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File ResidueShader.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| ResidueShader | 52 | 91 | 58 |
Contributing tests
This file is covered by 151 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.renderer; | |
| 22 | ||
| 23 | import jalview.analysis.AlignmentUtils; | |
| 24 | import jalview.analysis.Conservation; | |
| 25 | import jalview.api.ViewStyleI; | |
| 26 | import jalview.datamodel.AnnotatedCollectionI; | |
| 27 | import jalview.datamodel.ProfileI; | |
| 28 | import jalview.datamodel.ProfilesI; | |
| 29 | import jalview.datamodel.SequenceCollectionI; | |
| 30 | import jalview.datamodel.SequenceI; | |
| 31 | import jalview.schemes.ColourSchemeI; | |
| 32 | import jalview.util.ColorUtils; | |
| 33 | import jalview.util.Comparison; | |
| 34 | import jalview.util.Constants; | |
| 35 | ||
| 36 | import java.awt.Color; | |
| 37 | import java.util.Map; | |
| 38 | ||
| 39 | /** | |
| 40 | * A class that computes the colouring of an alignment (or subgroup). Currently | |
| 41 | * the factors that may influence residue colouring are | |
| 42 | * <ul> | |
| 43 | * <li>the colour scheme that provides a colour for each aligned residue</li> | |
| 44 | * <li>any threshold for colour, based on percentage identity with | |
| 45 | * consensus</li> | |
| 46 | * <li>any graduation based on conservation of physico-chemical properties</li> | |
| 47 | * </ul> | |
| 48 | * | |
| 49 | * @author gmcarstairs | |
| 50 | * | |
| 51 | */ | |
| 52 | public class ResidueShader implements ResidueShaderI | |
| 53 | { | |
| 54 | private static final int INITIAL_CONSERVATION = 30; | |
| 55 | ||
| 56 | /* | |
| 57 | * the colour scheme that gives the colour of each residue | |
| 58 | * before applying any conservation or PID shading | |
| 59 | */ | |
| 60 | private ColourSchemeI colourScheme; | |
| 61 | ||
| 62 | /* | |
| 63 | * the consensus data for each column | |
| 64 | */ | |
| 65 | private ProfilesI consensus; | |
| 66 | ||
| 67 | /* | |
| 68 | * the ss consensus data for each column for each source | |
| 69 | */ | |
| 70 | private Map<String, ProfilesI> ssConsensusProfileMap; | |
| 71 | ||
| 72 | /* | |
| 73 | * if true, apply shading of colour by conservation | |
| 74 | */ | |
| 75 | private boolean conservationColouring; | |
| 76 | ||
| 77 | private boolean consensusSecondaryStructureColouring; | |
| 78 | ||
| 79 | 5 |  @Override |
| 80 | public boolean isConsensusSecondaryStructureColouring() | |
| 81 | { | |
| 82 | 5 | return consensusSecondaryStructureColouring; |
| 83 | } | |
| 84 | ||
| 85 | /* | |
| 86 | * the physico-chemical property conservation scores for columns, with values | |
| 87 | * 0-9, '+' (all properties conserved), '*' (residue fully conserved) or '-' (gap) | |
| 88 | * (may be null if colour by conservation is not selected) | |
| 89 | */ | |
| 90 | private char[] conservation; | |
| 91 | ||
| 92 | /* | |
| 93 | * minimum percentage identity for colour to be applied; | |
| 94 | * if above zero, residue must match consensus (or joint consensus) | |
| 95 | * and column have >= pidThreshold identity with the residue | |
| 96 | */ | |
| 97 | private int pidThreshold; | |
| 98 | ||
| 99 | /* | |
| 100 | * if true, ignore gaps in percentage identity calculation | |
| 101 | */ | |
| 102 | private boolean ignoreGaps; | |
| 103 | ||
| 104 | /* | |
| 105 | * setting of the By Conservation slider | |
| 106 | */ | |
| 107 | private int conservationIncrement = INITIAL_CONSERVATION; | |
| 108 | ||
| 109 | private int consensusSecondaryStructureThreshold = 30; | |
| 110 | ||
| 111 | 946 | public ResidueShader(ColourSchemeI cs) |
