Coverage Report
File AlignmentViewport.java
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21% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignmentViewport | 90 | 738 | 454 |
Contributing tests
This file is covered by 326 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.Connectivity; | |
| 37 | import jalview.analysis.Conservation; | |
| 38 | import jalview.analysis.TreeModel; | |
| 39 | import jalview.api.AlignCalcManagerI; | |
| 40 | import jalview.api.AlignExportSettingsI; | |
| 41 | import jalview.api.AlignViewportI; | |
| 42 | import jalview.api.AlignmentViewPanel; | |
| 43 | import jalview.api.FeaturesDisplayedI; | |
| 44 | import jalview.api.ViewStyleI; | |
| 45 | import jalview.bin.Console; | |
| 46 | import jalview.commands.CommandI; | |
| 47 | import jalview.datamodel.AlignedCodonFrame; | |
| 48 | import jalview.datamodel.AlignmentAnnotation; | |
| 49 | import jalview.datamodel.AlignmentExportData; | |
| 50 | import jalview.datamodel.AlignmentI; | |
| 51 | import jalview.datamodel.AlignmentView; | |
| 52 | import jalview.datamodel.Annotation; | |
| 53 | import jalview.datamodel.ColumnSelection; | |
| 54 | import jalview.datamodel.ContactListI; | |
| 55 | import jalview.datamodel.ContactMatrixI; | |
| 56 | import jalview.datamodel.HiddenColumns; | |
| 57 | import jalview.datamodel.HiddenSequences; | |
| 58 | import jalview.datamodel.ProfilesI; | |
| 59 | import jalview.datamodel.SearchResultsI; | |
| 60 | import jalview.datamodel.Sequence; | |
| 61 | import jalview.datamodel.SequenceCollectionI; | |
| 62 | import jalview.datamodel.SequenceGroup; | |
| 63 | import jalview.datamodel.SequenceI; | |
| 64 | import jalview.gui.QuitHandler; | |
| 65 | import jalview.project.Jalview2XML; | |
| 66 | import jalview.renderer.ResidueShader; | |
| 67 | import jalview.renderer.ResidueShaderI; | |
| 68 | import jalview.schemes.ColourSchemeI; | |
| 69 | import jalview.structure.CommandListener; | |
| 70 | import jalview.structure.StructureSelectionManager; | |
| 71 | import jalview.structure.VamsasSource; | |
| 72 | import jalview.util.Comparison; | |
| 73 | import jalview.util.MapList; | |
| 74 | import jalview.util.MappingUtils; | |
| 75 | import jalview.util.MessageManager; | |
| 76 | import jalview.viewmodel.styles.ViewStyle; | |
| 77 | import jalview.workers.AlignCalcManager; | |
| 78 | import jalview.workers.ComplementConsensusThread; | |
| 79 | import jalview.workers.ConsensusThread; | |
| 80 | import jalview.workers.SecondaryStructureConsensusThread; | |
| 81 | import jalview.workers.StrucConsensusThread; | |
| 82 | ||
| 83 | /** | |
| 84 | * base class holding visualization and analysis attributes and common logic for | |
| 85 | * an active alignment view displayed in the GUI | |
| 86 | * | |
| 87 | * @author jimp | |
| 88 | * | |
| 89 | */ | |
| 90 | public abstract class AlignmentViewport | |
| 91 | implements AlignViewportI, CommandListener, VamsasSource | |
| 92 | { | |
| 93 | protected ViewportRanges ranges; | |
| 94 | ||
| 95 | protected ViewStyleI viewStyle = new ViewStyle(); | |
| 96 | ||
| 97 | /** | |
| 98 | * A viewport that hosts the cDna view of this (protein), or vice versa (if | |
| 99 | * set). | |
| 100 | */ | |
| 101 | AlignViewportI codingComplement = null; | |
| 102 | ||
| 103 | FeaturesDisplayedI featuresDisplayed = null; | |
| 104 | ||
| 105 | protected Deque<CommandI> historyList = new ArrayDeque<>(); | |
| 106 | ||
| 107 | protected Deque<CommandI> redoList = new ArrayDeque<>(); | |
| 108 | ||
| 109 | /** | |
| 110 | * used to determine if quit should be confirmed | |
| 111 | */ | |
| 112 | private boolean savedUpToDate = false; | |
| 113 | ||
| 114 | /** | |
| 115 | * alignment displayed in the viewport. Please use get/setter | |
| 116 | */ | |
| 117 | protected AlignmentI alignment; | |
| 118 | ||
| 119 | 508 |  public AlignmentViewport(AlignmentI al) |
| 120 | { | |
| 121 | 508 | setAlignment(al); |
| 122 | 508 | ranges = new ViewportRanges(al); |
| 123 | } | |
| 124 | ||
| 125 | /** | |
| 126 | * @param name | |
| 127 | * @see jalview.api.ViewStyleI#setFontName(java.lang.String) | |
| 128 | */ | |
| 129 | 0 | @Override |
| 130 | public void setFontName(String name) | |
| 131 | { | |
| 132 | 0 | viewStyle.setFontName(name); |
| 133 | } | |
| 134 | ||
| 135 | /** | |
| 136 | * @param style | |
| 137 | * @see jalview.api.ViewStyleI#setFontStyle(int) | |
| 138 | */ | |
| 139 | 0 | @Override |
| 140 | public void setFontStyle(int style) | |
| 141 | { | |
| 142 | 0 | viewStyle.setFontStyle(style); |
| 143 | } | |
| 144 | ||
| 145 | /** | |
| 146 | * @param size | |
| 147 | * @see jalview.api.ViewStyleI#setFontSize(int) | |
| 148 | */ | |
| 149 | 0 | @Override |
| 150 | public void setFontSize(int size) | |
| 151 | { | |
| 152 | 0 | viewStyle.setFontSize(size); |
| 153 | } | |
| 154 | ||
| 155 | /** | |
| 156 | * @return | |
| 157 | * @see jalview.api.ViewStyleI#getFontStyle() | |
| 158 | */ | |
| 159 | 0 | @Override |
| 160 | public int getFontStyle() | |
| 161 | { | |
| 162 | 0 | return viewStyle.getFontStyle(); |
| 163 | } | |
| 164 | ||
| 165 | /** | |
| 166 | * @return | |
| 167 | * @see jalview.api.ViewStyleI#getFontName() | |
| 168 | */ | |
| 169 | 0 | @Override |
| 170 | public String getFontName() | |
| 171 | { | |
| 172 | 0 | return viewStyle.getFontName(); |
| 173 | } | |
| 174 | ||
| 175 | /** | |
| 176 | * @return | |
| 177 | * @see jalview.api.ViewStyleI#getFontSize() | |
| 178 | */ | |
| 179 | 0 | @Override |
| 180 | public int getFontSize() | |
| 181 | { | |
| 182 | 0 | return viewStyle.getFontSize(); |
| 183 | } | |
| 184 | ||
| 185 | /** | |
| 186 | * @param upperCasebold | |
| 187 | * @see jalview.api.ViewStyleI#setUpperCasebold(boolean) | |
| 188 | */ | |
| 189 | 0 | @Override |
| 190 | public void setUpperCasebold(boolean upperCasebold) | |
| 191 | { | |
| 192 | 0 | viewStyle.setUpperCasebold(upperCasebold); |
| 193 | } | |
| 194 | ||
| 195 | /** | |
| 196 | * @return | |
| 197 | * @see jalview.api.ViewStyleI#isUpperCasebold() | |
| 198 | */ | |
| 199 | 0 | @Override |
| 200 | public boolean isUpperCasebold() | |
| 201 | { | |
| 202 | 0 | return viewStyle.isUpperCasebold(); |
| 203 | } | |
| 204 | ||
| 205 | /** | |
| 206 | * @return | |
| 207 | * @see jalview.api.ViewStyleI#isSeqNameItalics() | |
| 208 | */ | |
| 209 | 3051 | @Override |
| 210 | public boolean isSeqNameItalics() | |
| 211 | { | |
| 212 | 3051 | return viewStyle.isSeqNameItalics(); |
| 213 | } | |
| 214 | ||
| 215 | /** | |
| 216 | * @param colourByReferenceSeq | |
| 217 | * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean) | |
| 218 | */ | |
| 219 | 10 | @Override |
| 220 | public void setColourByReferenceSeq(boolean colourByReferenceSeq) | |
| 221 | { | |
| 222 | 10 | viewStyle.setColourByReferenceSeq(colourByReferenceSeq); |
| 223 | } | |
| 224 | ||
| 225 | /** | |
| 226 | * @param b | |
| 227 | * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean) | |
| 228 | */ | |
| 229 | 693 | @Override |
| 230 | public void setColourAppliesToAllGroups(boolean b) | |
| 231 | { | |
| 232 | 693 | viewStyle.setColourAppliesToAllGroups(b); |
| 233 | } | |
| 234 | ||
| 235 | /** | |
| 236 | * @return | |
| 237 | * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups() | |
| 238 | */ | |
| 239 | 962 | @Override |
| 240 | public boolean getColourAppliesToAllGroups() | |
| 241 | { | |
| 242 | 962 | return viewStyle.getColourAppliesToAllGroups(); |
| 243 | } | |
| 244 | ||
| 245 | /** | |
| 246 | * @return | |
| 247 | * @see jalview.api.ViewStyleI#getAbovePIDThreshold() | |
| 248 | */ | |
| 249 | 878 | @Override |
| 250 | public boolean getAbovePIDThreshold() | |
| 251 | { | |
| 252 | 878 | return viewStyle.getAbovePIDThreshold(); |
| 253 | } | |
| 254 | ||
| 255 | /** | |
| 256 | * @param inc | |
| 257 | * @see jalview.api.ViewStyleI#setIncrement(int) | |
| 258 | */ | |
| 259 | 85 | @Override |
| 260 | public void setIncrement(int inc) | |
| 261 | { | |
| 262 | 85 | viewStyle.setIncrement(inc); |
| 263 | } | |
| 264 | ||
| 265 | /** | |
| 266 | * @return | |
| 267 | * @see jalview.api.ViewStyleI#getIncrement() | |
| 268 | */ | |
| 269 | 0 | @Override |
| 270 | public int getIncrement() | |
| 271 | { | |
| 272 | 0 | return viewStyle.getIncrement(); |
| 273 | } | |
| 274 | ||
| 275 | /** | |
| 276 | * @param b | |
| 277 | * @see jalview.api.ViewStyleI#setConservationSelected(boolean) | |
| 278 | */ | |
| 279 | 93 | @Override |
| 280 | public void setConservationSelected(boolean b) | |
| 281 | { | |
| 282 | 93 | viewStyle.setConservationSelected(b); |
| 283 | } | |
| 284 | ||
| 285 | /** | |
| 286 | * @param show | |
| 287 | * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean) | |
| 288 | */ | |
| 289 | 0 | @Override |
| 290 | public void setShowHiddenMarkers(boolean show) | |
| 291 | { | |
| 292 | 0 | viewStyle.setShowHiddenMarkers(show); |
| 293 | } | |
| 294 | ||
| 295 | /** | |
| 296 | * @return | |
| 297 | * @see jalview.api.ViewStyleI#getShowHiddenMarkers() | |
| 298 | */ | |
| 299 | 6509 | @Override |
| 300 | public boolean getShowHiddenMarkers() | |
| 301 | { | |
| 302 | 6509 | return viewStyle.getShowHiddenMarkers(); |
| 303 | } | |
| 304 | ||
| 305 | /** | |
| 306 | * @param b | |
| 307 | * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean) | |
| 308 | */ | |
| 309 | 9 | @Override |
| 310 | public void setScaleRightWrapped(boolean b) | |
| 311 | { | |
| 312 | 9 | viewStyle.setScaleRightWrapped(b); |
| 313 | } | |
| 314 | ||
| 315 | /** | |
| 316 | * @param b | |
| 317 | * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean) | |
| 318 | */ | |
| 319 | 11 | @Override |
| 320 | public void setScaleLeftWrapped(boolean b) | |
| 321 | { | |
| 322 | 11 | viewStyle.setScaleLeftWrapped(b); |
| 323 | } | |
| 324 | ||
| 325 | /** | |
| 326 | * @param b | |
| 327 | * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean) | |
| 328 | */ | |
| 329 | 9 | @Override |
| 330 | public void setScaleAboveWrapped(boolean b) | |
| 331 | { | |
| 332 | 9 | viewStyle.setScaleAboveWrapped(b); |
| 333 | } | |
| 334 | ||
| 335 | /** | |
| 336 | * @return | |
| 337 | * @see jalview.api.ViewStyleI#getScaleLeftWrapped() | |
| 338 | */ | |
| 339 | 1415 | @Override |
| 340 | public boolean getScaleLeftWrapped() | |
| 341 | { | |
| 342 | 1415 | return viewStyle.getScaleLeftWrapped(); |
| 343 | } | |
| 344 | ||
| 345 | /** | |
| 346 | * @return | |
| 347 | * @see jalview.api.ViewStyleI#getScaleAboveWrapped() | |
| 348 | */ | |
| 349 | 991 | @Override |
| 350 | public boolean getScaleAboveWrapped() | |
| 351 | { | |
| 352 | 991 | return viewStyle.getScaleAboveWrapped(); |
| 353 | } | |
| 354 | ||
| 355 | /** | |
| 356 | * @return | |
| 357 | * @see jalview.api.ViewStyleI#getScaleRightWrapped() | |
| 358 | */ | |
| 359 | 2310 | @Override |
| 360 | public boolean getScaleRightWrapped() | |
| 361 | { | |
| 362 | 2310 | return viewStyle.getScaleRightWrapped(); |
| 363 | } | |
| 364 | ||
| 365 | /** | |
| 366 | * @param b | |
| 367 | * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean) | |
| 368 | */ | |
| 369 | 94 | @Override |
| 370 | public void setAbovePIDThreshold(boolean b) | |
| 371 | { | |
| 372 | 94 | viewStyle.setAbovePIDThreshold(b); |
| 373 | } | |
| 374 | ||
| 375 | /** | |
| 376 | * @param thresh | |
| 377 | * @see jalview.api.ViewStyleI#setThreshold(int) | |
| 378 | */ | |
| 379 | 106 | @Override |
| 380 | public void setThreshold(int thresh) | |
| 381 | { | |
| 382 | 106 | viewStyle.setThreshold(thresh); |
| 383 | } | |
| 384 | ||
| 385 | /** | |
| 386 | * @return | |
| 387 | * @see jalview.api.ViewStyleI#getThreshold() | |
| 388 | */ | |
| 389 | 0 | @Override |
| 390 | public int getThreshold() | |
| 391 | { | |
| 392 | 0 | return viewStyle.getThreshold(); |
| 393 | } | |
| 394 | ||
| 395 | /** | |
| 396 | * @return | |
| 397 | * @see jalview.api.ViewStyleI#getShowJVSuffix() | |
| 398 | */ | |
| 399 | 47069 | @Override |
| 400 | public boolean getShowJVSuffix() | |
| 401 | { | |
| 402 | 47069 | return viewStyle.getShowJVSuffix(); |
| 403 | } | |
| 404 | ||
| 405 | /** | |
| 406 | * @param b | |
| 407 | * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean) | |
| 408 | */ | |
| 409 | 86 | @Override |
| 410 | public void setShowJVSuffix(boolean b) | |
| 411 | { | |
| 412 | 86 | viewStyle.setShowJVSuffix(b); |
| 413 | } | |
| 414 | ||
| 415 | /** | |
| 416 | * @param state | |
| 417 | * @see jalview.api.ViewStyleI#setWrapAlignment(boolean) | |
| 418 | */ | |
| 419 | 97 | @Override |
| 420 | public void setWrapAlignment(boolean state) | |
| 421 | { | |
| 422 | 97 | viewStyle.setWrapAlignment(state); |
| 423 | 97 | ranges.setWrappedMode(state); |
| 424 | } | |
| 425 | ||
| 426 | /** | |
| 427 | * @param state | |
| 428 | * @see jalview.api.ViewStyleI#setShowText(boolean) | |
| 429 | */ | |
| 430 | 85 | @Override |
| 431 | public void setShowText(boolean state) | |
| 432 | { | |
| 433 | 85 | viewStyle.setShowText(state); |
| 434 | } | |
| 435 | ||
| 436 | /** | |
| 437 | * @param state | |
| 438 | * @see jalview.api.ViewStyleI#setRenderGaps(boolean) | |
| 439 | */ | |
| 440 | 85 | @Override |
| 441 | public void setRenderGaps(boolean state) | |
| 442 | { | |
| 443 | 85 | viewStyle.setRenderGaps(state); |
| 444 | } | |
| 445 | ||
| 446 | /** | |
| 447 | * @return | |
| 448 | * @see jalview.api.ViewStyleI#getColourText() | |
| 449 | */ | |
| 450 | 368964 | @Override |
| 451 | public boolean getColourText() | |
| 452 | { | |
| 453 | 368964 | return viewStyle.getColourText(); |
| 454 | } | |
| 455 | ||
| 456 | /** | |
| 457 | * @param state | |
