Coverage Report
File AlignViewController.java
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43% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignViewController | 47 | 180 | 74 |
Contributing tests
This file is covered by 181 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.controller; | |
| 22 | ||
| 23 | import java.awt.Color; | |
| 24 | import java.util.BitSet; | |
| 25 | import java.util.List; | |
| 26 | ||
| 27 | import jalview.analysis.AlignmentSorter; | |
| 28 | import jalview.api.AlignViewControllerGuiI; | |
| 29 | import jalview.api.AlignViewControllerI; | |
| 30 | import jalview.api.AlignViewportI; | |
| 31 | import jalview.api.AlignmentViewPanel; | |
| 32 | import jalview.api.FeatureRenderer; | |
| 33 | import jalview.commands.OrderCommand; | |
| 34 | import jalview.datamodel.AlignmentI; | |
| 35 | import jalview.datamodel.ColumnSelection; | |
| 36 | import jalview.datamodel.SearchResultsI; | |
| 37 | import jalview.datamodel.SequenceCollectionI; | |
| 38 | import jalview.datamodel.SequenceFeature; | |
| 39 | import jalview.datamodel.SequenceGroup; | |
| 40 | import jalview.datamodel.SequenceI; | |
| 41 | import jalview.gui.Desktop; | |
| 42 | import jalview.io.DataSourceType; | |
| 43 | import jalview.io.FeaturesFile; | |
| 44 | import jalview.schemes.ColourSchemeI; | |
| 45 | import jalview.util.MessageManager; | |
| 46 | ||
| 47 | public class AlignViewController implements AlignViewControllerI | |
| 48 | { | |
| 49 | AlignViewportI viewport = null; | |
| 50 | ||
| 51 | AlignmentViewPanel alignPanel = null; | |
| 52 | ||
| 53 | /** | |
| 54 | * the GUI container that is handling interactions with the user | |
| 55 | */ | |
| 56 | private AlignViewControllerGuiI avcg; | |
| 57 | ||
| 58 | 950 |  public AlignViewController(AlignViewControllerGuiI alignFrame, |
| 59 | AlignViewportI vp, AlignmentViewPanel ap) | |
| 60 | { | |
| 61 | 950 | this.avcg = alignFrame; |
| 62 | 950 | this.viewport = vp; |
| 63 | 950 | this.alignPanel = ap; |
| 64 | } | |
| 65 | ||
| 66 | 104 | @Override |
| 67 | public void setViewportAndAlignmentPanel(AlignViewportI vp, | |
| 68 | AlignmentViewPanel ap) | |
| 69 | { | |
| 70 | 104 | this.alignPanel = ap; |
| 71 | 104 | this.viewport = vp; |
| 72 | } | |
| 73 | ||
| 74 | 0 | @Override |
| 75 | public boolean makeGroupsFromSelection() | |
| 76 | { | |
| 77 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
| 78 | 0 | ColumnSelection cs = viewport.getColumnSelection(); |
| 79 | 0 | SequenceGroup[] gps = null; |
| 80 | 0 | if (sg != null && (cs == null || cs.isEmpty())) |
| 81 | { | |
| 82 | 0 | gps = jalview.analysis.Grouping.makeGroupsFrom( |
| 83 | viewport.getSequenceSelection(), | |
| 84 | viewport.getAlignmentView(true) | |
| 85 | .getSequenceStrings(viewport.getGapCharacter()), | |
| 86 | viewport.getAlignment().getGroups()); | |
| 87 | } | |
| 88 | else | |
| 89 | { | |
| 90 | 0 | if (cs != null) |
| 91 | { | |
| 92 | 0 | gps = jalview.analysis.Grouping.makeGroupsFromCols( |
| 93 | 0 | (sg == null) ? viewport.getAlignment().getSequencesArray() |
| 94 | : sg.getSequences().toArray(new SequenceI[0]), | |
| 95 | cs, viewport.getAlignment().getGroups()); | |
| 96 | } | |
