = visible; |
| 1760 | } | |
| 1761 | } | |
| 1762 | } | |
| 1763 | } | |
| 1764 | ||
| 1765 | 5 | public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) |
| 1766 | { | |
| 1767 | 5 | int sSize = sg.getSize(); |
| 1768 | 5 | if (sSize < 2) |
| 1769 | { | |
| 1770 | 0 | return; |
| 1771 | } | |
| 1772 | ||
| 1773 | 5 | if (hiddenRepSequences == null) |
| 1774 | { | |
| 1775 | 5 | hiddenRepSequences = new Hashtable<>(); |
| 1776 | } | |
| 1777 | ||
| 1778 | 5 | hiddenRepSequences.put(repSequence, sg); |
| 1779 | ||
| 1780 | // Hide all sequences except the repSequence | |
| 1781 | 5 | SequenceI[] seqs = new SequenceI[sSize - 1]; |
| 1782 | 5 | int index = 0; |
| 1783 | 16 | for (int i = 0; i < sSize; i++) |
| 1784 | { | |
| 1785 | 11 | if (sg.getSequenceAt(i) != repSequence) |
| 1786 | { | |
| 1787 | 6 | if (index == sSize - 1) |
| 1788 | { | |
| 1789 | 0 | return; |
| 1790 | } | |
| 1791 | ||
| 1792 | 6 | seqs[index++] = sg.getSequenceAt(i); |
| 1793 | } | |
| 1794 | } | |
| 1795 | 5 | sg.setSeqrep(repSequence); // note: not done in 2.7applet |
| 1796 | 5 | sg.setHidereps(true); // note: not done in 2.7applet |
| 1797 | 5 | hideSequence(seqs); |
| 1798 | ||
| 1799 | } | |
| 1800 | ||
| 1801 | /** | |
| 1802 | * | |
| 1803 | * @return null or the current reference sequence | |
| 1804 | */ | |
| 1805 | 0 | public SequenceI getReferenceSeq() |
| 1806 | { | |
| 1807 | 0 | return alignment.getSeqrep(); |
| 1808 | } | |
| 1809 | ||
| 1810 | /** | |
| 1811 | * @param seq | |
| 1812 | * @return true iff seq is the reference for the alignment | |
| 1813 | */ | |
| 1814 | 3839 | public boolean isReferenceSeq(SequenceI seq) |
| 1815 | { | |
| 1816 | 3839 | return alignment.getSeqrep() == seq; |
| 1817 | } | |
| 1818 | ||
| 1819 | /** | |
| 1820 | * | |
| 1821 | * @param seq | |
| 1822 | * @return true if there are sequences represented by this sequence that are | |
| 1823 | * currently hidden | |
| 1824 | */ | |
| 1825 | 3923 | public boolean isHiddenRepSequence(SequenceI seq) |
| 1826 | { | |
| 1827 | 3923 | return (hiddenRepSequences != null |
| 1828 | && hiddenRepSequences.containsKey(seq)); | |
| 1829 | } | |
| 1830 | ||
| 1831 | /** | |
| 1832 | * | |
| 1833 | * @param seq | |
| 1834 | * @return null or a sequence group containing the sequences that seq | |
| 1835 | * represents | |
| 1836 | */ | |
| 1837 | 2 | public SequenceGroup getRepresentedSequences(SequenceI seq) |
| 1838 | { | |
| 1839 | 2 | return (SequenceGroup) (hiddenRepSequences == null ? null |
| 1840 | : hiddenRepSequences.get(seq)); | |
| 1841 | } | |
| 1842 | ||
| 1843 | 0 | @Override |
| 1844 | public int adjustForHiddenSeqs(int alignmentIndex) | |
| 1845 | { | |
| 1846 | 0 | return alignment.getHiddenSequences() |
| 1847 | .adjustForHiddenSeqs(alignmentIndex); | |
| 1848 | } | |
| 1849 | ||
| 1850 | 0 | @Override |
| 1851 | public void invertColumnSelection() | |
| 1852 | { | |
| 1853 | 0 | colSel.invertColumnSelection(0, alignment.getWidth(), alignment); |
| 1854 | 0 | isColSelChanged(true); |
| 1855 | } | |
| 1856 | ||
| 1857 | 4 | @Override |
| 1858 | public SequenceI[] getSelectionAsNewSequence() | |
| 1859 | { | |
| 1860 | 4 | SequenceI[] sequences; |
| 1861 | // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - | |
| 1862 | // this was the only caller in the applet for this method | |
| 1863 | // JBPNote: in applet, this method returned references to the alignment | |
| 1864 | // sequences, and it did not honour the presence/absence of annotation | |
| 1865 | // attached to the alignment (probably!) | |
| 1866 | 4 | if (selectionGroup == null || selectionGroup.getSize() == 0) |
| 1867 | { | |
| 1868 | 2 | sequences = alignment.getSequencesArray(); |
| 1869 | 2 | AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); |
| 1870 | 4 | for (int i = 0; i < sequences.length; i++) |
| 1871 | { | |
| 1872 | // construct new sequence with subset of visible annotation | |
| 1873 | 2 | sequences[i] = new Sequence(sequences[i], annots); |
| 1874 | } | |
| 1875 | } | |
| 1876 | else | |
| 1877 | { | |
| 1878 | 2 | sequences = selectionGroup.getSelectionAsNewSequences(alignment); |
| 1879 | } | |
| 1880 | ||
| 1881 | 4 | return sequences; |
| 1882 | } | |
| 1883 | ||
| 1884 | 28 | @Override |
| 1885 | public SequenceI[] getSequenceSelection() | |
| 1886 | { | |
| 1887 | 28 | SequenceI[] sequences = null; |
| 1888 | 28 | if (selectionGroup != null) |
| 1889 | { | |
| 1890 | 4 | sequences = selectionGroup.getSequencesInOrder(alignment); |
| 1891 | } | |
| 1892 | 28 | if (sequences == null) |
| 1893 | { | |
| 1894 | 24 | sequences = alignment.getSequencesArray(); |
| 1895 | } | |
| 1896 | 28 | return sequences; |
| 1897 | } | |
| 1898 | ||
| 1899 | 25 | @Override |
| 1900 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 1901 | boolean selectedOnly) | |
| 1902 | { | |
| 1903 | 25 | return getAlignmentView(selectedOnly, false); |
| 1904 | } | |
| 1905 | ||
| 1906 | 26 | @Override |
| 1907 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 1908 | boolean selectedOnly, boolean markGroups) | |
| 1909 | { | |
| 1910 | 26 | return new AlignmentView(alignment, alignment.getHiddenColumns(), |
| 1911 | selectionGroup, | |
| 1912 | alignment.getHiddenColumns() != null | |
| 1913 | && alignment.getHiddenColumns().hasHiddenColumns(), | |
| 1914 | selectedOnly, markGroups); | |
| 1915 | } | |
| 1916 | ||
| 1917 | 24 | @Override |
| 1918 | public String[] getViewAsString(boolean selectedRegionOnly) | |
| 1919 | { | |
| 1920 | 24 | return getViewAsString(selectedRegionOnly, true); |
| 1921 | } | |
| 1922 | ||
| 1923 | 24 | @Override |
| 1924 | public String[] getViewAsString(boolean selectedRegionOnly, | |
| 1925 | boolean exportHiddenSeqs) | |
| 1926 | { | |
| 1927 | 24 | String[] selection = null; |
| 1928 | 24 | SequenceI[] seqs = null; |
| 1929 | 24 | int i, iSize; |
| 1930 | 24 | int start = 0, end = 0; |
| 1931 | 24 | if (selectedRegionOnly && selectionGroup != null) |
| 1932 | { | |
| 1933 | 0 | iSize = selectionGroup.getSize(); |
| 1934 | 0 | seqs = selectionGroup.getSequencesInOrder(alignment); |
| 1935 | 0 | start = selectionGroup.getStartRes(); |
| 1936 | 0 | end = selectionGroup.getEndRes() + 1; |
| 1937 | } | |
| 1938 | else | |
| 1939 | { | |
| 1940 | 24 | if (hasHiddenRows() && exportHiddenSeqs) |
| 1941 | { | |
| 1942 | 0 | AlignmentI fullAlignment = alignment.getHiddenSequences() |
| 1943 | .getFullAlignment(); | |
| 1944 | 0 | iSize = fullAlignment.getHeight(); |
| 1945 | 0 | seqs = fullAlignment.getSequencesArray(); |
| 1946 | 0 | end = fullAlignment.getWidth(); |
| 1947 | } | |
| 1948 | else | |
| 1949 | { | |
| 1950 | 24 | iSize = alignment.getHeight(); |
| 1951 | 24 | seqs = alignment.getSequencesArray(); |
| 1952 | 24 | end = alignment.getWidth(); |
| 1953 | } | |
| 1954 | } | |
| 1955 | ||
| 1956 | 24 | selection = new String[iSize]; |
| 1957 | 24 | if (alignment.getHiddenColumns() != null |
| 1958 | && alignment.getHiddenColumns().hasHiddenColumns()) | |
| 1959 | { | |
| 1960 | 206 | for (i = 0; i < iSize; i++) |
| 1961 | { | |
| 1962 | 188 | Iterator<int[]> blocks = alignment.getHiddenColumns() |
| 1963 | .getVisContigsIterator(start, end + 1, false); | |
| 1964 | 188 | selection[i] = seqs[i].getSequenceStringFromIterator(blocks); |
| 1965 | } | |
| 1966 | } | |
| 1967 | else | |
| 1968 | { | |
| 1969 | 36 | for (i = 0; i < iSize; i++) |
| 1970 | { | |
| 1971 | 30 | selection[i] = seqs[i].getSequenceAsString(start, end); |
| 1972 | } | |
| 1973 | ||
| 1974 | } | |
| 1975 | 24 | return selection; |
