Coverage Report
File StructureChooser.java
Coverage histogram
49% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| StructureChooser | 100 | 629 | 225 | ||
| StructureChooser.PDBEntryTableModel | 1662 | 26 | 15 | ||
| StructureChooser.CachedPDB | 1738 | 7 | 5 |
Contributing tests
This file is covered by 36 tests.
.
Source view
| 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 | ||
| 22 | package jalview.gui; | |
| 23 | ||
| 24 | import java.awt.event.ActionEvent; | |
| 25 | import java.awt.event.ActionListener; | |
| 26 | import java.awt.event.ItemEvent; | |
| 27 | import java.io.File; | |
| 28 | import java.io.IOException; | |
| 29 | import java.util.ArrayList; | |
| 30 | import java.util.Collection; | |
| 31 | import java.util.HashSet; | |
| 32 | import java.util.LinkedHashMap; | |
| 33 | import java.util.LinkedHashSet; | |
| 34 | import java.util.List; | |
| 35 | import java.util.Locale; | |
| 36 | import java.util.Map; | |
| 37 | import java.util.concurrent.Executors; | |
| 38 | ||
| 39 | import javax.swing.JCheckBox; | |
| 40 | import javax.swing.JComboBox; | |
| 41 | import javax.swing.JLabel; | |
| 42 | import javax.swing.JMenu; | |
| 43 | import javax.swing.JMenuItem; | |
| 44 | import javax.swing.JPopupMenu; | |
| 45 | import javax.swing.JProgressBar; | |
| 46 | import javax.swing.JTable; | |
| 47 | import javax.swing.SwingUtilities; | |
| 48 | import javax.swing.table.AbstractTableModel; | |
| 49 | ||
| 50 | import com.stevesoft.pat.Regex; | |
| 51 | ||
| 52 | import jalview.analysis.AlignmentUtils; | |
| 53 | import jalview.api.AlignmentViewPanel; | |
| 54 | import jalview.api.structures.JalviewStructureDisplayI; | |
| 55 | import jalview.bin.Cache; | |
| 56 | import jalview.bin.Console; | |
| 57 | import jalview.bin.Jalview; | |
| 58 | import jalview.datamodel.AlignmentAnnotation; | |
| 59 | import jalview.datamodel.AlignmentI; | |
| 60 | import jalview.datamodel.PDBEntry; | |
| 61 | import jalview.datamodel.SequenceGroup; | |
| 62 | import jalview.datamodel.SequenceI; | |
| 63 | import jalview.ext.jmol.JmolParser; | |
| 64 | import jalview.fts.api.FTSData; | |
| 65 | import jalview.fts.api.FTSDataColumnI; | |
| 66 | import jalview.fts.api.FTSRestClientI; | |
| 67 | import jalview.fts.core.FTSDataColumnPreferences; | |
| 68 | import jalview.fts.core.FTSRestRequest; | |
| 69 | import jalview.fts.core.FTSRestResponse; | |
| 70 | import jalview.fts.service.pdb.PDBFTSRestClient; | |
| 71 | import jalview.fts.service.threedbeacons.TDB_FTSData; | |
| 72 | import jalview.gui.StructureViewer.ViewerType; | |
| 73 | import jalview.gui.structurechooser.PDBStructureChooserQuerySource; | |
| 74 | import jalview.gui.structurechooser.StructureChooserQuerySource; | |
| 75 | import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; | |
| 76 | import jalview.io.DataSourceType; | |
| 77 | import jalview.io.JalviewFileChooser; | |
| 78 | import jalview.io.JalviewFileView; | |
| 79 | import jalview.jbgui.FilterOption; | |
| 80 | import jalview.jbgui.GStructureChooser; | |
| 81 | import jalview.structure.StructureImportSettings.TFType; | |
| 82 | import jalview.structure.StructureMapping; | |
| 83 | import jalview.structure.StructureSelectionManager; | |
| 84 | import jalview.util.MessageManager; | |
| 85 | import jalview.util.Platform; | |
| 86 | import jalview.util.StringUtils; | |
| 87 | import jalview.ws.DBRefFetcher; | |
| 88 | import jalview.ws.DBRefFetcher.FetchFinishedListenerI; | |
| 89 | import jalview.ws.datamodel.alphafold.PAEContactMatrix; | |
| 90 | import jalview.ws.seqfetcher.DbSourceProxy; | |
| 91 | import jalview.ws.sifts.SiftsSettings; | |
| 92 | ||
| 93 | /** | |
| 94 | * Provides the behaviors for the Structure chooser Panel | |
| 95 | * | |
| 96 | * @author tcnofoegbu | |
| 97 | * | |
| 98 | */ | |
| 99 | @SuppressWarnings("serial") | |
| 100 | public class StructureChooser extends GStructureChooser | |
| 101 | implements IProgressIndicator | |
| 102 | { | |
| 103 | public static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; | |
| 104 | ||
| 105 | /** | |
| 106 | * warn user if need to fetch more than this many uniprot records at once | |
| 107 | */ | |
| 108 | private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20; | |
| 109 | private SequenceI selectedSequence; | |
| 110 | ||
| 111 | private SequenceI[] selectedSequences; | |
| 112 | ||
| 113 | private IProgressIndicator progressIndicator; | |
| 114 | ||
| 115 | private Collection<FTSData> discoveredStructuresSet; | |
| 116 | ||
| 117 | private StructureChooserQuerySource data; | |
| 118 | ||
| 119 | 57 |  @Override |
| 120 | protected FTSDataColumnPreferences getFTSDocFieldPrefs() | |
| 121 | { | |
| 122 | 57 | return data.getDocFieldPrefs(); |
| 123 | } | |
| 124 | ||
| 125 | private String selectedPdbFileName; | |
| 126 | ||
| 127 | private String localPdbPaeMatrixFileName; | |
| 128 | ||
| 129 | private boolean isValidPBDEntry; | |
| 130 | ||
| 131 | private boolean cachedPDBExists; | |
| 132 | ||
| 133 | private Collection<FTSData> lastDiscoveredStructuresSet; | |
| 134 | ||
| 135 | private boolean canQueryTDB = false; | |
| 136 | ||
| 137 | private boolean notQueriedTDBYet = true; | |
| 138 | ||
| 139 | List<SequenceI> seqsWithoutSourceDBRef = null; | |
| 140 | ||
| 141 | private boolean showChooserGUI = true; | |
| 142 | ||
| 143 | /** | |
| 144 | * when true, queries to external services are supressed (no SIFTs, no PDBe, | |
| 145 | * no 3D-Beacons, etc) | |
| 146 | */ | |
| 147 | private boolean dontQueryServices = false; | |
| 148 | ||
| 149 | protected static StructureViewer lastTargetedView = null; | |
| 150 | ||
| 151 | 3 | public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, |
| 152 | AlignmentPanel ap) | |
| 153 | { | |
| 154 | 3 | this(selectedSeqs, selectedSeq, ap, true); |
| 155 | } | |
| 156 | ||
| 157 | 3 | public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, |
| 158 | AlignmentPanel ap, boolean showGUI) | |
| 159 | { | |
| 160 | 3 | this(selectedSeqs, selectedSeq, ap, showGUI, false); |
| 161 | } | |
| 162 | ||
| 163 | 57 | public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, |
| 164 | AlignmentPanel ap, boolean showGUI, boolean dontQueryServices) | |
| 165 | { | |
| 166 | ||
| 167 | // which FTS engine to use | |
| 168 | 57 | data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs); |
| 169 | 57 | initDialog(); |
| 170 | ||
| 171 | 57 | this.ap = ap; |
| 172 | 57 | this.selectedSequence = selectedSeq; |
| 173 | 57 | this.selectedSequences = selectedSeqs; |
| 174 | 57 | this.progressIndicator = (ap == null) ? null : ap.alignFrame; |
| 175 | 57 | this.showChooserGUI = showGUI; |
| 176 | 57 | this.dontQueryServices = dontQueryServices; |
| 177 | 57 | init(); |
| 178 | ||
| 179 | } | |
| 180 | ||
| 181 | /** | |
| 182 | * sets canQueryTDB if protein sequences without a canonical uniprot ref or at | |
| 183 | * least one structure are discovered. | |
| 184 | */ | |
| 185 | 3 | private void populateSeqsWithoutSourceDBRef() |
| 186 | { | |
| 187 | 3 | seqsWithoutSourceDBRef = new ArrayList<SequenceI>(); |
| 188 | 3 | boolean needCanonical = false; |
| 189 | 3 | for (SequenceI seq : selectedSequences) |
| 190 | { | |
| 191 | 3 | if (seq.isProtein()) |
| 192 | { | |
| 193 | 3 | int dbRef = ThreeDBStructureChooserQuerySource |
| 194 | .checkUniprotRefs(seq.getDBRefs()); | |
| 195 | 3 | if (dbRef < 0) |
| 196 | { | |
| 197 | 2 | if (dbRef == -1) |
| 198 | { | |
| 199 | // need to retrieve canonicals | |
| 200 | 1 | needCanonical = true; |
| 201 | 1 | seqsWithoutSourceDBRef.add(seq); |
| 202 | } | |
| 203 | else | |
| 204 | { | |
| 205 | // could be a sequence with pdb ref | |
| 206 | 1 | if (seq.getAllPDBEntries() == null |
| 207 | || seq.getAllPDBEntries().size() == 0) | |
| 208 | { | |
| 209 | 0 | seqsWithoutSourceDBRef.add(seq); |
| 210 | } | |
| 211 | } | |
| 212 | } | |
| 213 | } | |
| 214 | } | |
| 215 | // retrieve database refs for protein sequences | |
| 216 | 3 | if (!seqsWithoutSourceDBRef.isEmpty()) |
| 217 | { | |
| 218 | 1 | canQueryTDB = true; |
| 219 | 1 | if (needCanonical) |
| 220 | { | |
| 221 | // triggers display of the 'Query TDB' button | |
| 222 | 1 | notQueriedTDBYet = true; |
| 223 | } | |
| 224 | } | |
| 225 | }; | |
| 226 | ||
| 227 | /** | |
| 228 | * Initializes parameters used by the Structure Chooser Panel | |
| 229 | */ | |
| 230 | 57 | protected void init() |
| 231 | { | |
| 232 | 57 | if (!Jalview.isHeadlessMode()) |
| 233 | { | |
| 234 | 55 | progressBar = new ProgressBar(this.statusPanel, this.statusBar); |
| 235 | } | |
| 236 | ||
| 237 | 57 | chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); |
| 238 | 57 | btn_queryTDB.addActionListener(new ActionListener() |
| 239 | { | |
| 240 | ||
| 241 | 0 | @Override |
| 242 | public void actionPerformed(ActionEvent e) | |
| 243 | { | |
| 244 | 0 | promptForTDBFetch(false); |
| 245 | } | |
| 246 | }); | |
| 247 | ||
| 248 | 57 | if (!dontQueryServices) |
| 249 | { | |
| 250 | 3 | Executors.defaultThreadFactory().newThread(new Runnable() |
| 251 | { | |
| 252 | 3 | @Override |
| 253 | public void run() | |
| 254 | { | |
| 255 | 3 | populateSeqsWithoutSourceDBRef(); |
| 256 | 3 | initialStructureDiscovery(); |
| 257 | } | |
| 258 | ||
| 259 | }).start(); | |
| 260 | } | |
| 261 | else | |
| 262 | { | |
| 263 | 54 | Console.debug( |
| 264 | "Structure chooser not querying services to discover metadata."); | |
| 265 | } | |
| 266 | } | |
| 267 | ||
| 268 | // called by init | |
| 269 | 3 | private void initialStructureDiscovery() |
| 270 | { | |
| 271 | // check which FTS engine to use | |
| 272 | 3 | data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences); |
| 273 | ||
| 274 | // ensure a filter option is in force for search | |
| 275 | 3 | populateFilterComboBox(true, cachedPDBExists); |
| 276 | ||
| 277 | // looks for any existing structures already loaded | |
| 278 | // for the sequences (the cached ones) | |