| 97 | } | |
| 98 | 0 | if (gps != null) |
| 99 | { | |
| 100 | 0 | viewport.getAlignment().deleteAllGroups(); |
| 101 | 0 | viewport.clearSequenceColours(); |
| 102 | 0 | viewport.setSelectionGroup(null); |
| 103 | 0 | ColourSchemeI colours = viewport.getGlobalColourScheme(); |
| 104 | // set view properties for each group | |
| 105 | 0 | for (int g = 0; g < gps.length; g++) |
| 106 | { | |
| 107 | // gps[g].setShowunconserved(viewport.getShowUnconserved()); | |
| 108 | 0 | gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); |
| 109 | 0 | viewport.getAlignment().addGroup(gps[g]); |
| 110 | 0 | if (colours != null) |
| 111 | { | |
| 112 | 0 | gps[g].setColourScheme(colours.getInstance(viewport, gps[g])); |
| 113 | } | |
| 114 | 0 | Color col = new Color((int) (Math.random() * 255), |
| 115 | (int) (Math.random() * 255), (int) (Math.random() * 255)); | |
| 116 | 0 | gps[g].idColour = col; |
| 117 | 0 | viewport.setUpdateStructures(true); |
| 118 | 0 | viewport.addSequenceGroup(gps[g]); |
| 119 | } | |
| 120 | 0 | return true; |
| 121 | } | |
| 122 | 0 | return false; |
| 123 | } | |
| 124 | ||
| 125 | 0 | @Override |
| 126 | public boolean createGroup() | |
| 127 | { | |
| 128 | ||
| 129 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
| 130 | 0 | if (sg != null) |
| 131 | { | |
| 132 | 0 | viewport.getAlignment().addGroup(sg); |
| 133 | 0 | return true; |
| 134 | } | |
| 135 | 0 | return false; |
| 136 | } | |
| 137 | ||
| 138 | 0 | @Override |
| 139 | public boolean unGroup() | |
| 140 | { | |
| 141 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
| 142 | 0 | if (sg != null) |
| 143 | { | |
| 144 | 0 | viewport.getAlignment().deleteGroup(sg); |
| 145 | 0 | return true; |
| 146 | } | |
| 147 | 0 | return false; |
| 148 | } | |
| 149 | ||
| 150 | 0 | @Override |
| 151 | public boolean deleteGroups() | |
| 152 | { | |
| 153 | 0 | if (viewport.getAlignment().getGroups() != null |
| 154 | && viewport.getAlignment().getGroups().size() > 0) | |
| 155 | { | |
| 156 | 0 | viewport.getAlignment().deleteAllGroups(); |
| 157 | 0 | viewport.clearSequenceColours(); |
| 158 | 0 | viewport.setSelectionGroup(null); |
| 159 | 0 | return true; |
| 160 | } | |
| 161 | 0 | return false; |
| 162 | } | |
| 163 | ||
| 164 | 12 | @Override |
| 165 | public boolean markColumnsContainingFeatures(boolean invert, | |
| 166 | boolean extendCurrent, boolean toggle, String featureType) | |
| 167 | { | |
| 168 | // JBPNote this routine could also mark rows, not just columns. | |
| 169 | // need a decent query structure to allow all types of feature searches | |
| 170 | 12 | BitSet bs = new BitSet(); |
| 171 | 12 | boolean searchSelection = viewport.getSelectionGroup() != null |
| 172 | && !extendCurrent; | |
| 173 | 12 | SequenceCollectionI sqcol = searchSelection |
| 174 | ? viewport.getSelectionGroup() | |
| 175 | : viewport.getAlignment(); | |
| 176 | ||
| 177 | 12 | int nseq = findColumnsWithFeature(featureType, sqcol, bs); |
| 178 | ||
| 179 | 12 | ColumnSelection cs = viewport.getColumnSelection(); |
| 180 | 12 | if (cs == null) |
| 181 | { | |
| 182 | 0 | cs = new ColumnSelection(); |
| 183 | } | |
| 184 | ||
| 185 | 12 | if (bs.cardinality() > 0 || invert) |