| 1976 | } | |
| 1977 | ||
| 1978 | 0 | @Override |
| 1979 | public List<int[]> getVisibleRegionBoundaries(int min, int max) | |
| 1980 | { | |
| 1981 | 0 | ArrayList<int[]> regions = new ArrayList<>(); |
| 1982 | 0 | int start = min; |
| 1983 | 0 | int end = max; |
| 1984 | ||
| 1985 | 0 | do |
| 1986 | { | |
| 1987 | 0 | HiddenColumns hidden = alignment.getHiddenColumns(); |
| 1988 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 1989 | { | |
| 1990 | 0 | if (start == 0) |
| 1991 | { | |
| 1992 | 0 | start = hidden.visibleToAbsoluteColumn(start); |
| 1993 | } | |
| 1994 | ||
| 1995 | 0 | end = hidden.getNextHiddenBoundary(false, start); |
| 1996 | 0 | if (start == end) |
| 1997 | { | |
| 1998 | 0 | end = max; |
| 1999 | } | |
| 2000 | 0 | if (end > max) |
| 2001 | { | |
| 2002 | 0 | end = max; |
| 2003 | } | |
| 2004 | } | |
| 2005 | ||
| 2006 | 0 | regions.add(new int[] { start, end }); |
| 2007 | ||
| 2008 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 2009 | { | |
| 2010 | 0 | start = hidden.visibleToAbsoluteColumn(end); |
| 2011 | 0 | start = hidden.getNextHiddenBoundary(true, start) + 1; |
| 2012 | } | |
| 2013 | 0 | } while (end < max); |
| 2014 | ||
| 2015 | // int[][] startEnd = new int[regions.size()][2]; | |
| 2016 | ||
| 2017 | 0 | return regions; |
| 2018 | } | |
| 2019 | ||
| 2020 | 1 | @Override |
| 2021 | public List<AlignmentAnnotation> getVisibleAlignmentAnnotation( | |
| 2022 | boolean selectedOnly) | |
| 2023 | { | |
| 2024 | 1 | ArrayList<AlignmentAnnotation> ala = new ArrayList<>(); |
| 2025 | 1 | AlignmentAnnotation[] aa; |
| 2026 | ? | if ((aa = alignment.getAlignmentAnnotation()) != null) |
| 2027 | { | |
| 2028 | 1 | for (AlignmentAnnotation annot : aa) |
| 2029 | { | |
| 2030 | 4 | AlignmentAnnotation clone = new AlignmentAnnotation(annot); |
| 2031 | 4 | if (selectedOnly && selectionGroup != null) |
| 2032 | { | |
| 2033 | 4 | clone.makeVisibleAnnotation(selectionGroup.getStartRes(), |
| 2034 | selectionGroup.getEndRes(), alignment.getHiddenColumns()); | |
| 2035 | } | |
| 2036 | else | |
| 2037 | { | |
| 2038 | 0 | clone.makeVisibleAnnotation(alignment.getHiddenColumns()); |
| 2039 | } | |
| 2040 | 4 | ala.add(clone); |
| 2041 | } | |
| 2042 | } | |
| 2043 | 1 | return ala; |
| 2044 | } | |
| 2045 | ||
| 2046 | 2084 | @Override |
| 2047 | public boolean isPadGaps() | |
| 2048 | { | |
| 2049 | 2084 | return padGaps; |
| 2050 | } | |
| 2051 | ||
| 2052 | 531 | @Override |
| 2053 | public void setPadGaps(boolean padGaps) | |
| 2054 | { | |
| 2055 | 531 | this.padGaps = padGaps; |
| 2056 | } | |
| 2057 | ||
| 2058 | /** | |
| 2059 | * apply any post-edit constraints and trigger any calculations needed after | |
| 2060 | * an edit has been performed on the alignment | |
| 2061 | * | |
| 2062 | * @param ap | |
| 2063 | */ | |
| 2064 | 901 | @Override |
| 2065 | public void alignmentChanged(AlignmentViewPanel ap) | |
| 2066 | { | |
| 2067 | 901 | if (isPadGaps()) |
| 2068 | { | |
| 2069 | 505 | alignment.padGaps(); |
| 2070 | } | |
| 2071 | 901 | if (autoCalculateConsensus) |
| 2072 | { | |
| 2073 | 901 | updateConsensus(ap); |
| 2074 | 901 | updateSecondaryStructureConsensus(ap); |
| 2075 | } | |
| 2076 | 901 | if (hconsensus != null && autoCalculateConsensus) |
| 2077 | { | |
| 2078 | 883 | updateConservation(ap); |
| 2079 | } | |
| 2080 | 901 | if (autoCalculateStrucConsensus) |
| 2081 | { | |
| 2082 | 901 | updateStrucConsensus(ap); |
| 2083 | } | |
| 2084 | ||
| 2085 | // Reset endRes of groups if beyond alignment width | |
| 2086 | 901 | int alWidth = alignment.getWidth(); |
| 2087 | 901 | List<SequenceGroup> groups = alignment.getGroups(); |
| 2088 | 901 | if (groups != null) |
| 2089 | { | |
| 2090 | 901 | for (SequenceGroup sg : groups) |
| 2091 | { | |
| 2092 | 197 | if (sg.getEndRes() > alWidth) |
| 2093 | { | |
| 2094 | 0 | sg.setEndRes(alWidth - 1); |
| 2095 | } | |
| 2096 | } | |
| 2097 | } | |
| 2098 | ||
| 2099 | 901 | if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) |
| 2100 | { | |
| 2101 | 0 | selectionGroup.setEndRes(alWidth - 1); |
| 2102 | } | |
| 2103 | ||
| 2104 | 901 | updateAllColourSchemes(); |
| 2105 | 901 | calculator.restartWorkers(); |
| 2106 | // alignment.adjustSequenceAnnotations(); | |
| 2107 | } | |
| 2108 | ||
| 2109 | /** | |
| 2110 | * reset scope and do calculations for all applied colourschemes on alignment | |
| 2111 | */ | |
| 2112 | 901 | void updateAllColourSchemes() |
| 2113 | { | |
| 2114 | 901 | ResidueShaderI rs = residueShading; |
| 2115 | 901 | if (rs != null) |
| 2116 | { | |
| 2117 | 901 | rs.alignmentChanged(alignment, hiddenRepSequences); |
| 2118 | ||
| 2119 | 901 | rs.setConsensus(hconsensus); |
| 2120 | 901 | if (rs.conservationApplied()) |
| 2121 | { | |
| 2122 | 3 | rs.setConservation(Conservation.calculateConservation("All", |
| 2123 | alignment.getSequences(), 0, alignment.getWidth(), false, | |
| 2124 | getConsPercGaps(), false)); | |
| 2125 | } | |
| 2126 | } | |
| 2127 | ||
| 2128 | 901 | for (SequenceGroup sg : alignment.getGroups()) |
| 2129 | { | |
| 2130 | 197 | if (sg.cs != null) |
| 2131 | { | |
| 2132 | 197 | sg.cs.alignmentChanged(sg, hiddenRepSequences); |
| 2133 | } | |
| 2134 | 197 | sg.recalcConservation(); |
| 2135 | } | |
| 2136 | } | |
| 2137 | ||
| 2138 | 531 | protected void initAutoAnnotation() |
| 2139 | { | |
| 2140 | // TODO: add menu option action that nulls or creates consensus object | |
| 2141 | // depending on if the user wants to see the annotation or not in a | |
| 2142 | // specific alignment | |
| 2143 | ||
| 2144 | 531 | if (hconsensus == null && !isDataset) |
| 2145 | { | |
| 2146 | 531 | if (!alignment.isNucleotide()) |
| 2147 | { | |
| 2148 | 420 | initConservation(); |
| 2149 | 420 | initQuality(); |
| 2150 | } | |
| 2151 | else | |
| 2152 | { | |
| 2153 | 111 | initRNAStructure(); |
| 2154 | } | |
| 2155 | 531 | consensus = new AlignmentAnnotation("Consensus", |
| 2156 | MessageManager.getString("label.consensus_descr"), | |
| 2157 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2158 | 531 | setSecondaryStructureSources(alignment.getAlignmentAnnotation()); |
| 2159 | ||
| 2160 | 531 | List<String> secondaryStructureSources = getSecondaryStructureSources(); |
| 2161 | 531 | boolean singleProvider = false; |
| 2162 | ||
| 2163 | 531 | if (secondaryStructureSources != null) |
| 2164 | { | |
| 2165 | 531 | if(secondaryStructureSources.size() == 2) |
| 2166 | { | |
| 2167 | 18 | singleProvider = true; //Single provider if size is 2 (All, Provider 1) |
| 2168 | } | |
| 2169 | ||
| 2170 | 531 | AlignmentUtils.assignColorsForSecondaryStructureProviders(secondaryStructureSources); |
| 2171 | ||
| 2172 | 531 | secondaryStructureConsensus = new ArrayList<AlignmentAnnotation>(); |
| 2173 | 531 | for (String ssSource : secondaryStructureSources) |
| 2174 | { | |
| 2175 | ||
| 2176 | 473 | AlignmentAnnotation ssConsensus = new AlignmentAnnotation( |
| 2177 | MessageManager.getString("label.ssconsensus_label") + " " | |
| 2178 | + ssSource, | |
| 2179 | ssSource + " " | |
| 2180 | + MessageManager | |
| 2181 | .getString("label.ssconsensus_descr"), | |
| 2182 | new Annotation[1], 0f, 100f, | |
| 2183 | AlignmentAnnotation.BAR_GRAPH); | |
| 2184 | 473 | ssConsensus.autoCalculated=true; |
| 2185 | 473 | ssConsensus.hasData=false; |
| 2186 | 473 | ssConsensus.hasText=true; |
| 2187 | // Hide global ss consensus for all providers if only one provider is present | |
| 2188 | 473 | ssConsensus.visible = ssSource.equals(Constants.SS_ALL_PROVIDERS) && singleProvider ? false : true; |