| 112 | { | |
| 113 | 946 | colourScheme = cs; |
| 114 | } | |
| 115 | ||
| 116 | /** | |
| 117 | * Default constructor | |
| 118 | */ | |
| 119 | 405 | public ResidueShader() |
| 120 | { | |
| 121 | } | |
| 122 | ||
| 123 | /** | |
| 124 | * Constructor given view style settings | |
| 125 | * | |
| 126 | * @param viewStyle | |
| 127 | */ | |
| 128 | 0 | public ResidueShader(ViewStyleI viewStyle) |
| 129 | { | |
| 130 | // TODO remove duplicated storing of conservation / pid thresholds? | |
| 131 | 0 | this(); |
| 132 | 0 | setConservationApplied(viewStyle.isConservationColourSelected()); |
| 133 | // setThreshold(viewStyle.getThreshold()); | |
| 134 | } | |
| 135 | ||
| 136 | /** | |
| 137 | * Copy constructor | |
| 138 | */ | |
| 139 | 52 | public ResidueShader(ResidueShader rs) |
| 140 | { | |
| 141 | 52 | this.colourScheme = rs.colourScheme; |
| 142 | 52 | this.consensus = rs.consensus; |
| 143 | 52 | this.conservation = rs.conservation; |
| 144 | 52 | this.conservationColouring = rs.conservationColouring; |
| 145 | 52 | this.conservationIncrement = rs.conservationIncrement; |
| 146 | 52 | this.ignoreGaps = rs.ignoreGaps; |
| 147 | 52 | this.pidThreshold = rs.pidThreshold; |
| 148 | 52 | this.ssConsensusProfileMap = rs.ssConsensusProfileMap; |
| 149 | 52 | this.consensusSecondaryStructureColouring = rs.consensusSecondaryStructureColouring; |
| 150 | 52 | this.consensusSecondaryStructureThreshold = rs.consensusSecondaryStructureThreshold; |
| 151 | } | |
| 152 | ||
| 153 | /** | |
| 154 | * @see jalview.renderer.ResidueShaderI#setConsensus(jalview.datamodel.ProfilesI) | |
| 155 | */ | |
| 156 | 882 | @Override |
| 157 | public void setConsensus(ProfilesI cons) | |
| 158 | { | |
| 159 | 882 | consensus = cons; |
| 160 | ||
| 161 | } | |
| 162 | ||
| 163 | /** | |
| 164 | * @see jalview.renderer.ResidueShaderI#conservationApplied() | |
| 165 | */ | |
| 166 | 260 | @Override |
| 167 | public boolean conservationApplied() | |
| 168 | { | |
| 169 | 260 | return conservationColouring; |
| 170 | } | |
| 171 | ||
| 172 | /** | |
| 173 | * @see jalview.renderer.ResidueShaderI#setConservationApplied(boolean) | |
| 174 | */ | |
| 175 | 69 | @Override |
| 176 | public void setConservationApplied(boolean conservationApplied) | |
| 177 | { | |
| 178 | 69 | conservationColouring = conservationApplied; |
| 179 | } | |
| 180 | ||
| 181 | /** | |
| 182 | * @see jalview.renderer.ResidueShaderI#setConservation(jalview.analysis.Conservation) | |
| 183 | */ | |
| 184 | 21 | @Override |
| 185 | public void setConservation(Conservation cons) | |
| 186 | { | |
| 187 | 21 | if (cons == null) |
| 188 | { | |
| 189 | 0 | conservationColouring = false; |
| 190 | 0 | conservation = null; |
| 191 | } | |
| 192 | else | |
| 193 | { | |
| 194 | 21 | conservationColouring = true; |
| 195 | 21 | conservation = cons.getConsSequence().getSequenceAsString() |
| 196 | .toCharArray(); | |
| 197 | } | |
| 198 | ||
| 199 | } | |
| 200 | ||
| 201 | 1 | @Override |
| 202 | public void setConsensusSecondaryStructureColouring( | |
| 203 | boolean colourByConsensusSecondaryStructure) | |
| 204 | { | |
| 205 | ||
| 206 | 1 | consensusSecondaryStructureColouring = colourByConsensusSecondaryStructure; |
| 207 | ||
| 208 | } | |
| 209 | ||
| 210 | /** | |
| 211 | * @see jalview.renderer.ResidueShaderI#alignmentChanged(jalview.datamodel.AnnotatedCollectionI, | |
| 212 | * java.util.Map) | |
| 213 | */ | |
| 214 | 270 | @Override |
| 215 | public void alignmentChanged(AnnotatedCollectionI alignment, | |
| 216 | Map<SequenceI, SequenceCollectionI> hiddenReps) | |
| 217 | { | |