| 186 | { | |
| 187 | 10 | boolean changed = cs.markColumns(bs, sqcol.getStartRes(), |
| 188 | sqcol.getEndRes(), invert, extendCurrent, toggle); | |
| 189 | 10 | if (changed) |
| 190 | { | |
| 191 | 9 | viewport.setColumnSelection(cs); |
| 192 | 9 | alignPanel.paintAlignment(false, false); |
| 193 | 9 | int columnCount = invert |
| 194 | ? (sqcol.getEndRes() - sqcol.getStartRes() + 1) | |
| 195 | - bs.cardinality() | |
| 196 | : bs.cardinality(); | |
| 197 | 9 | avcg.setStatus(MessageManager.formatMessage( |
| 198 | "label.view_controller_toggled_marked", new String[] | |
| 199 | 9 | { toggle ? MessageManager.getString("label.toggled") |
| 200 | : MessageManager.getString("label.marked"), | |
| 201 | String.valueOf(columnCount), | |
| 202 | 9 | invert ? MessageManager |
| 203 | .getString("label.not_containing") | |
| 204 | : MessageManager.getString("label.containing"), | |
| 205 | featureType, Integer.valueOf(nseq).toString() })); | |
| 206 | 9 | return true; |
| 207 | } | |
| 208 | } | |
| 209 | else | |
| 210 | { | |
| 211 | 2 | String key = searchSelection ? "label.no_feature_found_selection" |
| 212 | : "label.no_feature_of_type_found"; | |
| 213 | 2 | avcg.setStatus( |
| 214 | MessageManager.formatMessage(key, new String[] | |
| 215 | { featureType })); | |
| 216 | 2 | if (!extendCurrent) |
| 217 | { | |
| 218 | 2 | cs.clear(); |
| 219 | 2 | alignPanel.paintAlignment(false, false); |
| 220 | } | |
| 221 | } | |
| 222 | 3 | return false; |
| 223 | } | |
| 224 | ||
| 225 | /** | |
| 226 | * Sets a bit in the BitSet for each column (base 0) in the sequence | |
| 227 | * collection which includes a visible feature of the specified feature type. | |
| 228 | * Returns the number of sequences which have the feature visible in the | |
| 229 | * selected range. | |
| 230 | * | |
| 231 | * @param featureType | |
| 232 | * @param sqcol | |
| 233 | * @param bs | |
| 234 | * @return | |
| 235 | */ | |
| 236 | 20 | int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol, |
| 237 | BitSet bs) | |
| 238 | { | |
| 239 | 20 | FeatureRenderer fr = alignPanel == null ? null |
| 240 | : alignPanel.getFeatureRenderer(); | |
| 241 | ||
| 242 | 20 | final int startColumn = sqcol.getStartRes() + 1; // converted to base 1 |
| 243 | 20 | final int endColumn = sqcol.getEndRes() + 1; |
| 244 | 20 | List<SequenceI> seqs = sqcol.getSequences(); |
| 245 | 20 | int nseq = 0; |
| 246 | 20 | for (SequenceI sq : seqs) |
| 247 | { | |
| 248 | 92 | if (sq != null) |
| 249 | { | |
| 250 | // int ist = sq.findPosition(sqcol.getStartRes()); | |
| 251 | 92 | List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn, |
| 252 | featureType); | |
| 253 | ||
| 254 | 92 | boolean found = false; |
| 255 | 92 | for (SequenceFeature sf : sfs) |
| 256 | { | |
| 257 | 545 | if (fr.getColour(sf) == null) |
| 258 | { | |
| 259 | 3 | continue; |
| 260 | } | |
| 261 | 542 | if (!found) |
| 262 | { | |
| 263 | 58 | nseq++; |
| 264 | } | |
| 265 | 542 | found = true; |
| 266 | ||
| 267 | 542 | int sfStartCol = sq.findIndex(sf.getBegin()); |
| 268 | 542 | int sfEndCol = sq.findIndex(sf.getEnd()); |
| 269 | ||
| 270 | 542 | if (sf.isContactFeature()) |