| 458 | * @see jalview.api.ViewStyleI#setColourText(boolean) | |
| 459 | */ | |
| 460 | 85 | @Override |
| 461 | public void setColourText(boolean state) | |
| 462 | { | |
| 463 | 85 | viewStyle.setColourText(state); |
| 464 | } | |
| 465 | ||
| 466 | /** | |
| 467 | * @return | |
| 468 | * @see jalview.api.ViewStyleI#getWrapAlignment() | |
| 469 | */ | |
| 470 | 29683 | @Override |
| 471 | public boolean getWrapAlignment() | |
| 472 | { | |
| 473 | 29683 | return viewStyle.getWrapAlignment(); |
| 474 | } | |
| 475 | ||
| 476 | /** | |
| 477 | * @return | |
| 478 | * @see jalview.api.ViewStyleI#getShowText() | |
| 479 | */ | |
| 480 | 369641 | @Override |
| 481 | public boolean getShowText() | |
| 482 | { | |
| 483 | 369641 | return viewStyle.getShowText(); |
| 484 | } | |
| 485 | ||
| 486 | /** | |
| 487 | * @return | |
| 488 | * @see jalview.api.ViewStyleI#getWrappedWidth() | |
| 489 | */ | |
| 490 | 2 | @Override |
| 491 | public int getWrappedWidth() | |
| 492 | { | |
| 493 | 2 | return viewStyle.getWrappedWidth(); |
| 494 | } | |
| 495 | ||
| 496 | /** | |
| 497 | * @param w | |
| 498 | * @see jalview.api.ViewStyleI#setWrappedWidth(int) | |
| 499 | */ | |
| 500 | 920 | @Override |
| 501 | public void setWrappedWidth(int w) | |
| 502 | { | |
| 503 | 920 | viewStyle.setWrappedWidth(w); |
| 504 | } | |
| 505 | ||
| 506 | /** | |
| 507 | * @return | |
| 508 | * @see jalview.api.ViewStyleI#getCharHeight() | |
| 509 | */ | |
| 510 | 108153 | @Override |
| 511 | public int getCharHeight() | |
| 512 | { | |
| 513 | 108153 | return viewStyle.getCharHeight(); |
| 514 | } | |
| 515 | ||
| 516 | /** | |
| 517 | * @param h | |
| 518 | * @see jalview.api.ViewStyleI#setCharHeight(int) | |
| 519 | */ | |
| 520 | 596 | @Override |
| 521 | public void setCharHeight(int h) | |
| 522 | { | |
| 523 | 596 | viewStyle.setCharHeight(h); |
| 524 | } | |
| 525 | ||
| 526 | /** | |
| 527 | * @return | |
| 528 | * @see jalview.api.ViewStyleI#getCharWidth() | |
| 529 | */ | |
| 530 | 1337911 | @Override |
| 531 | public int getCharWidth() | |
| 532 | { | |
| 533 | 1337933 | return viewStyle.getCharWidth(); |
| 534 | } | |
| 535 | ||
| 536 | /** | |
| 537 | * @param w | |
| 538 | * @see jalview.api.ViewStyleI#setCharWidth(int) | |
| 539 | */ | |
| 540 | 599 | @Override |
| 541 | public void setCharWidth(int w) | |
| 542 | { | |
| 543 | 599 | viewStyle.setCharWidth(w); |
| 544 | } | |
| 545 | ||
| 546 | /** | |
| 547 | * @return | |
| 548 | * @see jalview.api.ViewStyleI#getShowBoxes() | |
| 549 | */ | |
| 550 | 407194 | @Override |
| 551 | public boolean getShowBoxes() | |
| 552 | { | |
| 553 | 407195 | return viewStyle.getShowBoxes(); |
| 554 | } | |
| 555 | ||
| 556 | /** | |
| 557 | * @return | |
| 558 | * @see jalview.api.ViewStyleI#getShowUnconserved() | |
| 559 | */ | |
| 560 | 367185 | @Override |
| 561 | public boolean getShowUnconserved() | |
| 562 | { | |
| 563 | 367185 | return viewStyle.getShowUnconserved(); |
| 564 | } | |
| 565 | ||
| 566 | /** | |
| 567 | * @param showunconserved | |
| 568 | * @see jalview.api.ViewStyleI#setShowUnconserved(boolean) | |
| 569 | */ | |
| 570 | 85 | @Override |
| 571 | public void setShowUnconserved(boolean showunconserved) | |
| 572 | { | |
| 573 | 85 | viewStyle.setShowUnconserved(showunconserved); |
| 574 | } | |
| 575 | ||
| 576 | /** | |
| 577 | * @param default1 | |
| 578 | * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean) | |
| 579 | */ | |
| 580 | 0 | @Override |
| 581 | public void setSeqNameItalics(boolean default1) | |
| 582 | { | |
| 583 | 0 | viewStyle.setSeqNameItalics(default1); |
| 584 | } | |
| 585 | ||
| 586 | 192990 | @Override |
| 587 | public AlignmentI getAlignment() | |
| 588 | { | |
| 589 | 192990 | return alignment; |
| 590 | } | |
| 591 | ||
| 592 | 0 | @Override |
| 593 | public char getGapCharacter() | |
| 594 | { | |
| 595 | 0 | return alignment.getGapCharacter(); |
| 596 | } | |
| 597 | ||
| 598 | protected String sequenceSetID; | |
| 599 | ||
| 600 | /** | |
| 601 | * probably unused indicator that view is of a dataset rather than an | |
| 602 | * alignment | |
| 603 | */ | |
| 604 | protected boolean isDataset = false; | |
| 605 | ||
| 606 | 0 | public void setDataset(boolean b) |
| 607 | { | |
| 608 | 0 | isDataset = b; |
| 609 | } | |
| 610 | ||
| 611 | 478 | public boolean isDataset() |
| 612 | { | |
| 613 | 478 | return isDataset; |
| 614 | } | |
| 615 | ||
| 616 | private Map<SequenceI, SequenceCollectionI> hiddenRepSequences; | |
| 617 | ||
| 618 | protected ColumnSelection colSel = new ColumnSelection(); | |
| 619 | ||
| 620 | public boolean autoCalculateConsensus = true; | |
| 621 | ||
| 622 | protected boolean autoCalculateStrucConsensus = true; | |
| 623 | ||
| 624 | protected boolean ignoreGapsInConsensusCalculation = false; | |
| 625 | ||
| 626 | protected ResidueShaderI residueShading = new ResidueShader(); | |
| 627 | ||
| 628 | 274 | @Override |
| 629 | public void setGlobalColourScheme(ColourSchemeI cs) | |
| 630 | { | |
| 631 | // TODO: logic refactored from AlignFrame changeColour - | |
| 632 | // TODO: autorecalc stuff should be changed to rely on the worker system | |
| 633 | // check to see if we should implement a changeColour(cs) method rather than | |
| 634 | // put the logic in here | |
| 635 | // - means that caller decides if they want to just modify state and defer | |
| 636 | // calculation till later or to do all calculations in thread. | |
| 637 | // via changecolour | |
| 638 | ||
| 639 | /* | |
| 640 | * only instantiate alignment colouring once, thereafter update it; | |
| 641 | * this means that any conservation or PID threshold settings | |
| 642 | * persist when the alignment colour scheme is changed | |
| 643 | */ | |
| 644 | 274 | if (residueShading == null) |
| 645 | { | |
| 646 | 0 | residueShading = new ResidueShader(viewStyle); |
| 647 | } | |
| 648 | 274 | residueShading.setColourScheme(cs); |
| 649 | ||
| 650 | // TODO: do threshold and increment belong in ViewStyle or ResidueShader? | |
| 651 | // ...problem: groups need these, but do not currently have a ViewStyle | |
| 652 | ||
| 653 | 274 | if (cs != null) |
| 654 | { | |
| 655 | 81 | if (getConservationSelected()) |
| 656 | { | |
| 657 | 15 | residueShading.setConservation(hconservation); |
| 658 | } | |
| 659 | /* | |
| 660 | * reset conservation flag in case just set to false if | |
| 661 | * Conservation was null (calculation still in progress) | |
| 662 | */ | |
| 663 | 81 | residueShading.setConservationApplied(getConservationSelected()); |
| 664 | 81 | residueShading.alignmentChanged(alignment, hiddenRepSequences); |
| 665 | } | |
| 666 | ||
| 667 | /* | |
| 668 | * if 'apply colour to all groups' is selected... do so | |
| 669 | * (but don't transfer any colour threshold settings to groups) | |
| 670 | */ | |
| 671 | 274 | if (getColourAppliesToAllGroups()) |
| 672 | { | |
| 673 | 86 | for (SequenceGroup sg : getAlignment().getGroups()) |
| 674 | { | |
| 675 | /* | |
| 676 | * retain any colour thresholds per group while | |
| 677 | * changing choice of colour scheme (JAL-2386) | |
| 678 | */ | |
| 679 | 9 | sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg)); |
| 680 | 9 | if (cs != null) |
| 681 | { | |
| 682 | 8 | sg.getGroupColourScheme().alignmentChanged(sg, |
| 683 | hiddenRepSequences); | |
| 684 | } | |
| 685 | } | |
| 686 | } | |
| 687 | } | |
| 688 | ||
| 689 | 1399 | @Override |
| 690 | public ColourSchemeI getGlobalColourScheme() | |
| 691 | { | |
| 692 | 1399 | return residueShading == null ? null : residueShading.getColourScheme(); |
| 693 | } | |
| 694 | ||
| 695 | 411371 | @Override |
| 696 | public ResidueShaderI getResidueShading() | |
| 697 | { | |
| 698 | 411372 | return residueShading; |
| 699 | } | |
| 700 | ||
| 701 | protected AlignmentAnnotation consensus; | |
| 702 | ||
| 703 | protected AlignmentAnnotation secondaryStructureConsensus; | |
| 704 | ||
| 705 | protected AlignmentAnnotation complementConsensus; | |
| 706 | ||
| 707 | protected AlignmentAnnotation gapcounts; | |
| 708 | ||
| 709 | protected AlignmentAnnotation strucConsensus; | |
| 710 | ||
| 711 | protected AlignmentAnnotation conservation; | |
| 712 | ||
| 713 | protected AlignmentAnnotation quality; | |
| 714 | ||
| 715 | protected AlignmentAnnotation[] groupConsensus; | |
| 716 | ||
| 717 | protected AlignmentAnnotation[] groupSSConsensus; | |
| 718 | ||
| 719 | protected AlignmentAnnotation[] groupConservation; | |
| 720 | ||
| 721 | /** | |
| 722 | * results of alignment consensus analysis for visible portion of view | |
| 723 | */ | |
| 724 | protected ProfilesI hconsensus = null; | |
| 725 | ||
| 726 | protected ProfilesI hSSConsensus = null; | |
| 727 | ||
| 728 | /** | |
| 729 | * results of cDNA complement consensus visible portion of view | |
| 730 | */ | |
| 731 | protected Hashtable<String, Object>[] hcomplementConsensus = null; | |
| 732 | ||
| 733 | /** | |
| 734 | * results of secondary structure base pair consensus for visible portion of | |
| 735 | * view | |
| 736 | */ | |
| 737 | protected Hashtable<String, Object>[] hStrucConsensus = null; | |
| 738 | ||
| 739 | protected Conservation hconservation = null; | |
| 740 | ||
| 741 | 1001 | @Override |
| 742 | public void setConservation(Conservation cons) | |
| 743 | { | |
| 744 | 1001 | hconservation = cons; |
| 745 | } | |
| 746 | ||
| 747 | /** | |
| 748 | * percentage gaps allowed in a column before all amino acid properties should | |
| 749 | * be considered unconserved | |
| 750 | */ | |
| 751 | int ConsPercGaps = 25; // JBPNote : This should be a scalable property! | |
| 752 | ||
| 753 | 1849 | @Override |
| 754 | public int getConsPercGaps() | |
| 755 | { | |
| 756 | 1849 | return ConsPercGaps; |
| 757 | } | |
| 758 | ||
| 759 | 958 | @Override |
| 760 | public void setSequenceConsensusHash(ProfilesI hconsensus) | |
| 761 | { | |
| 762 | 958 | this.hconsensus = hconsensus; |
| 763 | } | |
| 764 | ||
| 765 | 970 | @Override |
| 766 | public void setSequenceSSConsensusHash(ProfilesI hSSConsensus) | |
| 767 | { | |
| 768 | 970 | this.hSSConsensus = hSSConsensus; |
| 769 | } | |
| 770 | ||
| 771 | 4 | @Override |
| 772 | public void setComplementConsensusHash( | |
| 773 | Hashtable<String, Object>[] hconsensus) | |
| 774 | { | |
| 775 | 4 | this.hcomplementConsensus = hconsensus; |
| 776 | } | |
| 777 | ||
| 778 | 3382 | @Override |
| 779 | public ProfilesI getSequenceConsensusHash() | |
| 780 | { | |
| 781 | 3382 | return hconsensus; |
| 782 | } | |
| 783 | ||
| 784 | 3378 | @Override |
| 785 | public ProfilesI getSequenceSSConsensusHash() | |
| 786 | { | |
| 787 | 3378 | return hSSConsensus; |
| 788 | } | |
| 789 | ||
| 790 | 2327 | @Override |
| 791 | public Hashtable<String, Object>[] getComplementConsensusHash() | |
| 792 | { | |
| 793 | 2327 | return hcomplementConsensus; |
| 794 | } | |
| 795 | ||
| 796 | 2328 | @Override |
| 797 | public Hashtable<String, Object>[] getRnaStructureConsensusHash() | |
| 798 | { | |
| 799 | 2328 | return hStrucConsensus; |
| 800 | } | |
| 801 | ||
| 802 | 5 | @Override |
| 803 | public void setRnaStructureConsensusHash( | |
| 804 | Hashtable<String, Object>[] hStrucConsensus) | |
| 805 | { | |
| 806 | 5 | this.hStrucConsensus = hStrucConsensus; |
| 807 | ||
| 808 | } | |
| 809 | ||
| 810 | 1448 | @Override |
| 811 | public AlignmentAnnotation getAlignmentQualityAnnot() | |
| 812 | { | |
| 813 | 1448 | return quality; |
| 814 | } | |
| 815 | ||
| 816 | 2277 | @Override |
| 817 | public AlignmentAnnotation getAlignmentConservationAnnotation() | |
| 818 | { | |
| 819 | 2277 | return conservation; |
| 820 | } | |
| 821 | ||
| 822 | 5629 | @Override |
| 823 | public AlignmentAnnotation getAlignmentConsensusAnnotation() | |
| 824 | { | |
| 825 | 5629 | return consensus; |
| 826 | } | |
| 827 | ||
| 828 | 5293 | @Override |
| 829 | public AlignmentAnnotation getAlignmentSecondaryStructureConsensusAnnotation() | |
| 830 | { | |
| 831 | 5293 | return secondaryStructureConsensus; |
| 832 | } | |
| 833 | ||
| 834 | 5925 | @Override |
| 835 | public AlignmentAnnotation getAlignmentGapAnnotation() | |
| 836 | { | |
| 837 | 5925 | return gapcounts; |
| 838 | } | |
| 839 | ||
| 840 | 2335 | @Override |
| 841 | public AlignmentAnnotation getComplementConsensusAnnotation() | |
| 842 | { | |
| 843 | 2335 | return complementConsensus; |
| 844 | } | |
| 845 | ||
| 846 | 2328 | @Override |
| 847 | public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() | |
| 848 | { | |
| 849 | 2328 | return strucConsensus; |
| 850 | } | |
| 851 | ||
| 852 | protected AlignCalcManagerI calculator = new AlignCalcManager(); | |
| 853 | ||
| 854 | /** | |
| 855 | * trigger update of conservation annotation | |
| 856 | */ | |
| 857 | 999 | public void updateConservation(final AlignmentViewPanel ap) |
| 858 | { | |
| 859 | // see note in mantis : issue number 8585 | |
| 860 | 999 | if (alignment.isNucleotide() |
| 861 | || (conservation == null && quality == null) | |
| 862 | || !autoCalculateConsensus) | |
| 863 | { | |
| 864 | 217 | return; |
| 865 | } | |
| 866 | 782 | if (calculator.getRegisteredWorkersOfClass( |
| 867 | jalview.workers.ConservationThread.class) == null) | |
| 868 | { | |
| 869 | 446 | calculator.registerWorker( |
| 870 | new jalview.workers.ConservationThread(this, ap)); | |
| 871 | } | |
| 872 | } | |
| 873 | ||
| 874 | /** | |
| 875 | * trigger update of consensus annotation | |
| 876 | */ | |
| 877 | 1009 | public void updateConsensus(final AlignmentViewPanel ap) |
| 878 | { | |
| 879 | // see note in mantis : issue number 8585 | |