| 218 | 270 | if (colourScheme != null) |
| 219 | { | |
| 220 | 52 | colourScheme.alignmentChanged(alignment, hiddenReps); |
| 221 | } | |
| 222 | } | |
| 223 | ||
| 224 | /** | |
| 225 | * @see jalview.renderer.ResidueShaderI#setThreshold(int, boolean) | |
| 226 | */ | |
| 227 | 35 | @Override |
| 228 | public void setThreshold(int consensusThreshold, boolean ignoreGaps) | |
| 229 | { | |
| 230 | 35 | pidThreshold = consensusThreshold; |
| 231 | 35 | this.ignoreGaps = ignoreGaps; |
| 232 | } | |
| 233 | ||
| 234 | /** | |
| 235 | * @see jalview.renderer.ResidueShaderI#setConservationInc(int) | |
| 236 | */ | |
| 237 | 22 | @Override |
| 238 | public void setConservationInc(int i) | |
| 239 | { | |
| 240 | 22 | conservationIncrement = i; |
| 241 | } | |
| 242 | ||
| 243 | /** | |
| 244 | * @see jalview.renderer.ResidueShaderI#getConservationInc() | |
| 245 | */ | |
| 246 | 28 | @Override |
| 247 | public int getConservationInc() | |
| 248 | { | |
| 249 | 28 | return conservationIncrement; |
| 250 | } | |
| 251 | ||
| 252 | 1 | @Override |
| 253 | public void setConsensusSecondaryStructureThreshold(int i) | |
| 254 | { | |
| 255 | 1 | consensusSecondaryStructureThreshold = i; |
| 256 | } | |
| 257 | ||
| 258 | 0 | @Override |
| 259 | public int getConsensusSecondaryStructureThreshold() | |
| 260 | { | |
| 261 | 0 | return consensusSecondaryStructureThreshold; |
| 262 | } | |
| 263 | ||
| 264 | /** | |
| 265 | * @see jalview.renderer.ResidueShaderI#getThreshold() | |
| 266 | */ | |
| 267 | 29 | @Override |
| 268 | public int getThreshold() | |
| 269 | { | |
| 270 | 29 | return pidThreshold; |
| 271 | } | |
| 272 | ||
| 273 | /** | |
| 274 | * @see jalview.renderer.ResidueShaderI#findColour(char, int, | |
| 275 | * jalview.datamodel.SequenceI) | |
| 276 | */ | |
| 277 | 12434 | @Override |
| 278 | public Color findColour(char symbol, int position, SequenceI seq) | |
| 279 | { | |
| 280 | 12435 | if (colourScheme == null) |
| 281 | { | |
| 282 | 0 | return Color.white; // Colour is 'None' |
| 283 | } | |
| 284 | ||
| 285 | /* | |
| 286 | * get 'base' colour | |
| 287 | */ | |
| 288 | 12435 | ProfileI profile = consensus == null ? null : consensus.get(position); |
| 289 | 12434 | String modalResidue = profile == null ? null |
| 290 | : profile.getModalResidue(); | |
| 291 | 12433 | float pid = profile == null ? 0f |
| 292 | : profile.getPercentageIdentity(ignoreGaps); | |
| 293 | 12435 | Color colour = colourScheme.findColour(symbol, position, seq, |
| 294 | modalResidue, pid); | |
| 295 | ||
| 296 | /* | |
| 297 | * apply PID threshold and consensus fading if in force | |
| 298 | */ | |
| 299 | 12435 | if (!Comparison.isGap(symbol)) |
| 300 | { | |
| 301 | 12177 | colour = adjustColour(symbol, position, colour, false); |
| 302 | } | |
| 303 | ||
| 304 | 12433 | return colour; |
| 305 | } | |
| 306 | ||
| 307 | 0 | @Override |
| 308 | public Color findSSColour(char symbol, int position) | |
| 309 | { | |
| 310 | 0 | if (colourScheme == null) |
| 311 | { | |
| 312 | 0 | return Color.white; // Colour is 'None' |
| 313 | } | |
| 314 | ||
| 315 | 0 | Color colour = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol); |
| 316 | ||
| 317 | /* | |
| 318 | * apply PID threshold and consensus fading if in force | |
| 319 | */ | |
| 320 | 0 | if (!Comparison.isGap(symbol)) |
| 321 | { | |
| 322 | 0 | colour = adjustColour(symbol, position, colour, true); |
| 323 | } | |
| 324 | ||
| 325 | 0 | return colour; |
| 326 | } | |
| 327 | ||
| 328 | /** | |
| 329 | * Adjusts colour by applying thresholding or conservation shading, if in | |
| 330 | * force. That is | |
| 331 | * <ul> | |
