src/jalview/gui/StructureChooser.java

   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 jalview.api.structures.JalviewStructureDisplayI;
  25 import jalview.bin.Cache;
  26 import jalview.bin.Jalview;
  27 import jalview.datamodel.DBRefEntry;
  28 import jalview.datamodel.DBRefSource;
  29 import jalview.datamodel.PDBEntry;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.fts.api.FTSData;
  32 import jalview.fts.api.FTSDataColumnI;
  33 import jalview.fts.api.FTSRestClientI;
  34 import jalview.fts.core.FTSDataColumnPreferences;
  35 import jalview.fts.core.FTSRestRequest;
  36 import jalview.fts.core.FTSRestResponse;
  37 import jalview.fts.service.pdb.PDBFTSRestClient;
  38 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  39 import jalview.gui.structurechooser.StructureChooserQuerySource;
  40 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  41 import jalview.io.DataSourceType;
  42 import jalview.jbgui.FilterOption;
  43 import jalview.jbgui.GStructureChooser;
  44 import jalview.structure.StructureMapping;
  45 import jalview.structure.StructureSelectionManager;
  46 import jalview.util.MessageManager;
  47 import jalview.ws.DBRefFetcher;
  48 import jalview.ws.sifts.SiftsSettings;
  49
  50 import java.awt.event.ItemEvent;
  51 import java.util.ArrayList;
  52 import java.util.Collection;
  53 import java.util.HashSet;
  54 import java.util.LinkedHashSet;
  55 import java.util.List;
  56 import java.util.Objects;
  57 import java.util.Set;
  58 import java.util.Vector;
  59 import java.util.concurrent.CompletableFuture;
  60 import java.util.concurrent.Executor;
  61 import java.util.concurrent.Executors;
  62
  63 import javax.swing.JCheckBox;
  64 import javax.swing.JComboBox;
  65 import javax.swing.JLabel;
  66 import javax.swing.JTable;
  67 import javax.swing.SwingUtilities;
  68 import javax.swing.table.AbstractTableModel;
  69
  70 /**
  71  * Provides the behaviors for the Structure chooser Panel
  72  *
  73  * @author tcnofoegbu
  74  *
  75  */
  76 @SuppressWarnings("serial")
  77 public class StructureChooser extends GStructureChooser
  78         implements IProgressIndicator
  79 {
  80   private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
  81
  82   private SequenceI selectedSequence;
  83
  84   private SequenceI[] selectedSequences;
  85
  86   private IProgressIndicator progressIndicator;
  87
  88   private Collection<FTSData> discoveredStructuresSet;
  89
  90   private StructureChooserQuerySource data;
  91
  92   @Override
  93   protected FTSDataColumnPreferences getFTSDocFieldPrefs()
  94   {
  95     return data.getDocFieldPrefs();
  96   }
  97
  98   private String selectedPdbFileName;
  99
 100   private boolean isValidPBDEntry;
 101
 102   private boolean cachedPDBExists;
 103
 104   private Collection<FTSData> lastDiscoveredStructuresSet;
 105
 106   private static StructureViewer lastTargetedView = null;
 107
 108   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
 109           AlignmentPanel ap)
 110   {
 111     // which FTS engine to use
 112     data = StructureChooserQuerySource
 113             .getQuerySourceFor(selectedSeqs);
 114     initDialog();
 115
 116     this.ap = ap;
 117     this.selectedSequence = selectedSeq;
 118     this.selectedSequences = selectedSeqs;
 119     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
 120     init();
 121
 122   }
 123
 124   /**
 125    * Initializes parameters used by the Structure Chooser Panel
 126    */
 127   protected void init()
 128   {
 129     if (!Jalview.isHeadlessMode())
 130     {
 131       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 132     }
 133
 134     chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
 135
 136     // ensure a filter option is in force for search
 137     populateFilterComboBox(true, cachedPDBExists);
 138     // todo change to futures I guess
 139
 140     final Runnable discoverPDBStructures = new Runnable()
 141     {
 142       @Override
 143       public void run()
 144       {
 145         // looks for any existing structures already loaded
 146         // for the sequences (the cached ones)
 147         // then queries the StructureChooserQuerySource to
 148         // discover more structures.
 149         //
 150         // Possible optimisation is to only begin querying
 151         // the structure chooser if there are no cached structures.