| 880 | 1009 | if (consensus == null || !autoCalculateConsensus) |
| 881 | { | |
| 882 | 0 | return; |
| 883 | } | |
| 884 | 1009 | if (calculator |
| 885 | .getRegisteredWorkersOfClass(ConsensusThread.class) == null) | |
| 886 | { | |
| 887 | 457 | calculator.registerWorker(new ConsensusThread(this, ap)); |
| 888 | } | |
| 889 | ||
| 890 | /* | |
| 891 | * A separate thread to compute cDNA consensus for a protein alignment | |
| 892 | * which has mapping to cDNA | |
| 893 | */ | |
| 894 | 1009 | final AlignmentI al = this.getAlignment(); |
| 895 | 1009 | if (!al.isNucleotide() && al.getCodonFrames() != null |
| 896 | && !al.getCodonFrames().isEmpty()) | |
| 897 | { | |
| 898 | /* | |
| 899 | * fudge - check first for protein-to-nucleotide mappings | |
| 900 | * (we don't want to do this for protein-to-protein) | |
| 901 | */ | |
| 902 | 4 | boolean doConsensus = false; |
| 903 | 4 | for (AlignedCodonFrame mapping : al.getCodonFrames()) |
| 904 | { | |
| 905 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 906 | 4 | MapList[] mapLists = mapping.getdnaToProt(); |
| 907 | // mapLists can be empty if project load has not finished resolving seqs | |
| 908 | 4 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 909 | { | |
| 910 | 4 | doConsensus = true; |
| 911 | 4 | break; |
| 912 | } | |
| 913 | } | |
| 914 | 4 | if (doConsensus) |
| 915 | { | |
| 916 | 4 | if (calculator.getRegisteredWorkersOfClass( |
| 917 | ComplementConsensusThread.class) == null) | |
| 918 | { | |
| 919 | 4 | calculator |
| 920 | .registerWorker(new ComplementConsensusThread(this, ap)); | |
| 921 | } | |
| 922 | } | |
| 923 | } | |
| 924 | } | |
| 925 | ||
| 926 | /** | |
| 927 | * trigger update of consensus annotation | |
| 928 | */ | |
| 929 | 1009 | public void updateSecondaryStructureConsensus(final AlignmentViewPanel ap) |
| 930 | { | |
| 931 | // see note in mantis : issue number 8585 | |
| 932 | 1009 | if (secondaryStructureConsensus == null || !autoCalculateConsensus) |
| 933 | { | |
| 934 | 0 | return; |
| 935 | } | |
| 936 | 1009 | if (calculator.getRegisteredWorkersOfClass( |
| 937 | SecondaryStructureConsensusThread.class) == null) | |
| 938 | { | |
| 939 | 459 | calculator.registerWorker( |
| 940 | new SecondaryStructureConsensusThread(this, ap)); | |
| 941 | } | |
| 942 | } | |
| 943 | ||
| 944 | // --------START Structure Conservation | |
| 945 | 1006 | public void updateStrucConsensus(final AlignmentViewPanel ap) |
| 946 | { | |
| 947 | 1006 | if (autoCalculateStrucConsensus && strucConsensus == null |
| 948 | && alignment.isNucleotide() && alignment.hasRNAStructure()) | |
| 949 | { | |
| 950 | // secondary structure has been added - so init the consensus line | |
| 951 | 0 | initRNAStructure(); |
| 952 | } | |
| 953 | ||
| 954 | // see note in mantis : issue number 8585 | |
| 955 | 1006 | if (strucConsensus == null || !autoCalculateStrucConsensus) |
| 956 | { | |
| 957 | 1003 | return; |
| 958 | } | |
| 959 | 3 | if (calculator.getRegisteredWorkersOfClass( |
| 960 | StrucConsensusThread.class) == null) | |
| 961 | { | |
| 962 | 3 | calculator.registerWorker(new StrucConsensusThread(this, ap)); |
| 963 | } | |
| 964 | } | |
| 965 | ||
| 966 | 2646 | public boolean isCalcInProgress() |
| 967 | { | |
| 968 | 2646 | return calculator.isWorking(); |
| 969 | } | |
| 970 | ||
| 971 | 9351 | @Override |
| 972 | public boolean isCalculationInProgress( | |
| 973 | AlignmentAnnotation alignmentAnnotation) | |
| 974 | { | |
| 975 | 9351 | if (!alignmentAnnotation.autoCalculated) |
| 976 | { | |
| 977 | 0 | return false; |
| 978 | } | |
| 979 | 9351 | if (calculator.workingInvolvedWith(alignmentAnnotation)) |
| 980 | { | |
| 981 | // jalview.bin.Console.errPrintln("grey out | |
| 982 | // ("+alignmentAnnotation.label+")"); | |
| 983 | 325 | return true; |
| 984 | } | |
| 985 | 9026 | return false; |
| 986 | } | |
| 987 | ||
| 988 | 761 | public void setAlignment(AlignmentI align) |
| 989 | { | |
| 990 | 761 | this.alignment = align; |
| 991 | } | |
| 992 | ||
| 993 | /** | |
| 994 | * Clean up references when this viewport is closed | |
| 995 | */ | |
| 996 | 253 | @Override |
| 997 | public void dispose() | |
| 998 | { | |
| 999 | /* | |
| 1000 | * defensively null out references to large objects in case | |
| 1001 | * this object is not garbage collected (as if!) | |
| 1002 | */ | |
| 1003 | 253 | consensus = null; |
| 1004 | 253 | complementConsensus = null; |
| 1005 | 253 | strucConsensus = null; |
| 1006 | 253 | secondaryStructureConsensus = null; |
| 1007 | 253 | conservation = null; |
| 1008 | 253 | quality = null; |
| 1009 | 253 | groupConsensus = null; |
| 1010 | 253 | groupConservation = null; |
| 1011 | 253 | hconsensus = null; |
| 1012 | 253 | hconservation = null; |
| 1013 | 253 | hcomplementConsensus = null; |
| 1014 | 253 | gapcounts = null; |
| 1015 | 253 | calculator = null; |
| 1016 | 253 | residueShading = null; // may hold a reference to Consensus |
| 1017 | 253 | changeSupport = null; |
| 1018 | 253 | ranges = null; |
| 1019 | 253 | currentTree = null; |
| 1020 | 253 | selectionGroup = null; |
| 1021 | 253 | colSel = null; |
| 1022 | 253 | setAlignment(null); |
| 1023 | } | |
| 1024 | ||
| 1025 | 3955 | @Override |
| 1026 | public boolean isClosed() | |
| 1027 | { | |
| 1028 | // TODO: check that this isClosed is only true after panel is closed, not | |
| 1029 | // before it is fully constructed. | |
| 1030 | 3955 | return alignment == null; |
| 1031 | } | |
| 1032 | ||
| 1033 | 3363 | @Override |
| 1034 | public AlignCalcManagerI getCalcManager() | |
| 1035 | { | |
| 1036 | 3363 | return calculator; |
| 1037 | } | |
| 1038 | ||
| 1039 | /** | |
| 1040 | * should conservation rows be shown for groups | |
| 1041 | */ | |
| 1042 | protected boolean showGroupConservation = false; | |
| 1043 | ||
| 1044 | /** | |
| 1045 | * should consensus rows be shown for groups | |
| 1046 | */ | |
| 1047 | protected boolean showGroupConsensus = false; | |
| 1048 | ||
| 1049 | /** | |
| 1050 | * should consensus profile be rendered by default | |
| 1051 | */ | |
| 1052 | protected boolean showSequenceLogo = false; | |
| 1053 | ||
| 1054 | protected boolean showSequenceSSLogo = false; | |
| 1055 | ||
| 1056 | /** | |
| 1057 | * should consensus profile be rendered normalised to row height | |
| 1058 | */ | |
| 1059 | protected boolean normaliseSequenceLogo = false; | |
| 1060 | ||
| 1061 | /** | |
| 1062 | * should consensus histograms be rendered by default | |
| 1063 | */ | |
| 1064 | protected boolean showConsensusHistogram = true; | |
| 1065 | ||
| 1066 | protected boolean showSSConsensusHistogram = true; | |
| 1067 | ||
| 1068 | 0 | public void setShowSSConsensusHistogram(boolean showSSConsensusHistogram) |
| 1069 | { | |
| 1070 | 0 | this.showSSConsensusHistogram = showSSConsensusHistogram; |
| 1071 | } | |
| 1072 | ||
| 1073 | /** | |
| 1074 | * @return the showConsensusProfile | |
| 1075 | */ | |
| 1076 | 5120 | @Override |
| 1077 | public boolean isShowSequenceLogo() | |
| 1078 | { | |
| 1079 | 5120 | return showSequenceLogo; |
| 1080 | } | |
| 1081 | ||
| 1082 | 130 | @Override |
| 1083 | public boolean isShowSequenceSSLogo() | |
| 1084 | { | |
| 1085 | 130 | return showSequenceSSLogo; |
| 1086 | } | |
| 1087 | ||
| 1088 | /** | |
| 1089 | * @param showSequenceLogo | |
| 1090 | * the new value | |
| 1091 | */ | |
| 1092 | 85 | public void setShowSequenceLogo(boolean showSequenceLogo) |
| 1093 | { | |
| 1094 | 85 | if (showSequenceLogo != this.showSequenceLogo) |
| 1095 | { | |
| 1096 | // TODO: decouple settings setting from calculation when refactoring | |
| 1097 | // annotation update method from alignframe to viewport | |
| 1098 | 16 | this.showSequenceLogo = showSequenceLogo; |
| 1099 | 16 | calculator.updateAnnotationFor(ConsensusThread.class); |
| 1100 | 16 | calculator.updateAnnotationFor(ComplementConsensusThread.class); |
| 1101 | 16 | calculator.updateAnnotationFor(StrucConsensusThread.class); |
| 1102 | } | |
| 1103 | 85 | this.showSequenceLogo = showSequenceLogo; |
| 1104 | } | |
| 1105 | ||
| 1106 | 0 | public void setShowSequenceSSLogo(boolean showSequenceSSLogo) |
| 1107 | { | |
| 1108 | 0 | if (showSequenceSSLogo != this.showSequenceSSLogo) |
| 1109 | { | |
| 1110 | // TODO: decouple settings setting from calculation when refactoring | |
| 1111 | // annotation update method from alignframe to viewport | |
| 1112 | 0 | this.showSequenceSSLogo = showSequenceSSLogo; |
| 1113 | 0 | calculator |
| 1114 | .updateAnnotationFor(SecondaryStructureConsensusThread.class); | |
| 1115 | } | |
| 1116 | 0 | this.showSequenceSSLogo = showSequenceSSLogo; |
| 1117 | } | |
| 1118 | ||
| 1119 | /** | |
| 1120 | * @param showConsensusHistogram | |
| 1121 | * the showConsensusHistogram to set | |
| 1122 | */ | |
| 1123 | 85 | public void setShowConsensusHistogram(boolean showConsensusHistogram) |
| 1124 | { | |
| 1125 | 85 | this.showConsensusHistogram = showConsensusHistogram; |
| 1126 | } | |
| 1127 | ||
| 1128 | /** | |
| 1129 | * @return the showGroupConservation | |
| 1130 | */ | |
| 1131 | 848 | public boolean isShowGroupConservation() |
| 1132 | { | |
| 1133 | 848 | return showGroupConservation; |
| 1134 | } | |
| 1135 | ||
| 1136 | /** | |
| 1137 | * @param showGroupConservation | |
| 1138 | * the showGroupConservation to set | |
| 1139 | */ | |
| 1140 | 85 | public void setShowGroupConservation(boolean showGroupConservation) |
| 1141 | { | |
| 1142 | 85 | this.showGroupConservation = showGroupConservation; |
| 1143 | } | |
| 1144 | ||
| 1145 | /** | |
| 1146 | * @return the showGroupConsensus | |
| 1147 | */ | |
| 1148 | 848 | public boolean isShowGroupConsensus() |
| 1149 | { | |
| 1150 | 848 | return showGroupConsensus; |
| 1151 | } | |
| 1152 | ||
| 1153 | /** | |
| 1154 | * @param showGroupConsensus | |
| 1155 | * the showGroupConsensus to set | |
| 1156 | */ | |
| 1157 | 85 | public void setShowGroupConsensus(boolean showGroupConsensus) |
| 1158 | { | |
| 1159 | 85 | this.showGroupConsensus = showGroupConsensus; |
| 1160 | } | |
| 1161 | ||
| 1162 | /** | |
| 1163 | * | |
| 1164 | * @return flag to indicate if the consensus histogram should be rendered by | |
| 1165 | * default | |
| 1166 | */ | |
| 1167 | 3171 | @Override |
| 1168 | public boolean isShowConsensusHistogram() | |
| 1169 | { | |
| 1170 | 3171 | return this.showConsensusHistogram; |
| 1171 | } | |
| 1172 | ||
| 1173 | 130 | @Override |
| 1174 | public boolean isShowSSConsensusHistogram() | |
| 1175 | { | |
| 1176 | 130 | return this.showSSConsensusHistogram; |
| 1177 | } | |
| 1178 | ||
| 1179 | /** | |
| 1180 | * when set, updateAlignment will always ensure sequences are of equal length | |
| 1181 | */ | |
| 1182 | private boolean padGaps = false; | |
| 1183 | ||
| 1184 | /** | |
| 1185 | * when set, alignment should be reordered according to a newly opened tree | |
| 1186 | */ | |
| 1187 | public boolean sortByTree = false; | |
| 1188 | ||
| 1189 | /** | |
| 1190 | * | |
| 1191 | * | |
| 1192 | * @return null or the currently selected sequence region | |
| 1193 | */ | |
| 1194 | 23849 | @Override |
| 1195 | public SequenceGroup getSelectionGroup() | |
| 1196 | { | |
| 1197 | 23849 | return selectionGroup; |
| 1198 | } | |
| 1199 | ||
| 1200 | /** | |
| 1201 | * Set the selection group for this window. Also sets the current alignment as | |
| 1202 | * the context for the group, if it does not already have one. | |
| 1203 | * | |
| 1204 | * @param sg | |
| 1205 | * - group holding references to sequences in this alignment view | |
| 1206 | * | |
| 1207 | */ | |
| 1208 | 140 | @Override |
| 1209 | public void setSelectionGroup(SequenceGroup sg) | |
| 1210 | { | |
| 1211 | 140 | selectionGroup = sg; |
| 1212 | 140 | if (sg != null && sg.getContext() == null) |
| 1213 | { | |
| 1214 | 36 | sg.setContext(alignment); |
| 1215 | } | |
| 1216 | } | |
| 1217 | ||
| 1218 | 1 | public void setHiddenColumns(HiddenColumns hidden) |
| 1219 | { | |
| 1220 | 1 | this.alignment.setHiddenColumns(hidden); |
| 1221 | } | |
| 1222 | ||
| 1223 | 4592 | @Override |
| 1224 | public ColumnSelection getColumnSelection() | |
| 1225 | { | |
| 1226 | 4592 | return colSel; |
| 1227 | } | |
| 1228 | ||
| 1229 | 13 | @Override |
| 1230 | public void setColumnSelection(ColumnSelection colSel) | |
| 1231 | { | |
| 1232 | 13 | this.colSel = colSel; |
| 1233 | 13 | if (colSel != null) |
| 1234 | { | |
| 1235 | 13 | updateHiddenColumns(); |
| 1236 | } | |
| 1237 | 13 | isColSelChanged(true); |
| 1238 | } | |
| 1239 | ||
| 1240 | /** | |
| 1241 | * | |
| 1242 | * @return | |
| 1243 | */ | |
| 1244 | 32 | @Override |
| 1245 | public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences() | |
| 1246 | { | |
| 1247 | 32 | return hiddenRepSequences; |
| 1248 | } | |
| 1249 | ||
| 1250 | 0 | @Override |
| 1251 | public void setHiddenRepSequences( | |
| 1252 | Map<SequenceI, SequenceCollectionI> hiddenRepSequences) | |
| 1253 | { | |
| 1254 | 0 | this.hiddenRepSequences = hiddenRepSequences; |
| 1255 | } | |
| 1256 | ||
| 1257 | 0 | @Override |
| 1258 | public boolean hasSelectedColumns() | |
| 1259 | { | |
| 1260 | 0 | ColumnSelection columnSelection = getColumnSelection(); |
| 1261 | 0 | return columnSelection != null && columnSelection.hasSelectedColumns(); |
| 1262 | } | |
| 1263 | ||
| 1264 | 8365 | @Override |
| 1265 | public boolean hasHiddenColumns() | |
| 1266 | { | |
| 1267 | 8365 | return alignment.getHiddenColumns() != null |
| 1268 | && alignment.getHiddenColumns().hasHiddenColumns(); | |
| 1269 | } | |