| 332 | * <li>if there is a threshold set for colouring, and the residue doesn't | |
| 333 | * match the consensus (or a joint consensus) residue, or the consensus score | |
| 334 | * is not above the threshold, then the colour is set to white</li> | |
| 335 | * <li>if conservation colouring is selected, the colour is faded by an amount | |
| 336 | * depending on the conservation score for the column, and the conservation | |
| 337 | * colour threshold</li> | |
| 338 | * </ul> | |
| 339 | * | |
| 340 | * @param symbol | |
| 341 | * @param column | |
| 342 | * @param colour | |
| 343 | * @return | |
| 344 | */ | |
| 345 | 12177 | protected Color adjustColour(char symbol, int column, Color colour, boolean isSecondaryStructure) |
| 346 | { | |
| 347 | 12177 | if (!isSecondaryStructure && !aboveThreshold(symbol, column)) |
| 348 | { | |
| 349 | 147 | colour = Color.white; |
| 350 | } | |
| 351 | ||
| 352 | 12177 | if (consensusSecondaryStructureColouring) |
| 353 | { | |
| 354 | 0 | colour = applyByConsensusSecondaryStructure(colour, column); |
| 355 | } | |
| 356 | ||
| 357 | 12176 | if (conservationColouring) |
| 358 | { | |
| 359 | 384 | colour = applyConservation(colour, column); |
| 360 | } | |
| 361 | 12176 | return colour; |
| 362 | } | |
| 363 | ||
| 364 | /** | |
| 365 | * Answers true if there is a consensus profile for the specified column, and | |
| 366 | * the given residue matches the consensus (or joint consensus) residue for | |
| 367 | * the column, and the percentage identity for the profile is equal to or | |
| 368 | * greater than the current threshold; else answers false. The percentage | |
| 369 | * calculation depends on whether or not we are ignoring gapped sequences. | |
| 370 | * | |
| 371 | * @param residue | |
| 372 | * @param column | |
| 373 | * (index into consensus profiles) | |
| 374 | * | |
| 375 | * @return | |
| 376 | * @see #setThreshold(int, boolean) | |
| 377 | */ | |
| 378 | 12193 | protected boolean aboveThreshold(char residue, int column) |
| 379 | { | |
| 380 | 12194 | if (pidThreshold == 0) |
| 381 | { | |
| 382 | 11797 | return true; |
| 383 | } | |
| 384 | 397 | if ('a' <= residue && residue <= 'z') |
| 385 | { | |
| 386 | // TO UPPERCASE !!! | |
| 387 | // Faster than toUpperCase | |
| 388 | 4 | residue -= ('a' - 'A'); |
| 389 | } | |
| 390 | ||
| 391 | 397 | if (consensus == null) |
| 392 | { | |
| 393 | 0 | return false; |
| 394 | } | |
| 395 | ||
| 396 | 397 | ProfileI profile = consensus.get(column); |
| 397 | ||
| 398 | /* | |
| 399 | * test whether this is the consensus (or joint consensus) residue | |
| 400 | */ | |
| 401 | 397 | if (profile != null |
| 402 | && profile.getModalResidue().contains(String.valueOf(residue))) | |
| 403 | { | |
| 404 | 253 | if (profile.getPercentageIdentity(ignoreGaps) >= pidThreshold) |
| 405 | { | |
| 406 | 243 | return true; |
| 407 | } | |
| 408 | } | |
| 409 | ||
| 410 | 154 | return false; |
| 411 | } | |
| 412 | ||
| 413 | /** | |
| 414 | * Applies a combination of column conservation score, and conservation | |
| 415 | * percentage slider, to 'bleach' out the residue colours towards white. | |
| 416 | * <p> | |
| 417 | * If a column is fully conserved (identical residues, conservation score 11, | |
| 418 | * shown as *), or all 10 physico-chemical properties are conserved | |
| 419 | * (conservation score 10, shown as +), then the colour is left unchanged. | |
| 420 | * <p> | |
| 421 | * Otherwise a 'bleaching' factor is computed and applied to the colour. This | |
| 422 | * is designed to fade colours for scores of 0-9 completely to white at slider | |
| 423 | * positions ranging from 18% - 100% respectively. | |