| 279 | // then queries the StructureChooserQuerySource to | |
| 280 | // discover more structures. | |
| 281 | // | |
| 282 | // Possible optimisation is to only begin querying | |
| 283 | // the structure chooser if there are no cached structures. | |
| 284 | ||
| 285 | 3 | long startTime = System.currentTimeMillis(); |
| 286 | 3 | updateProgressIndicator( |
| 287 | MessageManager.getString("status.loading_cached_pdb_entries"), | |
| 288 | startTime); | |
| 289 | 3 | loadLocalCachedPDBEntries(); |
| 290 | 3 | updateProgressIndicator(null, startTime); |
| 291 | 3 | updateProgressIndicator( |
| 292 | MessageManager.getString("status.searching_for_pdb_structures"), | |
| 293 | startTime); | |
| 294 | 3 | fetchStructuresMetaData(); |
| 295 | // revise filter options if no results were found | |
| 296 | 3 | populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); |
| 297 | 3 | discoverStructureViews(); |
| 298 | 2 | updateProgressIndicator(null, startTime); |
| 299 | 2 | mainFrame.setVisible(showChooserGUI); |
| 300 | 2 | updateCurrentView(); |
| 301 | } | |
| 302 | ||
| 303 | /** | |
| 304 | * raises dialog for Uniprot fetch followed by 3D beacons search | |
| 305 | * | |
| 306 | * @param ignoreGui | |
| 307 | * - when true, don't ask, just fetch | |
| 308 | */ | |
| 309 | 0 | public void promptForTDBFetch(boolean ignoreGui) |
| 310 | { | |
| 311 | 0 | final long progressId = System.currentTimeMillis(); |
| 312 | ||
| 313 | // final action after prompting and discovering db refs | |
| 314 | 0 | final Runnable strucDiscovery = new Runnable() |
| 315 | { | |
| 316 | 0 | @Override |
| 317 | public void run() | |
| 318 | { | |
| 319 | 0 | mainFrame.setEnabled(false); |
| 320 | 0 | cmb_filterOption.setEnabled(false); |
| 321 | 0 | progressBar.setProgressBar( |
| 322 | MessageManager.getString("status.searching_3d_beacons"), | |
| 323 | progressId); | |
| 324 | 0 | btn_queryTDB.setEnabled(false); |
| 325 | // TODO: warn if no accessions discovered | |
| 326 | 0 | populateSeqsWithoutSourceDBRef(); |
| 327 | // redo initial discovery - this time with 3d beacons | |
| 328 | // Executors. | |
| 329 | 0 | previousWantedFields = null; |
| 330 | 0 | lastSelected = (FilterOption) cmb_filterOption.getSelectedItem(); |
| 331 | 0 | cmb_filterOption.setSelectedItem(null); |
| 332 | 0 | cachedPDBExists=false; // reset to initial |
| 333 | 0 | initialStructureDiscovery(); |
| 334 | 0 | if (!isStructuresDiscovered()) |
| 335 | { | |
| 336 | 0 | progressBar.setProgressBar(MessageManager.getString( |
| 337 | "status.no_structures_discovered_from_3d_beacons"), | |
| 338 | progressId); | |
| 339 | 0 | btn_queryTDB.setToolTipText(MessageManager.getString( |
| 340 | "status.no_structures_discovered_from_3d_beacons")); | |
| 341 | 0 | btn_queryTDB.setEnabled(false); |
| 342 | 0 | pnl_queryTDB.setVisible(false); |
| 343 | } | |
| 344 | else | |
| 345 | { | |
| 346 | 0 | cmb_filterOption.setSelectedIndex(0); // select 'best' |
| 347 | 0 | btn_queryTDB.setVisible(false); |
| 348 | 0 | pnl_queryTDB.setVisible(false); |
| 349 | 0 | progressBar.setProgressBar(null, progressId); |
| 350 | } | |
| 351 | 0 | mainFrame.setEnabled(true); |
| 352 | 0 | cmb_filterOption.setEnabled(true); |
| 353 | } | |
| 354 | }; | |
| 355 | ||
| 356 | 0 | final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI() |
| 357 | { | |
| 358 | ||
| 359 | 0 | @Override |
| 360 | public void finished() | |
| 361 | { | |
| 362 | // filter has been selected, so we set flag to remove ourselves | |
| 363 | 0 | notQueriedTDBYet = false; |
| 364 | // new thread to discover structures - via 3d beacons | |
| 365 | 0 | Executors.defaultThreadFactory().newThread(strucDiscovery).start(); |
| 366 | ||
| 367 | } | |
| 368 | }; | |
| 369 | ||
| 370 | // fetch db refs if OK pressed | |
| 371 | 0 | final Runnable discoverCanonicalDBrefs = () -> { |
| 372 | 0 | btn_queryTDB.setEnabled(false); |
| 373 | 0 | populateSeqsWithoutSourceDBRef(); |
| 374 | ||
| 375 | 0 | final int y = seqsWithoutSourceDBRef.size(); |
| 376 | 0 | if (y > 0) |
| 377 | { | |
| 378 | 0 | final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef |
| 379 | .toArray(new SequenceI[y]); | |
| 380 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef, |
| 381 | progressBar, new DbSourceProxy[] | |
| 382 | { new jalview.ws.dbsources.Uniprot() }, null, false); | |
| 383 | 0 | dbRefFetcher.addListener(afterDbRefFetch); |
| 384 | // ideally this would also gracefully run with callbacks | |
| 385 | 0 | dbRefFetcher.fetchDBRefs(true); |
| 386 | } | |
| 387 | else | |
| 388 | { | |
| 389 | // call finished action directly | |
| 390 | 0 | afterDbRefFetch.finished(); |
| 391 | } | |
| 392 | }; | |
| 393 | 0 | final Runnable revertview = () -> { |
| 394 | 0 | if (lastSelected != null) |
| 395 | { | |
| 396 | 0 | cmb_filterOption.setSelectedItem(lastSelected); |
| 397 | } | |
| 398 | }; | |
| 399 | 0 | int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD", |
| 400 | THRESHOLD_WARN_UNIPROT_FETCH_NEEDED); | |
| 401 | 0 | Console.debug("Using Uniprot fetch threshold of " + threshold); |
| 402 | 0 | if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold) |
| 403 | { | |
| 404 | 0 | Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs); |
| 405 | 0 | return; |
| 406 | } | |
| 407 | // need cancel and no to result in the discoverPDB action - mocked is | |
| 408 | // 'cancel' TODO: mock should be OK | |
| 409 | 0 | StructureChooser thisSC = this; |
| 410 | 0 | JvOptionPane.newOptionDialog(thisSC.getFrame()) |
| 411 | .setResponseHandler(JvOptionPane.OK_OPTION, | |
| 412 | discoverCanonicalDBrefs) | |
| 413 | .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) | |
| 414 | .setResponseHandler(JvOptionPane.NO_OPTION, revertview) | |
| 415 | .showDialog( | |
| 416 | MessageManager.formatMessage( | |
| 417 | "label.fetch_references_for_3dbeacons", | |
| 418 | seqsWithoutSourceDBRef.size()), | |
| 419 | MessageManager | |
| 420 | .getString("label.3dbeacons"), | |
| 421 | JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE, | |
| 422 | null, new Object[] | |
| 423 | { MessageManager.getString("action.ok"), | |
| 424 | MessageManager.getString("action.cancel") }, | |
| 425 | MessageManager.getString("action.ok"), false); | |
| 426 | } | |
| 427 | ||
| 428 | /** | |
| 429 | * Builds a drop-down choice list of existing structure viewers to which new | |
| 430 | * structures may be added. If this list is empty then it, and the 'Add' | |
| 431 | * button, are hidden. | |
| 432 | */ | |
| 433 | 3 | private void discoverStructureViews() |
| 434 | { | |
| 435 | 3 | if (Desktop.getInstance() != null) |
| 436 | { | |
| 437 | 3 | targetView.removeAllItems(); |
| 438 | 3 | if (lastTargetedView != null && !lastTargetedView.isVisible()) |
| 439 | { | |
| 440 | 0 | lastTargetedView = null; |
| 441 | } | |
| 442 | 3 | int linkedViewsAt = 0; |
| 443 | 3 | for (StructureViewerBase view : Desktop.getInstance() |
| 444 | .getStructureViewers(null, null)) | |
| 445 | { | |
| 446 | 1 | StructureViewer viewHandler = (lastTargetedView != null |
| 447 | && lastTargetedView.sview == view) ? lastTargetedView | |
| 448 | : StructureViewer.reconfigure(view); | |
| 449 | ||
| 450 | 0 | if (view.isLinkedWith(ap)) |
| 451 | { | |
| 452 | 0 | targetView.insertItemAt(viewHandler, linkedViewsAt++); |
| 453 | } | |
| 454 | else | |
| 455 | { | |
| 456 | 0 | targetView.addItem(viewHandler); |
| 457 | } | |
| 458 | } | |
| 459 | ||
| 460 | /* | |
| 461 | * show option to Add to viewer if at least 1 viewer found | |
| 462 | */ | |
| 463 | 2 | targetView.setVisible(false); |
| 464 | 2 | if (targetView.getItemCount() > 0) |
| 465 | { | |
| 466 | 0 | targetView.setVisible(true); |
| 467 | 0 | if (lastTargetedView != null) |
| 468 | { | |
| 469 | 0 | targetView.setSelectedItem(lastTargetedView); |
| 470 | } | |
| 471 | else | |
| 472 | { | |
| 473 | 0 | targetView.setSelectedIndex(0); |
| 474 | } | |
| 475 | } | |
| 476 | 2 | btn_add.setVisible(targetView.isVisible()); |
| 477 | } | |
| 478 | } | |
| 479 | ||
| 480 | /** | |
| 481 | * Updates the progress indicator with the specified message | |
| 482 | * | |
| 483 | * @param message | |
| 484 | * displayed message for the operation | |
| 485 | * @param id | |
| 486 | * unique handle for this indicator | |
| 487 | */ | |
| 488 | 11 | protected void updateProgressIndicator(String message, long id) |
| 489 | { | |
| 490 | 11 | if (progressIndicator != null) |
| 491 | { | |
| 492 | 0 | progressIndicator.setProgressBar(message, id); |
| 493 | } | |
| 494 | } | |
| 495 | ||
| 496 | /** | |
| 497 | * Retrieve meta-data for all the structure(s) for a given sequence(s) in a | |
| 498 | * selection group | |
| 499 | */ | |
| 500 | 4 | void fetchStructuresMetaData() |
| 501 | { | |
| 502 | 4 | long startTime = System.currentTimeMillis(); |
| 503 | 4 | Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs() |
| 504 | .getStructureSummaryFields(); | |
| 505 | ||
| 506 | 4 | discoveredStructuresSet = new LinkedHashSet<>(); |
| 507 | 4 | HashSet<String> errors = new HashSet<>(); |
| 508 | ||
| 509 | 4 | FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
| 510 | .getSelectedItem()); | |
| 511 | ||
| 512 | 4 | for (SequenceI seq : selectedSequences) |
| 513 | { | |
| 514 | ||
| 515 | 4 | FTSRestResponse resultList; |
| 516 | 4 | try |
| 517 | { | |
| 518 | 4 | resultList = data.fetchStructuresMetaData(seq, wantedFields, |
| 519 | selectedFilterOpt, !chk_invertFilter.isSelected()); | |
| 520 | // null response means the FTSengine didn't yield a query for this | |
| 521 | // consider designing a special exception if we really wanted to be | |
| 522 | // OOCrazy | |
| 523 | 2 | if (resultList == null) |
| 524 | { | |
| 525 | 0 | continue; |
| 526 | } | |
| 527 | } catch (Exception e) | |
| 528 | { | |
| 529 | 2 | Console.printStackTrace(e); |
| 530 | 2 | errors.add(e.getMessage()); |
| 531 | 2 | continue; |
| 532 | } | |
| 533 | 2 | if (resultList.getSearchSummary() != null |