| 1270 | ||
| 1271 | 14 | public void updateHiddenColumns() |
| 1272 | { | |
| 1273 | // this method doesn't really do anything now. But - it could, since a | |
| 1274 | // column Selection could be in the process of modification | |
| 1275 | // hasHiddenColumns = colSel.hasHiddenColumns(); | |
| 1276 | } | |
| 1277 | ||
| 1278 | 4796 | @Override |
| 1279 | public boolean hasHiddenRows() | |
| 1280 | { | |
| 1281 | 4796 | return alignment.getHiddenSequences().getSize() > 0; |
| 1282 | } | |
| 1283 | ||
| 1284 | protected SequenceGroup selectionGroup; | |
| 1285 | ||
| 1286 | 85 | public void setSequenceSetId(String newid) |
| 1287 | { | |
| 1288 | 85 | if (sequenceSetID != null) |
| 1289 | { | |
| 1290 | 85 | jalview.bin.Console.errPrintln( |
| 1291 | "Warning - overwriting a sequenceSetId for a viewport!"); | |
| 1292 | } | |
| 1293 | 85 | sequenceSetID = new String(newid); |
| 1294 | } | |
| 1295 | ||
| 1296 | 5629 | @Override |
| 1297 | public String getSequenceSetId() | |
| 1298 | { | |
| 1299 | 5629 | if (sequenceSetID == null) |
| 1300 | { | |
| 1301 | 364 | sequenceSetID = alignment.hashCode() + ""; |
| 1302 | } | |
| 1303 | ||
| 1304 | 5629 | return sequenceSetID; |
| 1305 | } | |
| 1306 | ||
| 1307 | /** | |
| 1308 | * unique viewId for synchronizing state (e.g. with stored Jalview Project) | |
| 1309 | * | |
| 1310 | */ | |
| 1311 | protected String viewId = null; | |
| 1312 | ||
| 1313 | 598 | @Override |
| 1314 | public String getViewId() | |
| 1315 | { | |
| 1316 | 598 | if (viewId == null) |
| 1317 | { | |
| 1318 | 300 | viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; |
| 1319 | } | |
| 1320 | 598 | return viewId; |
| 1321 | } | |
| 1322 | ||
| 1323 | 88 | public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) |
| 1324 | { | |
| 1325 | 88 | ignoreGapsInConsensusCalculation = b; |
| 1326 | 88 | if (ap != null) |
| 1327 | { | |
| 1328 | 3 | updateConsensus(ap); |
| 1329 | 3 | updateSecondaryStructureConsensus(ap); |
| 1330 | 3 | if (residueShading != null) |
| 1331 | { | |
| 1332 | 3 | residueShading.setThreshold(residueShading.getThreshold(), |
| 1333 | ignoreGapsInConsensusCalculation); | |
| 1334 | } | |
| 1335 | } | |
| 1336 | ||
| 1337 | } | |
| 1338 | ||
| 1339 | private long sgrouphash = -1, colselhash = -1; | |
| 1340 | ||
| 1341 | /** | |
| 1342 | * checks current SelectionGroup against record of last hash value, and | |
| 1343 | * updates record. | |
| 1344 | * | |
| 1345 | * @param b | |
| 1346 | * update the record of last hash value | |
| 1347 | * | |
| 1348 | * @return true if SelectionGroup changed since last call (when b is true) | |
| 1349 | */ | |
| 1350 | 161 | public boolean isSelectionGroupChanged(boolean b) |
| 1351 | { | |
| 1352 | 161 | int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1 |
| 1353 | : selectionGroup.hashCode(); | |
| 1354 | 161 | if (hc != -1 && hc != sgrouphash) |
| 1355 | { | |
| 1356 | 9 | if (b) |
| 1357 | { | |
| 1358 | 9 | sgrouphash = hc; |
| 1359 | } | |
| 1360 | 9 | return true; |
| 1361 | } | |
| 1362 | 152 | return false; |
| 1363 | } | |
| 1364 | ||
| 1365 | /** | |
| 1366 | * checks current colsel against record of last hash value, and optionally | |
| 1367 | * updates record. | |
| 1368 | * | |
| 1369 | * @param b | |
| 1370 | * update the record of last hash value | |
| 1371 | * @return true if colsel changed since last call (when b is true) | |
| 1372 | */ | |
| 1373 | 173 | public boolean isColSelChanged(boolean b) |
| 1374 | { | |
| 1375 | 173 | int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode(); |
| 1376 | 173 | if (hc != -1 && hc != colselhash) |
| 1377 | { | |
| 1378 | 17 | if (b) |
| 1379 | { | |
| 1380 | 17 | colselhash = hc; |
| 1381 | } | |
| 1382 | 17 | return true; |
| 1383 | } | |
| 1384 | 156 | return false; |
| 1385 | } | |
| 1386 | ||
| 1387 | 4342 | @Override |
| 1388 | public boolean isIgnoreGapsConsensus() | |
| 1389 | { | |
| 1390 | 4342 | return ignoreGapsInConsensusCalculation; |
| 1391 | } | |
| 1392 | ||
| 1393 | // property change stuff | |
| 1394 | // JBPNote Prolly only need this in the applet version. | |
| 1395 | private PropertyChangeSupport changeSupport = new PropertyChangeSupport( | |
| 1396 | this); | |
| 1397 | ||
| 1398 | protected boolean showConservation = true; | |
| 1399 | ||
| 1400 | protected boolean showQuality = true; | |
| 1401 | ||
| 1402 | protected boolean showConsensus = true; | |
| 1403 | ||
| 1404 | protected boolean showSSConsensus = false; | |
| 1405 | ||
| 1406 | protected boolean showOccupancy = true; | |
| 1407 | ||
| 1408 | private Map<SequenceI, Color> sequenceColours = new HashMap<>(); | |
| 1409 | ||
| 1410 | protected SequenceAnnotationOrder sortAnnotationsBy = null; | |
| 1411 | ||
| 1412 | protected boolean showAutocalculatedAbove; | |
| 1413 | ||
| 1414 | /** | |
| 1415 | * when set, view will scroll to show the highlighted position | |
| 1416 | */ | |
| 1417 | private boolean followHighlight = true; | |
| 1418 | ||
| 1419 | /** | |
| 1420 | * Property change listener for changes in alignment | |
| 1421 | * | |
| 1422 | * @param listener | |
| 1423 | * DOCUMENT ME! | |
| 1424 | */ | |
| 1425 | 492 | public void addPropertyChangeListener( |
| 1426 | java.beans.PropertyChangeListener listener) | |
| 1427 | { | |
| 1428 | 492 | changeSupport.addPropertyChangeListener(listener); |
| 1429 | } | |
| 1430 | ||
| 1431 | /** | |
| 1432 | * DOCUMENT ME! | |
| 1433 | * | |
| 1434 | * @param listener | |
| 1435 | * DOCUMENT ME! | |
| 1436 | */ | |
| 1437 | 265 | public void removePropertyChangeListener( |
| 1438 | java.beans.PropertyChangeListener listener) | |
| 1439 | { | |
| 1440 | 265 | if (changeSupport != null) |
| 1441 | { | |
| 1442 | 264 | changeSupport.removePropertyChangeListener(listener); |
| 1443 | } | |
| 1444 | } | |
| 1445 | ||
| 1446 | /** | |
| 1447 | * Property change listener for changes in alignment | |
| 1448 | * | |
| 1449 | * @param prop | |
| 1450 | * DOCUMENT ME! | |
| 1451 | * @param oldvalue | |
| 1452 | * DOCUMENT ME! | |
| 1453 | * @param newvalue | |
| 1454 | * DOCUMENT ME! | |
| 1455 | */ | |
| 1456 | 78 | public void firePropertyChange(String prop, Object oldvalue, |
| 1457 | Object newvalue) | |
| 1458 | { | |
| 1459 | 78 | changeSupport.firePropertyChange(prop, oldvalue, newvalue); |
| 1460 | } | |
| 1461 | ||
| 1462 | 0 | @Override |
| 1463 | public void notifyAlignmentChanged() | |
| 1464 | { | |
| 1465 | 0 | firePropertyChange("alignment", null, alignment); |
| 1466 | } | |
| 1467 | ||
| 1468 | // common hide/show column stuff | |
| 1469 | ||
| 1470 | 6 | public void hideSelectedColumns() |
| 1471 | { | |
| 1472 | 6 | if (colSel.isEmpty()) |
| 1473 | { | |
| 1474 | 2 | return; |
| 1475 | } | |
| 1476 | ||
| 1477 | 4 | colSel.hideSelectedColumns(alignment); |
| 1478 | 4 | setSelectionGroup(null); |
| 1479 | 4 | isColSelChanged(true); |
| 1480 | } | |
| 1481 | ||
| 1482 | 71 | public void hideColumns(int start, int end) |
| 1483 | { | |
| 1484 | 71 | if (start == end) |
| 1485 | { | |
| 1486 | 2 | colSel.hideSelectedColumns(start, alignment.getHiddenColumns()); |
| 1487 | } | |
| 1488 | else | |
| 1489 | { | |
| 1490 | 69 | alignment.getHiddenColumns().hideColumns(start, end); |
| 1491 | } | |
| 1492 | 71 | isColSelChanged(true); |
| 1493 | } | |
| 1494 | ||
| 1495 | 1 | public void showColumn(int col) |
| 1496 | { | |
| 1497 | 1 | alignment.getHiddenColumns().revealHiddenColumns(col, colSel); |
| 1498 | 1 | isColSelChanged(true); |
| 1499 | } | |
| 1500 | ||
| 1501 | 5 | public void showAllHiddenColumns() |
| 1502 | { | |
| 1503 | 5 | alignment.getHiddenColumns().revealAllHiddenColumns(colSel); |
| 1504 | 5 | isColSelChanged(true); |
| 1505 | } | |
| 1506 | ||
| 1507 | // common hide/show seq stuff | |
| 1508 | 1 | public void showAllHiddenSeqs() |
| 1509 | { | |
| 1510 | 1 | int startSeq = ranges.getStartSeq(); |
| 1511 | 1 | int endSeq = ranges.getEndSeq(); |
| 1512 | ||
| 1513 | 1 | if (alignment.getHiddenSequences().getSize() > 0) |
| 1514 | { | |
| 1515 | 1 | if (selectionGroup == null) |
| 1516 | { | |
| 1517 | 0 | selectionGroup = new SequenceGroup(); |
| 1518 | 0 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1519 | } | |
| 1520 | 1 | List<SequenceI> tmp = alignment.getHiddenSequences() |
| 1521 | .showAll(hiddenRepSequences); | |
| 1522 | 1 | for (SequenceI seq : tmp) |
| 1523 | { | |
| 1524 | 2 | selectionGroup.addSequence(seq, false); |
| 1525 | 2 | setSequenceAnnotationsVisible(seq, true); |
| 1526 | } | |
| 1527 | ||
| 1528 | 1 | hiddenRepSequences = null; |
| 1529 | ||
| 1530 | 1 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1531 | ||
| 1532 | 1 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1533 | // used to set hasHiddenRows/hiddenRepSequences here, after the property | |
| 1534 | // changed event | |
| 1535 | 1 | sendSelection(); |
| 1536 | } | |
| 1537 | } | |
| 1538 | ||
| 1539 | 2 | public void showSequence(int index) |
| 1540 | { | |
| 1541 | 2 | int startSeq = ranges.getStartSeq(); |
| 1542 | 2 | int endSeq = ranges.getEndSeq(); |
| 1543 | ||
| 1544 | 2 | List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index, |
| 1545 | hiddenRepSequences); | |
| 1546 | 2 | if (tmp.size() > 0) |
| 1547 | { | |
| 1548 | 2 | if (selectionGroup == null) |
| 1549 | { | |
| 1550 | 2 | selectionGroup = new SequenceGroup(); |
| 1551 | 2 | selectionGroup.setEndRes(alignment.getWidth() - 1); |
| 1552 | } | |
| 1553 | ||
| 1554 | 2 | for (SequenceI seq : tmp) |
| 1555 | { | |
| 1556 | 3 | selectionGroup.addSequence(seq, false); |
| 1557 | 3 | setSequenceAnnotationsVisible(seq, true); |
| 1558 | } | |
| 1559 | ||
| 1560 | 2 | ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); |
| 1561 | ||
| 1562 | 2 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1563 | 2 | sendSelection(); |
| 1564 | } | |
| 1565 | } | |
| 1566 | ||
| 1567 | 0 | public void hideAllSelectedSeqs() |
| 1568 | { | |
| 1569 | 0 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1570 | { | |
| 1571 | 0 | return; |
| 1572 | } | |
| 1573 | ||
| 1574 | 0 | SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); |
| 1575 | ||
| 1576 | 0 | hideSequence(seqs); |
| 1577 | ||
| 1578 | 0 | setSelectionGroup(null); |
| 1579 | } | |
| 1580 | ||
| 1581 | 54 | public void hideSequence(SequenceI[] seq) |
| 1582 | { | |
| 1583 | /* | |
| 1584 | * cache offset to first visible sequence | |
| 1585 | */ | |
| 1586 | 54 | int startSeq = ranges.getStartSeq(); |
| 1587 | ||
| 1588 | 54 | if (seq != null) |
| 1589 | { | |
| 1590 | 252 | for (int i = 0; i < seq.length; i++) |
| 1591 | { | |
| 1592 | 198 | alignment.getHiddenSequences().hideSequence(seq[i]); |
| 1593 | 198 | setSequenceAnnotationsVisible(seq[i], false); |
| 1594 | } | |
| 1595 | 54 | ranges.setStartSeq(startSeq); |
| 1596 | 54 | firePropertyChange("alignment", null, alignment.getSequences()); |
| 1597 | } | |
| 1598 | } | |
| 1599 | ||
| 1600 | /** | |
| 1601 | * Hides the specified sequence, or the sequences it represents | |
| 1602 | * | |
| 1603 | * @param sequence | |
| 1604 | * the sequence to hide, or keep as representative | |
| 1605 | * @param representGroup | |
| 1606 | * if true, hide the current selection group except for the | |
| 1607 | * representative sequence | |
| 1608 | */ | |
| 1609 | 3 | public void hideSequences(SequenceI sequence, boolean representGroup) |
| 1610 | { | |
| 1611 | 3 | if (selectionGroup == null || selectionGroup.getSize() < 1) |
| 1612 | { | |
| 1613 | 0 | hideSequence(new SequenceI[] { sequence }); |
| 1614 | 0 | return; |
| 1615 | } | |
| 1616 | ||
| 1617 | 3 | if (representGroup) |
| 1618 | { | |
| 1619 | 3 | hideRepSequences(sequence, selectionGroup); |
| 1620 | 3 | setSelectionGroup(null); |
| 1621 | 3 | return; |
| 1622 | } | |
| 1623 | ||
| 1624 | 0 | int gsize = selectionGroup.getSize(); |
| 1625 | 0 | SequenceI[] hseqs = selectionGroup.getSequences() |
| 1626 | .toArray(new SequenceI[gsize]); | |
| 1627 | ||
| 1628 | 0 | hideSequence(hseqs); |
| 1629 | 0 | setSelectionGroup(null); |
| 1630 | 0 | sendSelection(); |
| 1631 | } | |
| 1632 | ||
| 1633 | /** | |
| 1634 | * Set visibility for any annotations for the given sequence. | |
| 1635 | * | |
| 1636 | * @param sequenceI | |
| 1637 | */ | |
| 1638 | 203 | protected void setSequenceAnnotationsVisible(SequenceI sequenceI, |
| 1639 | boolean visible) | |
| 1640 | { | |
| 1641 | 203 | AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation(); |
| 1642 | 203 | if (anns != null) |
| 1643 | { | |
| 1644 | 203 | for (AlignmentAnnotation ann : anns) |
| 1645 | { | |
| 1646 | 1033 | if (ann.sequenceRef == sequenceI) |
| 1647 | { | |
| 1648 | 0 | ann.visible = visible; |
| 1649 | } | |
| 1650 | } | |
| 1651 | } | |
| 1652 | } | |
| 1653 | ||
| 1654 | 5 | public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) |
| 1655 | { | |
| 1656 | 5 | int sSize = sg.getSize(); |
| 1657 | 5 | if (sSize < 2) |
| 1658 | { | |
| 1659 | 0 | return; |
| 1660 | } | |
| 1661 | ||
| 1662 | 5 | if (hiddenRepSequences == null) |
| 1663 | { | |
| 1664 | 5 | hiddenRepSequences = new Hashtable<>(); |
| 1665 | } | |
| 1666 | ||
| 1667 | 5 | hiddenRepSequences.put(repSequence, sg); |
| 1668 | ||
| 1669 | // Hide all sequences except the repSequence | |
| 1670 | 5 | SequenceI[] seqs = new SequenceI[sSize - 1]; |
| 1671 | 5 | int index = 0; |
| 1672 | 16 | for (int i = 0; i < sSize; i++) |
| 1673 | { | |
| 1674 | 11 | if (sg.getSequenceAt(i) != repSequence) |
| 1675 | { | |
| 1676 | 6 | if (index == sSize - 1) |
| 1677 | { | |
| 1678 | 0 | return; |
| 1679 | } | |
| 1680 | ||