| 2189 | ||
| 2190 | 473 | secondaryStructureConsensus.add(ssConsensus); |
| 2191 | } | |
| 2192 | ||
| 2193 | } | |
| 2194 | ||
| 2195 | 531 | initConsensus(consensus); |
| 2196 | 531 | initSSConsensus(secondaryStructureConsensus); |
| 2197 | 531 | initGapCounts(); |
| 2198 | 531 | initComplementConsensus(); |
| 2199 | } | |
| 2200 | } | |
| 2201 | ||
| 2202 | /** | |
| 2203 | * If this is a protein alignment and there are mappings to cDNA, adds the | |
| 2204 | * cDNA consensus annotation and returns true, else returns false. | |
| 2205 | */ | |
| 2206 | 541 | public boolean initComplementConsensus() |
| 2207 | { | |
| 2208 | 541 | if (!alignment.isNucleotide()) |
| 2209 | { | |
| 2210 | 429 | final List<AlignedCodonFrame> codonMappings = alignment |
| 2211 | .getCodonFrames(); | |
| 2212 | 429 | if (codonMappings != null && !codonMappings.isEmpty()) |
| 2213 | { | |
| 2214 | 4 | boolean doConsensus = false; |
| 2215 | 4 | for (AlignedCodonFrame mapping : codonMappings) |
| 2216 | { | |
| 2217 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 2218 | 4 | MapList[] mapLists = mapping.getdnaToProt(); |
| 2219 | // mapLists can be empty if project load has not finished resolving | |
| 2220 | // seqs | |
| 2221 | 4 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 2222 | { | |
| 2223 | 4 | doConsensus = true; |
| 2224 | 4 | break; |
| 2225 | } | |
| 2226 | } | |
| 2227 | 4 | if (doConsensus) |
| 2228 | { | |
| 2229 | 4 | Iterable<AlignmentAnnotation> annots = alignment |
| 2230 | .findAnnotations(null, null, "cDNA Consensus"); | |
| 2231 | 4 | if (annots != null && (complementConsensus == null)) |
| 2232 | { | |
| 2233 | 4 | for (AlignmentAnnotation ann : annots) |
| 2234 | { | |
| 2235 | 0 | if (ann.autoCalculated) |
| 2236 | { | |
| 2237 | 0 | complementConsensus = ann; |
| 2238 | } | |
| 2239 | } | |
| 2240 | } | |
| 2241 | 4 | if (complementConsensus == null) |
| 2242 | { | |
| 2243 | 4 | complementConsensus = new AlignmentAnnotation("cDNA Consensus", |
| 2244 | MessageManager | |
| 2245 | .getString("label.complement_consensus_descr"), | |
| 2246 | new Annotation[1], 0f, 100f, | |
| 2247 | AlignmentAnnotation.BAR_GRAPH); | |
| 2248 | 4 | initConsensus(complementConsensus); |
| 2249 | } | |
| 2250 | 4 | return true; |
| 2251 | } | |
| 2252 | } | |
| 2253 | } | |
| 2254 | 537 | return false; |
| 2255 | } | |
| 2256 | ||
| 2257 | 535 | private void initConsensus(AlignmentAnnotation aa) |
| 2258 | { | |
| 2259 | 535 | aa.hasText = true; |
| 2260 | 535 | aa.autoCalculated = true; |
| 2261 | ||
| 2262 | 535 | if (showConsensus) |
| 2263 | { | |
| 2264 | 534 | alignment.addAnnotation(aa); |
| 2265 | } | |
| 2266 | } | |
| 2267 | ||
| 2268 | 531 | private void initSSConsensus( |
| 2269 | List<AlignmentAnnotation> secondaryStructureConsensuses) | |
| 2270 | { | |
| 2271 | 531 | if (secondaryStructureConsensuses == null) |
| 2272 | { | |
| 2273 | 0 | return; |
| 2274 | } | |
| 2275 | 531 | for (AlignmentAnnotation aa : secondaryStructureConsensuses) |
| 2276 | { | |
| 2277 | 473 | aa.hasText = true; |
| 2278 | 473 | aa.autoCalculated = true; |
| 2279 | ||
| 2280 | 473 | if (showSSConsensus) |
| 2281 | { | |
| 2282 | 0 | alignment.addAnnotation(aa); |
| 2283 | } | |
| 2284 | ||
| 2285 | } | |
| 2286 | } | |
| 2287 | ||
| 2288 | // these should be extracted from the view model - style and settings for | |
| 2289 | // derived annotation | |
| 2290 | 531 | private void initGapCounts() |
| 2291 | { | |
| 2292 | 531 | if (showOccupancy) |
| 2293 | { | |
| 2294 | 527 | gapcounts = new AlignmentAnnotation("Occupancy", |
| 2295 | MessageManager.getString("label.occupancy_descr"), | |
| 2296 | new Annotation[1], 0f, alignment.getHeight(), | |
| 2297 | AlignmentAnnotation.BAR_GRAPH); | |
| 2298 | 527 | gapcounts.hasText = true; |
| 2299 | 527 | gapcounts.autoCalculated = true; |
| 2300 | 527 | gapcounts.scaleColLabel = true; |
| 2301 | 527 | gapcounts.graph = AlignmentAnnotation.BAR_GRAPH; |
| 2302 | ||
| 2303 | 527 | alignment.addAnnotation(gapcounts); |
| 2304 | } | |
| 2305 | } | |
| 2306 | ||
| 2307 | 420 | private void initConservation() |
| 2308 | { | |
| 2309 | 420 | if (showConservation) |
| 2310 | { | |
| 2311 | 419 | if (conservation == null) |
| 2312 | { | |
| 2313 | 419 | conservation = new AlignmentAnnotation("Conservation", |
| 2314 | MessageManager.formatMessage("label.conservation_descr", | |
| 2315 | getConsPercGaps()), | |
| 2316 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2317 | 419 | conservation.hasText = true; |
| 2318 | 419 | conservation.autoCalculated = true; |
| 2319 | 419 | alignment.addAnnotation(conservation); |
| 2320 | } | |
| 2321 | } | |
| 2322 | } | |
| 2323 | ||
| 2324 | 420 | private void initQuality() |
| 2325 | { | |
| 2326 | 420 | if (showQuality) |
| 2327 | { | |
| 2328 | 420 | if (quality == null) |
| 2329 | { | |
| 2330 | 420 | quality = new AlignmentAnnotation("Quality", |
| 2331 | MessageManager.getString("label.quality_descr"), | |
| 2332 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2333 | 420 | quality.hasText = true; |
| 2334 | 420 | quality.autoCalculated = true; |
| 2335 | 420 | alignment.addAnnotation(quality); |
| 2336 | } | |
| 2337 | } | |
| 2338 | } | |
| 2339 | ||
| 2340 | 111 | private void initRNAStructure() |
| 2341 | { | |
| 2342 | 111 | if (alignment.hasRNAStructure() && strucConsensus == null) |
| 2343 | { | |
| 2344 | 2 | strucConsensus = new AlignmentAnnotation("StrucConsensus", |
| 2345 | MessageManager.getString("label.strucconsensus_descr"), | |
| 2346 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2347 | 2 | strucConsensus.hasText = true; |
| 2348 | 2 | strucConsensus.autoCalculated = true; |
| 2349 | ||
| 2350 | 2 | if (showConsensus) |
| 2351 | { | |
| 2352 | 2 | alignment.addAnnotation(strucConsensus); |
| 2353 | } | |
| 2354 | } | |
| 2355 | } | |
| 2356 | ||
| 2357 | /* | |
| 2358 | * (non-Javadoc) | |
| 2359 | * | |
| 2360 | * @see jalview.api.AlignViewportI#calcPanelHeight() | |
| 2361 | */ | |
| 2362 | 7469 | @Override |
| 2363 | public int calcPanelHeight() | |
| 2364 | { | |
| 2365 | // setHeight of panels | |
| 2366 | 7469 | AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation(); |
| 2367 | 7468 | int height = 0; |
| 2368 | 7468 | int charHeight = getCharHeight(); |
| 2369 | 7467 | if (anns != null) |
| 2370 | { | |
| 2371 | 7467 | BitSet graphgrp = new BitSet(); |
| 2372 | 7467 | for (AlignmentAnnotation aa : anns) |
| 2373 | { | |
| 2374 | 38865 | if (aa == null) |
| 2375 | { | |
| 2376 | 0 | jalview.bin.Console.errPrintln("Null annotation row: ignoring."); |
| 2377 | 0 | continue; |
| 2378 | } | |
| 2379 | 38865 | if (!aa.isForDisplay()) |
| 2380 | { | |
| 2381 | 5374 | continue; |
| 2382 | } | |
| 2383 | 33492 | if (aa.graphGroup > -1) |
| 2384 | { | |
| 2385 | 720 | if (graphgrp.get(aa.graphGroup)) |
| 2386 | { | |
| 2387 | 360 | continue; |
| 2388 | } | |
| 2389 | else | |
| 2390 | { | |
| 2391 | 360 | graphgrp.set(aa.graphGroup); |
| 2392 | } | |
| 2393 | } | |
| 2394 | 33132 | aa.height = 0; |
| 2395 | ||
| 2396 | 33132 | if (aa.hasText) |
| 2397 | { | |
| 2398 | 28799 | aa.height += charHeight; |
| 2399 | } | |
| 2400 | ||
| 2401 | 33132 | if (aa.hasIcons) |
| 2402 | { | |
| 2403 | 2555 | aa.height += 16; |
| 2404 | } | |
| 2405 | ||
| 2406 | 33132 | if (aa.graph > 0) |
| 2407 | { | |
| 2408 | 29577 | aa.height += aa.graphHeight + 20; |
| 2409 | } | |
| 2410 | ||
| 2411 | 33132 | if (aa.height == 0) |