| 534 | && !resultList.getSearchSummary().isEmpty()) | |
| 535 | { | |
| 536 | 2 | discoveredStructuresSet.addAll(resultList.getSearchSummary()); |
| 537 | } | |
| 538 | } | |
| 539 | ||
| 540 | 4 | int noOfStructuresFound = 0; |
| 541 | 4 | String totalTime = (System.currentTimeMillis() - startTime) |
| 542 | + " milli secs"; | |
| 543 | 4 | if (discoveredStructuresSet != null |
| 544 | && !discoveredStructuresSet.isEmpty()) | |
| 545 | { | |
| 546 | 2 | getResultTable() |
| 547 | .setModel(data.getTableModel(discoveredStructuresSet)); | |
| 548 | ||
| 549 | 2 | noOfStructuresFound = discoveredStructuresSet.size(); |
| 550 | 2 | lastDiscoveredStructuresSet = discoveredStructuresSet; |
| 551 | 2 | mainFrame.setTitle(MessageManager.formatMessage( |
| 552 | "label.structure_chooser_no_of_structures", | |
| 553 | noOfStructuresFound, totalTime)); | |
| 554 | } | |
| 555 | else | |
| 556 | { | |
| 557 | 2 | mainFrame.setTitle(MessageManager |
| 558 | .getString("label.structure_chooser_manual_association")); | |
| 559 | 2 | if (errors.size() > 0) |
| 560 | { | |
| 561 | 2 | StringBuilder errorMsg = new StringBuilder(); |
| 562 | 2 | for (String error : errors) |
| 563 | { | |
| 564 | 2 | errorMsg.append(error).append("\n"); |
| 565 | } | |
| 566 | 2 | if (!Jalview.isHeadlessMode()) |
| 567 | { | |
| 568 | 2 | JvOptionPane.showMessageDialog(this, errorMsg.toString(), |
| 569 | MessageManager.getString("label.pdb_web-service_error"), | |
| 570 | JvOptionPane.ERROR_MESSAGE); | |
| 571 | } | |
| 572 | else | |
| 573 | { | |
| 574 | 0 | Console.error( |
| 575 | MessageManager.getString("label.pdb_web-service_error")); | |
| 576 | 0 | Console.debug(errorMsg.toString()); |
| 577 | } | |
| 578 | } | |
| 579 | } | |
| 580 | } | |
| 581 | ||
| 582 | 3 | protected void loadLocalCachedPDBEntries() |
| 583 | { | |
| 584 | 3 | ArrayList<CachedPDB> entries = new ArrayList<>(); |
| 585 | 3 | for (SequenceI seq : selectedSequences) |
| 586 | { | |
| 587 | 3 | if (seq.getDatasetSequence() != null |
| 588 | && seq.getDatasetSequence().getAllPDBEntries() != null) | |
| 589 | { | |
| 590 | 3 | for (PDBEntry pdbEntry : seq.getDatasetSequence() |
| 591 | .getAllPDBEntries()) | |
| 592 | { | |
| 593 | 0 | if (pdbEntry.getFile() != null) |
| 594 | { | |
| 595 | 0 | entries.add(new CachedPDB(seq, pdbEntry)); |
| 596 | } | |
| 597 | } | |
| 598 | } | |
| 599 | } | |
| 600 | 3 | cachedPDBExists = !entries.isEmpty(); |
| 601 | 3 | PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); |
| 602 | 3 | tbl_local_pdb.setModel(tableModelx); |
| 603 | } | |
| 604 | ||
| 605 | /** | |
| 606 | * Filters a given list of discovered structures based on supplied argument | |
| 607 | * | |
| 608 | * @param fieldToFilterBy | |
| 609 | * the field to filter by | |
| 610 | */ | |
| 611 | 1 | void filterResultSet(final String fieldToFilterBy) |
| 612 | { | |
| 613 | 1 | Thread filterThread = new Thread(new Runnable() |
| 614 | { | |
| 615 | ||
| 616 | 1 | @Override |
| 617 | public void run() | |
| 618 | { | |
| 619 | 1 | long startTime = System.currentTimeMillis(); |
| 620 | 1 | lbl_loading.setVisible(true); |
| 621 | 1 | Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs() |
| 622 | .getStructureSummaryFields(); | |
| 623 | 1 | Collection<FTSData> filteredResponse = new HashSet<>(); |
| 624 | 1 | HashSet<String> errors = new HashSet<>(); |
| 625 | ||
| 626 | 1 | for (SequenceI seq : selectedSequences) |
| 627 | { | |
| 628 | ||
| 629 | 1 | FTSRestResponse resultList; |
| 630 | 1 | try |
| 631 | { | |
| 632 | 1 | resultList = data.selectFirstRankedQuery(seq, |
| 633 | discoveredStructuresSet, wantedFields, fieldToFilterBy, | |
| 634 | !chk_invertFilter.isSelected()); | |
| 635 | ||
| 636 | } catch (Exception e) | |
| 637 | { | |
| 638 | 0 | Console.debugPrintStackTrace(e); |
| 639 | 0 | errors.add(e.getMessage()); |
| 640 | 0 | continue; |
| 641 | } | |
| 642 | 1 | if (resultList.getSearchSummary() != null |
| 643 | && !resultList.getSearchSummary().isEmpty()) | |
| 644 | { | |
| 645 | 1 | filteredResponse.addAll(resultList.getSearchSummary()); |
| 646 | } | |
| 647 | } | |
| 648 | ||
| 649 | 1 | String totalTime = (System.currentTimeMillis() - startTime) |
| 650 | + " milli secs"; | |
| 651 | 1 | if (!filteredResponse.isEmpty()) |
| 652 | { | |
| 653 | 1 | final int filterResponseCount = filteredResponse.size(); |
| 654 | 1 | Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>(); |
| 655 | 1 | reorderedStructuresSet.addAll(filteredResponse); |
| 656 | 1 | reorderedStructuresSet.addAll(discoveredStructuresSet); |
| 657 | 1 | getResultTable() |
| 658 | .setModel(data.getTableModel(reorderedStructuresSet)); | |
| 659 | ||
| 660 | 1 | FTSRestResponse.configureTableColumn(getResultTable(), |
| 661 | wantedFields, tempUserPrefs); | |
| 662 | 1 | getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); |
| 663 | 1 | getResultTable().getColumn("Ref Sequence").setMinWidth(100); |
| 664 | 1 | getResultTable().getColumn("Ref Sequence").setMaxWidth(200); |
| 665 | // Update table selection model here | |
| 666 | 1 | getResultTable().addRowSelectionInterval(0, |
| 667 | filterResponseCount - 1); | |
| 668 | 1 | mainFrame.setTitle(MessageManager.formatMessage( |
| 669 | "label.structure_chooser_filter_time", totalTime)); | |
| 670 | } | |
| 671 | else | |
| 672 | { | |
| 673 | 0 | mainFrame.setTitle(MessageManager.formatMessage( |
| 674 | "label.structure_chooser_filter_time", totalTime)); | |
| 675 | 0 | if (errors.size() > 0) |
| 676 | { | |
| 677 | 0 | StringBuilder errorMsg = new StringBuilder(); |
| 678 | 0 | for (String error : errors) |
| 679 | { | |
| 680 | 0 | errorMsg.append(error).append("\n"); |
| 681 | } | |
| 682 | 0 | JvOptionPane.showMessageDialog(null, errorMsg.toString(), |
| 683 | MessageManager.getString("label.pdb_web-service_error"), | |
| 684 | JvOptionPane.ERROR_MESSAGE); | |
| 685 | } | |
| 686 | } | |
| 687 | ||
| 688 | 1 | lbl_loading.setVisible(false); |
| 689 | ||
| 690 | 1 | validateSelections(); |
| 691 | } | |
| 692 | }); | |
| 693 | 1 | filterThread.start(); |
| 694 | } | |
| 695 | ||
| 696 | /** | |
| 697 | * Handles action event for btn_pdbFromFile | |
| 698 | */ | |
| 699 | 0 | @Override |
| 700 | protected void pdbFromFile_actionPerformed() | |
| 701 | { | |
| 702 | // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and | |
| 703 | // StructureChooser | |
| 704 | // works | |
| 705 | 0 | JalviewFileChooser chooser = new JalviewFileChooser( |
| 706 | Cache.getProperty("LAST_DIRECTORY")); | |
| 707 | 0 | chooser.setFileView(new JalviewFileView()); |
| 708 | 0 | chooser.setDialogTitle( |
| 709 | MessageManager.formatMessage("label.select_pdb_file_for", | |
| 710 | selectedSequence.getDisplayId(false))); | |
| 711 | 0 | chooser.setToolTipText(MessageManager.formatMessage( |
| 712 | "label.load_pdb_file_associate_with_sequence", | |
| 713 | selectedSequence.getDisplayId(false))); | |
| 714 | ||
| 715 | 0 | int value = chooser.showOpenDialog(null); |
| 716 | 0 | if (value == JalviewFileChooser.APPROVE_OPTION) |
| 717 | { | |
| 718 | 0 | selectedPdbFileName = chooser.getSelectedFile().getPath(); |
| 719 | 0 | Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); |
| 720 | 0 | boolean guessTFType = localPdbPaeMatrixFileName == null; |
| 721 | 0 | localPdbPaeMatrixFileName = guessPAEFilename(); |
| 722 | 0 | guessTFType |= localPdbPaeMatrixFileName != null; |
| 723 | 0 | Regex alphaFold = JmolParser.getNewAlphafoldValidator(); |
| 724 | 0 | if (guessTFType |
| 725 | && alphaFold.search(new File(selectedPdbFileName).getName()) | |
| 726 | && !tempFacAsChanged) | |
| 727 | { | |
| 728 | // localPdbPaeMatrixFileName was null and now isn't and filename could | |
| 729 | // well be AlphaFold and user hasn't adjusted the tempFacType | |
| 730 | 0 | combo_tempFacAs.setSelectedItem(TFType.PLDDT); |
| 731 | } | |
| 732 | 0 | validateSelections(); |
| 733 | } | |
| 734 | } | |
| 735 | ||
| 736 | /** | |
| 737 | * Handles action event for btn_paeMatrixFile | |
| 738 | */ | |
| 739 | 0 | @Override |
| 740 | protected void paeMatrixFile_actionPerformed() | |
| 741 | { | |
| 742 | 0 | File pdbFile = new File(selectedPdbFileName); |
| 743 | 0 | String setFile = Cache.getProperty("LAST_DIRECTORY"); |
| 744 | 0 | if (localPdbPaeMatrixFileName != null) |
| 745 | { | |
| 746 | 0 | File paeFile = new File(localPdbPaeMatrixFileName); |
| 747 | 0 | if (paeFile.exists()) |
| 748 | 0 | setFile = paeFile.getAbsolutePath(); |
| 749 | 0 | else if (paeFile.getParentFile().exists()) |
| 750 | 0 | setFile = paeFile.getParentFile().getAbsolutePath(); |
| 751 | } | |
| 752 | else | |
| 753 | { | |
| 754 | 0 | String guess = guessPAEFilename(); |
| 755 | 0 | if (guess != null) |
| 756 | 0 | setFile = guess; |
| 757 | } | |
| 758 | 0 | JalviewFileChooser chooser = new JalviewFileChooser(setFile); |
| 759 | 0 | chooser.setFileView(new JalviewFileView()); |
| 760 | 0 | chooser.setDialogTitle(MessageManager.formatMessage( |
| 761 | "label.select_pae_matrix_file_for", pdbFile.getName())); | |
| 762 | 0 | chooser.setToolTipText(MessageManager.formatMessage( |
| 763 | "label.load_pae_matrix_file_associate_with_structure", | |
| 764 | pdbFile.getName())); | |
| 765 | ||
| 766 | // TODO convert to Callable/Promise | |
| 767 | 0 | int value = chooser.showOpenDialog(null); |
| 768 | 0 | if (value == JalviewFileChooser.APPROVE_OPTION) |
| 769 | { | |
| 770 | 0 | String fileName = chooser.getSelectedFile().getPath(); |
| 771 | 0 | try |
| 772 | { | |
| 773 | 0 | PAEContactMatrix.validateContactMatrixFile(fileName); |
| 774 | } catch (Exception thr) | |
| 775 | { | |
| 776 | 0 | JvOptionPane.showInternalMessageDialog(this, MessageManager |
| 777 | .formatMessage("label.couldnt_load_file", new Object[] | |
| 778 | { fileName }) + "<br>" + thr.getLocalizedMessage(), | |
| 779 | MessageManager.getString("label.error_loading_file"), | |
| 780 | JvOptionPane.WARNING_MESSAGE); | |