| 424 | * | |
| 425 | * @param currentColour | |
| 426 | * @param column | |
| 427 | * | |
| 428 | * @return bleached (or unmodified) colour | |
| 429 | */ | |
| 430 | 425 | protected Color applyConservation(Color currentColour, int column) |
| 431 | { | |
| 432 | 425 | if (conservation == null || conservation.length <= column) |
| 433 | { | |
| 434 | 2 | return currentColour; |
| 435 | } | |
| 436 | 423 | char conservationScore = conservation[column]; |
| 437 | ||
| 438 | /* | |
| 439 | * if residues are fully conserved (* or 11), or all properties | |
| 440 | * are conserved (+ or 10), leave colour unchanged | |
| 441 | */ | |
| 442 | 423 | if (conservationScore == '*' || conservationScore == '+' |
| 443 | || conservationScore == (char) 10 | |
| 444 | || conservationScore == (char) 11) | |
| 445 | { | |
| 446 | 22 | return currentColour; |
| 447 | } | |
| 448 | ||
| 449 | 401 | if (Comparison.isGap(conservationScore)) |
| 450 | { | |
| 451 | 114 | return Color.white; |
| 452 | } | |
| 453 | ||
| 454 | /* | |
| 455 | * convert score 0-9 to a bleaching factor 1.1 - 0.2 | |
| 456 | */ | |
| 457 | 287 | float bleachFactor = (11 - (conservationScore - '0')) / 10f; |
| 458 | ||
| 459 | /* | |
| 460 | * scale this up by 0-5 (percentage slider / 20) | |
| 461 | * as a result, scores of: 0 1 2 3 4 5 6 7 8 9 | |
| 462 | * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100% | |
| 463 | */ | |
| 464 | 287 | bleachFactor *= (conservationIncrement / 20f); |
| 465 | ||
| 466 | 287 | return ColorUtils.bleachColour(currentColour, bleachFactor); |
| 467 | } | |
| 468 | ||
| 469 | 0 | protected Color applyByConsensusSecondaryStructure(Color currentColour, |
| 470 | int column) | |
| 471 | { | |
| 472 | 0 | if (ssConsensusProfileMap == null && ssConsensusProfileMap |
| 473 | .get(Constants.SS_ALL_PROVIDERS) == null) | |
| 474 | { | |
| 475 | 0 | return currentColour; |
| 476 | } | |
| 477 | ||
| 478 | 0 | ProfilesI consensusSSProfileForAllSources = ssConsensusProfileMap |
| 479 | .get(Constants.SS_ALL_PROVIDERS); | |
| 480 | 0 | ProfileI profile = consensusSSProfileForAllSources.get(column); |
| 481 | ||
| 482 | 0 | if (profile != null) |
| 483 | { | |
| 484 | 0 | float pid = profile.getSSPercentageIdentity(ignoreGaps); |
| 485 | ||
| 486 | 0 | if (pid == 0) |
| 487 | { | |
| 488 | 0 | return Color.white; |
| 489 | } | |
| 490 | ||
| 491 | 0 | float bleachFactor = 1f - (pid / 100); |
| 492 | 0 | bleachFactor *= (consensusSecondaryStructureThreshold / 20); |
| 493 | ||
| 494 | 0 | return ColorUtils.bleachColour(currentColour, bleachFactor); |
| 495 | ||
| 496 | } | |
| 497 | ||
| 498 | 0 | return currentColour; |
| 499 | ||
| 500 | } | |
| 501 | ||
| 502 | /** | |
| 503 | * @see jalview.renderer.ResidueShaderI#getColourScheme() | |
| 504 | */ | |
| 505 | 80970 | @Override |
| 506 | public ColourSchemeI getColourScheme() | |
| 507 | { | |
| 508 | 80970 | return this.colourScheme; |
| 509 | } | |
| 510 | ||
| 511 | /** | |
| 512 | * @see jalview.renderer.ResidueShaderI#setColourScheme(jalview.schemes.ColourSchemeI) | |
| 513 | */ | |
| 514 | 95 | @Override |
| 515 | public void setColourScheme(ColourSchemeI cs) | |
| 516 | { | |
| 517 | 95 | colourScheme = cs; |
| 518 | } | |
| 519 | ||
| 520 | 0 | public Map<String, ProfilesI> getSSConsensusProfileMap() |
| 521 | { | |
| 522 | 0 | return ssConsensusProfileMap; |
| 523 | } | |
| 524 | ||
| 525 | 709 | public void setSSConsensusProfileMap( |
| 526 | Map<String, ProfilesI> ssConsensusProfileMap) | |
| 527 | { | |
| 528 | 709 | this.ssConsensusProfileMap = ssConsensusProfileMap; |
| 529 | } | |
| 530 | } |