| 2412 | { | |
| 2413 | 168 | aa.height = 20; |
| 2414 | } | |
| 2415 | ||
| 2416 | 33132 | height += aa.height; |
| 2417 | } | |
| 2418 | } | |
| 2419 | 7468 | if (height == 0) |
| 2420 | { | |
| 2421 | // set minimum | |
| 2422 | 37 | height = 20; |
| 2423 | } | |
| 2424 | 7468 | return height; |
| 2425 | } | |
| 2426 | ||
| 2427 | 135 | @Override |
| 2428 | public void updateGroupAnnotationSettings(boolean applyGlobalSettings, | |
| 2429 | boolean preserveNewGroupSettings) | |
| 2430 | { | |
| 2431 | 135 | boolean updateCalcs = false; |
| 2432 | 135 | boolean conv = isShowGroupConservation(); |
| 2433 | 135 | boolean cons = isShowGroupConsensus(); |
| 2434 | 135 | boolean sscons = isShowGroupSSConsensus(); |
| 2435 | 135 | boolean showprf = isShowSequenceLogo(); |
| 2436 | 135 | boolean showConsHist = isShowConsensusHistogram(); |
| 2437 | 135 | boolean normLogo = isNormaliseSequenceLogo(); |
| 2438 | ||
| 2439 | /** | |
| 2440 | * TODO reorder the annotation rows according to group/sequence ordering on | |
| 2441 | * alignment | |
| 2442 | */ | |
| 2443 | // boolean sortg = true; | |
| 2444 | ||
| 2445 | // remove old automatic annotation | |
| 2446 | // add any new annotation | |
| 2447 | ||
| 2448 | // intersect alignment annotation with alignment groups | |
| 2449 | ||
| 2450 | 135 | AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation(); |
| 2451 | 135 | List<SequenceGroup> oldrfs = new ArrayList<>(); |
| 2452 | 135 | if (aan != null) |
| 2453 | { | |
| 2454 | 1375 | for (int an = 0; an < aan.length; an++) |
| 2455 | { | |
| 2456 | 1240 | if (aan[an].autoCalculated && aan[an].groupRef != null) |
| 2457 | { | |
| 2458 | 0 | oldrfs.add(aan[an].groupRef); |
| 2459 | 0 | alignment.deleteAnnotation(aan[an], false); |
| 2460 | } | |
| 2461 | } | |
| 2462 | } | |
| 2463 | 135 | if (alignment.getGroups() != null) |
| 2464 | { | |
| 2465 | 135 | for (SequenceGroup sg : alignment.getGroups()) |
| 2466 | { | |
| 2467 | 70 | updateCalcs = false; |
| 2468 | 70 | if (applyGlobalSettings |
| 2469 | || (!preserveNewGroupSettings && !oldrfs.contains(sg))) | |
| 2470 | { | |
| 2471 | // set defaults for this group's conservation/consensus | |
| 2472 | 11 | sg.setshowSequenceLogo(showprf); |
| 2473 | 11 | sg.setShowConsensusHistogram(showConsHist); |
| 2474 | 11 | sg.setNormaliseSequenceLogo(normLogo); |
| 2475 | } | |
| 2476 | 70 | if (conv) |
| 2477 | { | |
| 2478 | 0 | updateCalcs = true; |
| 2479 | 0 | alignment.addAnnotation(sg.getConservationRow(), 0); |
| 2480 | } | |
| 2481 | 70 | if (cons) |
| 2482 | { | |
| 2483 | 24 | updateCalcs = true; |
| 2484 | 24 | alignment.addAnnotation(sg.getConsensus(), 0); |
| 2485 | } | |
| 2486 | 70 | if (sscons) |
| 2487 | { | |
| 2488 | 0 | updateCalcs = true; |
| 2489 | 0 | List<String> secondaryStructureSources = getSecondaryStructureSources(); |
| 2490 | 0 | if (secondaryStructureSources != null) |
| 2491 | { | |
| 2492 | 0 | List<AlignmentAnnotation> ssAa = sg |
| 2493 | .getSSConsensus(secondaryStructureSources); | |
| 2494 | 0 | if (ssAa != null) |
| 2495 | { | |
| 2496 | 0 | for (AlignmentAnnotation aa : ssAa) |
| 2497 | { | |
| 2498 | // Setting annotation visibility to true for the secondary | |
| 2499 | // structure consensus for all providers | |
| 2500 | 0 | if (aa.label.contains(Constants.SS_ALL_PROVIDERS)) |
| 2501 | { | |
| 2502 | 0 | aa.visible = true; |
| 2503 | } | |
| 2504 | 0 | alignment.addAnnotation(aa, 0); |
| 2505 | } | |
| 2506 | } | |
| 2507 | } | |
| 2508 | } | |
| 2509 | // refresh the annotation rows | |
| 2510 | 70 | if (updateCalcs) |
| 2511 | { | |
| 2512 | 24 | sg.recalcConservation(); |
| 2513 | } | |
| 2514 | } | |
| 2515 | } | |
| 2516 | 135 | oldrfs.clear(); |
| 2517 | } | |
| 2518 | ||
| 2519 | 22140 | @Override |
| 2520 | public boolean isDisplayReferenceSeq() | |
| 2521 | { | |
| 2522 | 22140 | return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq(); |
| 2523 | } | |
| 2524 | ||
| 2525 | 10 | @Override |
| 2526 | public void setDisplayReferenceSeq(boolean displayReferenceSeq) | |
| 2527 | { | |
| 2528 | 10 | viewStyle.setDisplayReferenceSeq(displayReferenceSeq); |
| 2529 | } | |
| 2530 | ||
| 2531 | 5 | @Override |
| 2532 | public boolean isColourByReferenceSeq() | |
| 2533 | { | |
| 2534 | 5 | return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq(); |
| 2535 | } | |
| 2536 | ||
| 2537 | 35174 | @Override |
| 2538 | public Color getSequenceColour(SequenceI seq) | |
| 2539 | { | |
| 2540 | 35174 | Color sqc = sequenceColours.get(seq); |
| 2541 | 35174 | return (sqc == null ? Color.white : sqc); |
| 2542 | } | |
| 2543 | ||
| 2544 | 1303 | @Override |
| 2545 | public void setSequenceColour(SequenceI seq, Color col) | |
| 2546 | { | |
| 2547 | 1303 | if (col == null) |
| 2548 | { | |
| 2549 | 0 | sequenceColours.remove(seq); |
| 2550 | } | |
| 2551 | else | |
| 2552 | { | |
| 2553 | 1303 | sequenceColours.put(seq, col); |
| 2554 | } | |
| 2555 | } | |
| 2556 | ||
| 2557 | 9 | @Override |
| 2558 | public void updateSequenceIdColours() | |
| 2559 | { | |
| 2560 | 9 | for (SequenceGroup sg : alignment.getGroups()) |
| 2561 | { | |
| 2562 | 5 | if (sg.idColour != null) |
| 2563 | { | |
| 2564 | 0 | for (SequenceI s : sg.getSequences(getHiddenRepSequences())) |
| 2565 | { | |
| 2566 | 0 | sequenceColours.put(s, sg.idColour); |
| 2567 | } | |
| 2568 | } | |
| 2569 | } | |
| 2570 | } | |
| 2571 | ||
| 2572 | 1 | @Override |
| 2573 | public void clearSequenceColours() | |
| 2574 | { | |
| 2575 | 1 | sequenceColours.clear(); |
| 2576 | } | |
| 2577 | ||
| 2578 | ||
| 2579 | 0 | @Override |
| 2580 | public Color getAnnotationColour(AlignmentAnnotation annot) | |
| 2581 | { | |
| 2582 | 0 | Color annotColor = annotationColours.get(annot); |
| 2583 | 0 | return (annotColor == null ? Color.white : annotColor); |
| 2584 | } | |
| 2585 | ||
| 2586 | 12 | @Override |
| 2587 | public void setAnnotationColour(AlignmentAnnotation annot, Color col) | |
| 2588 | { | |
| 2589 | 12 | if (col == null) |
| 2590 | { | |
| 2591 | 0 | annotationColours.remove(annot); |
| 2592 | 0 | annot.setAnnotationGroupColour(Color.WHITE); |
| 2593 | } | |
| 2594 | else | |
| 2595 | { | |
| 2596 | 12 | annotationColours.put(annot, col); |
| 2597 | 12 | annot.setAnnotationGroupColour(col); |
| 2598 | } | |
| 2599 | } | |
| 2600 | ||
| 2601 | 1261 | @Override |
| 2602 | public void updateAnnotationColours() | |
| 2603 | { | |
| 2604 | 1261 | for (SequenceGroup sg : alignment.getGroups()) |
| 2605 | { | |
| 2606 | 930 | if (sg.idColour != null) |
| 2607 | { | |
| 2608 | 925 | for (AlignmentAnnotation annot : sg.getAlignmentAnnotation()) |
| 2609 | { | |
| 2610 | 384 | annotationColours.put(annot, sg.idColour); |
| 2611 | 384 | annot.setAnnotationGroupColour(sg.idColour); |
| 2612 | } | |
| 2613 | } | |
| 2614 | } | |
| 2615 | } | |
| 2616 | ||
| 2617 | 1 | @Override |
| 2618 | public void clearAnnotationColours() | |
| 2619 | { | |
| 2620 | 1 | for (AlignmentAnnotation annot : annotationColours.keySet()) |
| 2621 | { | |
| 2622 | 4 | annot.setAnnotationGroupColour(Color.WHITE); |
| 2623 | } | |
| 2624 | 1 | annotationColours.clear(); |
| 2625 | } | |
| 2626 | ||
| 2627 | 0 | @Override |
| 2628 | public Map<AlignmentAnnotation, Color> getAnnotationColours() | |
| 2629 | { | |
| 2630 | 0 | return annotationColours; |
| 2631 | } | |
| 2632 | ||
| 2633 | 0 | @Override |
| 2634 | public void setAnnotationColours( | |
| 2635 | Map<AlignmentAnnotation, Color> annotationColours) | |
| 2636 | { | |
| 2637 | 0 | this.annotationColours = annotationColours; |