| 781 | 0 | Console.error("Couldn't import " + fileName + " as a PAE matrix", |
| 782 | thr); | |
| 783 | 0 | return; |
| 784 | } | |
| 785 | 0 | localPdbPaeMatrixFileName = fileName; |
| 786 | 0 | Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName); |
| 787 | } | |
| 788 | 0 | validateAssociationFromFile(); |
| 789 | } | |
| 790 | ||
| 791 | 0 | private String guessPAEFilename() |
| 792 | { | |
| 793 | 0 | if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb") |
| 794 | || selectedPdbFileName.toLowerCase(Locale.ROOT) | |
| 795 | .endsWith(".cif")) | |
| 796 | { | |
| 797 | 0 | String jsonExt = selectedPdbFileName.substring(0, |
| 798 | selectedPdbFileName.length() - 4) + ".json"; | |
| 799 | // AlphaFold naming scheme | |
| 800 | 0 | String guessFile1 = StringUtils.replaceLast(jsonExt, "model", |
| 801 | "predicted_aligned_error"); | |
| 802 | // nf-core mode naming scheme | |
| 803 | 0 | String guessFile2 = StringUtils.replaceLast(jsonExt, ".json", |
| 804 | "_scores.json"); | |
| 805 | 0 | if (new File(guessFile1).exists()) |
| 806 | { | |
| 807 | 0 | return guessFile1; |
| 808 | } | |
| 809 | 0 | else if (new File(jsonExt).exists()) |
| 810 | { | |
| 811 | 0 | return jsonExt; |
| 812 | } | |
| 813 | 0 | else if (new File(guessFile2).exists()) |
| 814 | { | |
| 815 | 0 | return guessFile2; |
| 816 | } | |
| 817 | } | |
| 818 | 0 | return null; |
| 819 | } | |
| 820 | ||
| 821 | /** | |
| 822 | * Populates the filter combo-box options dynamically depending on discovered | |
| 823 | * structures | |
| 824 | */ | |
| 825 | 9 | protected void populateFilterComboBox(boolean haveData, |
| 826 | boolean cachedPDBExist) | |
| 827 | { | |
| 828 | 9 | populateFilterComboBox(haveData, cachedPDBExist, null); |
| 829 | } | |
| 830 | ||
| 831 | /** | |
| 832 | * Populates the filter combo-box options dynamically depending on discovered | |
| 833 | * structures | |
| 834 | */ | |
| 835 | 9 | protected void populateFilterComboBox(boolean haveData, |
| 836 | boolean cachedPDBExist, FilterOption lastSel) | |
| 837 | { | |
| 838 | ||
| 839 | /* | |
| 840 | * temporarily suspend the change listener behaviour | |
| 841 | */ | |
| 842 | 9 | cmb_filterOption.removeItemListener(this); |
| 843 | 9 | int selSet = -1; |
| 844 | 9 | cmb_filterOption.removeAllItems(); |
| 845 | 9 | if (haveData) |
| 846 | { | |
| 847 | 6 | List<FilterOption> filters = data |
| 848 | .getAvailableFilterOptions(VIEWS_FILTER); | |
| 849 | 6 | data.updateAvailableFilterOptions(VIEWS_FILTER, filters, |
| 850 | lastDiscoveredStructuresSet); | |
| 851 | 6 | int p = 0; |
| 852 | 6 | for (FilterOption filter : filters) |
| 853 | { | |
| 854 | 39 | if (lastSel != null && filter.equals(lastSel)) |
| 855 | { | |
| 856 | 0 | selSet = p; |
| 857 | } | |
| 858 | 39 | p++; |
| 859 | 39 | cmb_filterOption.addItem(filter); |
| 860 | } | |
| 861 | } | |
| 862 | ||
| 863 | 9 | cmb_filterOption.addItem( |
| 864 | new FilterOption(MessageManager.getString("label.enter_pdb_id"), | |
| 865 | "-", VIEWS_ENTER_ID, false, null)); | |
| 866 | 9 | cmb_filterOption.addItem( |
| 867 | new FilterOption(MessageManager.getString("label.from_file"), | |
| 868 | "-", VIEWS_FROM_FILE, false, null)); | |
| 869 | 9 | if (canQueryTDB && notQueriedTDBYet) |
| 870 | { | |
| 871 | 2 | btn_queryTDB.setVisible(true); |
| 872 | 2 | pnl_queryTDB.setVisible(true); |
| 873 | } | |
| 874 | ||
| 875 | 9 | if (cachedPDBExist) |
| 876 | { | |
| 877 | 1 | FilterOption cachedOption = new FilterOption( |
| 878 | MessageManager.getString("label.cached_structures"), "-", | |
| 879 | VIEWS_LOCAL_PDB, false, null); | |
| 880 | 1 | cmb_filterOption.addItem(cachedOption); |
| 881 | 1 | if (selSet == -1) |
| 882 | { | |
| 883 | 1 | cmb_filterOption.setSelectedItem(cachedOption); |
| 884 | } | |
| 885 | } | |
| 886 | 9 | if (selSet > -1) |
| 887 | { | |
| 888 | 0 | cmb_filterOption.setSelectedIndex(selSet); |
| 889 | } | |
| 890 | 9 | cmb_filterOption.addItemListener(this); |
| 891 | } | |
| 892 | ||
| 893 | /** | |
| 894 | * Updates the displayed view based on the selected filter option | |
| 895 | */ | |
| 896 | 2 | protected void updateCurrentView() |
| 897 | { | |
| 898 | 2 | FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
| 899 | .getSelectedItem()); | |
| 900 | ||
| 901 | 2 | if (lastSelected == selectedFilterOpt) |
| 902 | { | |
| 903 | // don't need to do anything, probably | |
| 904 | 0 | return; |
| 905 | } | |
| 906 | // otherwise, record selection | |
| 907 | // and update the layout and dialog accordingly | |
| 908 | 2 | lastSelected = selectedFilterOpt; |
| 909 | ||
| 910 | 2 | layout_switchableViews.show(pnl_switchableViews, |
| 911 | selectedFilterOpt.getView()); | |
| 912 | 2 | String filterTitle = mainFrame.getTitle(); |
| 913 | 2 | mainFrame.setTitle(frameTitle); |
| 914 | 2 | chk_invertFilter.setVisible(false); |
| 915 | ||
| 916 | 2 | if (selectedFilterOpt.getView() == VIEWS_FILTER) |
| 917 | { | |
| 918 | 1 | mainFrame.setTitle(filterTitle); |
| 919 | // TDB Query has no invert as yet | |
| 920 | 1 | chk_invertFilter.setVisible(selectedFilterOpt |
| 921 | .getQuerySource() instanceof PDBStructureChooserQuerySource); | |
| 922 | ||
| 923 | 1 | if (data != selectedFilterOpt.getQuerySource() |
| 924 | || data.needsRefetch(selectedFilterOpt)) | |
| 925 | { | |
| 926 | 0 | data = selectedFilterOpt.getQuerySource(); |
| 927 | // rebuild the views completely, since prefs will also change | |
| 928 | 0 | tabRefresh(); |
| 929 | 0 | return; |
| 930 | } | |
| 931 | else | |
| 932 | { | |
| 933 | 1 | filterResultSet(selectedFilterOpt.getValue()); |
| 934 | } | |
| 935 | } | |
| 936 | 1 | else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID |
| 937 | || selectedFilterOpt.getView() == VIEWS_FROM_FILE) | |
| 938 | { | |
| 939 | 1 | mainFrame.setTitle(MessageManager |
| 940 | .getString("label.structure_chooser_manual_association")); | |
| 941 | 1 | idInputAssSeqPanel.loadCmbAssSeq(); |
| 942 | 1 | fileChooserAssSeqPanel.loadCmbAssSeq(); |
| 943 | } | |
| 944 | 2 | validateSelections(); |
| 945 | } | |
| 946 | ||
| 947 | /** | |
| 948 | * Validates user selection and enables the 'Add' and 'New View' buttons if | |
| 949 | * all parameters are correct (the Add button will only be visible if there is | |
| 950 | * at least one existing structure viewer open). This basically means at least | |
| 951 | * one structure selected and no error messages. | |
| 952 | * <p> | |
| 953 | * The 'Superpose Structures' option is enabled if either more than one | |
| 954 | * structure is selected, or the 'Add' to existing view option is enabled, and | |
| 955 | * disabled if the only option is to open a new view of a single structure. | |
| 956 | */ | |
| 957 | 5 | @Override |
| 958 | protected void validateSelections() | |
| 959 | { | |
| 960 | 5 | FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
| 961 | .getSelectedItem()); | |
| 962 | 5 | btn_add.setEnabled(false); |
| 963 | 5 | String currentView = selectedFilterOpt.getView(); |
| 964 | 5 | int selectedCount = 0; |
| 965 | 5 | if (currentView == VIEWS_FILTER) |
| 966 | { | |
| 967 | 2 | selectedCount = getResultTable().getSelectedRows().length; |
| 968 | 2 | if (selectedCount > 0) |
| 969 | { | |
| 970 | 1 | btn_add.setEnabled(true); |
| 971 | } | |
| 972 | } | |
| 973 | 3 | else if (currentView == VIEWS_LOCAL_PDB) |
| 974 | { | |
| 975 | 0 | selectedCount = tbl_local_pdb.getSelectedRows().length; |
| 976 | 0 | if (selectedCount > 0) |
| 977 | { | |
| 978 | 0 | btn_add.setEnabled(true); |
| 979 | } | |
| 980 | } | |
| 981 | 3 | else if (currentView == VIEWS_ENTER_ID) |
| 982 | { | |
| 983 | 3 | validateAssociationEnterPdb(); |
| 984 | } | |
| 985 | 0 | else if (currentView == VIEWS_FROM_FILE) |
| 986 | { | |
| 987 | 0 | validateAssociationFromFile(); |
| 988 | } | |
| 989 | ||
| 990 | 5 | btn_newView.setEnabled(btn_add.isEnabled()); |
| 991 | ||
| 992 | /* | |
| 993 | * enable 'Superpose' option if more than one structure is selected, | |
| 994 | * or there are view(s) available to add structure(s) to | |
| 995 | */ | |
| 996 | 5 | chk_superpose |
| 997 | .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); | |
| 998 | } | |
| 999 | ||
| 1000 | 0 | @Override |
| 1001 | protected boolean showPopupFor(int selectedRow, int x, int y) | |
| 1002 | { | |
| 1003 | 0 | FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
| 1004 | .getSelectedItem()); | |
| 1005 | 0 | String currentView = selectedFilterOpt.getView(); |
| 1006 | 0 | if (currentView == VIEWS_FILTER |
| 1007 | && data instanceof ThreeDBStructureChooserQuerySource) | |
| 1008 | { | |
| 1009 | 0 | TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data) |
| 1010 | .getFTSDataFor(getResultTable(), selectedRow, | |
| 1011 | discoveredStructuresSet); | |
| 1012 | 0 | String pageUrl = row.getModelViewUrl(); |
| 1013 | ||
| 1014 | 0 | JPopupMenu popup = new JPopupMenu("3D Beacons"); |
| 1015 | 0 | JMenuItem viewUrl = new JMenuItem("View model web page"); |
| 1016 | 0 | if (pageUrl == null || "".equals(pageUrl.trim())) |
| 1017 | { | |
| 1018 | 0 | viewUrl.setEnabled(false); |
| 1019 | 0 | viewUrl.setText("No model page available."); |
| 1020 | } | |
| 1021 | 0 | viewUrl.addActionListener(new ActionListener() |
| 1022 | { | |
| 1023 | 0 | @Override |
| 1024 | public void actionPerformed(ActionEvent e) | |
| 1025 | { | |
| 1026 | 0 | Desktop.showUrl(pageUrl); |
| 1027 | } | |
| 1028 | }); | |
| 1029 | 0 | popup.add(viewUrl); |
| 1030 | 0 | SwingUtilities.invokeLater(new Runnable() |
| 1031 | { | |
| 1032 | 0 | @Override |
| 1033 | public void run() | |
| 1034 | { | |
| 1035 | 0 | popup.show(getResultTable(), x, y); |
| 1036 | } | |
| 1037 | }); | |
| 1038 | 0 | return true; |
| 1039 | } | |
| 1040 | // event not handled by us | |
| 1041 | 0 | return false; |
| 1042 | } | |
| 1043 | /** | |
| 1044 | * Validates inputs from the Manual PDB entry panel | |
| 1045 | */ | |
| 1046 | 3 | protected void validateAssociationEnterPdb() |