| 271 | { | |
| 272 | /* | |
| 273 | * 'contact' feature - check for 'start' or 'end' | |
| 274 | * position within the selected region | |
| 275 | */ | |
| 276 | 1 | if (sfStartCol >= startColumn && sfStartCol <= endColumn) |
| 277 | { | |
| 278 | 1 | bs.set(sfStartCol - 1); |
| 279 | } | |
| 280 | 1 | if (sfEndCol >= startColumn && sfEndCol <= endColumn) |
| 281 | { | |
| 282 | 1 | bs.set(sfEndCol - 1); |
| 283 | } | |
| 284 | 1 | continue; |
| 285 | } | |
| 286 | ||
| 287 | /* | |
| 288 | * contiguous feature - select feature positions (if any) | |
| 289 | * within the selected region | |
| 290 | */ | |
| 291 | 541 | if (sfStartCol < startColumn) |
| 292 | { | |
| 293 | 1 | sfStartCol = startColumn; |
| 294 | } | |
| 295 | // not sure what the point of this is | |
| 296 | // if (sfStartCol < ist) | |
| 297 | // { | |
| 298 | // sfStartCol = ist; | |
| 299 | // } | |
| 300 | 541 | if (sfEndCol > endColumn) |
| 301 | { | |
| 302 | 4 | sfEndCol = endColumn; |
| 303 | } | |
| 304 | 25219 | for (; sfStartCol <= sfEndCol; sfStartCol++) |
| 305 | { | |
| 306 | 24678 | bs.set(sfStartCol - 1); // convert to base 0 |
| 307 | } | |
| 308 | } | |
| 309 | } | |
| 310 | } | |
| 311 | 20 | return nseq; |
| 312 | } | |
| 313 | ||
| 314 | 0 | @Override |
| 315 | public void sortAlignmentByFeatureDensity(List<String> typ) | |
| 316 | { | |
| 317 | 0 | String methodText = MessageManager.getString("label.sort_by_density"); |
| 318 | 0 | sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY); |
| 319 | } | |
| 320 | ||
| 321 | /** | |
| 322 | * Sorts the alignment (or current selection) by either average score or | |
| 323 | * density of the specified feature types, and adds to the command history. If | |
| 324 | * {@code types} is null, all visible feature types are used for the sort. If | |
| 325 | * no feature types apply, does nothing. | |
| 326 | * | |
| 327 | * @param types | |
| 328 | * @param methodText | |
| 329 | * - text shown in Undo/Redo command | |
| 330 | * @param method | |
| 331 | * - passed to jalview.analysis.AlignmentSorter.sortByFeatures() | |
| 332 | */ | |
| 333 | 0 | protected void sortByFeatures(List<String> types, String methodText, |
| 334 | final String method) | |
| 335 | { | |
| 336 | 0 | FeatureRenderer fr = alignPanel.getFeatureRenderer(); |
| 337 | 0 | if (types == null && fr != null) |
| 338 | { | |
| 339 | 0 | types = fr.getDisplayedFeatureTypes(); |
| 340 | } | |
| 341 | 0 | if (types.isEmpty()) |
| 342 | { | |
| 343 | 0 | return; // nothing to do |
| 344 | } | |
| 345 | 0 | List<String> gps = null; |
| 346 | 0 | if (fr != null) |
| 347 | { | |
| 348 | 0 | gps = fr.getDisplayedFeatureGroups(); |
| 349 | } | |
| 350 | 0 | AlignmentI al = viewport.getAlignment(); |
| 351 | ||
| 352 | 0 | int start, stop; |
| 353 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
| 354 | 0 | if (sg != null) |
| 355 | { | |
| 356 | 0 | start = sg.getStartRes(); |
| 357 | 0 | stop = sg.getEndRes(); |
| 358 | } | |
| 359 | else | |
| 360 | { | |
| 361 | 0 | start = 0; |
| 362 | 0 | stop = al.getWidth(); |
| 363 | } | |
| 364 | 0 | SequenceI[] oldOrder = al.getSequencesArray(); |
| 365 | 0 | AlignmentSorter.sortByFeature(types, gps, start, stop, al, method); |