| 2638 | } | |
| 2639 | ||
| 2640 | 1195 | @Override |
| 2641 | public AlignViewportI getCodingComplement() | |
| 2642 | { | |
| 2643 | 1195 | return this.codingComplement; |
| 2644 | } | |
| 2645 | ||
| 2646 | /** | |
| 2647 | * Set this as the (cDna/protein) complement of the given viewport. Also | |
| 2648 | * ensures the reverse relationship is set on the given viewport. | |
| 2649 | */ | |
| 2650 | 6 | @Override |
| 2651 | public void setCodingComplement(AlignViewportI av) | |
| 2652 | { | |
| 2653 | 6 | if (this == av) |
| 2654 | { | |
| 2655 | 0 | jalview.bin.Console |
| 2656 | .errPrintln("Ignoring recursive setCodingComplement request"); | |
| 2657 | } | |
| 2658 | else | |
| 2659 | { | |
| 2660 | 6 | this.codingComplement = av; |
| 2661 | // avoid infinite recursion! | |
| 2662 | 6 | if (av.getCodingComplement() != this) |
| 2663 | { | |
| 2664 | 3 | av.setCodingComplement(this); |
| 2665 | } | |
| 2666 | } | |
| 2667 | } | |
| 2668 | ||
| 2669 | 25 | @Override |
| 2670 | public boolean isNucleotide() | |
| 2671 | { | |
| 2672 | 25 | return getAlignment() == null ? false : getAlignment().isNucleotide(); |
| 2673 | } | |
| 2674 | ||
| 2675 | 2036552 | @Override |
| 2676 | public FeaturesDisplayedI getFeaturesDisplayed() | |
| 2677 | { | |
| 2678 | 2038032 | return featuresDisplayed; |
| 2679 | } | |
| 2680 | ||
| 2681 | 129 | @Override |
| 2682 | public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) | |
| 2683 | { | |
| 2684 | 129 | featuresDisplayed = featuresDisplayedI; |
| 2685 | } | |
| 2686 | ||
| 2687 | 83 | @Override |
| 2688 | public boolean areFeaturesDisplayed() | |
| 2689 | { | |
| 2690 | 83 | return featuresDisplayed != null |
| 2691 | && featuresDisplayed.getRegisteredFeaturesCount() > 0; | |
| 2692 | } | |
| 2693 | ||
| 2694 | /** | |
| 2695 | * set the flag | |
| 2696 | * | |
| 2697 | * @param b | |
| 2698 | * features are displayed if true | |
| 2699 | */ | |
| 2700 | 149 | @Override |
| 2701 | public void setShowSequenceFeatures(boolean b) | |
| 2702 | { | |
| 2703 | 149 | viewStyle.setShowSequenceFeatures(b); |
| 2704 | } | |
| 2705 | ||
| 2706 | 523850 | @Override |
| 2707 | public boolean isShowSequenceFeatures() | |
| 2708 | { | |
| 2709 | 523862 | return viewStyle.isShowSequenceFeatures(); |
| 2710 | } | |
| 2711 | ||
| 2712 | 0 | @Override |
| 2713 | public void setShowSequenceFeaturesHeight(boolean selected) | |
| 2714 | { | |
| 2715 | 0 | viewStyle.setShowSequenceFeaturesHeight(selected); |
| 2716 | } | |
| 2717 | ||
| 2718 | 0 | @Override |
| 2719 | public boolean isShowSequenceFeaturesHeight() | |
| 2720 | { | |
| 2721 | 0 | return viewStyle.isShowSequenceFeaturesHeight(); |
| 2722 | } | |
| 2723 | ||
| 2724 | 711 | @Override |
| 2725 | public void setShowAnnotation(boolean b) | |
| 2726 | { | |
| 2727 | 711 | viewStyle.setShowAnnotation(b); |
| 2728 | } | |
| 2729 | ||
| 2730 | 4298 | @Override |
| 2731 | public boolean isShowAnnotation() | |
| 2732 | { | |
| 2733 | 4298 | return viewStyle.isShowAnnotation(); |
| 2734 | } | |
| 2735 | ||
| 2736 | 14225 | @Override |
| 2737 | public boolean isRightAlignIds() | |
| 2738 | { | |
| 2739 | 14225 | return viewStyle.isRightAlignIds(); |
| 2740 | } | |
| 2741 | ||
| 2742 | 620 | @Override |
| 2743 | public void setRightAlignIds(boolean rightAlignIds) | |
| 2744 | { | |
| 2745 | 620 | viewStyle.setRightAlignIds(rightAlignIds); |
| 2746 | } | |
| 2747 | ||
| 2748 | 1087 | @Override |
| 2749 | public boolean getConservationSelected() | |
| 2750 | { | |
| 2751 | 1087 | return viewStyle.getConservationSelected(); |
| 2752 | } | |
| 2753 | ||
| 2754 | 89 | @Override |
| 2755 | public void setShowBoxes(boolean state) | |
| 2756 | { | |
| 2757 | 89 | viewStyle.setShowBoxes(state); |
| 2758 | } | |
| 2759 | ||
| 2760 | /** | |
| 2761 | * @return | |
| 2762 | * @see jalview.api.ViewStyleI#getTextColour() | |
| 2763 | */ | |
| 2764 | 707059 | @Override |
| 2765 | public Color getTextColour() | |
| 2766 | { | |
| 2767 | 707059 | return viewStyle.getTextColour(); |
| 2768 | } | |
| 2769 | ||
| 2770 | /** | |
| 2771 | * @return | |
| 2772 | * @see jalview.api.ViewStyleI#getTextColour2() | |
| 2773 | */ | |
| 2774 | 48 | @Override |
| 2775 | public Color getTextColour2() | |
| 2776 | { | |
| 2777 | 48 | return viewStyle.getTextColour2(); |
| 2778 | } | |
| 2779 | ||
| 2780 | /** | |
| 2781 | * @return | |
| 2782 | * @see jalview.api.ViewStyleI#getThresholdTextColour() | |
| 2783 | */ | |
| 2784 | 468903 | @Override |
| 2785 | public int getThresholdTextColour() | |
| 2786 | { | |
| 2787 | 468903 | return viewStyle.getThresholdTextColour(); |
| 2788 | } | |
| 2789 | ||
| 2790 | /** | |
| 2791 | * @return | |
| 2792 | * @see jalview.api.ViewStyleI#isConservationColourSelected() | |
| 2793 | */ | |
| 2794 | 0 | @Override |
| 2795 | public boolean isConservationColourSelected() | |
| 2796 | { | |
| 2797 | 0 | return viewStyle.isConservationColourSelected(); |
| 2798 | } | |
| 2799 | ||
| 2800 | /** | |
| 2801 | * @return | |
| 2802 | * @see jalview.api.ViewStyleI#isRenderGaps() | |
| 2803 | */ | |
| 2804 | 3608 | @Override |
| 2805 | public boolean isRenderGaps() | |
| 2806 | { | |
| 2807 | 3608 | return viewStyle.isRenderGaps(); |
| 2808 | } | |
| 2809 | ||
| 2810 | /** | |
| 2811 | * @return | |
| 2812 | * @see jalview.api.ViewStyleI#isShowColourText() | |
| 2813 | */ | |
| 2814 | 703 | @Override |
| 2815 | public boolean isShowColourText() | |
| 2816 | { | |
| 2817 | 703 | return viewStyle.isShowColourText(); |
| 2818 | } | |
| 2819 | ||
| 2820 | /** | |
| 2821 | * @param conservationColourSelected | |
| 2822 | * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean) | |
| 2823 | */ | |
| 2824 | 0 | @Override |
| 2825 | public void setConservationColourSelected( | |
| 2826 | boolean conservationColourSelected) | |
| 2827 | { | |
| 2828 | 0 | viewStyle.setConservationColourSelected(conservationColourSelected); |
| 2829 | } | |
| 2830 | ||
| 2831 | /** | |
| 2832 | * @param showColourText | |
| 2833 | * @see jalview.api.ViewStyleI#setShowColourText(boolean) | |
| 2834 | */ | |
| 2835 | 0 | @Override |
| 2836 | public void setShowColourText(boolean showColourText) | |
| 2837 | { | |
| 2838 | 0 | viewStyle.setShowColourText(showColourText); |
| 2839 | } | |
| 2840 | ||
| 2841 | /** | |
| 2842 | * @param textColour | |
| 2843 | * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color) | |
| 2844 | */ | |
| 2845 | 89 | @Override |
| 2846 | public void setTextColour(Color textColour) | |
| 2847 | { | |
| 2848 | 89 | viewStyle.setTextColour(textColour); |
| 2849 | } | |
| 2850 | ||
| 2851 | /** | |
| 2852 | * @param thresholdTextColour | |
| 2853 | * @see jalview.api.ViewStyleI#setThresholdTextColour(int) | |
| 2854 | */ | |
| 2855 | 89 | @Override |
| 2856 | public void setThresholdTextColour(int thresholdTextColour) | |
| 2857 | { | |
| 2858 | 89 | viewStyle.setThresholdTextColour(thresholdTextColour); |
| 2859 | } | |
| 2860 | ||
| 2861 | /** | |
| 2862 | * @param textColour2 | |
| 2863 | * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color) | |
| 2864 | */ | |
| 2865 | 89 | @Override |
| 2866 | public void setTextColour2(Color textColour2) | |
| 2867 | { | |
| 2868 | 89 | viewStyle.setTextColour2(textColour2); |
| 2869 | } | |
| 2870 | ||
| 2871 | 149 | @Override |
| 2872 | public ViewStyleI getViewStyle() | |
| 2873 | { | |
| 2874 | 149 | return new ViewStyle(viewStyle); |
| 2875 | } | |
| 2876 | ||
| 2877 | 90 | @Override |
| 2878 | public void setViewStyle(ViewStyleI settingsForView) | |