| 1681 | 6 | seqs[index++] = sg.getSequenceAt(i); |
| 1682 | } | |
| 1683 | } | |
| 1684 | 5 | sg.setSeqrep(repSequence); // note: not done in 2.7applet |
| 1685 | 5 | sg.setHidereps(true); // note: not done in 2.7applet |
| 1686 | 5 | hideSequence(seqs); |
| 1687 | ||
| 1688 | } | |
| 1689 | ||
| 1690 | /** | |
| 1691 | * | |
| 1692 | * @return null or the current reference sequence | |
| 1693 | */ | |
| 1694 | 0 | public SequenceI getReferenceSeq() |
| 1695 | { | |
| 1696 | 0 | return alignment.getSeqrep(); |
| 1697 | } | |
| 1698 | ||
| 1699 | /** | |
| 1700 | * @param seq | |
| 1701 | * @return true iff seq is the reference for the alignment | |
| 1702 | */ | |
| 1703 | 4816 | public boolean isReferenceSeq(SequenceI seq) |
| 1704 | { | |
| 1705 | 4816 | return alignment.getSeqrep() == seq; |
| 1706 | } | |
| 1707 | ||
| 1708 | /** | |
| 1709 | * | |
| 1710 | * @param seq | |
| 1711 | * @return true if there are sequences represented by this sequence that are | |
| 1712 | * currently hidden | |
| 1713 | */ | |
| 1714 | 4878 | public boolean isHiddenRepSequence(SequenceI seq) |
| 1715 | { | |
| 1716 | 4878 | return (hiddenRepSequences != null |
| 1717 | && hiddenRepSequences.containsKey(seq)); | |
| 1718 | } | |
| 1719 | ||
| 1720 | /** | |
| 1721 | * | |
| 1722 | * @param seq | |
| 1723 | * @return null or a sequence group containing the sequences that seq | |
| 1724 | * represents | |
| 1725 | */ | |
| 1726 | 2 | public SequenceGroup getRepresentedSequences(SequenceI seq) |
| 1727 | { | |
| 1728 | 2 | return (SequenceGroup) (hiddenRepSequences == null ? null |
| 1729 | : hiddenRepSequences.get(seq)); | |
| 1730 | } | |
| 1731 | ||
| 1732 | 0 | @Override |
| 1733 | public int adjustForHiddenSeqs(int alignmentIndex) | |
| 1734 | { | |
| 1735 | 0 | return alignment.getHiddenSequences() |
| 1736 | .adjustForHiddenSeqs(alignmentIndex); | |
| 1737 | } | |
| 1738 | ||
| 1739 | 0 | @Override |
| 1740 | public void invertColumnSelection() | |
| 1741 | { | |
| 1742 | 0 | colSel.invertColumnSelection(0, alignment.getWidth(), alignment); |
| 1743 | 0 | isColSelChanged(true); |
| 1744 | } | |
| 1745 | ||
| 1746 | 4 | @Override |
| 1747 | public SequenceI[] getSelectionAsNewSequence() | |
| 1748 | { | |
| 1749 | 4 | SequenceI[] sequences; |
| 1750 | // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - | |
| 1751 | // this was the only caller in the applet for this method | |
| 1752 | // JBPNote: in applet, this method returned references to the alignment | |
| 1753 | // sequences, and it did not honour the presence/absence of annotation | |
| 1754 | // attached to the alignment (probably!) | |
| 1755 | 4 | if (selectionGroup == null || selectionGroup.getSize() == 0) |
| 1756 | { | |
| 1757 | 2 | sequences = alignment.getSequencesArray(); |
| 1758 | 2 | AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); |
| 1759 | 4 | for (int i = 0; i < sequences.length; i++) |
| 1760 | { | |
| 1761 | // construct new sequence with subset of visible annotation | |
| 1762 | 2 | sequences[i] = new Sequence(sequences[i], annots); |
| 1763 | } | |
| 1764 | } | |
| 1765 | else | |
| 1766 | { | |
| 1767 | 2 | sequences = selectionGroup.getSelectionAsNewSequences(alignment); |
| 1768 | } | |
| 1769 | ||
| 1770 | 4 | return sequences; |
| 1771 | } | |
| 1772 | ||
| 1773 | 28 | @Override |
| 1774 | public SequenceI[] getSequenceSelection() | |
| 1775 | { | |
| 1776 | 28 | SequenceI[] sequences = null; |
| 1777 | 28 | if (selectionGroup != null) |
| 1778 | { | |
| 1779 | 4 | sequences = selectionGroup.getSequencesInOrder(alignment); |
| 1780 | } | |
| 1781 | 28 | if (sequences == null) |
| 1782 | { | |
| 1783 | 24 | sequences = alignment.getSequencesArray(); |
| 1784 | } | |
| 1785 | 28 | return sequences; |
| 1786 | } | |
| 1787 | ||
| 1788 | 20 | @Override |
| 1789 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 1790 | boolean selectedOnly) | |
| 1791 | { | |
| 1792 | 20 | return getAlignmentView(selectedOnly, false); |
| 1793 | } | |
| 1794 | ||
| 1795 | 21 | @Override |
| 1796 | public jalview.datamodel.AlignmentView getAlignmentView( | |
| 1797 | boolean selectedOnly, boolean markGroups) | |
| 1798 | { | |
| 1799 | 21 | return new AlignmentView(alignment, alignment.getHiddenColumns(), |
| 1800 | selectionGroup, | |
| 1801 | alignment.getHiddenColumns() != null | |
| 1802 | && alignment.getHiddenColumns().hasHiddenColumns(), | |
| 1803 | selectedOnly, markGroups); | |
| 1804 | } | |
| 1805 | ||
| 1806 | 24 | @Override |
| 1807 | public String[] getViewAsString(boolean selectedRegionOnly) | |
| 1808 | { | |
| 1809 | 24 | return getViewAsString(selectedRegionOnly, true); |
| 1810 | } | |
| 1811 | ||
| 1812 | 24 | @Override |
| 1813 | public String[] getViewAsString(boolean selectedRegionOnly, | |
| 1814 | boolean exportHiddenSeqs) | |
| 1815 | { | |
| 1816 | 24 | String[] selection = null; |
| 1817 | 24 | SequenceI[] seqs = null; |
| 1818 | 24 | int i, iSize; |
| 1819 | 24 | int start = 0, end = 0; |
| 1820 | 24 | if (selectedRegionOnly && selectionGroup != null) |
| 1821 | { | |
| 1822 | 0 | iSize = selectionGroup.getSize(); |
| 1823 | 0 | seqs = selectionGroup.getSequencesInOrder(alignment); |
| 1824 | 0 | start = selectionGroup.getStartRes(); |
| 1825 | 0 | end = selectionGroup.getEndRes() + 1; |
| 1826 | } | |
| 1827 | else | |
| 1828 | { | |
| 1829 | 24 | if (hasHiddenRows() && exportHiddenSeqs) |
| 1830 | { | |
| 1831 | 0 | AlignmentI fullAlignment = alignment.getHiddenSequences() |
| 1832 | .getFullAlignment(); | |
| 1833 | 0 | iSize = fullAlignment.getHeight(); |
| 1834 | 0 | seqs = fullAlignment.getSequencesArray(); |
| 1835 | 0 | end = fullAlignment.getWidth(); |
| 1836 | } | |
| 1837 | else | |
| 1838 | { | |
| 1839 | 24 | iSize = alignment.getHeight(); |
| 1840 | 24 | seqs = alignment.getSequencesArray(); |
| 1841 | 24 | end = alignment.getWidth(); |
| 1842 | } | |
| 1843 | } | |
| 1844 | ||
| 1845 | 24 | selection = new String[iSize]; |
| 1846 | 24 | if (alignment.getHiddenColumns() != null |
| 1847 | && alignment.getHiddenColumns().hasHiddenColumns()) | |
| 1848 | { | |
| 1849 | 206 | for (i = 0; i < iSize; i++) |
| 1850 | { | |
| 1851 | 188 | Iterator<int[]> blocks = alignment.getHiddenColumns() |
| 1852 | .getVisContigsIterator(start, end + 1, false); | |
| 1853 | 188 | selection[i] = seqs[i].getSequenceStringFromIterator(blocks); |
| 1854 | } | |
| 1855 | } | |
| 1856 | else | |
| 1857 | { | |
| 1858 | 36 | for (i = 0; i < iSize; i++) |
| 1859 | { | |
| 1860 | 30 | selection[i] = seqs[i].getSequenceAsString(start, end); |
| 1861 | } | |
| 1862 | ||
| 1863 | } | |
| 1864 | 24 | return selection; |
| 1865 | } | |
| 1866 | ||
| 1867 | 0 | @Override |
| 1868 | public List<int[]> getVisibleRegionBoundaries(int min, int max) | |
| 1869 | { | |
| 1870 | 0 | ArrayList<int[]> regions = new ArrayList<>(); |
| 1871 | 0 | int start = min; |
| 1872 | 0 | int end = max; |
| 1873 | ||
| 1874 | 0 | do |
| 1875 | { | |
| 1876 | 0 | HiddenColumns hidden = alignment.getHiddenColumns(); |
| 1877 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 1878 | { | |
| 1879 | 0 | if (start == 0) |
| 1880 | { | |
| 1881 | 0 | start = hidden.visibleToAbsoluteColumn(start); |
| 1882 | } | |
| 1883 | ||
| 1884 | 0 | end = hidden.getNextHiddenBoundary(false, start); |
| 1885 | 0 | if (start == end) |
| 1886 | { | |
| 1887 | 0 | end = max; |
| 1888 | } | |
| 1889 | 0 | if (end > max) |
| 1890 | { | |
| 1891 | 0 | end = max; |
| 1892 | } | |
| 1893 | } | |
| 1894 | ||
| 1895 | 0 | regions.add(new int[] { start, end }); |
| 1896 | ||
| 1897 | 0 | if (hidden != null && hidden.hasHiddenColumns()) |
| 1898 | { | |
| 1899 | 0 | start = hidden.visibleToAbsoluteColumn(end); |
| 1900 | 0 | start = hidden.getNextHiddenBoundary(true, start) + 1; |
| 1901 | } | |
| 1902 | 0 | } while (end < max); |
| 1903 | ||
| 1904 | // int[][] startEnd = new int[regions.size()][2]; | |
| 1905 | ||
| 1906 | 0 | return regions; |
| 1907 | } | |
| 1908 | ||
| 1909 | 1 | @Override |
| 1910 | public List<AlignmentAnnotation> getVisibleAlignmentAnnotation( | |
| 1911 | boolean selectedOnly) | |
| 1912 | { | |
| 1913 | 1 | ArrayList<AlignmentAnnotation> ala = new ArrayList<>(); |
| 1914 | 1 | AlignmentAnnotation[] aa; |
| 1915 | ? | if ((aa = alignment.getAlignmentAnnotation()) != null) |
| 1916 | { | |
| 1917 | 1 | for (AlignmentAnnotation annot : aa) |
| 1918 | { | |
| 1919 | 4 | AlignmentAnnotation clone = new AlignmentAnnotation(annot); |
| 1920 | 4 | if (selectedOnly && selectionGroup != null) |
| 1921 | { | |
| 1922 | 4 | clone.makeVisibleAnnotation(selectionGroup.getStartRes(), |
| 1923 | selectionGroup.getEndRes(), alignment.getHiddenColumns()); | |
| 1924 | } | |
| 1925 | else | |
| 1926 | { | |
| 1927 | 0 | clone.makeVisibleAnnotation(alignment.getHiddenColumns()); |
| 1928 | } | |
| 1929 | 4 | ala.add(clone); |
| 1930 | } | |
| 1931 | } | |
| 1932 | 1 | return ala; |
| 1933 | } | |
| 1934 | ||
| 1935 | 1678 | @Override |
| 1936 | public boolean isPadGaps() | |
| 1937 | { | |
| 1938 | 1678 | return padGaps; |
| 1939 | } | |
| 1940 | ||
| 1941 | 508 | @Override |
| 1942 | public void setPadGaps(boolean padGaps) | |
| 1943 | { | |
| 1944 | 508 | this.padGaps = padGaps; |
| 1945 | } | |
| 1946 | ||
| 1947 | /** | |
| 1948 | * apply any post-edit constraints and trigger any calculations needed after | |
| 1949 | * an edit has been performed on the alignment | |
| 1950 | * | |
| 1951 | * @param ap | |
| 1952 | */ | |
| 1953 | 549 | @Override |
| 1954 | public void alignmentChanged(AlignmentViewPanel ap) | |
| 1955 | { | |
| 1956 | 549 | if (isPadGaps()) |
| 1957 | { | |
| 1958 | 310 | alignment.padGaps(); |
| 1959 | } | |
| 1960 | 549 | if (autoCalculateConsensus) |
| 1961 | { | |
| 1962 | 549 | updateConsensus(ap); |
| 1963 | 549 | updateSecondaryStructureConsensus(ap); |
| 1964 | } | |
| 1965 | 549 | if (hconsensus != null && autoCalculateConsensus) |
| 1966 | { | |
| 1967 | 542 | updateConservation(ap); |
| 1968 | } | |
| 1969 | 549 | if (autoCalculateStrucConsensus) |
| 1970 | { | |
| 1971 | 549 | updateStrucConsensus(ap); |
| 1972 | } | |
| 1973 | ||
| 1974 | // Reset endRes of groups if beyond alignment width | |
| 1975 | 549 | int alWidth = alignment.getWidth(); |
| 1976 | 549 | List<SequenceGroup> groups = alignment.getGroups(); |
| 1977 | 549 | if (groups != null) |
| 1978 | { | |
| 1979 | 549 | for (SequenceGroup sg : groups) |
| 1980 | { | |
| 1981 | 175 | if (sg.getEndRes() > alWidth) |
| 1982 | { | |
| 1983 | 0 | sg.setEndRes(alWidth - 1); |
| 1984 | } | |
| 1985 | } | |
| 1986 | } | |
| 1987 | ||
| 1988 | 549 | if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) |
| 1989 | { | |
| 1990 | 0 | selectionGroup.setEndRes(alWidth - 1); |
| 1991 | } | |
| 1992 | ||
| 1993 | 549 | updateAllColourSchemes(); |
| 1994 | 549 | calculator.restartWorkers(); |
| 1995 | // alignment.adjustSequenceAnnotations(); | |
| 1996 | } | |
| 1997 | ||
| 1998 | /** | |
| 1999 | * reset scope and do calculations for all applied colourschemes on alignment | |
| 2000 | */ | |
| 2001 | 549 | void updateAllColourSchemes() |
| 2002 | { | |
| 2003 | 549 | ResidueShaderI rs = residueShading; |
| 2004 | 549 | if (rs != null) |
| 2005 | { | |
| 2006 | 549 | rs.alignmentChanged(alignment, hiddenRepSequences); |
| 2007 | ||
| 2008 | 549 | rs.setConsensus(hconsensus); |
| 2009 | 549 | if (rs.conservationApplied()) |
| 2010 | { | |
| 2011 | 3 | rs.setConservation(Conservation.calculateConservation("All", |
| 2012 | alignment.getSequences(), 0, alignment.getWidth(), false, | |
| 2013 | getConsPercGaps(), false)); | |
| 2014 | } | |
| 2015 | } | |
| 2016 | ||
| 2017 | 549 | for (SequenceGroup sg : alignment.getGroups()) |
| 2018 | { | |
| 2019 | 175 | if (sg.cs != null) |
| 2020 | { | |
| 2021 | 175 | sg.cs.alignmentChanged(sg, hiddenRepSequences); |
| 2022 | } | |
| 2023 | 175 | sg.recalcConservation(); |
| 2024 | } | |
| 2025 | } | |
| 2026 | ||
| 2027 | 508 | protected void initAutoAnnotation() |
| 2028 | { | |
| 2029 | // TODO: add menu option action that nulls or creates consensus object | |
| 2030 | // depending on if the user wants to see the annotation or not in a | |
| 2031 | // specific alignment | |
| 2032 | ||
| 2033 | 508 | if (hconsensus == null && !isDataset) |
| 2034 | { | |
| 2035 | 508 | if (!alignment.isNucleotide()) |
| 2036 | { | |
| 2037 | 397 | initConservation(); |
| 2038 | 397 | initQuality(); |
| 2039 | } | |
| 2040 | else | |
| 2041 | { | |
| 2042 | 111 | initRNAStructure(); |
| 2043 | } | |
| 2044 | 508 | consensus = new AlignmentAnnotation("Consensus", |
| 2045 | MessageManager.getString("label.consensus_descr"), | |
| 2046 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2047 | ||
| 2048 | 508 | secondaryStructureConsensus = new AlignmentAnnotation( |
| 2049 | MessageManager.getString("label.ssconsensus_label"), | |
| 2050 | MessageManager.getString("label.ssconsensus_descr"), | |
| 2051 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2052 | ||
| 2053 | 508 | initConsensus(consensus); |
| 2054 | 508 | initSSConsensus(secondaryStructureConsensus); |
| 2055 | 508 | initGapCounts(); |
| 2056 | 508 | initComplementConsensus(); |
| 2057 | } | |
| 2058 | } | |
| 2059 | ||
| 2060 | /** | |
| 2061 | * If this is a protein alignment and there are mappings to cDNA, adds the | |
| 2062 | * cDNA consensus annotation and returns true, else returns false. | |
| 2063 | */ | |
| 2064 | 518 | public boolean initComplementConsensus() |
| 2065 | { | |
| 2066 | 518 | if (!alignment.isNucleotide()) |
| 2067 | { | |