 152
 153         long startTime = System.currentTimeMillis();
 154         updateProgressIndicator(MessageManager
 155                 .getString("status.loading_cached_pdb_entries"), startTime);
 156         loadLocalCachedPDBEntries();
 157         updateProgressIndicator(null, startTime);
 158         updateProgressIndicator(MessageManager.getString(
 159                 "status.searching_for_pdb_structures"), startTime);
 160         fetchStructuresMetaData();
 161         // revise filter options if no results were found
 162         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
 163         discoverStructureViews();
 164         updateProgressIndicator(null, startTime);
 165         mainFrame.setVisible(true);
 166         updateCurrentView();
 167       }
 168     };
 169     final List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
 170
 171     final Runnable discoverCanonicalDBrefs = new Runnable()
 172     {
 173       @Override
 174       public void run()
 175       {
 176         long progressId = System.currentTimeMillis();
 177
 178         int y = seqsWithoutSourceDBRef.size();
 179         setProgressBar(MessageManager.formatMessage(
 180                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
 181                 y), progressId);
 182         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
 183                 .toArray(new SequenceI[y]);
 184         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
 185         dbRefFetcher.fetchDBRefs(true);
 186
 187         setProgressBar("Fetch complete.", progressId); // todo i18n
 188
 189         SwingUtilities.invokeLater(discoverPDBStructures);
 190       }
 191     };
 192
 193     Executors.defaultThreadFactory().newThread(new Runnable()
 194     {
 195       public void run()
 196       {
 197
 198         for (SequenceI seq : selectedSequences)
 199         {
 200           if (seq.isProtein())
 201           {
 202             int dbRef = ThreeDBStructureChooserQuerySource
 203                     .checkUniprotRefs(seq.getDBRefs());
 204             if (dbRef < 0)
 205             {
 206               seqsWithoutSourceDBRef.add(seq);
 207             }
 208           }
 209         }
 210         // retrieve database refs for protein sequences
 211         if (!seqsWithoutSourceDBRef.isEmpty())
 212         {
 213           JvOptionPane.newOptionDialog(Desktop.getDesktop())
 214                   .setResponseHandler(0, discoverCanonicalDBrefs)
 215                   .setResponseHandler(1, discoverPDBStructures)
 216                   .showDialog(MessageManager.formatMessage("label.fetch_references_for",seqsWithoutSourceDBRef.size()), MessageManager.getString(
 217                           "label.fetch_uniprot_references"),
 218                           JvOptionPane.YES_NO_OPTION,
 219                           JvOptionPane.PLAIN_MESSAGE, null, new Object[]
 220                           { MessageManager.getString("action.ok"),
 221                               MessageManager.getString("action.cancel") },
 222                           MessageManager.getString("action.ok"));
 223         } else {
 224           // get structures directly
 225           Executors.defaultThreadFactory().newThread(discoverPDBStructures).start();
 226         }
 227       };
 228     }).start();;
 229
 230   }
 231
 232   /**
 233    * Builds a drop-down choice list of existing structure viewers to which new
 234    * structures may be added. If this list is empty then it, and the 'Add'
 235    * button, are hidden.
 236    */
 237   private void discoverStructureViews()
 238   {
 239     if (Desktop.instance != null)
 240     {
 241       targetView.removeAllItems();
 242       if (lastTargetedView != null && !lastTargetedView.isVisible())
 243       {
 244         lastTargetedView = null;
 245       }
 246       int linkedViewsAt = 0;
 247       for (StructureViewerBase view : Desktop.instance
 248               .getStructureViewers(null, null))
 249       {
 250         StructureViewer viewHandler = (lastTargetedView != null
 251                 && lastTargetedView.sview == view) ? lastTargetedView
 252                         : StructureViewer.reconfigure(view);
 253
 254         if (view.isLinkedWith(ap))
 255         {
 256           targetView.insertItemAt(viewHandler, linkedViewsAt++);
 257         }
 258         else
 259         {
 260           targetView.addItem(viewHandler);
 261         }
 262       }
 263
 264       /*