| 2879 | { | |
| 2880 | 90 | viewStyle = new ViewStyle(settingsForView); |
| 2881 | 90 | if (residueShading != null) |
| 2882 | { | |
| 2883 | 90 | residueShading.setConservationApplied( |
| 2884 | settingsForView.isConservationColourSelected()); | |
| 2885 | } | |
| 2886 | } | |
| 2887 | ||
| 2888 | 0 | @Override |
| 2889 | public boolean sameStyle(ViewStyleI them) | |
| 2890 | { | |
| 2891 | 0 | return viewStyle.sameStyle(them); |
| 2892 | } | |
| 2893 | ||
| 2894 | /** | |
| 2895 | * @return | |
| 2896 | * @see jalview.api.ViewStyleI#getIdWidth() | |
| 2897 | */ | |
| 2898 | 6947 | @Override |
| 2899 | public int getIdWidth() | |
| 2900 | { | |
| 2901 | 6947 | return viewStyle.getIdWidth(); |
| 2902 | } | |
| 2903 | ||
| 2904 | /** | |
| 2905 | * @param i | |
| 2906 | * @see jalview.api.ViewStyleI#setIdWidth(int) | |
| 2907 | */ | |
| 2908 | 694 | @Override |
| 2909 | public void setIdWidth(int i) | |
| 2910 | { | |
| 2911 | 694 | viewStyle.setIdWidth(i); |
| 2912 | } | |
| 2913 | ||
| 2914 | /** | |
| 2915 | * @return | |
| 2916 | * @see jalview.api.ViewStyleI#isCentreColumnLabels() | |
| 2917 | */ | |
| 2918 | 703 | @Override |
| 2919 | public boolean isCentreColumnLabels() | |
| 2920 | { | |
| 2921 | 703 | return viewStyle.isCentreColumnLabels(); |
| 2922 | } | |
| 2923 | ||
| 2924 | /** | |
| 2925 | * @param centreColumnLabels | |
| 2926 | * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean) | |
| 2927 | */ | |
| 2928 | 620 | @Override |
| 2929 | public void setCentreColumnLabels(boolean centreColumnLabels) | |
| 2930 | { | |
| 2931 | 620 | viewStyle.setCentreColumnLabels(centreColumnLabels); |
| 2932 | } | |
| 2933 | ||
| 2934 | /** | |
| 2935 | * @param showdbrefs | |
| 2936 | * @see jalview.api.ViewStyleI#setShowDBRefs(boolean) | |
| 2937 | */ | |
| 2938 | 620 | @Override |
| 2939 | public void setShowDBRefs(boolean showdbrefs) | |
| 2940 | { | |
| 2941 | 620 | viewStyle.setShowDBRefs(showdbrefs); |
| 2942 | } | |
| 2943 | ||
| 2944 | /** | |
| 2945 | * @return | |
| 2946 | * @see jalview.api.ViewStyleI#isShowDBRefs() | |
| 2947 | */ | |
| 2948 | 751 | @Override |
| 2949 | public boolean isShowDBRefs() | |
| 2950 | { | |
| 2951 | 751 | return viewStyle.isShowDBRefs(); |
| 2952 | } | |
| 2953 | ||
| 2954 | /** | |
| 2955 | * @return | |
| 2956 | * @see jalview.api.ViewStyleI#isShowNPFeats() | |
| 2957 | */ | |
| 2958 | 751 | @Override |
| 2959 | public boolean isShowNPFeats() | |
| 2960 | { | |
| 2961 | 751 | return viewStyle.isShowNPFeats(); |
| 2962 | } | |
| 2963 | ||
| 2964 | /** | |
| 2965 | * @param shownpfeats | |
| 2966 | * @see jalview.api.ViewStyleI#setShowNPFeats(boolean) | |
| 2967 | */ | |
| 2968 | 620 | @Override |
| 2969 | public void setShowNPFeats(boolean shownpfeats) | |
| 2970 | { | |
| 2971 | 620 | viewStyle.setShowNPFeats(shownpfeats); |
| 2972 | } | |
| 2973 | ||
| 2974 | public abstract StructureSelectionManager getStructureSelectionManager(); | |
| 2975 | ||
| 2976 | /** | |
| 2977 | * Add one command to the command history list. | |
| 2978 | * | |
| 2979 | * @param command | |
| 2980 | */ | |
| 2981 | 1 | public void addToHistoryList(CommandI command) |
| 2982 | { | |
| 2983 | 1 | if (this.historyList != null) |
| 2984 | { | |
| 2985 | 1 | this.historyList.push(command); |
| 2986 | 1 | broadcastCommand(command, false); |
| 2987 | 1 | setSavedUpToDate(false); |
| 2988 | 1 | Jalview2XML.setStateSavedUpToDate(false); |
| 2989 | } | |
| 2990 | } | |
| 2991 | ||
| 2992 | 1 | protected void broadcastCommand(CommandI command, boolean undo) |
| 2993 | { | |
| 2994 | 1 | getStructureSelectionManager().commandPerformed(command, undo, |
| 2995 | getVamsasSource()); | |
| 2996 | } | |
| 2997 | ||
| 2998 | /** | |
| 2999 | * Add one command to the command redo list. | |
| 3000 | * | |
| 3001 | * @param command | |
| 3002 | */ | |
| 3003 | 0 | public void addToRedoList(CommandI command) |
| 3004 | { | |
| 3005 | 0 | if (this.redoList != null) |
| 3006 | { | |
| 3007 | 0 | this.redoList.push(command); |
| 3008 | } | |
| 3009 | 0 | broadcastCommand(command, true); |
| 3010 | } | |
| 3011 | ||
| 3012 | /** | |
| 3013 | * Clear the command redo list. | |
| 3014 | */ | |
| 3015 | 0 | public void clearRedoList() |
| 3016 | { | |
| 3017 | 0 | if (this.redoList != null) |
| 3018 | { | |
| 3019 | 0 | this.redoList.clear(); |
| 3020 | } | |
| 3021 | } | |
| 3022 | ||
| 3023 | 53 | public void setHistoryList(Deque<CommandI> list) |
| 3024 | { | |
| 3025 | 53 | this.historyList = list; |
| 3026 | } | |
| 3027 | ||
| 3028 | 1648 | public Deque<CommandI> getHistoryList() |
| 3029 | { | |
| 3030 | 1648 | return this.historyList; |
| 3031 | } | |
| 3032 | ||
| 3033 | 53 | public void setRedoList(Deque<CommandI> list) |
| 3034 | { | |
| 3035 | 53 | this.redoList = list; |
| 3036 | } | |
| 3037 | ||
| 3038 | 1648 | public Deque<CommandI> getRedoList() |
| 3039 | { | |
| 3040 | 1648 | return this.redoList; |
| 3041 | } | |
| 3042 | ||
| 3043 | 1 | @Override |
| 3044 | public VamsasSource getVamsasSource() | |
| 3045 | { | |
| 3046 | 1 | return this; |
| 3047 | } | |
| 3048 | ||
| 3049 | 8297 | public SequenceAnnotationOrder getSortAnnotationsBy() |
| 3050 | { | |
| 3051 | 8297 | return sortAnnotationsBy; |
| 3052 | } | |
| 3053 | ||
| 3054 | 0 | public void setSortAnnotationsBy( |
| 3055 | SequenceAnnotationOrder sortAnnotationsBy) | |
| 3056 | { | |
| 3057 | 0 | this.sortAnnotationsBy = sortAnnotationsBy; |
| 3058 | } | |
| 3059 | ||
| 3060 | 8297 | public boolean isShowAutocalculatedAbove() |
| 3061 | { | |
| 3062 | 8297 | return showAutocalculatedAbove; |
| 3063 | } | |
| 3064 | ||
| 3065 | 475 | public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) |
| 3066 | { | |
| 3067 | 475 | this.showAutocalculatedAbove = showAutocalculatedAbove; |
| 3068 | } | |
| 3069 | ||
| 3070 | 3 | @Override |
| 3071 | public boolean isScaleProteinAsCdna() | |
| 3072 | { | |
| 3073 | 3 | return viewStyle.isScaleProteinAsCdna(); |
| 3074 | } | |
| 3075 | ||
| 3076 | 0 | @Override |
| 3077 | public void setScaleProteinAsCdna(boolean b) | |
| 3078 | { | |
| 3079 | 0 | viewStyle.setScaleProteinAsCdna(b); |
| 3080 | } | |
| 3081 | ||
| 3082 | 0 | @Override |
| 3083 | public boolean isProteinFontAsCdna() | |
| 3084 | { | |
| 3085 | 0 | return viewStyle.isProteinFontAsCdna(); |
| 3086 | } | |
| 3087 | ||
| 3088 | 0 | @Override |
| 3089 | public void setProteinFontAsCdna(boolean b) | |
| 3090 | { | |
| 3091 | 0 | viewStyle.setProteinFontAsCdna(b); |
| 3092 | } | |
| 3093 | ||
| 3094 | 89 | @Override |
| 3095 | public void setShowComplementFeatures(boolean b) | |
| 3096 | { | |
| 3097 | 89 | viewStyle.setShowComplementFeatures(b); |
| 3098 | } | |
| 3099 | ||
| 3100 | 528985 | @Override |
| 3101 | public boolean isShowComplementFeatures() | |
| 3102 | { | |
| 3103 | 529033 | return viewStyle.isShowComplementFeatures(); |
| 3104 | } | |
| 3105 | ||
| 3106 | 89 | @Override |
| 3107 | public void setShowComplementFeaturesOnTop(boolean b) | |
| 3108 | { | |
| 3109 | 89 | viewStyle.setShowComplementFeaturesOnTop(b); |
| 3110 | } | |
| 3111 | ||
| 3112 | 49 | @Override |
| 3113 | public boolean isShowComplementFeaturesOnTop() | |
| 3114 | { | |
| 3115 | 49 | return viewStyle.isShowComplementFeaturesOnTop(); |
| 3116 | } | |
| 3117 | ||
| 3118 | /** | |
| 3119 | * @return true if view should scroll to show the highlighted region of a | |
| 3120 | * sequence | |
| 3121 | * @return | |
| 3122 | */ | |
| 3123 | 51 | @Override |
| 3124 | public final boolean isFollowHighlight() | |