| 2068 | 406 | final List<AlignedCodonFrame> codonMappings = alignment |
| 2069 | .getCodonFrames(); | |
| 2070 | 406 | if (codonMappings != null && !codonMappings.isEmpty()) |
| 2071 | { | |
| 2072 | 4 | boolean doConsensus = false; |
| 2073 | 4 | for (AlignedCodonFrame mapping : codonMappings) |
| 2074 | { | |
| 2075 | // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame? | |
| 2076 | 4 | MapList[] mapLists = mapping.getdnaToProt(); |
| 2077 | // mapLists can be empty if project load has not finished resolving | |
| 2078 | // seqs | |
| 2079 | 4 | if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3) |
| 2080 | { | |
| 2081 | 4 | doConsensus = true; |
| 2082 | 4 | break; |
| 2083 | } | |
| 2084 | } | |
| 2085 | 4 | if (doConsensus) |
| 2086 | { | |
| 2087 | 4 | complementConsensus = new AlignmentAnnotation("cDNA Consensus", |
| 2088 | MessageManager | |
| 2089 | .getString("label.complement_consensus_descr"), | |
| 2090 | new Annotation[1], 0f, 100f, | |
| 2091 | AlignmentAnnotation.BAR_GRAPH); | |
| 2092 | 4 | initConsensus(complementConsensus); |
| 2093 | 4 | return true; |
| 2094 | } | |
| 2095 | } | |
| 2096 | } | |
| 2097 | 514 | return false; |
| 2098 | } | |
| 2099 | ||
| 2100 | 512 | private void initConsensus(AlignmentAnnotation aa) |
| 2101 | { | |
| 2102 | 512 | aa.hasText = true; |
| 2103 | 512 | aa.autoCalculated = true; |
| 2104 | ||
| 2105 | 512 | if (showConsensus) |
| 2106 | { | |
| 2107 | 511 | alignment.addAnnotation(aa); |
| 2108 | } | |
| 2109 | } | |
| 2110 | ||
| 2111 | 508 | private void initSSConsensus(AlignmentAnnotation aa) |
| 2112 | { | |
| 2113 | 508 | aa.hasText = true; |
| 2114 | 508 | aa.autoCalculated = true; |
| 2115 | ||
| 2116 | 508 | if (showSSConsensus) |
| 2117 | { | |
| 2118 | 0 | alignment.addAnnotation(aa); |
| 2119 | } | |
| 2120 | } | |
| 2121 | ||
| 2122 | // these should be extracted from the view model - style and settings for | |
| 2123 | // derived annotation | |
| 2124 | 508 | private void initGapCounts() |
| 2125 | { | |
| 2126 | 508 | if (showOccupancy) |
| 2127 | { | |
| 2128 | 504 | gapcounts = new AlignmentAnnotation("Occupancy", |
| 2129 | MessageManager.getString("label.occupancy_descr"), | |
| 2130 | new Annotation[1], 0f, alignment.getHeight(), | |
| 2131 | AlignmentAnnotation.BAR_GRAPH); | |
| 2132 | 504 | gapcounts.hasText = true; |
| 2133 | 504 | gapcounts.autoCalculated = true; |
| 2134 | 504 | gapcounts.scaleColLabel = true; |
| 2135 | 504 | gapcounts.graph = AlignmentAnnotation.BAR_GRAPH; |
| 2136 | ||
| 2137 | 504 | alignment.addAnnotation(gapcounts); |
| 2138 | } | |
| 2139 | } | |
| 2140 | ||
| 2141 | 397 | private void initConservation() |
| 2142 | { | |
| 2143 | 397 | if (showConservation) |
| 2144 | { | |
| 2145 | 396 | if (conservation == null) |
| 2146 | { | |
| 2147 | 396 | conservation = new AlignmentAnnotation("Conservation", |
| 2148 | MessageManager.formatMessage("label.conservation_descr", | |
| 2149 | getConsPercGaps()), | |
| 2150 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2151 | 396 | conservation.hasText = true; |
| 2152 | 396 | conservation.autoCalculated = true; |
| 2153 | 396 | alignment.addAnnotation(conservation); |
| 2154 | } | |
| 2155 | } | |
| 2156 | } | |
| 2157 | ||
| 2158 | 397 | private void initQuality() |
| 2159 | { | |
| 2160 | 397 | if (showQuality) |
| 2161 | { | |
| 2162 | 397 | if (quality == null) |
| 2163 | { | |
| 2164 | 397 | quality = new AlignmentAnnotation("Quality", |
| 2165 | MessageManager.getString("label.quality_descr"), | |
| 2166 | new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); | |
| 2167 | 397 | quality.hasText = true; |
| 2168 | 397 | quality.autoCalculated = true; |
| 2169 | 397 | alignment.addAnnotation(quality); |
| 2170 | } | |
| 2171 | } | |
| 2172 | } | |
| 2173 | ||
| 2174 | 111 | private void initRNAStructure() |
| 2175 | { | |
| 2176 | 111 | if (alignment.hasRNAStructure() && strucConsensus == null) |
| 2177 | { | |
| 2178 | 2 | strucConsensus = new AlignmentAnnotation("StrucConsensus", |
| 2179 | MessageManager.getString("label.strucconsensus_descr"), | |
| 2180 | new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); | |
| 2181 | 2 | strucConsensus.hasText = true; |
| 2182 | 2 | strucConsensus.autoCalculated = true; |
| 2183 | ||
| 2184 | 2 | if (showConsensus) |
| 2185 | { | |
| 2186 | 2 | alignment.addAnnotation(strucConsensus); |
| 2187 | } | |
| 2188 | } | |
| 2189 | } | |
| 2190 | ||
| 2191 | /* | |
| 2192 | * (non-Javadoc) | |
| 2193 | * | |
| 2194 | * @see jalview.api.AlignViewportI#calcPanelHeight() | |
| 2195 | */ | |
| 2196 | 3867 | @Override |
| 2197 | public int calcPanelHeight() | |
| 2198 | { | |
| 2199 | // setHeight of panels | |
| 2200 | 3867 | AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation(); |
| 2201 | 3867 | int height = 0; |
| 2202 | 3867 | int charHeight = getCharHeight(); |
| 2203 | 3867 | if (anns != null) |
| 2204 | { | |
| 2205 | 3867 | BitSet graphgrp = new BitSet(); |
| 2206 | 3867 | for (AlignmentAnnotation aa : anns) |
| 2207 | { | |
| 2208 | 18151 | if (aa == null) |
| 2209 | { | |
| 2210 | 0 | jalview.bin.Console.errPrintln("Null annotation row: ignoring."); |
| 2211 | 0 | continue; |
| 2212 | } | |
| 2213 | 18151 | if (!aa.visible) |
| 2214 | { | |
| 2215 | 1377 | continue; |
| 2216 | } | |
| 2217 | 16774 | if (aa.graphGroup > -1) |
| 2218 | { | |
| 2219 | 300 | if (graphgrp.get(aa.graphGroup)) |
| 2220 | { | |
| 2221 | 150 | continue; |
| 2222 | } | |
| 2223 | else | |
| 2224 | { | |
| 2225 | 150 | graphgrp.set(aa.graphGroup); |
| 2226 | } | |
| 2227 | } | |
| 2228 | 16623 | aa.height = 0; |
| 2229 | ||
| 2230 | 16623 | if (aa.hasText) |
| 2231 | { | |
| 2232 | 14690 | aa.height += charHeight; |
| 2233 | } | |
| 2234 | ||
| 2235 | 16624 | if (aa.hasIcons) |
| 2236 | { | |
| 2237 | 667 | aa.height += 16; |
| 2238 | } | |
| 2239 | ||
| 2240 | 16624 | if (aa.graph > 0) |
| 2241 | { | |
| 2242 | 15567 | aa.height += aa.graphHeight + 20; |
| 2243 | } | |
| 2244 | ||
| 2245 | 16623 | if (aa.height == 0) |
| 2246 | { | |
| 2247 | 156 | aa.height = 20; |
| 2248 | } | |
| 2249 | ||
| 2250 | 16623 | height += aa.height; |
| 2251 | } | |
| 2252 | } | |
| 2253 | 3867 | if (height == 0) |
| 2254 | { | |
| 2255 | // set minimum | |
| 2256 | 18 | height = 20; |
| 2257 | } | |
| 2258 | 3867 | return height; |
| 2259 | } | |
| 2260 | ||
| 2261 | 130 | @Override |
| 2262 | public void updateGroupAnnotationSettings(boolean applyGlobalSettings, | |
| 2263 | boolean preserveNewGroupSettings) | |
| 2264 | { | |
| 2265 | 130 | boolean updateCalcs = false; |
| 2266 | 130 | boolean conv = isShowGroupConservation(); |
| 2267 | 130 | boolean cons = isShowGroupConsensus(); |
| 2268 | 130 | boolean showprf = isShowSequenceLogo(); |
| 2269 | 130 | boolean showSSprf = isShowSequenceSSLogo(); |
| 2270 | 130 | boolean showConsHist = isShowConsensusHistogram(); |
| 2271 | 130 | boolean showSSConsHist = isShowSSConsensusHistogram(); |
| 2272 | 130 | boolean normLogo = isNormaliseSequenceLogo(); |
| 2273 | ||
| 2274 | /** | |
| 2275 | * TODO reorder the annotation rows according to group/sequence ordering on | |
| 2276 | * alignment | |
| 2277 | */ | |
| 2278 | // boolean sortg = true; | |
| 2279 | ||
| 2280 | // remove old automatic annotation | |
| 2281 | // add any new annotation | |
| 2282 | ||
| 2283 | // intersect alignment annotation with alignment groups | |
| 2284 | ||
| 2285 | 130 | AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation(); |
| 2286 | 130 | List<SequenceGroup> oldrfs = new ArrayList<>(); |
| 2287 | 130 | if (aan != null) |
| 2288 | { | |
| 2289 | 1021 | for (int an = 0; an < aan.length; an++) |
| 2290 | { | |
| 2291 | 891 | if (aan[an].autoCalculated && aan[an].groupRef != null) |
| 2292 | { | |
| 2293 | 0 | oldrfs.add(aan[an].groupRef); |
| 2294 | 0 | alignment.deleteAnnotation(aan[an], false); |
| 2295 | } | |
| 2296 | } | |
| 2297 | } | |
| 2298 | 130 | if (alignment.getGroups() != null) |
| 2299 | { | |
| 2300 | 130 | for (SequenceGroup sg : alignment.getGroups()) |
| 2301 | { | |
| 2302 | 56 | updateCalcs = false; |
| 2303 | 56 | if (applyGlobalSettings |
| 2304 | || (!preserveNewGroupSettings && !oldrfs.contains(sg))) | |
| 2305 | { | |
| 2306 | // set defaults for this group's conservation/consensus | |
| 2307 | 9 | sg.setshowSequenceLogo(showprf); |
| 2308 | 9 | sg.setshowSequenceSSLogo(showSSprf); |
| 2309 | 9 | sg.setShowConsensusHistogram(showConsHist); |
| 2310 | 9 | sg.setShowSSConsensusHistogram(showSSConsHist); |
| 2311 | 9 | sg.setNormaliseSequenceLogo(normLogo); |
| 2312 | } | |
| 2313 | 56 | if (conv) |
| 2314 | { | |
| 2315 | 0 | updateCalcs = true; |
| 2316 | 0 | alignment.addAnnotation(sg.getConservationRow(), 0); |
| 2317 | } | |
| 2318 | 56 | if (cons) |
| 2319 | { | |
| 2320 | 24 | updateCalcs = true; |
| 2321 | 24 | alignment.addAnnotation(sg.getConsensus(), 0); |
| 2322 | 24 | alignment.addAnnotation(sg.getSSConsensus(), 0); |
| 2323 | } | |
| 2324 | // refresh the annotation rows | |
| 2325 | 56 | if (updateCalcs) |
| 2326 | { | |
| 2327 | 24 | sg.recalcConservation(); |
| 2328 | } | |
| 2329 | } | |
| 2330 | } | |
| 2331 | 130 | oldrfs.clear(); |
| 2332 | } | |
| 2333 | ||
| 2334 | 24633 | @Override |
| 2335 | public boolean isDisplayReferenceSeq() | |
| 2336 | { | |
| 2337 | 24633 | return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq(); |
| 2338 | } | |
| 2339 | ||
| 2340 | 10 | @Override |
| 2341 | public void setDisplayReferenceSeq(boolean displayReferenceSeq) | |
| 2342 | { | |
| 2343 | 10 | viewStyle.setDisplayReferenceSeq(displayReferenceSeq); |
| 2344 | } | |
| 2345 | ||
| 2346 | 5 | @Override |
| 2347 | public boolean isColourByReferenceSeq() | |
| 2348 | { | |
| 2349 | 5 | return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq(); |
| 2350 | } | |
| 2351 | ||
| 2352 | 18999 | @Override |
| 2353 | public Color getSequenceColour(SequenceI seq) | |
| 2354 | { | |
| 2355 | 18999 | Color sqc = sequenceColours.get(seq); |
| 2356 | 18999 | return (sqc == null ? Color.white : sqc); |
| 2357 | } | |
| 2358 | ||
| 2359 | 1192 | @Override |
| 2360 | public void setSequenceColour(SequenceI seq, Color col) | |
| 2361 | { | |
| 2362 | 1192 | if (col == null) |
| 2363 | { | |
| 2364 | 0 | sequenceColours.remove(seq); |
| 2365 | } | |
| 2366 | else | |
| 2367 | { | |
| 2368 | 1192 | sequenceColours.put(seq, col); |
| 2369 | } | |
| 2370 | } | |
| 2371 | ||
| 2372 | 5 | @Override |
| 2373 | public void updateSequenceIdColours() | |
| 2374 | { | |
| 2375 | 5 | for (SequenceGroup sg : alignment.getGroups()) |
| 2376 | { | |
| 2377 | 5 | if (sg.idColour != null) |
| 2378 | { | |
| 2379 | 0 | for (SequenceI s : sg.getSequences(getHiddenRepSequences())) |
| 2380 | { | |
| 2381 | 0 | sequenceColours.put(s, sg.idColour); |
| 2382 | } | |
| 2383 | } | |
| 2384 | } | |
| 2385 | } | |
| 2386 | ||
| 2387 | 0 | @Override |
| 2388 | public void clearSequenceColours() | |
| 2389 | { | |
| 2390 | 0 | sequenceColours.clear(); |
| 2391 | } | |
| 2392 | ||
| 2393 | 1048 | @Override |
| 2394 | public AlignViewportI getCodingComplement() | |
| 2395 | { | |
| 2396 | 1048 | return this.codingComplement; |
| 2397 | } | |
| 2398 | ||
| 2399 | /** | |
| 2400 | * Set this as the (cDna/protein) complement of the given viewport. Also | |
| 2401 | * ensures the reverse relationship is set on the given viewport. | |
| 2402 | */ | |
| 2403 | 6 | @Override |
| 2404 | public void setCodingComplement(AlignViewportI av) | |
| 2405 | { | |
| 2406 | 6 | if (this == av) |
| 2407 | { | |
| 2408 | 0 | jalview.bin.Console |
| 2409 | .errPrintln("Ignoring recursive setCodingComplement request"); | |
| 2410 | } | |
| 2411 | else | |
| 2412 | { | |
| 2413 | 6 | this.codingComplement = av; |
| 2414 | // avoid infinite recursion! | |
| 2415 | 6 | if (av.getCodingComplement() != this) |
| 2416 | { | |
| 2417 | 3 | av.setCodingComplement(this); |
| 2418 | } | |
| 2419 | } | |
| 2420 | } | |
| 2421 | ||
| 2422 | 25 | @Override |
| 2423 | public boolean isNucleotide() | |
| 2424 | { | |
| 2425 | 25 | return getAlignment() == null ? false : getAlignment().isNucleotide(); |
| 2426 | } | |
| 2427 | ||
| 2428 | 1697888 | @Override |
| 2429 | public FeaturesDisplayedI getFeaturesDisplayed() | |
| 2430 | { | |
| 2431 | 1698089 | return featuresDisplayed; |
| 2432 | } | |
| 2433 | ||
| 2434 | 112 | @Override |
| 2435 | public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) | |
| 2436 | { | |
| 2437 | 112 | featuresDisplayed = featuresDisplayedI; |
| 2438 | } | |
| 2439 | ||
| 2440 | 83 | @Override |
| 2441 | public boolean areFeaturesDisplayed() | |
| 2442 | { | |
| 2443 | 83 | return featuresDisplayed != null |
| 2444 | && featuresDisplayed.getRegisteredFeaturesCount() > 0; | |
| 2445 | } | |
| 2446 | ||
| 2447 | /** | |
| 2448 | * set the flag | |
| 2449 | * | |
| 2450 | * @param b | |
| 2451 | * features are displayed if true | |
| 2452 | */ | |
| 2453 | 141 | @Override |
| 2454 | public void setShowSequenceFeatures(boolean b) | |
| 2455 | { | |
| 2456 | 141 | viewStyle.setShowSequenceFeatures(b); |
| 2457 | } | |
| 2458 | ||
| 2459 | 435352 | @Override |
| 2460 | public boolean isShowSequenceFeatures() | |
| 2461 | { | |
| 2462 | 435398 | return viewStyle.isShowSequenceFeatures(); |
| 2463 | } | |
| 2464 | ||
| 2465 | 0 | @Override |
| 2466 | public void setShowSequenceFeaturesHeight(boolean selected) | |
| 2467 | { | |
| 2468 | 0 | viewStyle.setShowSequenceFeaturesHeight(selected); |
| 2469 | } | |
| 2470 | ||
| 2471 | 0 | @Override |
| 2472 | public boolean isShowSequenceFeaturesHeight() | |