 265        * show option to Add to viewer if at least 1 viewer found
 266        */
 267       targetView.setVisible(false);
 268       if (targetView.getItemCount() > 0)
 269       {
 270         targetView.setVisible(true);
 271         if (lastTargetedView != null)
 272         {
 273           targetView.setSelectedItem(lastTargetedView);
 274         }
 275         else
 276         {
 277           targetView.setSelectedIndex(0);
 278         }
 279       }
 280       btn_add.setVisible(targetView.isVisible());
 281     }
 282   }
 283
 284   /**
 285    * Updates the progress indicator with the specified message
 286    *
 287    * @param message
 288    *          displayed message for the operation
 289    * @param id
 290    *          unique handle for this indicator
 291    */
 292   protected void updateProgressIndicator(String message, long id)
 293   {
 294     if (progressIndicator != null)
 295     {
 296       progressIndicator.setProgressBar(message, id);
 297     }
 298   }
 299
 300   /**
 301    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
 302    * selection group
 303    */
 304   void fetchStructuresMetaData()
 305   {
 306     long startTime = System.currentTimeMillis();
 307     Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 308             .getStructureSummaryFields();
 309
 310     discoveredStructuresSet = new LinkedHashSet<>();
 311     HashSet<String> errors = new HashSet<>();
 312
 313     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 314             .getSelectedItem());
 315
 316     for (SequenceI seq : selectedSequences)
 317     {
 318
 319       FTSRestResponse resultList;
 320       try
 321       {
 322         resultList = data.fetchStructuresMetaData(seq, wantedFields,
 323                 selectedFilterOpt, !chk_invertFilter.isSelected());
 324         // null response means the FTSengine didn't yield a query for this
 325         // consider designing a special exception if we really wanted to be OOCrazy
 326         if (resultList==null)
 327         {
 328           continue;
 329         }
 330       } catch (Exception e)
 331       {
 332         e.printStackTrace();
 333         errors.add(e.getMessage());
 334         continue;
 335       }
 336       if (resultList.getSearchSummary() != null
 337               && !resultList.getSearchSummary().isEmpty())
 338       {
 339         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 340       }
 341     }
 342
 343     int noOfStructuresFound = 0;
 344     String totalTime = (System.currentTimeMillis() - startTime)
 345             + " milli secs";
 346     if (discoveredStructuresSet != null
 347             && !discoveredStructuresSet.isEmpty())
 348     {
 349       getResultTable()
 350               .setModel(data.getTableModel(discoveredStructuresSet));
 351
 352       noOfStructuresFound = discoveredStructuresSet.size();
 353       lastDiscoveredStructuresSet=discoveredStructuresSet;
 354       mainFrame.setTitle(MessageManager.formatMessage(
 355               "label.structure_chooser_no_of_structures",
 356               noOfStructuresFound, totalTime));
 357     }
 358     else
 359     {
 360       mainFrame.setTitle(MessageManager
 361               .getString("label.structure_chooser_manual_association"));
 362       if (errors.size() > 0)
 363       {
 364         StringBuilder errorMsg = new StringBuilder();
 365         for (String error : errors)
 366         {
 367           errorMsg.append(error).append("\n");
 368         }
 369         JvOptionPane.showMessageDialog(this, errorMsg.toString(),
 370                 MessageManager.getString("label.pdb_web-service_error"),
 371                 JvOptionPane.ERROR_MESSAGE);
 372       }
 373     }
 374   }
 375
 376   protected void loadLocalCachedPDBEntries()
 377   {
 378     ArrayList<CachedPDB> entries = new ArrayList<>();
 379     for (SequenceI seq : selectedSequences)
 380     {
 381       if (seq.getDatasetSequence() != null
 382               && seq.getDatasetSequence().getAllPDBEntries() != null)
 383       {
 384         for (PDBEntry pdbEntry : seq.getDatasetSequence()
 385                 .getAllPDBEntries())
 386         {
 387           if (pdbEntry.getFile() != null)
 388           {
 389             entries.add(new CachedPDB(seq, pdbEntry));
 390           }
 391         }
 392       }
 393     }
 394     cachedPDBExists = !entries.isEmpty();
 395     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
 396     tbl_local_pdb.setModel(tableModelx);