| 3125 | { | |
| 3126 | 51 | return followHighlight; |
| 3127 | } | |
| 3128 | ||
| 3129 | 89 | @Override |
| 3130 | public final void setFollowHighlight(boolean b) | |
| 3131 | { | |
| 3132 | 89 | this.followHighlight = b; |
| 3133 | } | |
| 3134 | ||
| 3135 | 43887 | @Override |
| 3136 | public ViewportRanges getRanges() | |
| 3137 | { | |
| 3138 | 43887 | return ranges; |
| 3139 | } | |
| 3140 | ||
| 3141 | /** | |
| 3142 | * Helper method to populate the SearchResults with the location in the | |
| 3143 | * complementary alignment to scroll to, in order to match this one. | |
| 3144 | * | |
| 3145 | * @param sr | |
| 3146 | * the SearchResults to add to | |
| 3147 | * @return the offset (below top of visible region) of the matched sequence | |
| 3148 | */ | |
| 3149 | 757 | protected int findComplementScrollTarget(SearchResultsI sr) |
| 3150 | { | |
| 3151 | 757 | final AlignViewportI complement = getCodingComplement(); |
| 3152 | 757 | if (complement == null || !complement.isFollowHighlight()) |
| 3153 | { | |
| 3154 | 755 | return 0; |
| 3155 | } | |
| 3156 | 2 | boolean iAmProtein = !getAlignment().isNucleotide(); |
| 3157 | 2 | AlignmentI proteinAlignment = iAmProtein ? getAlignment() |
| 3158 | : complement.getAlignment(); | |
| 3159 | 2 | if (proteinAlignment == null) |
| 3160 | { | |
| 3161 | 0 | return 0; |
| 3162 | } | |
| 3163 | 2 | final List<AlignedCodonFrame> mappings = proteinAlignment |
| 3164 | .getCodonFrames(); | |
| 3165 | ||
| 3166 | /* | |
| 3167 | * Heuristic: find the first mapped sequence (if any) with a non-gapped | |
| 3168 | * residue in the middle column of the visible region. Scroll the | |
| 3169 | * complementary alignment to line up the corresponding residue. | |
| 3170 | */ | |
| 3171 | 2 | int seqOffset = 0; |
| 3172 | 2 | SequenceI sequence = null; |
| 3173 | ||
| 3174 | /* | |
| 3175 | * locate 'middle' column (true middle if an odd number visible, left of | |
| 3176 | * middle if an even number visible) | |
| 3177 | */ | |
| 3178 | 2 | int middleColumn = ranges.getStartRes() |
| 3179 | + (ranges.getEndRes() - ranges.getStartRes()) / 2; | |
| 3180 | 2 | final HiddenSequences hiddenSequences = getAlignment() |
| 3181 | .getHiddenSequences(); | |
| 3182 | ||
| 3183 | /* | |
| 3184 | * searching to the bottom of the alignment gives smoother scrolling across | |
| 3185 | * all gapped visible regions | |
| 3186 | */ | |
| 3187 | 2 | int lastSeq = alignment.getHeight() - 1; |
| 3188 | 2 | List<AlignedCodonFrame> seqMappings = null; |
| 3189 | 2 | for (int seqNo = ranges |
| 3190 | 2 | .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) |
| 3191 | { | |
| 3192 | 2 | sequence = getAlignment().getSequenceAt(seqNo); |
| 3193 | 2 | if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) |
| 3194 | { | |
| 3195 | 0 | continue; |
| 3196 | } | |
| 3197 | 2 | if (Comparison.isGap(sequence.getCharAt(middleColumn))) |
| 3198 | { | |
| 3199 | 0 | continue; |
| 3200 | } | |
| 3201 | 2 | seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence, |
| 3202 | mappings, | |
| 3203 | getCodingComplement().getAlignment().getSequences()); | |
| 3204 | 2 | if (!seqMappings.isEmpty()) |
| 3205 | { | |
| 3206 | 2 | break; |
| 3207 | } | |
| 3208 | } | |
| 3209 | ||
| 3210 | 2 | if (sequence == null || seqMappings == null || seqMappings.isEmpty()) |
| 3211 | { | |
| 3212 | /* | |
| 3213 | * No ungapped mapped sequence in middle column - do nothing | |
| 3214 | */ | |
| 3215 | 0 | return 0; |
| 3216 | } | |
| 3217 | 2 | MappingUtils.addSearchResults(sr, sequence, |
| 3218 | sequence.findPosition(middleColumn), seqMappings); | |
| 3219 | 2 | return seqOffset; |
| 3220 | } | |
| 3221 | ||
| 3222 | /** | |
| 3223 | * synthesize a column selection if none exists so it covers the given | |
| 3224 | * selection group. if wholewidth is false, no column selection is made if the | |
| 3225 | * selection group covers the whole alignment width. | |
| 3226 | * | |
| 3227 | * @param sg | |
| 3228 | * @param wholewidth | |
| 3229 | */ | |
| 3230 | 0 | public void expandColSelection(SequenceGroup sg, boolean wholewidth) |
| 3231 | { | |
| 3232 | 0 | int sgs, sge; |
| 3233 | 0 | if (sg != null && (sgs = sg.getStartRes()) >= 0 |
| 3234 | && sg.getStartRes() <= (sge = sg.getEndRes()) | |
| 3235 | && !this.hasSelectedColumns()) | |
| 3236 | { | |
| 3237 | 0 | if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) |
| 3238 | { | |
| 3239 | // do nothing | |
| 3240 | 0 | return; |
| 3241 | } | |
| 3242 | 0 | if (colSel == null) |
| 3243 | { | |
| 3244 | 0 | colSel = new ColumnSelection(); |
| 3245 | } | |
| 3246 | 0 | for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) |
| 3247 | { | |
| 3248 | 0 | colSel.addElement(cspos); |
| 3249 | } | |
| 3250 | } | |
| 3251 | } | |
| 3252 | ||
| 3253 | /** | |
| 3254 | * hold status of current selection group - defined on alignment or not. | |
| 3255 | */ | |
| 3256 | private boolean selectionIsDefinedGroup = false; | |
| 3257 | ||
| 3258 | 0 | @Override |
| 3259 | public boolean isSelectionDefinedGroup() | |
| 3260 | { | |
| 3261 | 0 | if (selectionGroup == null) |
| 3262 | { | |
| 3263 | 0 | return false; |
| 3264 | } | |
| 3265 | 0 | if (isSelectionGroupChanged(true)) |
| 3266 | { | |
| 3267 | 0 | selectionIsDefinedGroup = false; |
| 3268 | 0 | List<SequenceGroup> gps = alignment.getGroups(); |
| 3269 | 0 | if (gps == null || gps.size() == 0) |
| 3270 | { | |
| 3271 | 0 | selectionIsDefinedGroup = false; |
| 3272 | } | |
| 3273 | else | |
| 3274 | { | |
| 3275 | 0 | selectionIsDefinedGroup = gps.contains(selectionGroup); |
| 3276 | } | |
| 3277 | } | |
| 3278 | 0 | return selectionGroup.isDefined() || selectionIsDefinedGroup; |
| 3279 | } | |
| 3280 | ||
| 3281 | /** | |
| 3282 | * null, or currently highlighted results on this view | |
| 3283 | */ | |
| 3284 | private SearchResultsI searchResults = null; | |
| 3285 | ||
| 3286 | protected TreeModel currentTree = null; | |
| 3287 | ||
| 3288 | 12504 | @Override |
| 3289 | public boolean hasSearchResults() | |
| 3290 | { | |
| 3291 | 12504 | return searchResults != null; |
| 3292 | } | |
| 3293 | ||
| 3294 | 7 | @Override |
| 3295 | public void setSearchResults(SearchResultsI results) | |
| 3296 | { | |
| 3297 | 7 | searchResults = results; |
| 3298 | } | |
| 3299 | ||
| 3300 | 54 | @Override |
| 3301 | public SearchResultsI getSearchResults() | |
| 3302 | { | |
| 3303 | 54 | return searchResults; |
| 3304 | } | |
| 3305 | ||
| 3306 | 4916 | @Override |
| 3307 | public ContactListI getContactList(AlignmentAnnotation _aa, int column) | |
| 3308 | { | |
| 3309 | 4916 | return alignment.getContactListFor(_aa, column); |
| 3310 | } | |
| 3311 | ||
| 3312 | 307 | @Override |
| 3313 | public ContactMatrixI getContactMatrix( | |
| 3314 | AlignmentAnnotation alignmentAnnotation) | |
| 3315 | { | |
| 3316 | 307 | return alignment.getContactMatrixFor(alignmentAnnotation); |
| 3317 | } | |
| 3318 | ||
| 3319 | /** | |
| 3320 | * get the consensus sequence as displayed under the PID consensus annotation | |
| 3321 | * row. | |
| 3322 | * | |
| 3323 | * @return consensus sequence as a new sequence object | |
| 3324 | */ | |
| 3325 | 1 | public SequenceI getConsensusSeq() |
| 3326 | { | |
| 3327 | 1 | if (consensus == null) |
| 3328 | { | |
| 3329 | 0 | updateConsensus(null); |
| 3330 | } | |
| 3331 | 1 | if (consensus == null) |
| 3332 | { | |
| 3333 | 0 | return null; |
| 3334 | } | |
| 3335 | 1 | StringBuffer seqs = new StringBuffer(); |