| 2473 | { | |
| 2474 | 0 | return viewStyle.isShowSequenceFeaturesHeight(); |
| 2475 | } | |
| 2476 | ||
| 2477 | 680 | @Override |
| 2478 | public void setShowAnnotation(boolean b) | |
| 2479 | { | |
| 2480 | 680 | viewStyle.setShowAnnotation(b); |
| 2481 | } | |
| 2482 | ||
| 2483 | 5204 | @Override |
| 2484 | public boolean isShowAnnotation() | |
| 2485 | { | |
| 2486 | 5204 | return viewStyle.isShowAnnotation(); |
| 2487 | } | |
| 2488 | ||
| 2489 | 18791 | @Override |
| 2490 | public boolean isRightAlignIds() | |
| 2491 | { | |
| 2492 | 18791 | return viewStyle.isRightAlignIds(); |
| 2493 | } | |
| 2494 | ||
| 2495 | 593 | @Override |
| 2496 | public void setRightAlignIds(boolean rightAlignIds) | |
| 2497 | { | |
| 2498 | 593 | viewStyle.setRightAlignIds(rightAlignIds); |
| 2499 | } | |
| 2500 | ||
| 2501 | 1040 | @Override |
| 2502 | public boolean getConservationSelected() | |
| 2503 | { | |
| 2504 | 1040 | return viewStyle.getConservationSelected(); |
| 2505 | } | |
| 2506 | ||
| 2507 | 85 | @Override |
| 2508 | public void setShowBoxes(boolean state) | |
| 2509 | { | |
| 2510 | 85 | viewStyle.setShowBoxes(state); |
| 2511 | } | |
| 2512 | ||
| 2513 | /** | |
| 2514 | * @return | |
| 2515 | * @see jalview.api.ViewStyleI#getTextColour() | |
| 2516 | */ | |
| 2517 | 644943 | @Override |
| 2518 | public Color getTextColour() | |
| 2519 | { | |
| 2520 | 644944 | return viewStyle.getTextColour(); |
| 2521 | } | |
| 2522 | ||
| 2523 | /** | |
| 2524 | * @return | |
| 2525 | * @see jalview.api.ViewStyleI#getTextColour2() | |
| 2526 | */ | |
| 2527 | 46 | @Override |
| 2528 | public Color getTextColour2() | |
| 2529 | { | |
| 2530 | 46 | return viewStyle.getTextColour2(); |
| 2531 | } | |
| 2532 | ||
| 2533 | /** | |
| 2534 | * @return | |
| 2535 | * @see jalview.api.ViewStyleI#getThresholdTextColour() | |
| 2536 | */ | |
| 2537 | 368957 | @Override |
| 2538 | public int getThresholdTextColour() | |
| 2539 | { | |
| 2540 | 368957 | return viewStyle.getThresholdTextColour(); |
| 2541 | } | |
| 2542 | ||
| 2543 | /** | |
| 2544 | * @return | |
| 2545 | * @see jalview.api.ViewStyleI#isConservationColourSelected() | |
| 2546 | */ | |
| 2547 | 0 | @Override |
| 2548 | public boolean isConservationColourSelected() | |
| 2549 | { | |
| 2550 | 0 | return viewStyle.isConservationColourSelected(); |
| 2551 | } | |
| 2552 | ||
| 2553 | /** | |
| 2554 | * @return | |
| 2555 | * @see jalview.api.ViewStyleI#isRenderGaps() | |
| 2556 | */ | |
| 2557 | 3227 | @Override |
| 2558 | public boolean isRenderGaps() | |
| 2559 | { | |
| 2560 | 3227 | return viewStyle.isRenderGaps(); |
| 2561 | } | |
| 2562 | ||
| 2563 | /** | |
| 2564 | * @return | |
| 2565 | * @see jalview.api.ViewStyleI#isShowColourText() | |
| 2566 | */ | |
| 2567 | 672 | @Override |
| 2568 | public boolean isShowColourText() | |
| 2569 | { | |
| 2570 | 672 | return viewStyle.isShowColourText(); |
| 2571 | } | |
| 2572 | ||
| 2573 | /** | |
| 2574 | * @param conservationColourSelected | |
| 2575 | * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean) | |
| 2576 | */ | |
| 2577 | 0 | @Override |
| 2578 | public void setConservationColourSelected( | |
| 2579 | boolean conservationColourSelected) | |
| 2580 | { | |
| 2581 | 0 | viewStyle.setConservationColourSelected(conservationColourSelected); |
| 2582 | } | |
| 2583 | ||
| 2584 | /** | |
| 2585 | * @param showColourText | |
| 2586 | * @see jalview.api.ViewStyleI#setShowColourText(boolean) | |
| 2587 | */ | |
| 2588 | 0 | @Override |
| 2589 | public void setShowColourText(boolean showColourText) | |
| 2590 | { | |
| 2591 | 0 | viewStyle.setShowColourText(showColourText); |
| 2592 | } | |
| 2593 | ||
| 2594 | /** | |
| 2595 | * @param textColour | |
| 2596 | * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color) | |
| 2597 | */ | |
| 2598 | 85 | @Override |
| 2599 | public void setTextColour(Color textColour) | |
| 2600 | { | |
| 2601 | 85 | viewStyle.setTextColour(textColour); |
| 2602 | } | |
| 2603 | ||
| 2604 | /** | |
| 2605 | * @param thresholdTextColour | |
| 2606 | * @see jalview.api.ViewStyleI#setThresholdTextColour(int) | |
| 2607 | */ | |
| 2608 | 85 | @Override |
| 2609 | public void setThresholdTextColour(int thresholdTextColour) | |
| 2610 | { | |
| 2611 | 85 | viewStyle.setThresholdTextColour(thresholdTextColour); |
| 2612 | } | |
| 2613 | ||
| 2614 | /** | |
| 2615 | * @param textColour2 | |
| 2616 | * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color) | |
| 2617 | */ | |
| 2618 | 85 | @Override |
| 2619 | public void setTextColour2(Color textColour2) | |
| 2620 | { | |
| 2621 | 85 | viewStyle.setTextColour2(textColour2); |
| 2622 | } | |
| 2623 | ||
| 2624 | 143 | @Override |
| 2625 | public ViewStyleI getViewStyle() | |
| 2626 | { | |
| 2627 | 143 | return new ViewStyle(viewStyle); |
| 2628 | } | |
| 2629 | ||
| 2630 | 86 | @Override |
| 2631 | public void setViewStyle(ViewStyleI settingsForView) | |
| 2632 | { | |
| 2633 | 86 | viewStyle = new ViewStyle(settingsForView); |
| 2634 | 86 | if (residueShading != null) |
| 2635 | { | |
| 2636 | 86 | residueShading.setConservationApplied( |
| 2637 | settingsForView.isConservationColourSelected()); | |
| 2638 | } | |
| 2639 | } | |
| 2640 | ||
| 2641 | 0 | @Override |
| 2642 | public boolean sameStyle(ViewStyleI them) | |
| 2643 | { | |
| 2644 | 0 | return viewStyle.sameStyle(them); |
| 2645 | } | |
| 2646 | ||
| 2647 | /** | |
| 2648 | * @return | |
| 2649 | * @see jalview.api.ViewStyleI#getIdWidth() | |
| 2650 | */ | |
| 2651 | 6205 | @Override |
| 2652 | public int getIdWidth() | |
| 2653 | { | |
| 2654 | 6205 | return viewStyle.getIdWidth(); |
| 2655 | } | |
| 2656 | ||
| 2657 | /** | |
| 2658 | * @param i | |
| 2659 | * @see jalview.api.ViewStyleI#setIdWidth(int) | |
| 2660 | */ | |
| 2661 | 1031 | @Override |
| 2662 | public void setIdWidth(int i) | |
| 2663 | { | |
| 2664 | 1031 | viewStyle.setIdWidth(i); |
| 2665 | } | |
| 2666 | ||
| 2667 | /** | |
| 2668 | * @return | |
| 2669 | * @see jalview.api.ViewStyleI#isCentreColumnLabels() | |
| 2670 | */ | |
| 2671 | 672 | @Override |
| 2672 | public boolean isCentreColumnLabels() | |
| 2673 | { | |
| 2674 | 672 | return viewStyle.isCentreColumnLabels(); |
| 2675 | } | |
| 2676 | ||
| 2677 | /** | |
| 2678 | * @param centreColumnLabels | |
| 2679 | * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean) | |
| 2680 | */ | |
| 2681 | 593 | @Override |
| 2682 | public void setCentreColumnLabels(boolean centreColumnLabels) | |
| 2683 | { | |
| 2684 | 593 | viewStyle.setCentreColumnLabels(centreColumnLabels); |
| 2685 | } | |
| 2686 | ||
| 2687 | /** | |
| 2688 | * @param showdbrefs | |
| 2689 | * @see jalview.api.ViewStyleI#setShowDBRefs(boolean) | |
| 2690 | */ | |
| 2691 | 593 | @Override |
| 2692 | public void setShowDBRefs(boolean showdbrefs) | |
| 2693 | { | |
| 2694 | 593 | viewStyle.setShowDBRefs(showdbrefs); |
| 2695 | } | |
| 2696 | ||
| 2697 | /** | |
| 2698 | * @return | |
| 2699 | * @see jalview.api.ViewStyleI#isShowDBRefs() | |
| 2700 | */ | |
| 2701 | 718 | @Override |
| 2702 | public boolean isShowDBRefs() | |
| 2703 | { | |
| 2704 | 718 | return viewStyle.isShowDBRefs(); |
| 2705 | } | |
| 2706 | ||
| 2707 | /** | |
| 2708 | * @return | |
| 2709 | * @see jalview.api.ViewStyleI#isShowNPFeats() | |
| 2710 | */ | |
| 2711 | 718 | @Override |
| 2712 | public boolean isShowNPFeats() | |
| 2713 | { | |
| 2714 | 718 | return viewStyle.isShowNPFeats(); |
| 2715 | } | |
| 2716 | ||
| 2717 | /** | |
| 2718 | * @param shownpfeats | |
| 2719 | * @see jalview.api.ViewStyleI#setShowNPFeats(boolean) | |
| 2720 | */ | |
| 2721 | 593 | @Override |
| 2722 | public void setShowNPFeats(boolean shownpfeats) | |
| 2723 | { | |
| 2724 | 593 | viewStyle.setShowNPFeats(shownpfeats); |
| 2725 | } | |
| 2726 | ||
| 2727 | public abstract StructureSelectionManager getStructureSelectionManager(); | |
| 2728 | ||
| 2729 | /** | |
| 2730 | * Add one command to the command history list. | |
| 2731 | * | |
| 2732 | * @param command | |
| 2733 | */ | |
| 2734 | 1 | public void addToHistoryList(CommandI command) |
| 2735 | { | |
| 2736 | 1 | if (this.historyList != null) |
| 2737 | { | |
| 2738 | 1 | this.historyList.push(command); |
| 2739 | 1 | broadcastCommand(command, false); |
| 2740 | 1 | setSavedUpToDate(false); |
| 2741 | 1 | Jalview2XML.setStateSavedUpToDate(false); |
| 2742 | } | |
| 2743 | } | |
| 2744 | ||
| 2745 | 1 | protected void broadcastCommand(CommandI command, boolean undo) |
| 2746 | { | |
| 2747 | 1 | getStructureSelectionManager().commandPerformed(command, undo, |
| 2748 | getVamsasSource()); | |
| 2749 | } | |
| 2750 | ||
| 2751 | /** | |
| 2752 | * Add one command to the command redo list. | |
| 2753 | * | |
| 2754 | * @param command | |
| 2755 | */ | |
| 2756 | 0 | public void addToRedoList(CommandI command) |
| 2757 | { | |
| 2758 | 0 | if (this.redoList != null) |
| 2759 | { | |
| 2760 | 0 | this.redoList.push(command); |
| 2761 | } | |
| 2762 | 0 | broadcastCommand(command, true); |
| 2763 | } | |
| 2764 | ||
| 2765 | /** | |
| 2766 | * Clear the command redo list. | |
| 2767 | */ | |
| 2768 | 1 | public void clearRedoList() |
| 2769 | { | |
| 2770 | 1 | if (this.redoList != null) |
| 2771 | { | |
| 2772 | 1 | this.redoList.clear(); |
| 2773 | } | |
| 2774 | } | |
| 2775 | ||
| 2776 | 53 | public void setHistoryList(Deque<CommandI> list) |
| 2777 | { | |
| 2778 | 53 | this.historyList = list; |
| 2779 | } | |
| 2780 | ||
| 2781 | 1277 | public Deque<CommandI> getHistoryList() |
| 2782 | { | |
| 2783 | 1277 | return this.historyList; |
| 2784 | } | |
| 2785 | ||
| 2786 | 53 | public void setRedoList(Deque<CommandI> list) |
| 2787 | { | |
| 2788 | 53 | this.redoList = list; |
| 2789 | } | |
| 2790 | ||
| 2791 | 1275 | public Deque<CommandI> getRedoList() |
| 2792 | { | |
| 2793 | 1275 | return this.redoList; |
| 2794 | } | |
| 2795 | ||
| 2796 | 1 | @Override |
| 2797 | public VamsasSource getVamsasSource() | |
| 2798 | { | |
| 2799 | 1 | return this; |
| 2800 | } | |
| 2801 | ||
| 2802 | 4559 | public SequenceAnnotationOrder getSortAnnotationsBy() |
| 2803 | { | |
| 2804 | 4559 | return sortAnnotationsBy; |
| 2805 | } | |
| 2806 | ||
| 2807 | 0 | public void setSortAnnotationsBy( |
| 2808 | SequenceAnnotationOrder sortAnnotationsBy) | |
| 2809 | { | |
| 2810 | 0 | this.sortAnnotationsBy = sortAnnotationsBy; |
| 2811 | } | |
| 2812 | ||
| 2813 | 4559 | public boolean isShowAutocalculatedAbove() |
| 2814 | { | |
| 2815 | 4559 | return showAutocalculatedAbove; |
| 2816 | } | |
| 2817 | ||
| 2818 | 452 | public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) |
| 2819 | { | |
| 2820 | 452 | this.showAutocalculatedAbove = showAutocalculatedAbove; |
| 2821 | } | |
| 2822 | ||
| 2823 | 3 | @Override |
| 2824 | public boolean isScaleProteinAsCdna() | |
| 2825 | { | |
| 2826 | 3 | return viewStyle.isScaleProteinAsCdna(); |
| 2827 | } | |
| 2828 | ||
| 2829 | 0 | @Override |
| 2830 | public void setScaleProteinAsCdna(boolean b) | |
| 2831 | { | |
| 2832 | 0 | viewStyle.setScaleProteinAsCdna(b); |
| 2833 | } | |
| 2834 | ||
| 2835 | 0 | @Override |
| 2836 | public boolean isProteinFontAsCdna() | |
| 2837 | { | |
| 2838 | 0 | return viewStyle.isProteinFontAsCdna(); |
| 2839 | } | |
| 2840 | ||
| 2841 | 0 | @Override |
| 2842 | public void setProteinFontAsCdna(boolean b) | |
| 2843 | { | |
| 2844 | 0 | viewStyle.setProteinFontAsCdna(b); |
| 2845 | } | |
| 2846 | ||
| 2847 | 85 | @Override |
| 2848 | public void setShowComplementFeatures(boolean b) | |
| 2849 | { | |
| 2850 | 85 | viewStyle.setShowComplementFeatures(b); |
| 2851 | } | |
| 2852 | ||
| 2853 | 439339 | @Override |
| 2854 | public boolean isShowComplementFeatures() | |
| 2855 | { | |
| 2856 | 439394 | return viewStyle.isShowComplementFeatures(); |
| 2857 | } | |
| 2858 | ||
| 2859 | 85 | @Override |
| 2860 | public void setShowComplementFeaturesOnTop(boolean b) | |
| 2861 | { | |
| 2862 | 85 | viewStyle.setShowComplementFeaturesOnTop(b); |
| 2863 | } | |
| 2864 | ||
| 2865 | 47 | @Override |
| 2866 | public boolean isShowComplementFeaturesOnTop() | |
| 2867 | { | |
| 2868 | 47 | return viewStyle.isShowComplementFeaturesOnTop(); |
| 2869 | } | |
| 2870 | ||
| 2871 | /** | |
| 2872 | * @return true if view should scroll to show the highlighted region of a | |
| 2873 | * sequence | |
| 2874 | * @return | |
| 2875 | */ | |
| 2876 | 51 | @Override |
| 2877 | public final boolean isFollowHighlight() | |
| 2878 | { | |
| 2879 | 51 | return followHighlight; |
| 2880 | } | |
| 2881 | ||
| 2882 | 85 | @Override |
| 2883 | public final void setFollowHighlight(boolean b) | |
| 2884 | { | |
| 2885 | 85 | this.followHighlight = b; |
| 2886 | } | |
| 2887 | ||
| 2888 | 38412 | @Override |
| 2889 | public ViewportRanges getRanges() | |
| 2890 | { | |
| 2891 | 38412 | return ranges; |
| 2892 | } | |
| 2893 | ||
| 2894 | /** | |
| 2895 | * Helper method to populate the SearchResults with the location in the | |
| 2896 | * complementary alignment to scroll to, in order to match this one. | |
| 2897 | * | |
| 2898 | * @param sr | |
| 2899 | * the SearchResults to add to | |
| 2900 | * @return the offset (below top of visible region) of the matched sequence | |
| 2901 | */ | |
| 2902 | 628 | protected int findComplementScrollTarget(SearchResultsI sr) |
| 2903 | { | |
| 2904 | 628 | final AlignViewportI complement = getCodingComplement(); |
| 2905 | 628 | if (complement == null || !complement.isFollowHighlight()) |
| 2906 | { | |
| 2907 | 624 | return 0; |
| 2908 | } | |
| 2909 | 4 | boolean iAmProtein = !getAlignment().isNucleotide(); |