 397   }
 398
 399   /**
 400    * Filters a given list of discovered structures based on supplied argument
 401    *
 402    * @param fieldToFilterBy
 403    *          the field to filter by
 404    */
 405   void filterResultSet(final String fieldToFilterBy)
 406   {
 407     Thread filterThread = new Thread(new Runnable()
 408     {
 409
 410       @Override
 411       public void run()
 412       {
 413         long startTime = System.currentTimeMillis();
 414         lbl_loading.setVisible(true);
 415         Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs()
 416                 .getStructureSummaryFields();
 417         Collection<FTSData> filteredResponse = new HashSet<>();
 418         HashSet<String> errors = new HashSet<>();
 419
 420         for (SequenceI seq : selectedSequences)
 421         {
 422
 423           FTSRestResponse resultList;
 424           try
 425           {
 426             resultList = data.selectFirstRankedQuery(seq, discoveredStructuresSet,wantedFields,
 427                     fieldToFilterBy, !chk_invertFilter.isSelected());
 428
 429           } catch (Exception e)
 430           {
 431             e.printStackTrace();
 432             errors.add(e.getMessage());
 433             continue;
 434           }
 435           if (resultList.getSearchSummary() != null
 436                   && !resultList.getSearchSummary().isEmpty())
 437           {
 438             filteredResponse.addAll(resultList.getSearchSummary());
 439           }
 440         }
 441
 442         String totalTime = (System.currentTimeMillis() - startTime)
 443                 + " milli secs";
 444         if (!filteredResponse.isEmpty())
 445         {
 446           final int filterResponseCount = filteredResponse.size();
 447           Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
 448           reorderedStructuresSet.addAll(filteredResponse);
 449           reorderedStructuresSet.addAll(discoveredStructuresSet);
 450           getResultTable()
 451                   .setModel(data.getTableModel(reorderedStructuresSet));
 452
 453           FTSRestResponse.configureTableColumn(getResultTable(),
 454                   wantedFields, tempUserPrefs);
 455           getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
 456           getResultTable().getColumn("Ref Sequence").setMinWidth(100);
 457           getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
 458           // Update table selection model here
 459           getResultTable().addRowSelectionInterval(0,
 460                   filterResponseCount - 1);
 461           mainFrame.setTitle(MessageManager.formatMessage(
 462                   "label.structure_chooser_filter_time", totalTime));
 463         }
 464         else
 465         {
 466           mainFrame.setTitle(MessageManager.formatMessage(
 467                   "label.structure_chooser_filter_time", totalTime));
 468           if (errors.size() > 0)
 469           {
 470             StringBuilder errorMsg = new StringBuilder();
 471             for (String error : errors)
 472             {
 473               errorMsg.append(error).append("\n");
 474             }
 475             JvOptionPane.showMessageDialog(null, errorMsg.toString(),
 476                     MessageManager.getString("label.pdb_web-service_error"),
 477                     JvOptionPane.ERROR_MESSAGE);
 478           }
 479         }
 480
 481         lbl_loading.setVisible(false);
 482
 483         validateSelections();
 484       }
 485     });
 486     filterThread.start();
 487   }
 488
 489   /**
 490    * Handles action event for btn_pdbFromFile
 491    */
 492   @Override
 493   protected void pdbFromFile_actionPerformed()
 494   {
 495     // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
 496     // StructureChooser
 497     // works
 498     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 499             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 500     chooser.setFileView(new jalview.io.JalviewFileView());
 501     chooser.setDialogTitle(
 502             MessageManager.formatMessage("label.select_pdb_file_for",
 503                     selectedSequence.getDisplayId(false)));
 504     chooser.setToolTipText(MessageManager.formatMessage(
 505             "label.load_pdb_file_associate_with_sequence",
 506             selectedSequence.getDisplayId(false)));
 507
 508     int value = chooser.showOpenDialog(null);
 509     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 510     {