| 366 | 0 | avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, |
| 367 | viewport.getAlignment())); | |
| 368 | 0 | alignPanel.paintAlignment(true, false); |
| 369 | ||
| 370 | } | |
| 371 | ||
| 372 | 0 | @Override |
| 373 | public void sortAlignmentByFeatureScore(List<String> typ) | |
| 374 | { | |
| 375 | 0 | String methodText = MessageManager.getString("label.sort_by_score"); |
| 376 | 0 | sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE); |
| 377 | } | |
| 378 | ||
| 379 | 4 | @Override |
| 380 | public boolean parseFeaturesFile(Object file, DataSourceType protocol, | |
| 381 | boolean relaxedIdMatching) | |
| 382 | { | |
| 383 | 4 | boolean featuresAdded = false; |
| 384 | 4 | FeatureRenderer fr = alignPanel.getFeatureRenderer(); |
| 385 | 4 | try |
| 386 | { | |
| 387 | 4 | featuresAdded = new FeaturesFile(false, file, protocol).parse( |
| 388 | viewport.getAlignment().getDataset(), fr.getFeatureColours(), | |
| 389 | fr.getFeatureFilters(), false, relaxedIdMatching); | |
| 390 | } catch (Exception ex) | |
| 391 | { | |
| 392 | 0 | ex.printStackTrace(); |
| 393 | } | |
| 394 | ||
| 395 | 4 | if (featuresAdded) |
| 396 | { | |
| 397 | 4 | avcg.refreshFeatureUI(true); |
| 398 | 4 | if (fr != null) |
| 399 | { | |
| 400 | // update the min/max ranges where necessary | |
| 401 | 4 | fr.findAllFeatures(true); |
| 402 | } | |
| 403 | 4 | if (avcg.getFeatureSettingsUI() != null) |
| 404 | { | |
| 405 | 0 | avcg.getFeatureSettingsUI().discoverAllFeatureData(); |
| 406 | } | |
| 407 | 4 | alignPanel.paintAlignment(true, true); |
| 408 | } | |
| 409 | ||
| 410 | 4 | return featuresAdded; |
| 411 | ||
| 412 | } | |
| 413 | ||
| 414 | 2 | @Override |
| 415 | public boolean markHighlightedColumns(boolean invert, | |
| 416 | boolean extendCurrent, boolean toggle) | |
| 417 | { | |
| 418 | 2 | if (!viewport.hasSearchResults()) |
| 419 | { | |
| 420 | // do nothing if no selection exists | |
| 421 | 0 | return false; |
| 422 | } | |
| 423 | // JBPNote this routine could also mark rows, not just columns. | |
| 424 | 2 | BitSet bs = new BitSet(); |
| 425 | 2 | SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null |
| 426 | || extendCurrent) ? viewport.getAlignment() | |
| 427 | : viewport.getSelectionGroup(); | |
| 428 | ||
| 429 | // this could be a lambda... - the remains of the method is boilerplate, | |
| 430 | // except for the different messages for reporting selection. | |
| 431 | 2 | int nseq = viewport.getSearchResults().markColumns(sqcol, bs); |
| 432 | ||
| 433 | 2 | ColumnSelection cs = viewport.getColumnSelection(); |
| 434 | 2 | if (cs == null) |
| 435 | { | |
| 436 | 0 | cs = new ColumnSelection(); |
| 437 | } | |
| 438 | ||
| 439 | 2 | if (bs.cardinality() > 0 || invert) |
| 440 | { | |
| 441 | 2 | boolean changed = cs.markColumns(bs, sqcol.getStartRes(), |
| 442 | sqcol.getEndRes(), invert, extendCurrent, toggle); | |
| 443 | 2 | if (changed) |
| 444 | { | |
| 445 | 2 | viewport.setColumnSelection(cs); |
| 446 | 2 | alignPanel.paintAlignment(false, false); |
| 447 | 2 | int columnCount = invert |
| 448 | ? (sqcol.getEndRes() - sqcol.getStartRes() + 1) | |