| 1047 | { | |
| 1048 | 3 | AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel |
| 1049 | .getCmb_assSeq().getSelectedItem(); | |
| 1050 | 3 | lbl_pdbManualFetchStatus.setIcon(errorImage); |
| 1051 | 3 | lbl_pdbManualFetchStatus.setToolTipText(""); |
| 1052 | 3 | if (txt_search.getText().length() > 0) |
| 1053 | { | |
| 1054 | 0 | lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, |
| 1055 | MessageManager.formatMessage("info.no_pdb_entry_found_for", | |
| 1056 | txt_search.getText()))); | |
| 1057 | } | |
| 1058 | ||
| 1059 | 3 | if (errorWarning.length() > 0) |
| 1060 | { | |
| 1061 | 0 | lbl_pdbManualFetchStatus.setIcon(warningImage); |
| 1062 | 0 | lbl_pdbManualFetchStatus.setToolTipText( |
| 1063 | JvSwingUtils.wrapTooltip(true, errorWarning.toString())); | |
| 1064 | } | |
| 1065 | ||
| 1066 | 3 | if (selectedSequences.length == 1 || !assSeqOpt.getName() |
| 1067 | .equalsIgnoreCase("-Select Associated Seq-")) | |
| 1068 | { | |
| 1069 | 3 | txt_search.setEnabled(true); |
| 1070 | // JBPNote - temporary workaround the PDB SOLR endpoint issue | |
| 1071 | // probably need to create a feature flag... | |
| 1072 | 3 | if (txt_search.getText().length()>=4) { |
| 1073 | 0 | isValidPBDEntry=true; |
| 1074 | } | |
| 1075 | 3 | if (isValidPBDEntry) |
| 1076 | { | |
| 1077 | 0 | btn_add.setEnabled(true); |
| 1078 | 0 | lbl_pdbManualFetchStatus.setToolTipText(""); |
| 1079 | 0 | lbl_pdbManualFetchStatus.setIcon(goodImage); |
| 1080 | } | |
| 1081 | } | |
| 1082 | else | |
| 1083 | { | |
| 1084 | 0 | txt_search.setEnabled(false); |
| 1085 | 0 | lbl_pdbManualFetchStatus.setIcon(errorImage); |
| 1086 | } | |
| 1087 | } | |
| 1088 | ||
| 1089 | /** | |
| 1090 | * Validates inputs for the manual PDB file selection options | |
| 1091 | */ | |
| 1092 | 0 | protected void validateAssociationFromFile() |
| 1093 | { | |
| 1094 | 0 | AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel |
| 1095 | .getCmb_assSeq().getSelectedItem(); | |
| 1096 | // lbl_fromFileStatus.setIcon(errorImage); | |
| 1097 | 0 | String pdbFileString = ""; |
| 1098 | 0 | String pdbFileTooltip = ""; |
| 1099 | 0 | if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt |
| 1100 | .getName().equalsIgnoreCase("-Select Associated Seq-"))) | |
| 1101 | { | |
| 1102 | 0 | btn_pdbFromFile.setEnabled(true); |
| 1103 | 0 | if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) |
| 1104 | { | |
| 1105 | 0 | btn_add.setEnabled(true); |
| 1106 | // lbl_fromFileStatus.setIcon(goodImage); | |
| 1107 | 0 | pdbFileString = new File(selectedPdbFileName).getName(); |
| 1108 | 0 | pdbFileTooltip = new File(selectedPdbFileName).getAbsolutePath(); |
| 1109 | 0 | setPdbOptionsEnabled(true); |
| 1110 | } | |
| 1111 | else | |
| 1112 | { | |
| 1113 | 0 | pdbFileString = MessageManager.getString("label.none"); |
| 1114 | 0 | pdbFileTooltip = MessageManager.getString("label.nothing_selected"); |
| 1115 | 0 | setPdbOptionsEnabled(false); |
| 1116 | } | |
| 1117 | } | |
| 1118 | else | |
| 1119 | { | |
| 1120 | 0 | btn_pdbFromFile.setEnabled(false); |
| 1121 | 0 | setPdbOptionsEnabled(false); |
| 1122 | // lbl_fromFileStatus.setIcon(errorImage); | |
| 1123 | 0 | pdbFileString = MessageManager.getString("label.none"); |
| 1124 | 0 | pdbFileTooltip = MessageManager.getString("label.nothing_selected"); |
| 1125 | } | |
| 1126 | 0 | lbl_pdbFile.setText(pdbFileString); |
| 1127 | 0 | lbl_pdbFile.setToolTipText(pdbFileTooltip); |
| 1128 | ||
| 1129 | // PAE file choice | |
| 1130 | 0 | String paeFileString = ""; |
| 1131 | 0 | String paeFileTooltip = ""; |
| 1132 | 0 | if (localPdbPaeMatrixFileName != null |
| 1133 | && localPdbPaeMatrixFileName.length() > 0) | |
| 1134 | { | |
| 1135 | 0 | paeFileString = new File(localPdbPaeMatrixFileName).getName(); |
| 1136 | 0 | paeFileTooltip = new File(localPdbPaeMatrixFileName) |
| 1137 | .getAbsolutePath(); | |
| 1138 | } | |
| 1139 | else | |
| 1140 | { | |
| 1141 | 0 | paeFileString = MessageManager.getString("label.none"); |
| 1142 | 0 | paeFileTooltip = MessageManager.getString("label.nothing_selected"); |
| 1143 | } | |
| 1144 | 0 | lbl_paeFile.setText(paeFileString); |
| 1145 | 0 | lbl_paeFile.setToolTipText(paeFileTooltip); |
| 1146 | } | |
| 1147 | ||
| 1148 | 2 | @Override |
| 1149 | protected void cmbAssSeqStateChanged() | |
| 1150 | { | |
| 1151 | 2 | validateSelections(); |
| 1152 | } | |
| 1153 | private FilterOption lastSelected=null; | |
| 1154 | /** | |
| 1155 | * Handles the state change event for the 'filter' combo-box and 'invert' | |
| 1156 | * check-box | |
| 1157 | */ | |
| 1158 | 0 | @Override |
| 1159 | protected void stateChanged(ItemEvent e) | |
| 1160 | { | |
| 1161 | 0 | if (e.getSource() instanceof JCheckBox) |
| 1162 | { | |
| 1163 | 0 | updateCurrentView(); |
| 1164 | } | |
| 1165 | else | |
| 1166 | { | |
| 1167 | 0 | if (e.getStateChange() == ItemEvent.SELECTED) |
| 1168 | { | |
| 1169 | 0 | updateCurrentView(); |
| 1170 | } | |
| 1171 | } | |
| 1172 | ||
| 1173 | } | |
| 1174 | ||
| 1175 | /** | |
| 1176 | * select structures for viewing by their PDB IDs | |
| 1177 | * | |
| 1178 | * @param pdbids | |
| 1179 | * @return true if structures were found and marked as selected | |
| 1180 | */ | |
| 1181 | 0 | public boolean selectStructure(String... pdbids) |
| 1182 | { | |
| 1183 | 0 | boolean found = false; |
| 1184 | ||
| 1185 | 0 | FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
| 1186 | .getSelectedItem()); | |
| 1187 | 0 | String currentView = selectedFilterOpt.getView(); |
| 1188 | 0 | JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() |
| 1189 | 0 | : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null; |
| 1190 | ||
| 1191 | 0 | if (restable == null) |
| 1192 | { | |
| 1193 | // can't select (enter PDB ID, or load file - need to also select which | |
| 1194 | // sequence to associate with) | |
| 1195 | 0 | return false; |
| 1196 | } | |
| 1197 | ||
| 1198 | 0 | int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex(); |
| 1199 | 0 | for (int r = 0; r < restable.getRowCount(); r++) |
| 1200 | { | |
| 1201 | 0 | for (int p = 0; p < pdbids.length; p++) |
| 1202 | { | |
| 1203 | 0 | if (String.valueOf(restable.getValueAt(r, pdbIdColIndex)) |
| 1204 | .equalsIgnoreCase(pdbids[p])) | |
| 1205 | { | |
| 1206 | 0 | restable.setRowSelectionInterval(r, r); |
| 1207 | 0 | found = true; |
| 1208 | } | |
| 1209 | } | |
| 1210 | } | |
| 1211 | 0 | return found; |
| 1212 | } | |
| 1213 | ||
| 1214 | /** | |
| 1215 | * Handles the 'New View' action | |
| 1216 | */ | |
| 1217 | 0 | @Override |
| 1218 | protected void newView_ActionPerformed() | |
| 1219 | { | |
| 1220 | 0 | targetView.setSelectedItem(null); |
| 1221 | 0 | showStructures(false); |
| 1222 | } | |
| 1223 | ||
| 1224 | /** | |
| 1225 | * Handles the 'Add to existing viewer' action | |
| 1226 | */ | |
| 1227 | 0 | @Override |
| 1228 | protected void add_ActionPerformed() | |
| 1229 | { | |
| 1230 | 0 | showStructures(false); |
| 1231 | } | |
| 1232 | ||
| 1233 | /** | |
| 1234 | * structure viewer opened by this dialog, or null | |
| 1235 | */ | |
| 1236 | private StructureViewer sViewer = null; | |
| 1237 | ||
| 1238 | 0 | public void showStructures(boolean waitUntilFinished) |
| 1239 | { | |
| 1240 | ||
| 1241 | 0 | final StructureSelectionManager ssm = ap.getStructureSelectionManager(); |
| 1242 | 0 | final StructureViewer theViewer = getTargetedStructureViewer(ssm); |
| 1243 | 0 | boolean superimpose = chk_superpose.isSelected(); |
| 1244 | 0 | final int preferredHeight = pnl_filter.getHeight(); |
| 1245 | 0 | btn_add.setEnabled(false); |
| 1246 | 0 | btn_newView.setEnabled(false); |
| 1247 | 0 | btn_cancel.setEnabled(false); |
| 1248 | 0 | actionsPanel.setEnabled(false); |
| 1249 | ||
| 1250 | 0 | final String progress = MessageManager |
| 1251 | .getString("label.working_ellipsis"); | |
| 1252 | 0 | setProgressBar(progress, progress.hashCode()); |
| 1253 | 0 | Runnable viewStruc = new Runnable() |
| 1254 | { | |
| 1255 | 0 | @Override |
| 1256 | public void run() | |
| 1257 | { | |
| 1258 | 0 | FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
| 1259 | .getSelectedItem()); | |
| 1260 | 0 | String currentView = selectedFilterOpt.getView(); |
| 1261 | 0 | JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() |
| 1262 | : tbl_local_pdb; | |
| 1263 | ||
| 1264 | 0 | if (currentView == VIEWS_FILTER) |
| 1265 | { | |
| 1266 | 0 | int[] selectedRows = restable.getSelectedRows(); |
| 1267 | 0 | PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; |
| 1268 | 0 | List<SequenceI> selectedSeqsToView = new ArrayList<>(); |
| 1269 | 0 | pdbEntriesToView = data.collectSelectedRows(restable, |
| 1270 | selectedRows, selectedSeqsToView); | |
| 1271 | ||
| 1272 | 0 | SequenceI[] selectedSeqs = selectedSeqsToView |
| 1273 | .toArray(new SequenceI[selectedSeqsToView.size()]); | |
| 1274 | 0 | sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, |
| 1275 | selectedSeqs, superimpose, theViewer, progressBar); | |
| 1276 | } | |
| 1277 | 0 | else if (currentView == VIEWS_LOCAL_PDB) |
| 1278 | { | |
| 1279 | 0 | int[] selectedRows = tbl_local_pdb.getSelectedRows(); |
| 1280 | 0 | PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; |
| 1281 | 0 | int count = 0; |
| 1282 | 0 | int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") |
| 1283 | .getModelIndex(); | |
| 1284 | 0 | int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") |
| 1285 | .getModelIndex(); | |
| 1286 | 0 | List<SequenceI> selectedSeqsToView = new ArrayList<>(); |
| 1287 | 0 | for (int row : selectedRows) |
| 1288 | { | |
| 1289 | 0 | PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb |
| 1290 | .getModel()).getPDBEntryAt(row).getPdbEntry(); | |
| 1291 | ||
| 1292 | 0 | pdbEntriesToView[count++] = pdbEntry; |
| 1293 | 0 | SequenceI selectedSeq = (SequenceI) tbl_local_pdb |
| 1294 | .getValueAt(row, refSeqColIndex); | |
| 1295 | 0 | selectedSeqsToView.add(selectedSeq); |