 511       selectedPdbFileName = chooser.getSelectedFile().getPath();
 512       jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
 513       validateSelections();
 514     }
 515   }
 516
 517   /**
 518    * Populates the filter combo-box options dynamically depending on discovered
 519    * structures
 520    */
 521   protected void populateFilterComboBox(boolean haveData,
 522           boolean cachedPDBExist)
 523   {
 524     populateFilterComboBox(haveData, cachedPDBExist, null);
 525   }
 526   /**
 527    * Populates the filter combo-box options dynamically depending on discovered
 528    * structures
 529    */
 530   protected void populateFilterComboBox(boolean haveData,
 531           boolean cachedPDBExist, FilterOption lastSel)
 532   {
 533
 534     /*
 535      * temporarily suspend the change listener behaviour
 536      */
 537     cmb_filterOption.removeItemListener(this);
 538     int selSet=-1;
 539     cmb_filterOption.removeAllItems();
 540     if (haveData)
 541     {
 542       List<FilterOption> filters = data.getAvailableFilterOptions(VIEWS_FILTER);
 543       data.updateAvailableFilterOptions(VIEWS_FILTER, filters, lastDiscoveredStructuresSet);
 544       int p=0;
 545       for (FilterOption filter:filters)
 546       {
 547         if (lastSel!=null && filter.equals(lastSel)) {
 548           selSet=p;
 549         }
 550         p++;
 551         cmb_filterOption.addItem(filter);
 552       }
 553     }
 554     cmb_filterOption.addItem(
 555             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
 556                     "-", VIEWS_ENTER_ID, false,null));
 557     cmb_filterOption.addItem(
 558             new FilterOption(MessageManager.getString("label.from_file"),
 559                     "-", VIEWS_FROM_FILE, false,null));
 560
 561     if (cachedPDBExist)
 562     {
 563       FilterOption cachedOption = new FilterOption(
 564               MessageManager.getString("label.cached_structures"), "-",
 565               VIEWS_LOCAL_PDB, false,null);
 566       cmb_filterOption.addItem(cachedOption);
 567       if (selSet==-1) {
 568         cmb_filterOption.setSelectedItem(cachedOption);
 569       }
 570     }
 571     if (selSet>-1)
 572     {
 573       cmb_filterOption.setSelectedIndex(selSet);
 574     }
 575     cmb_filterOption.addItemListener(this);
 576   }
 577
 578   /**
 579    * Updates the displayed view based on the selected filter option
 580    */
 581   protected void updateCurrentView()
 582   {
 583     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 584             .getSelectedItem());
 585     layout_switchableViews.show(pnl_switchableViews,
 586             selectedFilterOpt.getView());
 587     String filterTitle = mainFrame.getTitle();
 588     mainFrame.setTitle(frameTitle);
 589     chk_invertFilter.setVisible(false);
 590     if (selectedFilterOpt.getView() == VIEWS_FILTER)
 591     {
 592       mainFrame.setTitle(filterTitle);
 593       // TDB Query has no invert as yet
 594       chk_invertFilter.setVisible(selectedFilterOpt.getQuerySource() instanceof PDBStructureChooserQuerySource);
 595
 596       if (data!=selectedFilterOpt.getQuerySource() || data.needsRefetch(selectedFilterOpt))
 597       {
 598         data = selectedFilterOpt.getQuerySource();
 599         // rebuild the views completely, since prefs will also change
 600         tabRefresh();
 601         return;
 602       } else {
 603         filterResultSet(selectedFilterOpt.getValue());
 604       }
 605     }
 606     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
 607             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
 608     {
 609       mainFrame.setTitle(MessageManager
 610               .getString("label.structure_chooser_manual_association"));
 611       idInputAssSeqPanel.loadCmbAssSeq();
 612       fileChooserAssSeqPanel.loadCmbAssSeq();
 613     }
 614     validateSelections();
 615   }
 616
 617   /**
 618    * Validates user selection and enables the 'Add' and 'New View' buttons if
 619    * all parameters are correct (the Add button will only be visible if there is
 620    * at least one existing structure viewer open). This basically means at least
 621    * one structure selected and no error messages.
 622    * <p>
 623    * The 'Superpose Structures' option is enabled if either more than one
 624    * structure is selected, or the 'Add' to existing view option is enabled, and
 625    * disabled if the only option is to open a new view of a single structure.