| 3336 | 4 | for (int i = 0; i < consensus.annotations.length; i++) |
| 3337 | { | |
| 3338 | 3 | Annotation annotation = consensus.annotations[i]; |
| 3339 | 3 | if (annotation != null) |
| 3340 | { | |
| 3341 | 3 | String description = annotation.description; |
| 3342 | 3 | if (description != null && description.startsWith("[")) |
| 3343 | { | |
| 3344 | // consensus is a tie - just pick the first one | |
| 3345 | 1 | seqs.append(description.charAt(1)); |
| 3346 | } | |
| 3347 | else | |
| 3348 | { | |
| 3349 | 2 | seqs.append(annotation.displayCharacter); |
| 3350 | } | |
| 3351 | } | |
| 3352 | } | |
| 3353 | ||
| 3354 | 1 | SequenceI sq = new Sequence("Consensus", seqs.toString()); |
| 3355 | 1 | sq.setDescription("Percentage Identity Consensus " |
| 3356 | 1 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3357 | 1 | return sq; |
| 3358 | } | |
| 3359 | ||
| 3360 | // to do jal-4386 | |
| 3361 | 0 | public SequenceI getSSConsensusSeq() |
| 3362 | { | |
| 3363 | 0 | if (secondaryStructureConsensus == null) |
| 3364 | { | |
| 3365 | 0 | updateSecondaryStructureConsensus(null); |
| 3366 | } | |
| 3367 | 0 | if (secondaryStructureConsensus == null) |
| 3368 | { | |
| 3369 | 0 | return null; |
| 3370 | } | |
| 3371 | 0 | StringBuffer seqs = new StringBuffer(); |
| 3372 | // for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++) | |
| 3373 | // { | |
| 3374 | // Annotation annotation = secondaryStructureConsensus.annotations[i]; | |
| 3375 | // if (annotation != null) | |
| 3376 | // { | |
| 3377 | // String description = annotation.description; | |
| 3378 | // if (description != null && description.startsWith("[")) | |
| 3379 | // { | |
| 3380 | // // consensus is a tie - just pick the first one | |
| 3381 | // seqs.append(description.charAt(1)); | |
| 3382 | // } | |
| 3383 | // else | |
| 3384 | // { | |
| 3385 | // seqs.append(annotation.displayCharacter); | |
| 3386 | // } | |
| 3387 | // } | |
| 3388 | // } | |
| 3389 | ||
| 3390 | 0 | SequenceI sq = new Sequence("Sec Str Consensus", seqs.toString()); |
| 3391 | 0 | sq.setDescription("Percentage Identity Sec Str Consensus " |
| 3392 | 0 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3393 | 0 | return sq; |
| 3394 | } | |
| 3395 | ||
| 3396 | 24 | @Override |
| 3397 | public void setCurrentTree(TreeModel tree) | |
| 3398 | { | |
| 3399 | 24 | currentTree = tree; |
| 3400 | } | |
| 3401 | ||
| 3402 | 54 | @Override |
| 3403 | public TreeModel getCurrentTree() | |
| 3404 | { | |
| 3405 | 54 | return currentTree; |
| 3406 | } | |
| 3407 | ||
| 3408 | 121 | @Override |
| 3409 | public AlignmentExportData getAlignExportData( | |
| 3410 | AlignExportSettingsI options) | |
| 3411 | { | |
| 3412 | 121 | AlignmentI alignmentToExport = null; |
| 3413 | 121 | String[] omitHidden = null; |
| 3414 | 121 | alignmentToExport = null; |
| 3415 | ||
| 3416 | 121 | if (hasHiddenColumns() && !options.isExportHiddenColumns()) |
| 3417 | { | |
| 3418 | 0 | omitHidden = getViewAsString(false, |
| 3419 | options.isExportHiddenSequences()); | |
| 3420 | } | |
| 3421 | ||
| 3422 | 121 | int[] alignmentStartEnd = new int[2]; |
| 3423 | 121 | if (hasHiddenRows() && options.isExportHiddenSequences()) |
| 3424 | { | |
| 3425 | 0 | alignmentToExport = getAlignment().getHiddenSequences() |
| 3426 | .getFullAlignment(); | |
| 3427 | } | |
| 3428 | else | |
| 3429 | { | |
| 3430 | 121 | alignmentToExport = getAlignment(); |
| 3431 | } | |
| 3432 | 121 | alignmentStartEnd = getAlignment().getHiddenColumns() |
| 3433 | .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); | |
| 3434 | 121 | AlignmentExportData ed = new AlignmentExportData(alignmentToExport, |
| 3435 | omitHidden, alignmentStartEnd); | |
| 3436 | 121 | return ed; |
| 3437 | } | |
| 3438 | ||
| 3439 | /** | |
| 3440 | * flag set to indicate if structure views might be out of sync with sequences | |
| 3441 | * in the alignment | |
| 3442 | */ | |
| 3443 | ||
| 3444 | private boolean needToUpdateStructureViews = false; | |
| 3445 | ||
| 3446 | 0 | @Override |
| 3447 | public boolean isUpdateStructures() | |
| 3448 | { | |
| 3449 | 0 | return needToUpdateStructureViews; |
| 3450 | } | |
| 3451 | ||
| 3452 | 3 | @Override |
| 3453 | public void setUpdateStructures(boolean update) | |
| 3454 | { | |
| 3455 | 3 | needToUpdateStructureViews = update; |
| 3456 | } | |
| 3457 | ||
| 3458 | 4275 | @Override |
| 3459 | public boolean needToUpdateStructureViews() | |
| 3460 | { | |
| 3461 | 4275 | boolean update = needToUpdateStructureViews; |
| 3462 | 4275 | needToUpdateStructureViews = false; |
| 3463 | 4275 | return update; |
| 3464 | } | |
| 3465 | ||
| 3466 | 2 | @Override |
| 3467 | public void addSequenceGroup(SequenceGroup sequenceGroup) | |
| 3468 | { | |
| 3469 | 2 | alignment.addGroup(sequenceGroup); |
| 3470 | ||
| 3471 | 2 | Color col = sequenceGroup.idColour; |
| 3472 | 2 | if (col != null) |
| 3473 | { | |
| 3474 | 2 | col = col.brighter(); |
| 3475 | ||
| 3476 | 2 | for (SequenceI sq : sequenceGroup.getSequences()) |
| 3477 | { | |
| 3478 | 15 | setSequenceColour(sq, col); |
| 3479 | } | |
| 3480 | ||
| 3481 | 2 | List<AlignmentAnnotation> annotations = sequenceGroup.getAnnotationsFromTree(); |
| 3482 | 2 | if (annotations != null) { |
| 3483 | 2 | for (AlignmentAnnotation annot : annotations) { |
| 3484 | 4 | setAnnotationColour(annot, col); |
| 3485 | } | |
| 3486 | } | |
| 3487 | } | |
| 3488 | ||
| 3489 | 2 | if (codingComplement != null) |
| 3490 | { | |
| 3491 | 0 | SequenceGroup mappedGroup = MappingUtils |
| 3492 | .mapSequenceGroup(sequenceGroup, this, codingComplement); | |
| 3493 | 0 | if (mappedGroup.getSequences().size() > 0) |
| 3494 | { | |
| 3495 | 0 | codingComplement.getAlignment().addGroup(mappedGroup); |
| 3496 | ||
| 3497 | 0 | if (col != null) |
| 3498 | { | |
| 3499 | 0 | for (SequenceI seq : mappedGroup.getSequences()) |
| 3500 | { | |
| 3501 | 0 | codingComplement.setSequenceColour(seq, col); |
| 3502 | } | |
| 3503 | } | |
| 3504 | } | |
| 3505 | // propagate the structure view update flag according to our own setting | |
| 3506 | 0 | codingComplement.setUpdateStructures(needToUpdateStructureViews); |
| 3507 | } | |
| 3508 | } | |
| 3509 | ||
| 3510 | 34 | @Override |
| 3511 | public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly) | |
| 3512 | { | |
| 3513 | 34 | int start = 0; |
| 3514 | 34 | int end = 0; |
| 3515 | 34 | if (selectedRegionOnly && selectionGroup != null) |
| 3516 | { | |
| 3517 | 4 | start = selectionGroup.getStartRes(); |
| 3518 | 4 | end = selectionGroup.getEndRes() + 1; |
| 3519 | } | |
| 3520 | else | |
| 3521 | { | |
| 3522 | 30 | end = alignment.getWidth(); |
| 3523 | } | |
| 3524 | 34 | return (alignment.getHiddenColumns().getVisContigsIterator(start, end, |
| 3525 | false)); | |
| 3526 | } | |
| 3527 | ||
| 3528 | 133 | public void setSavedUpToDate(boolean s) |
| 3529 | { | |
| 3530 | 133 | setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES); |
| 3531 | } | |
| 3532 | ||
| 3533 | 471 | public void setSavedUpToDate(boolean s, QuitHandler.Message m) |
| 3534 | { | |
| 3535 | 471 | Console.debug( |
| 3536 | "Setting " + this.getViewId() + " setSavedUpToDate to " + s); | |
| 3537 | 471 | savedUpToDate = s; |
| 3538 | 471 | QuitHandler.setMessage(m); |
| 3539 | } | |
| 3540 | ||
| 3541 | 4 | public boolean savedUpToDate() |
| 3542 | { | |
| 3543 | 4 | Console.debug("Returning " + this.getViewId() + " savedUpToDate value: " |
| 3544 | + savedUpToDate); | |
| 3545 | 4 | return savedUpToDate; |
| 3546 | } | |
| 3547 | } |