| 1296 | } | |
| 1297 | 0 | SequenceI[] selectedSeqs = selectedSeqsToView |
| 1298 | .toArray(new SequenceI[selectedSeqsToView.size()]); | |
| 1299 | 0 | sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, |
| 1300 | selectedSeqs, superimpose, theViewer, progressBar); | |
| 1301 | } | |
| 1302 | 0 | else if (currentView == VIEWS_ENTER_ID) |
| 1303 | { | |
| 1304 | 0 | SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel |
| 1305 | .getCmb_assSeq().getSelectedItem()).getSequence(); | |
| 1306 | 0 | if (userSelectedSeq != null) |
| 1307 | { | |
| 1308 | 0 | selectedSequence = userSelectedSeq; |
| 1309 | } | |
| 1310 | 0 | String pdbIdStr = txt_search.getText(); |
| 1311 | 0 | PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); |
| 1312 | 0 | if (pdbEntry == null) |
| 1313 | { | |
| 1314 | 0 | pdbEntry = new PDBEntry(); |
| 1315 | 0 | if (pdbIdStr.split(":").length > 1) |
| 1316 | { | |
| 1317 | 0 | pdbEntry.setId(pdbIdStr.split(":")[0]); |
| 1318 | 0 | pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); |
| 1319 | } | |
| 1320 | else | |
| 1321 | { | |
| 1322 | 0 | pdbEntry.setId(pdbIdStr); |
| 1323 | } | |
| 1324 | 0 | pdbEntry.setType(PDBEntry.Type.PDB); |
| 1325 | 0 | selectedSequence.getDatasetSequence().addPDBId(pdbEntry); |
| 1326 | } | |
| 1327 | ||
| 1328 | 0 | PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; |
| 1329 | 0 | sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView, |
| 1330 | new SequenceI[] | |
| 1331 | { selectedSequence }, superimpose, theViewer, | |
| 1332 | progressBar); | |
| 1333 | } | |
| 1334 | 0 | else if (currentView == VIEWS_FROM_FILE) |
| 1335 | { | |
| 1336 | 0 | StructureChooser sc = StructureChooser.this; |
| 1337 | 0 | String chainCodes = sc.chains.getText(); |
| 1338 | 0 | TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem(); |
| 1339 | 0 | String paeFilename = sc.localPdbPaeMatrixFileName; |
| 1340 | 0 | AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel |
| 1341 | .getCmb_assSeq().getSelectedItem(); | |
| 1342 | 0 | SequenceI userSelectedSeq = assSeqOpt.getSequence(); |
| 1343 | 0 | if (userSelectedSeq != null) |
| 1344 | { | |
| 1345 | 0 | selectedSequence = userSelectedSeq; |
| 1346 | } | |
| 1347 | // TODO: JAL-4107 - do we still need to resolve via AssociatePdbFileWithSeq ? | |
| 1348 | //PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName, | |
| 1349 | // DataSourceType.FILE, selectedSequence, true); | |
| 1350 | ||
| 1351 | // sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry }, | |
| 1352 | // new SequenceI[] { selectedSequence }, superimpose, theViewer, | |
| 1353 | // progressBar); | |
| 1354 | 0 | String lbn_filename; |
| 1355 | ||
| 1356 | 0 | String[] chainCodeSet= null; |
| 1357 | 0 | SequenceI[] selSeq=new SequenceI[] {selectedSequence }; |
| 1358 | 0 | if (chainCodes.length()>0 && chainCodes.trim().length()>0 && !"*".equals(chainCodes.trim())) |
| 1359 | { | |
| 1360 | 0 | chainCodeSet=chainCodes.split(","); |
| 1361 | } | |
| 1362 | ||
| 1363 | 0 | String pdbFilename = selectedPdbFileName; |
| 1364 | 0 | StructureChooser.openStructureForASequence(ssm, sc, ap, |
| 1365 | selectedSequence, true,pdbFilename,DataSourceType.FILE, chainCodeSet,tft, | |
| 1366 | paeFilename, | |
| 1367 | false, true, false, | |
| 1368 | getTargetedStructureViewer(ssm).getViewerType()); | |
| 1369 | } | |
| 1370 | 0 | SwingUtilities.invokeLater(new Runnable() |
| 1371 | { | |
| 1372 | 0 | @Override |
| 1373 | public void run() | |
| 1374 | { | |
| 1375 | 0 | setProgressBar("Complete.", progress.hashCode()); |
| 1376 | 0 | closeAction(preferredHeight); |
| 1377 | 0 | mainFrame.dispose(); |
| 1378 | } | |
| 1379 | }); | |
| 1380 | } | |
| 1381 | }; | |
| 1382 | 0 | Thread runner = new Thread(viewStruc); |
| 1383 | 0 | runner.start(); |
| 1384 | 0 | if (waitUntilFinished) |
| 1385 | { | |
| 1386 | 0 | while (sViewer == null ? runner.isAlive() |
| 1387 | 0 | : (sViewer.sview == null ? true |
| 1388 | : !sViewer.sview.hasMapping())) | |
| 1389 | { | |
| 1390 | 0 | try |
| 1391 | { | |
| 1392 | 0 | Thread.sleep(300); |
| 1393 | } catch (InterruptedException ie) | |
| 1394 | { | |
| 1395 | ||
| 1396 | } | |
| 1397 | } | |
| 1398 | } | |
| 1399 | } | |
| 1400 | ||
| 1401 | /** | |
| 1402 | * Answers a structure viewer (new or existing) configured to superimpose | |
| 1403 | * added structures or not according to the user's choice | |
| 1404 | * | |
| 1405 | * @param ssm | |
| 1406 | * @return | |
| 1407 | */ | |
| 1408 | 38 | StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm) |
| 1409 | { | |
| 1410 | 38 | Object sv = targetView.getSelectedItem(); |
| 1411 | ||
| 1412 | 38 | return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; |
| 1413 | } | |
| 1414 | ||
| 1415 | /** | |
| 1416 | * Adds PDB structures to a new or existing structure viewer | |
| 1417 | * | |
| 1418 | * @param ssm | |
| 1419 | * @param pdbEntriesToView | |
| 1420 | * @param alignPanel | |
| 1421 | * @param sequences | |
| 1422 | * @return | |
| 1423 | */ | |
| 1424 | 0 | private StructureViewer launchStructureViewer( |
| 1425 | StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, | |
| 1426 | final AlignmentPanel alignPanel, SequenceI[] sequences) | |
| 1427 | { | |
| 1428 | 0 | return launchStructureViewer(ssm, pdbEntriesToView, alignPanel, |
| 1429 | sequences, null); | |
| 1430 | } | |
| 1431 | ||
| 1432 | 33 | public StructureViewer launchStructureViewer( |
| 1433 | StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, | |
| 1434 | final AlignmentPanel alignPanel, SequenceI[] sequences, | |
| 1435 | ViewerType viewerType) | |
| 1436 | { | |
| 1437 | 33 | return launchStructureViewer(ssm, pdbEntriesToView, alignPanel, |
| 1438 | sequences, viewerType, chk_superpose.isSelected()); | |
| 1439 | } | |
| 1440 | ||
| 1441 | 38 | public StructureViewer launchStructureViewer( |
| 1442 | StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, | |
| 1443 | final AlignmentPanel alignPanel, SequenceI[] sequences, | |
| 1444 | ViewerType viewerType, boolean thisSuperimpose) | |
| 1445 | { | |
| 1446 | 38 | long progressId = sequences.hashCode(); |
| 1447 | 38 | setProgressBar(MessageManager |
| 1448 | .getString("status.launching_3d_structure_viewer"), progressId); | |
| 1449 | 38 | final StructureViewer theViewer = getTargetedStructureViewer(ssm); |
| 1450 | 38 | theViewer.setSuperpose(thisSuperimpose); |
| 1451 | ||
| 1452 | // if we're running in --headless mode make this viewer synchronous | |
| 1453 | 38 | if (Jalview.isHeadlessMode()) |
| 1454 | { | |
| 1455 | 2 | theViewer.setAsync(false); |
| 1456 | } | |
| 1457 | ||
| 1458 | /* | |
| 1459 | * remember user's choice of superimpose or not | |
| 1460 | */ | |
| 1461 | 38 | Cache.setProperty(AUTOSUPERIMPOSE, |
| 1462 | Boolean.valueOf(thisSuperimpose).toString()); | |
| 1463 | ||
| 1464 | 38 | setProgressBar(null, progressId); |
| 1465 | 38 | boolean localFiles=true; |
| 1466 | 38 | for (PDBEntry pe:pdbEntriesToView) |
| 1467 | { | |
| 1468 | 48 | if (pe.hasProvider() || (! pe.fakedPDBId() && pe.isAuthoritative())) |
| 1469 | { | |
| 1470 | 0 | localFiles=false; |
| 1471 | 0 | break; |
| 1472 | } | |
| 1473 | } | |
| 1474 | 38 | if (!localFiles && SiftsSettings.isMapWithSifts()) |
| 1475 | { | |
| 1476 | 0 | List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>(); |
| 1477 | 0 | int p = 0; |
| 1478 | // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a | |
| 1479 | // real PDB ID. For moment, we can also safely do this if there is already | |
| 1480 | // a known mapping between the PDBEntry and the sequence. | |
| 1481 | 0 | for (SequenceI seq : sequences) |
| 1482 | { | |
| 1483 | 0 | PDBEntry pdbe = pdbEntriesToView[p++]; |
| 1484 | 0 | if (pdbe != null && pdbe.getFile() != null) |
| 1485 | { | |
| 1486 | 0 | StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); |
| 1487 | 0 | if (smm != null && smm.length > 0) |
| 1488 | { | |
| 1489 | 0 | for (StructureMapping sm : smm) |
| 1490 | { | |
| 1491 | 0 | if (sm.getSequence() == seq) |
| 1492 | { | |
| 1493 | 0 | continue; |
| 1494 | } | |
| 1495 | } | |
| 1496 | } | |
| 1497 | } | |
| 1498 | 0 | if (seq.getPrimaryDBRefs().isEmpty() && seq.isProtein()) |
| 1499 | { | |
| 1500 | 0 | seqsWithoutSourceDBRef.add(seq); |
| 1501 | 0 | continue; |
| 1502 | } | |
| 1503 | } | |
| 1504 | 0 | if (!seqsWithoutSourceDBRef.isEmpty()) |
| 1505 | { | |
| 1506 | 0 | int y = seqsWithoutSourceDBRef.size(); |
| 1507 | 0 | setProgressBar(MessageManager.formatMessage( |
| 1508 | "status.fetching_dbrefs_for_sequences_without_valid_refs", | |
| 1509 | y), progressId); | |
| 1510 | 0 | SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef |
| 1511 | .toArray(new SequenceI[y]); | |
| 1512 | 0 | DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); |
| 1513 | 0 | dbRefFetcher.fetchDBRefs(true); |
| 1514 | ||
| 1515 | 0 | setProgressBar("Fetch complete.", progressId); // todo i18n |
| 1516 | } | |
| 1517 | } | |
| 1518 | 38 | if (pdbEntriesToView.length > 1) |
| 1519 | { | |
| 1520 | 5 | setProgressBar( |
| 1521 | MessageManager.getString( | |
| 1522 | "status.fetching_3d_structures_for_selected_entries"), | |
| 1523 | progressId); | |
| 1524 | 5 | theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel, |
| 1525 | viewerType); | |
| 1526 | } | |
| 1527 | else | |
| 1528 | { | |
| 1529 | 33 | setProgressBar(MessageManager.formatMessage( |
| 1530 | "status.fetching_3d_structures_for", | |
| 1531 | pdbEntriesToView[0].getId()), progressId); | |
| 1532 | // Can we pass a pre-computeMappinged pdbFile? | |
| 1533 | 33 | theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel, |
| 1534 | viewerType); | |
| 1535 | } | |
| 1536 | 38 | setProgressBar(null, progressId); |
| 1537 | // remember the last viewer we used... | |
| 1538 | 38 | lastTargetedView = theViewer; |
| 1539 | 38 | return theViewer; |
| 1540 | } | |
| 1541 | ||
| 1542 | /** | |