| 449 | - bs.cardinality() | |
| 450 | : bs.cardinality(); | |
| 451 | 2 | avcg.setStatus(MessageManager.formatMessage( |
| 452 | "label.view_controller_toggled_marked", new String[] | |
| 453 | 2 | { toggle ? MessageManager.getString("label.toggled") |
| 454 | : MessageManager.getString("label.marked"), | |
| 455 | String.valueOf(columnCount), | |
| 456 | 2 | invert ? MessageManager |
| 457 | .getString("label.not_containing") | |
| 458 | : MessageManager.getString("label.containing"), | |
| 459 | "Highlight", Integer.valueOf(nseq).toString() })); | |
| 460 | 2 | return true; |
| 461 | } | |
| 462 | } | |
| 463 | else | |
| 464 | { | |
| 465 | 0 | avcg.setStatus(MessageManager |
| 466 | .getString("label.no_highlighted_regions_marked")); | |
| 467 | 0 | if (!extendCurrent) |
| 468 | { | |
| 469 | 0 | cs.clear(); |
| 470 | 0 | alignPanel.paintAlignment(false, false); |
| 471 | } | |
| 472 | } | |
| 473 | 0 | return false; |
| 474 | } | |
| 475 | ||
| 476 | 0 | @Override |
| 477 | public boolean copyHighlightedRegionsToClipboard() | |
| 478 | { | |
| 479 | 0 | if (!viewport.hasSearchResults()) |
| 480 | { | |
| 481 | // do nothing if no selection exists | |
| 482 | 0 | return false; |
| 483 | } | |
| 484 | ||
| 485 | 0 | SearchResultsI searchResults = viewport.getSearchResults(); |
| 486 | 0 | if (searchResults.isEmpty()) |
| 487 | { | |
| 488 | 0 | return false; // shouldn't happen |
| 489 | } | |
| 490 | 0 | List<SequenceI> seqs = searchResults.getMatchingSubSequences(); |
| 491 | ||
| 492 | // TODO: pass in hiddenColumns according to intersection of searchResults | |
| 493 | // and visible columns. Currently this isn't done, since each contig becomes | |
| 494 | // a single subsequence | |
| 495 | 0 | Desktop.jalviewClipboard = new Object[] { |
| 496 | seqs.toArray(new SequenceI[0]), | |
| 497 | alignPanel.getAlignment().getDataset(), null }; | |
| 498 | 0 | avcg.setStatus(MessageManager.formatMessage( |
| 499 | "label.copied_sequences_to_clipboard", seqs.size())); | |
| 500 | // Technically we should return false, since view has not changed | |
| 501 | 0 | return false; |
| 502 | } | |
| 503 | ||
| 504 | 0 | @Override |
| 505 | public boolean justify_Region(boolean left) | |
| 506 | { | |
| 507 | 0 | AlignmentI al = viewport.getAlignment(); |
| 508 | 0 | SequenceGroup reg = viewport.getSelectionGroup(); |
| 509 | 0 | int from, to; |
| 510 | 0 | List<SequenceI> seqs; |
| 511 | ||
| 512 | 0 | from = 0; |
| 513 | 0 | to = al.getWidth() - 1; |
| 514 | 0 | seqs = al.getSequences(); |
| 515 | 0 | if (reg != null) |
| 516 | { | |
| 517 | 0 | seqs = reg.getSequences(); |
| 518 | 0 | from = reg.getStartRes(); |
| 519 | 0 | to = reg.getEndRes(); |
| 520 | } | |
| 521 | ||
| 522 | 0 | if ((to - from) < 1) |
| 523 | { | |
| 524 | 0 | return false; |
| 525 | } | |
| 526 | ||
| 527 | 0 | al.padGaps(); |
| 528 | 0 | jalview.commands.JustifyLeftOrRightCommand finalEdit = new jalview.commands.JustifyLeftOrRightCommand( |
| 529 | 0 | "Justify " + (left ? "Left" : "Right"), left, seqs, from, to, |
| 530 | al); | |
| 531 | 0 | avcg.addHistoryItem(finalEdit); |
| 532 | 0 | viewport.notifyAlignmentChanged(); |
| 533 | 0 | return true; |
| 534 | } | |
| 535 | } |