| 2910 | 4 | AlignmentI proteinAlignment = iAmProtein ? getAlignment() |
| 2911 | : complement.getAlignment(); | |
| 2912 | 4 | if (proteinAlignment == null) |
| 2913 | { | |
| 2914 | 0 | return 0; |
| 2915 | } | |
| 2916 | 4 | final List<AlignedCodonFrame> mappings = proteinAlignment |
| 2917 | .getCodonFrames(); | |
| 2918 | ||
| 2919 | /* | |
| 2920 | * Heuristic: find the first mapped sequence (if any) with a non-gapped | |
| 2921 | * residue in the middle column of the visible region. Scroll the | |
| 2922 | * complementary alignment to line up the corresponding residue. | |
| 2923 | */ | |
| 2924 | 4 | int seqOffset = 0; |
| 2925 | 4 | SequenceI sequence = null; |
| 2926 | ||
| 2927 | /* | |
| 2928 | * locate 'middle' column (true middle if an odd number visible, left of | |
| 2929 | * middle if an even number visible) | |
| 2930 | */ | |
| 2931 | 4 | int middleColumn = ranges.getStartRes() |
| 2932 | + (ranges.getEndRes() - ranges.getStartRes()) / 2; | |
| 2933 | 4 | final HiddenSequences hiddenSequences = getAlignment() |
| 2934 | .getHiddenSequences(); | |
| 2935 | ||
| 2936 | /* | |
| 2937 | * searching to the bottom of the alignment gives smoother scrolling across | |
| 2938 | * all gapped visible regions | |
| 2939 | */ | |
| 2940 | 4 | int lastSeq = alignment.getHeight() - 1; |
| 2941 | 4 | List<AlignedCodonFrame> seqMappings = null; |
| 2942 | 4 | for (int seqNo = ranges |
| 2943 | 4 | .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) |
| 2944 | { | |
| 2945 | 4 | sequence = getAlignment().getSequenceAt(seqNo); |
| 2946 | 4 | if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) |
| 2947 | { | |
| 2948 | 0 | continue; |
| 2949 | } | |
| 2950 | 4 | if (Comparison.isGap(sequence.getCharAt(middleColumn))) |
| 2951 | { | |
| 2952 | 0 | continue; |
| 2953 | } | |
| 2954 | 4 | seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence, |
| 2955 | mappings, | |
| 2956 | getCodingComplement().getAlignment().getSequences()); | |
| 2957 | 4 | if (!seqMappings.isEmpty()) |
| 2958 | { | |
| 2959 | 4 | break; |
| 2960 | } | |
| 2961 | } | |
| 2962 | ||
| 2963 | 4 | if (sequence == null || seqMappings == null || seqMappings.isEmpty()) |
| 2964 | { | |
| 2965 | /* | |
| 2966 | * No ungapped mapped sequence in middle column - do nothing | |
| 2967 | */ | |
| 2968 | 0 | return 0; |
| 2969 | } | |
| 2970 | 4 | MappingUtils.addSearchResults(sr, sequence, |
| 2971 | sequence.findPosition(middleColumn), seqMappings); | |
| 2972 | 4 | return seqOffset; |
| 2973 | } | |
| 2974 | ||
| 2975 | /** | |
| 2976 | * synthesize a column selection if none exists so it covers the given | |
| 2977 | * selection group. if wholewidth is false, no column selection is made if the | |
| 2978 | * selection group covers the whole alignment width. | |
| 2979 | * | |
| 2980 | * @param sg | |
| 2981 | * @param wholewidth | |
| 2982 | */ | |
| 2983 | 0 | public void expandColSelection(SequenceGroup sg, boolean wholewidth) |
| 2984 | { | |
| 2985 | 0 | int sgs, sge; |
| 2986 | 0 | if (sg != null && (sgs = sg.getStartRes()) >= 0 |
| 2987 | && sg.getStartRes() <= (sge = sg.getEndRes()) | |
| 2988 | && !this.hasSelectedColumns()) | |
| 2989 | { | |
| 2990 | 0 | if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) |
| 2991 | { | |
| 2992 | // do nothing | |
| 2993 | 0 | return; |
| 2994 | } | |
| 2995 | 0 | if (colSel == null) |
| 2996 | { | |
| 2997 | 0 | colSel = new ColumnSelection(); |
| 2998 | } | |
| 2999 | 0 | for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) |
| 3000 | { | |
| 3001 | 0 | colSel.addElement(cspos); |
| 3002 | } | |
| 3003 | } | |
| 3004 | } | |
| 3005 | ||
| 3006 | /** | |
| 3007 | * hold status of current selection group - defined on alignment or not. | |
| 3008 | */ | |
| 3009 | private boolean selectionIsDefinedGroup = false; | |
| 3010 | ||
| 3011 | 0 | @Override |
| 3012 | public boolean isSelectionDefinedGroup() | |
| 3013 | { | |
| 3014 | 0 | if (selectionGroup == null) |
| 3015 | { | |
| 3016 | 0 | return false; |
| 3017 | } | |
| 3018 | 0 | if (isSelectionGroupChanged(true)) |
| 3019 | { | |
| 3020 | 0 | selectionIsDefinedGroup = false; |
| 3021 | 0 | List<SequenceGroup> gps = alignment.getGroups(); |
| 3022 | 0 | if (gps == null || gps.size() == 0) |
| 3023 | { | |
| 3024 | 0 | selectionIsDefinedGroup = false; |
| 3025 | } | |
| 3026 | else | |
| 3027 | { | |
| 3028 | 0 | selectionIsDefinedGroup = gps.contains(selectionGroup); |
| 3029 | } | |
| 3030 | } | |
| 3031 | 0 | return selectionGroup.isDefined() || selectionIsDefinedGroup; |
| 3032 | } | |
| 3033 | ||
| 3034 | /** | |
| 3035 | * null, or currently highlighted results on this view | |
| 3036 | */ | |
| 3037 | private SearchResultsI searchResults = null; | |
| 3038 | ||
| 3039 | protected TreeModel currentTree = null; | |
| 3040 | ||
| 3041 | 11375 | @Override |
| 3042 | public boolean hasSearchResults() | |
| 3043 | { | |
| 3044 | 11375 | return searchResults != null; |
| 3045 | } | |
| 3046 | ||
| 3047 | 7 | @Override |
| 3048 | public void setSearchResults(SearchResultsI results) | |
| 3049 | { | |
| 3050 | 7 | searchResults = results; |
| 3051 | } | |
| 3052 | ||
| 3053 | 44 | @Override |
| 3054 | public SearchResultsI getSearchResults() | |
| 3055 | { | |
| 3056 | 44 | return searchResults; |
| 3057 | } | |
| 3058 | ||
| 3059 | 3473 | @Override |
| 3060 | public ContactListI getContactList(AlignmentAnnotation _aa, int column) | |
| 3061 | { | |
| 3062 | 3473 | return alignment.getContactListFor(_aa, column); |
| 3063 | } | |
| 3064 | ||
| 3065 | 145 | @Override |
| 3066 | public ContactMatrixI getContactMatrix( | |
| 3067 | AlignmentAnnotation alignmentAnnotation) | |
| 3068 | { | |
| 3069 | 145 | return alignment.getContactMatrixFor(alignmentAnnotation); |
| 3070 | } | |
| 3071 | ||
| 3072 | /** | |
| 3073 | * get the consensus sequence as displayed under the PID consensus annotation | |
| 3074 | * row. | |
| 3075 | * | |
| 3076 | * @return consensus sequence as a new sequence object | |
| 3077 | */ | |
| 3078 | 1 | public SequenceI getConsensusSeq() |
| 3079 | { | |
| 3080 | 1 | if (consensus == null) |
| 3081 | { | |
| 3082 | 0 | updateConsensus(null); |
| 3083 | } | |
| 3084 | 1 | if (consensus == null) |
| 3085 | { | |
| 3086 | 0 | return null; |
| 3087 | } | |
| 3088 | 1 | StringBuffer seqs = new StringBuffer(); |
| 3089 | 4 | for (int i = 0; i < consensus.annotations.length; i++) |
| 3090 | { | |
| 3091 | 3 | Annotation annotation = consensus.annotations[i]; |
| 3092 | 3 | if (annotation != null) |
| 3093 | { | |
| 3094 | 3 | String description = annotation.description; |
| 3095 | 3 | if (description != null && description.startsWith("[")) |
| 3096 | { | |
| 3097 | // consensus is a tie - just pick the first one | |
| 3098 | 1 | seqs.append(description.charAt(1)); |
| 3099 | } | |
| 3100 | else | |
| 3101 | { | |
| 3102 | 2 | seqs.append(annotation.displayCharacter); |
| 3103 | } | |
| 3104 | } | |
| 3105 | } | |
| 3106 | ||
| 3107 | 1 | SequenceI sq = new Sequence("Consensus", seqs.toString()); |
| 3108 | 1 | sq.setDescription("Percentage Identity Consensus " |
| 3109 | 1 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3110 | 1 | return sq; |
| 3111 | } | |
| 3112 | ||
| 3113 | 0 | public SequenceI getSSConsensusSeq() |
| 3114 | { | |
| 3115 | 0 | if (secondaryStructureConsensus == null) |
| 3116 | { | |
| 3117 | 0 | updateSecondaryStructureConsensus(null); |
| 3118 | } | |
| 3119 | 0 | if (secondaryStructureConsensus == null) |
| 3120 | { | |
| 3121 | 0 | return null; |
| 3122 | } | |
| 3123 | 0 | StringBuffer seqs = new StringBuffer(); |
| 3124 | 0 | for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++) |
| 3125 | { | |
| 3126 | 0 | Annotation annotation = secondaryStructureConsensus.annotations[i]; |
| 3127 | 0 | if (annotation != null) |
| 3128 | { | |
| 3129 | 0 | String description = annotation.description; |
| 3130 | 0 | if (description != null && description.startsWith("[")) |
| 3131 | { | |
| 3132 | // consensus is a tie - just pick the first one | |
| 3133 | 0 | seqs.append(description.charAt(1)); |
| 3134 | } | |
| 3135 | else | |
| 3136 | { | |
| 3137 | 0 | seqs.append(annotation.displayCharacter); |
| 3138 | } | |
| 3139 | } | |
| 3140 | } | |
| 3141 | ||
| 3142 | 0 | SequenceI sq = new Sequence("Sec Str Consensus", seqs.toString()); |
| 3143 | 0 | sq.setDescription("Percentage Identity Sec Str Consensus " |
| 3144 | 0 | + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); |
| 3145 | 0 | return sq; |
| 3146 | } | |
| 3147 | ||
| 3148 | 28 | @Override |
| 3149 | public void setCurrentTree(TreeModel tree) | |
| 3150 | { | |
| 3151 | 28 | currentTree = tree; |
| 3152 | } | |
| 3153 | ||
| 3154 | 50 | @Override |
| 3155 | public TreeModel getCurrentTree() | |
| 3156 | { | |
| 3157 | 50 | return currentTree; |
| 3158 | } | |
| 3159 | ||
| 3160 | 121 | @Override |
| 3161 | public AlignmentExportData getAlignExportData( | |
| 3162 | AlignExportSettingsI options) | |
| 3163 | { | |
| 3164 | 121 | AlignmentI alignmentToExport = null; |
| 3165 | 121 | String[] omitHidden = null; |
| 3166 | 121 | alignmentToExport = null; |
| 3167 | ||
| 3168 | 121 | if (hasHiddenColumns() && !options.isExportHiddenColumns()) |
| 3169 | { | |
| 3170 | 0 | omitHidden = getViewAsString(false, |
| 3171 | options.isExportHiddenSequences()); | |
| 3172 | } | |
| 3173 | ||
| 3174 | 121 | int[] alignmentStartEnd = new int[2]; |
| 3175 | 121 | if (hasHiddenRows() && options.isExportHiddenSequences()) |
| 3176 | { | |
| 3177 | 0 | alignmentToExport = getAlignment().getHiddenSequences() |
| 3178 | .getFullAlignment(); | |
| 3179 | } | |
| 3180 | else | |
| 3181 | { | |
| 3182 | 121 | alignmentToExport = getAlignment(); |
| 3183 | } | |
| 3184 | 121 | alignmentStartEnd = getAlignment().getHiddenColumns() |
| 3185 | .getVisibleStartAndEndIndex(alignmentToExport.getWidth()); | |
| 3186 | 121 | AlignmentExportData ed = new AlignmentExportData(alignmentToExport, |
| 3187 | omitHidden, alignmentStartEnd); | |
| 3188 | 121 | return ed; |
| 3189 | } | |
| 3190 | ||
| 3191 | /** | |
| 3192 | * flag set to indicate if structure views might be out of sync with sequences | |
| 3193 | * in the alignment | |
| 3194 | */ | |
| 3195 | ||
| 3196 | private boolean needToUpdateStructureViews = false; | |
| 3197 | ||
| 3198 | 0 | @Override |
| 3199 | public boolean isUpdateStructures() | |
| 3200 | { | |
| 3201 | 0 | return needToUpdateStructureViews; |
| 3202 | } | |
| 3203 | ||
| 3204 | 0 | @Override |
| 3205 | public void setUpdateStructures(boolean update) | |
| 3206 | { | |
| 3207 | 0 | needToUpdateStructureViews = update; |
| 3208 | } | |
| 3209 | ||
| 3210 | 741 | @Override |
| 3211 | public boolean needToUpdateStructureViews() | |
| 3212 | { | |
| 3213 | 741 | boolean update = needToUpdateStructureViews; |
| 3214 | 741 | needToUpdateStructureViews = false; |
| 3215 | 741 | return update; |
| 3216 | } | |
| 3217 | ||
| 3218 | 0 | @Override |
| 3219 | public void addSequenceGroup(SequenceGroup sequenceGroup) | |
| 3220 | { | |
| 3221 | 0 | alignment.addGroup(sequenceGroup); |
| 3222 | ||
| 3223 | 0 | Color col = sequenceGroup.idColour; |
| 3224 | 0 | if (col != null) |
| 3225 | { | |
| 3226 | 0 | col = col.brighter(); |
| 3227 | ||
| 3228 | 0 | for (SequenceI sq : sequenceGroup.getSequences()) |
| 3229 | { | |
| 3230 | 0 | setSequenceColour(sq, col); |
| 3231 | } | |
| 3232 | } | |
| 3233 | ||
| 3234 | 0 | if (codingComplement != null) |
| 3235 | { | |
| 3236 | 0 | SequenceGroup mappedGroup = MappingUtils |
| 3237 | .mapSequenceGroup(sequenceGroup, this, codingComplement); | |
| 3238 | 0 | if (mappedGroup.getSequences().size() > 0) |
| 3239 | { | |
| 3240 | 0 | codingComplement.getAlignment().addGroup(mappedGroup); |
| 3241 | ||
| 3242 | 0 | if (col != null) |
| 3243 | { | |
| 3244 | 0 | for (SequenceI seq : mappedGroup.getSequences()) |
| 3245 | { | |
| 3246 | 0 | codingComplement.setSequenceColour(seq, col); |
| 3247 | } | |
| 3248 | } | |
| 3249 | } | |
| 3250 | // propagate the structure view update flag according to our own setting | |
| 3251 | 0 | codingComplement.setUpdateStructures(needToUpdateStructureViews); |
| 3252 | } | |
| 3253 | } | |
| 3254 | ||
| 3255 | 34 | @Override |
| 3256 | public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly) | |
| 3257 | { | |
| 3258 | 34 | int start = 0; |
| 3259 | 34 | int end = 0; |
| 3260 | 34 | if (selectedRegionOnly && selectionGroup != null) |
| 3261 | { | |
| 3262 | 4 | start = selectionGroup.getStartRes(); |
| 3263 | 4 | end = selectionGroup.getEndRes() + 1; |
| 3264 | } | |
| 3265 | else | |
| 3266 | { | |
| 3267 | 30 | end = alignment.getWidth(); |
| 3268 | } | |
| 3269 | 34 | return (alignment.getHiddenColumns().getVisContigsIterator(start, end, |
| 3270 | false)); | |
| 3271 | } | |
| 3272 | ||
| 3273 | 133 | public void setSavedUpToDate(boolean s) |
| 3274 | { | |
| 3275 | 133 | setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES); |
| 3276 | } | |
| 3277 | ||
| 3278 | 452 | public void setSavedUpToDate(boolean s, QuitHandler.Message m) |
| 3279 | { | |
| 3280 | 452 | Console.debug( |
| 3281 | "Setting " + this.getViewId() + " setSavedUpToDate to " + s); | |
| 3282 | 452 | savedUpToDate = s; |
| 3283 | 452 | QuitHandler.setMessage(m); |
| 3284 | } | |
| 3285 | ||
| 3286 | 4 | public boolean savedUpToDate() |
| 3287 | { | |
| 3288 | 4 | Console.debug("Returning " + this.getViewId() + " savedUpToDate value: " |
| 3289 | + savedUpToDate); | |
| 3290 | 4 | return savedUpToDate; |
| 3291 | } | |
| 3292 | } |