| 1543 | * Populates the combo-box used in associating manually fetched structures to | |
| 1544 | * a unique sequence when more than one sequence selection is made. | |
| 1545 | */ | |
| 1546 | 2 | @Override |
| 1547 | protected void populateCmbAssociateSeqOptions( | |
| 1548 | JComboBox<AssociateSeqOptions> cmb_assSeq, | |
| 1549 | JLabel lbl_associateSeq) | |
| 1550 | { | |
| 1551 | 2 | cmb_assSeq.removeAllItems(); |
| 1552 | 2 | cmb_assSeq.addItem( |
| 1553 | new AssociateSeqOptions("-Select Associated Seq-", null)); | |
| 1554 | 2 | lbl_associateSeq.setVisible(false); |
| 1555 | 2 | if (selectedSequences.length > 1) |
| 1556 | { | |
| 1557 | 0 | for (SequenceI seq : selectedSequences) |
| 1558 | { | |
| 1559 | 0 | cmb_assSeq.addItem(new AssociateSeqOptions(seq)); |
| 1560 | } | |
| 1561 | } | |
| 1562 | else | |
| 1563 | { | |
| 1564 | 2 | String seqName = selectedSequence.getDisplayId(false); |
| 1565 | 2 | seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39); |
| 1566 | 2 | lbl_associateSeq.setText(seqName); |
| 1567 | 2 | lbl_associateSeq.setVisible(true); |
| 1568 | 2 | cmb_assSeq.setVisible(false); |
| 1569 | } | |
| 1570 | } | |
| 1571 | ||
| 1572 | 3 | protected boolean isStructuresDiscovered() |
| 1573 | { | |
| 1574 | 3 | return discoveredStructuresSet != null |
| 1575 | && !discoveredStructuresSet.isEmpty(); | |
| 1576 | } | |
| 1577 | ||
| 1578 | protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes | |
| 1579 | // this. | |
| 1580 | // Doing a search for "1" or "1c" is valuable? | |
| 1581 | // Those work but are enormously slow. | |
| 1582 | ||
| 1583 | 0 | @Override |
| 1584 | protected void txt_search_ActionPerformed() | |
| 1585 | { | |
| 1586 | 0 | String text = txt_search.getText().trim(); |
| 1587 | 0 | if (text.length() >= PDB_ID_MIN) |
| 1588 | 0 | new Thread() |
| 1589 | { | |
| 1590 | ||
| 1591 | 0 | @Override |
| 1592 | public void run() | |
| 1593 | { | |
| 1594 | 0 | errorWarning.setLength(0); |
| 1595 | 0 | isValidPBDEntry = false; |
| 1596 | 0 | if (text.length() > 0) |
| 1597 | { | |
| 1598 | // TODO move this pdb id search into the PDB specific | |
| 1599 | // FTSSearchEngine | |
| 1600 | // for moment, it will work fine as is because it is self-contained | |
| 1601 | 0 | String searchTerm = text.toLowerCase(Locale.ROOT); |
| 1602 | 0 | searchTerm = searchTerm.split(":")[0]; |
| 1603 | // jalview.bin.Console.outPrintln(">>>>> search term : " + | |
| 1604 | // searchTerm); | |
| 1605 | 0 | List<FTSDataColumnI> wantedFields = new ArrayList<>(); |
| 1606 | 0 | FTSRestRequest pdbRequest = new FTSRestRequest(); |
| 1607 | 0 | pdbRequest.setAllowEmptySeq(false); |
| 1608 | 0 | pdbRequest.setResponseSize(1); |
| 1609 | 0 | pdbRequest.setFieldToSearchBy("(pdb_id:"); |
| 1610 | 0 | pdbRequest.setWantedFields(wantedFields); |
| 1611 | 0 | pdbRequest.setSearchTerm(searchTerm + ")"); |
| 1612 | 0 | pdbRequest.setAssociatedSequence(selectedSequence); |
| 1613 | 0 | FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance(); |
| 1614 | 0 | wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); |
| 1615 | 0 | FTSRestResponse resultList; |
| 1616 | 0 | try |
| 1617 | { | |
| 1618 | 0 | resultList = pdbRestClient.executeRequest(pdbRequest); |
| 1619 | } catch (Exception e) | |
| 1620 | { | |
| 1621 | 0 | errorWarning.append(e.getMessage()); |
| 1622 | 0 | return; |
| 1623 | } finally | |
| 1624 | { | |
| 1625 | 0 | validateSelections(); |
| 1626 | } | |
| 1627 | 0 | if (resultList.getSearchSummary() != null |
| 1628 | && resultList.getSearchSummary().size() > 0) | |
| 1629 | { | |
| 1630 | 0 | isValidPBDEntry = true; |
| 1631 | } | |
| 1632 | } | |
| 1633 | 0 | validateSelections(); |
| 1634 | } | |
| 1635 | }.start(); | |
| 1636 | } | |
| 1637 | ||
| 1638 | 57 | @Override |
| 1639 | protected void tabRefresh() | |
| 1640 | { | |
| 1641 | 57 | if (selectedSequences != null) |
| 1642 | { | |
| 1643 | 0 | lbl_loading.setVisible(true); |
| 1644 | 0 | Thread refreshThread = new Thread(new Runnable() |
| 1645 | { | |
| 1646 | 0 | @Override |
| 1647 | public void run() | |
| 1648 | { | |
| 1649 | 0 | fetchStructuresMetaData(); |
| 1650 | // populateFilterComboBox(true, cachedPDBExists); | |
| 1651 | ||
| 1652 | 0 | filterResultSet( |
| 1653 | ((FilterOption) cmb_filterOption.getSelectedItem()) | |
| 1654 | .getValue()); | |
| 1655 | 0 | lbl_loading.setVisible(false); |
| 1656 | } | |
| 1657 | }); | |
| 1658 | 0 | refreshThread.start(); |
| 1659 | } | |
| 1660 | } | |
| 1661 | ||
| 1662 | public class PDBEntryTableModel extends AbstractTableModel | |
| 1663 | { | |
| 1664 | String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", | |
| 1665 | "File" }; | |
| 1666 | ||
| 1667 | private List<CachedPDB> pdbEntries; | |
| 1668 | ||
| 1669 | 3 | public PDBEntryTableModel(List<CachedPDB> pdbEntries) |
| 1670 | { | |
| 1671 | 3 | this.pdbEntries = new ArrayList<>(pdbEntries); |
| 1672 | } | |
| 1673 | ||
| 1674 | 15 | @Override |
| 1675 | public String getColumnName(int columnIndex) | |
| 1676 | { | |
| 1677 | 15 | return columns[columnIndex]; |
| 1678 | } | |
| 1679 | ||
| 1680 | 21 | @Override |
| 1681 | public int getRowCount() | |
| 1682 | { | |
| 1683 | 21 | return pdbEntries.size(); |
| 1684 | } | |
| 1685 | ||
| 1686 | 18 | @Override |
| 1687 | public int getColumnCount() | |
| 1688 | { | |
| 1689 | 18 | return columns.length; |
| 1690 | } | |
| 1691 | ||
| 1692 | 0 | @Override |
| 1693 | public boolean isCellEditable(int row, int column) | |
| 1694 | { | |
| 1695 | 0 | return false; |
| 1696 | } | |
| 1697 | ||
| 1698 | 0 | @Override |
| 1699 | public Object getValueAt(int rowIndex, int columnIndex) | |
| 1700 | { | |
| 1701 | 0 | Object value = "??"; |
| 1702 | 0 | CachedPDB entry = pdbEntries.get(rowIndex); |
| 1703 | 0 | switch (columnIndex) |
| 1704 | { | |
| 1705 | 0 | case 0: |
| 1706 | 0 | value = entry.getSequence(); |
| 1707 | 0 | break; |
| 1708 | 0 | case 1: |
| 1709 | 0 | value = entry.getQualifiedId(); |
| 1710 | 0 | break; |
| 1711 | 0 | case 2: |
| 1712 | 0 | value = entry.getPdbEntry().getChainCode() == null ? "_" |
| 1713 | : entry.getPdbEntry().getChainCode(); | |
| 1714 | 0 | break; |
| 1715 | 0 | case 3: |
| 1716 | 0 | value = entry.getPdbEntry().getType(); |
| 1717 | 0 | break; |
| 1718 | 0 | case 4: |
| 1719 | 0 | value = entry.getPdbEntry().getFile(); |
| 1720 | 0 | break; |
| 1721 | } | |
| 1722 | 0 | return value; |
| 1723 | } | |
| 1724 | ||
| 1725 | 0 | @Override |
| 1726 | public Class<?> getColumnClass(int columnIndex) | |
| 1727 | { | |
| 1728 | 0 | return columnIndex == 0 ? SequenceI.class : PDBEntry.class; |
| 1729 | } | |
| 1730 | ||
| 1731 | 0 | public CachedPDB getPDBEntryAt(int row) |
| 1732 | { | |
| 1733 | 0 | return pdbEntries.get(row); |
| 1734 | } | |
| 1735 | ||
| 1736 | } | |
| 1737 | ||
| 1738 | private class CachedPDB | |
| 1739 | { | |
| 1740 | private SequenceI sequence; | |
| 1741 | ||
| 1742 | private PDBEntry pdbEntry; | |
| 1743 | ||
| 1744 | 0 | public CachedPDB(SequenceI sequence, PDBEntry pdbEntry) |
| 1745 | { | |
| 1746 | 0 | this.sequence = sequence; |
| 1747 | 0 | this.pdbEntry = pdbEntry; |
| 1748 | } | |
| 1749 | ||
| 1750 | 0 | public String getQualifiedId() |
| 1751 | { | |
| 1752 | 0 | if (pdbEntry.hasProvider()) |
| 1753 | { | |
| 1754 | 0 | return pdbEntry.getProvider() + ":" + pdbEntry.getId(); |
| 1755 | } | |
| 1756 | 0 | return pdbEntry.toString(); |
| 1757 | } | |
| 1758 | ||
| 1759 | 0 | public SequenceI getSequence() |
| 1760 | { | |
| 1761 | 0 | return sequence; |
| 1762 | } | |
| 1763 | ||
| 1764 | 0 | public PDBEntry getPdbEntry() |
| 1765 | { | |
| 1766 | 0 | return pdbEntry; |
| 1767 | } | |
| 1768 | ||
| 1769 | } | |
| 1770 | ||
| 1771 | private IProgressIndicator progressBar; | |
| 1772 | ||
| 1773 | 152 | @Override |
| 1774 | public void setProgressBar(String message, long id) | |
| 1775 | { | |
| 1776 | 152 | if (!Platform.isHeadless() && progressBar != null) |
| 1777 | 144 | progressBar.setProgressBar(message, id); |
| 1778 | } | |
| 1779 | ||
| 1780 | 0 | @Override |
| 1781 | public void addProgressBar(long id, String message) | |
| 1782 | { | |
| 1783 | 0 | progressBar.addProgressBar(id, message); |
| 1784 | } | |
| 1785 | ||
| 1786 | 0 | @Override |
| 1787 | public void removeProgressBar(long id) | |
| 1788 | { | |
| 1789 | 0 | progressBar.removeProgressBar(id); |
| 1790 | } | |
| 1791 | ||
| 1792 | 0 | @Override |
| 1793 | public void registerHandler(long id, IProgressIndicatorHandler handler) | |
| 1794 | { | |
| 1795 | 0 | if (progressBar != null) |
| 1796 | 0 | progressBar.registerHandler(id, handler); |
| 1797 | } | |
| 1798 | ||
| 1799 | 0 | @Override |
| 1800 | public boolean operationInProgress() | |
| 1801 | { | |
| 1802 | 0 | return progressBar == null ? false : progressBar.operationInProgress(); |
| 1803 | } | |
| 1804 | ||
| 1805 | 0 | public JalviewStructureDisplayI getOpenedStructureViewer() |
| 1806 | { | |
| 1807 | 0 | return sViewer == null ? null : sViewer.sview; |
| 1808 | } | |
| 1809 | ||
| 1810 | 0 | @Override |
| 1811 | protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs) | |
| 1812 | { | |
| 1813 | 0 | data.setDocFieldPrefs(newPrefs); |
| 1814 | ||
| 1815 | } | |
| 1816 | ||
| 1817 | /** | |
| 1818 | * | |
| 1819 | * @return true when all initialisation threads have finished and dialog is | |
| 1820 | * visible | |
| 1821 | */ | |
| 1822 | 12 | public boolean isDialogVisible() |
| 1823 | { | |
| 1824 | 12 | return mainFrame != null && data != null && cmb_filterOption != null |
| 1825 | && mainFrame.isVisible() | |
| 1826 | && cmb_filterOption.getSelectedItem() != null; | |
| 1827 | } | |
| 1828 | /** | |
| 1829 | * | |
| 1830 | * @return true if the 3D-Beacons query button will/has been displayed | |
| 1831 | */ | |
| 1832 | 1 | public boolean isCanQueryTDB() |
| 1833 | { | |
| 1834 | 1 | return canQueryTDB; |
| 1835 | } | |
| 1836 | ||
| 1837 | 1 | public boolean isNotQueriedTDBYet() |
| 1838 | { | |
| 1839 | 1 | return notQueriedTDBYet; |
| 1840 | } | |
| 1841 | ||
| 1842 | /** | |
| 1843 | * Open a single structure file for a given sequence | |
| 1844 | */ | |
| 1845 | 0 | public static void openStructureFileForSequence( |
| 1846 | StructureSelectionManager ssm, StructureChooser sc, | |
| 1847 | AlignmentPanel ap, SequenceI seq, boolean prompt, | |
| 1848 | String sFilename, TFType tft, String paeFilename, | |
| 1849 | boolean doXferSettings) | |
| 1850 | { | |
| 1851 | 0 | openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft, |
| 1852 | paeFilename, false, true, doXferSettings, null); | |
| 1853 | } | |
| 1854 | ||
| 1855 | /** | |
| 1856 | * | |
| 1857 | * @param ssm | |
| 1858 | * @param sc | |
| 1859 | * @param ap | |
| 1860 | * @param seq | |
| 1861 | * @param prompt | |
| 1862 | * @param sFilename | |
| 1863 | * @param tft | |
| 1864 | * @param paeFilename | |
| 1865 | * @param forceHeadless | |
| 1866 | * @param showRefAnnotations | |
| 1867 | * @param doXferSettings | |
| 1868 | * @param viewerType | |
| 1869 | * - when not null means the viewer will be opened, providing | |
| 1870 | * forceHeadless/headless is not true | |
| 1871 | * @return | |
| 1872 | */ | |
| 1873 | 10 | public static StructureViewer openStructureFileForSequence( |
| 1874 | StructureSelectionManager ssm, StructureChooser sc, | |
| 1875 | AlignmentPanel ap, SequenceI seq, boolean prompt, | |
| 1876 | String sFilename, TFType tft, String paeFilename, | |
| 1877 | boolean forceHeadless, boolean showRefAnnotations, | |
| 1878 | boolean doXferSettings, ViewerType viewerType) | |
| 1879 | { | |
| 1880 | 10 | return openStructureForASequence(ssm, sc, ap, seq, prompt, sFilename, |
| 1881 | DataSourceType.FILE, tft, paeFilename, forceHeadless, | |
| 1882 | showRefAnnotations, doXferSettings, viewerType); | |
| 1883 | } | |
| 1884 | 47 | public static StructureViewer openStructureForASequence( |
| 1885 | StructureSelectionManager ssm, StructureChooser sc, | |
| 1886 | AlignmentPanel ap, SequenceI seq, boolean prompt, | |
| 1887 | String strucDloc, DataSourceType strucDsource, TFType tft, | |
| 1888 | String paeFileSource, boolean forceHeadless, | |
| 1889 | boolean showRefAnnotations, boolean doXferSettings, | |
| 1890 | ViewerType viewerType) | |
| 1891 | { | |
| 1892 | 47 | return openStructureForASequence(ssm, sc, ap, seq, prompt, strucDloc, strucDsource, null, |
| 1893 | tft, paeFileSource, forceHeadless, | |
| 1894 | showRefAnnotations, doXferSettings, viewerType); | |
| 1895 | } | |
| 1896 | /** | |
| 1897 | * Import and view structure data for one or more sequences | |
| 1898 | * | |
| 1899 | * @param ssm | |
| 1900 | * - null or a specific StructureSelectionManageer | |
| 1901 | * @param sc | |
| 1902 | * - null or a live StructureChooser instance to get data from | |
| 1903 | * @param ap | |
| 1904 | * - alignmentPanel to associate viewer with | |
| 1905 | * @param seq | |
| 1906 | * - sequence to associate structure with | |
| 1907 | * @param prompt | |
| 1908 | * - when true will raise an error dialog | |
| 1909 | * @param strucDloc | |
| 1910 | * - string resolving to structure data using strucDsoruce | |
| 1911 | * @param strucDsource | |
| 1912 | * - how to get data from strucDloc and paeFileSource or null if they | |
| 1913 | * are file paths | |
| 1914 | * @param chains | |
| 1915 | * - null or one or more chains to associated with the sequence | |
| 1916 | * @param tft | |
| 1917 | * - temperature factor type for the datasource | |
| 1918 | * @param paeFileSource | |
| 1919 | * - a PAE matrix for the structure data | |
| 1920 | * @param forceHeadless | |
| 1921 | * - when true override any and all gui ops | |
| 1922 | * @param showRefAnnotations | |
| 1923 | * - automatically display reference annotations associated with | |
| 1924 | * structure | |
| 1925 | * @param doXferSettings | |
| 1926 | * - TODO CLARIFY transfer specific import settings for structureData | |
| 1927 | * @param viewerType | |
| 1928 | * - when not null means the viewer will be opened, providing | |
| 1929 | * forceHeadless/headless is not true | |
| 1930 | * @return null or StructureViewer instance | |
| 1931 | */ | |
| 1932 | 49 | public static StructureViewer openStructureForASequence( |
| 1933 | StructureSelectionManager ssm, StructureChooser sc, | |
| 1934 | AlignmentPanel ap, SequenceI seq, boolean prompt, | |
| 1935 | String strucDloc, DataSourceType strucDsource, String[] chains, TFType tft, | |
| 1936 | String paeFileSource, boolean forceHeadless, | |
| 1937 | boolean showRefAnnotations, boolean doXferSettings, | |
| 1938 | ViewerType viewerType) | |
| 1939 | { | |
| 1940 | 49 | StructureViewer sv = null; |
| 1941 | 49 | boolean headless = forceHeadless; |
| 1942 | 49 | if (sc == null) |
| 1943 | { | |
| 1944 | // headless = true; | |
| 1945 | 49 | prompt = false; |
| 1946 | // suppress structure viewer's external service queries | |
| 1947 | 49 | sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false, |
| 1948 | true); | |
| 1949 | } | |
| 1950 | 49 | if (ssm == null) |
| 1951 | { | |
| 1952 | 49 | ssm = ap.getStructureSelectionManager(); |
| 1953 | 49 | StructureSelectionManager.doConfigureStructurePrefs(ssm); |
| 1954 | } | |
| 1955 | 49 | String paeFilename = null; |
| 1956 | 49 | if (paeFileSource != null) |
| 1957 | { | |
| 1958 | 32 | if (strucDsource == null || strucDsource.equals(DataSourceType.FILE)) |
| 1959 | { | |
| 1960 | 29 | paeFilename = paeFileSource; |
| 1961 | } | |
| 1962 | else | |
| 1963 | { | |
| 1964 | 3 | if (DataSourceType.URL.equals(strucDsource)) |
| 1965 | { | |
| 1966 | 3 | try |
| 1967 | { | |
| 1968 | 3 | File tfile = jalview.ws.dbsources.EBIAlfaFold |
| 1969 | .fetchAPAE_from(null, paeFileSource); | |
| 1970 | 3 | paeFilename = tfile.getAbsolutePath(); |
| 1971 | } catch (IOException ex) | |
| 1972 | { | |
| 1973 | 0 | Console.error( |
| 1974 | "Couldn't retrieve PAE file from URL " + paeFileSource, | |
| 1975 | ex); | |
| 1976 | } | |
| 1977 | ||
| 1978 | } | |
| 1979 | else | |
| 1980 | { | |
| 1981 | 0 | Console.warn("Can't handle PAE data location type " + strucDsource |
| 1982 | + " for given structure " + strucDloc); | |
| 1983 | 0 | ; |
| 1984 | } | |
| 1985 | } | |
| 1986 | } | |
| 1987 | 49 | List<PDBEntry> fileEntries=new ArrayList<PDBEntry>(); |
| 1988 | 49 | List<SequenceI> seqEntries=new ArrayList<SequenceI>(); |
| 1989 | 47 | if (chains!=null) { |
| 1990 | 0 | for (String chain:chains) |
| 1991 | { | |
| 1992 | ||
| 1993 | 0 | PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq( |
| 1994 | strucDloc, | |
| 1995 | 0 | strucDsource != null ? strucDsource : DataSourceType.FILE, |
| 1996 | seq, new String[] { chain }, prompt, Desktop.getInstance(), tft, paeFilename, | |
| 1997 | doXferSettings); | |
| 1998 | // why didn't associatePdbFile actually add a PDBEntry ? | |
| 1999 | // why didn't the fileEntry have a chaincode ? | |
| 2000 | 0 | fileEntry.setChainCode(chain); |
| 2001 | 0 | fileEntries.add(fileEntry); |
| 2002 | 0 | seq.addPDBId(fileEntry); |
| 2003 | 0 | seqEntries.add(seq); |
| 2004 | ||
| 2005 | } | |
| 2006 | } | |
| 2007 | else | |
| 2008 | { | |
| 2009 | ||
| 2010 | 47 | PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq( |
| 2011 | strucDloc, | |
| 2012 | 47 | strucDsource != null ? strucDsource : DataSourceType.FILE, |
| 2013 | seq, prompt, Desktop.getInstance(), tft, paeFilename, | |
| 2014 | doXferSettings); | |
| 2015 | 47 | fileEntries.add(fileEntry); |
| 2016 | 47 | seqEntries.add(seq); |
| 2017 | } | |
| 2018 | // if headless, "false" in the sc constructor above will avoid GUI behaviour | |
| 2019 | // in sc.launchStructureViewer() | |
| 2020 | 49 | if (!headless && !(viewerType == null)) |
| 2021 | { | |
| 2022 | 33 | sv = sc.launchStructureViewer(ssm, fileEntries.toArray(new PDBEntry[0]), ap, |
| 2023 | seqEntries.toArray(new SequenceI[0]), viewerType); | |
| 2024 | // foo | |
| 2025 | 33 | sv.getJalviewStructureDisplay().raiseViewer(); |
| 2026 | } | |
| 2027 | ||
| 2028 | 49 | sc.mainFrame.dispose(); |
| 2029 | ||
| 2030 | // TODO should honor preferences - only show reference annotation that is | |
| 2031 | // requested - JAL-4415 JAL-3124 | |
| 2032 | 49 | if (showRefAnnotations) |
| 2033 | { | |
| 2034 | 37 | showReferenceAnnotationsForSequence(ap.alignFrame, seq); |
| 2035 | } | |
| 2036 | ||
| 2037 | 49 | return sv; |
| 2038 | } | |
| 2039 | ||
| 2040 | 37 | public static void showReferenceAnnotationsForSequence(AlignFrame af, |
| 2041 | SequenceI sequence) | |
| 2042 | { | |
| 2043 | 37 | AlignViewport av = af.getCurrentView(); |
| 2044 | 37 | AlignmentI al = av.getAlignment(); |
| 2045 | ||
| 2046 | 37 | List<SequenceI> forSequences = new ArrayList<>(); |
| 2047 | 37 | forSequences.add(sequence); |
| 2048 | 37 | final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>(); |
| 2049 | 37 | AlignmentUtils.findAddableReferenceAnnotations(forSequences, null, |
| 2050 | candidates, al); | |
| 2051 | 37 | final SequenceGroup selectionGroup = av.getSelectionGroup(); |
| 2052 | 37 | AlignmentUtils.addReferenceAnnotations(candidates, al, selectionGroup); |
| 2053 | 37 | for (AlignmentViewPanel ap : af.getAlignPanels()) |
| 2054 | { | |
| 2055 | // required to readjust the height and position of the PAE | |
| 2056 | // annotation | |
| 2057 | 37 | ap.adjustAnnotationHeight(); |
| 2058 | } | |
| 2059 | ||
| 2060 | } | |
| 2061 | ||
| 2062 | 0 | @Override |
| 2063 | public JProgressBar getProgressBar(long id) | |
| 2064 | { | |
| 2065 | 0 | return progressBar.getProgressBar(id); |
| 2066 | } | |
| 2067 | ||
| 2068 | 0 | @Override |
| 2069 | public String getMessage(long id) | |
| 2070 | { | |
| 2071 | 0 | return progressIndicator.getMessage(id); |
| 2072 | } | |
| 2073 | ||
| 2074 | 0 | @Override |
| 2075 | public void setProgressBarMessage(long id, String message) | |
| 2076 | { | |
| 2077 | 0 | progressIndicator.setProgressBarMessage(id, message); |
| 2078 | } | |
| 2079 | } |