 626    */
 627   @Override
 628   protected void validateSelections()
 629   {
 630     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 631             .getSelectedItem());
 632     btn_add.setEnabled(false);
 633     String currentView = selectedFilterOpt.getView();
 634     int selectedCount = 0;
 635     if (currentView == VIEWS_FILTER)
 636     {
 637       selectedCount = getResultTable().getSelectedRows().length;
 638       if (selectedCount > 0)
 639       {
 640         btn_add.setEnabled(true);
 641       }
 642     }
 643     else if (currentView == VIEWS_LOCAL_PDB)
 644     {
 645       selectedCount = tbl_local_pdb.getSelectedRows().length;
 646       if (selectedCount > 0)
 647       {
 648         btn_add.setEnabled(true);
 649       }
 650     }
 651     else if (currentView == VIEWS_ENTER_ID)
 652     {
 653       validateAssociationEnterPdb();
 654     }
 655     else if (currentView == VIEWS_FROM_FILE)
 656     {
 657       validateAssociationFromFile();
 658     }
 659
 660     btn_newView.setEnabled(btn_add.isEnabled());
 661
 662     /*
 663      * enable 'Superpose' option if more than one structure is selected,
 664      * or there are view(s) available to add structure(s) to
 665      */
 666     chk_superpose
 667             .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
 668   }
 669
 670   /**
 671    * Validates inputs from the Manual PDB entry panel
 672    */
 673   protected void validateAssociationEnterPdb()
 674   {
 675     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
 676             .getCmb_assSeq().getSelectedItem();
 677     lbl_pdbManualFetchStatus.setIcon(errorImage);
 678     lbl_pdbManualFetchStatus.setToolTipText("");
 679     if (txt_search.getText().length() > 0)
 680     {
 681       lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
 682               MessageManager.formatMessage("info.no_pdb_entry_found_for",
 683                       txt_search.getText())));
 684     }
 685
 686     if (errorWarning.length() > 0)
 687     {
 688       lbl_pdbManualFetchStatus.setIcon(warningImage);
 689       lbl_pdbManualFetchStatus.setToolTipText(
 690               JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
 691     }
 692
 693     if (selectedSequences.length == 1 || !assSeqOpt.getName()
 694             .equalsIgnoreCase("-Select Associated Seq-"))
 695     {
 696       txt_search.setEnabled(true);
 697       if (isValidPBDEntry)
 698       {
 699         btn_add.setEnabled(true);
 700         lbl_pdbManualFetchStatus.setToolTipText("");
 701         lbl_pdbManualFetchStatus.setIcon(goodImage);
 702       }
 703     }
 704     else
 705     {
 706       txt_search.setEnabled(false);
 707       lbl_pdbManualFetchStatus.setIcon(errorImage);
 708     }
 709   }
 710
 711   /**
 712    * Validates inputs for the manual PDB file selection options
 713    */
 714   protected void validateAssociationFromFile()
 715   {
 716     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
 717             .getCmb_assSeq().getSelectedItem();
 718     lbl_fromFileStatus.setIcon(errorImage);
 719     if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
 720             .getName().equalsIgnoreCase("-Select Associated Seq-")))
 721     {
 722       btn_pdbFromFile.setEnabled(true);
 723       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
 724       {
 725         btn_add.setEnabled(true);
 726         lbl_fromFileStatus.setIcon(goodImage);
 727       }
 728     }
 729     else
 730     {
 731       btn_pdbFromFile.setEnabled(false);
 732       lbl_fromFileStatus.setIcon(errorImage);
 733     }
 734   }
 735
 736   @Override
 737   protected void cmbAssSeqStateChanged()
 738   {
 739     validateSelections();
 740   }
 741
 742   /**
 743    * Handles the state change event for the 'filter' combo-box and 'invert'
 744    * check-box
 745    */
 746   @Override
 747   protected void stateChanged(ItemEvent e)
 748   {
 749     if (e.getSource() instanceof JCheckBox)
 750     {
 751       updateCurrentView();
 752     }
 753     else
 754     {
 755       if (e.getStateChange() == ItemEvent.SELECTED)
 756       {
 757         updateCurrentView();
 758       }
 759     }
 760
 761   }
 762
 763   /**
 764    * select structures for viewing by their PDB IDs
 765    *
 766    * @param pdbids
 767    * @return true if structures were found and marked as selected
 768    */
 769   public boolean selectStructure(String... pdbids)
 770   {
 771     boolean found = false;
 772
 773     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 774             .getSelectedItem());
 775     String currentView = selectedFilterOpt.getView();
 776     JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 777             : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
 778
 779     if (restable == null)
 780     {
 781       // can't select (enter PDB ID, or load file - need to also select which
 782       // sequence to associate with)
 783       return false;
 784     }
 785
 786     int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
 787     for (int r = 0; r < restable.getRowCount(); r++)
 788     {
 789       for (int p = 0; p < pdbids.length; p++)
 790       {
 791         if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
 792                 .equalsIgnoreCase(pdbids[p]))
 793         {
 794           restable.setRowSelectionInterval(r, r);
 795           found = true;
 796         }
 797       }
 798     }
 799     return found;
 800   }
 801
 802   /**
 803    * Handles the 'New View' action
 804    */
 805   @Override
 806   protected void newView_ActionPerformed()
 807   {
 808     targetView.setSelectedItem(null);
 809     showStructures(false);
 810   }
 811
 812   /**
 813    * Handles the 'Add to existing viewer' action
 814    */
 815   @Override
 816   protected void add_ActionPerformed()
 817   {
 818     showStructures(false);
 819   }
 820
 821   /**
 822    * structure viewer opened by this dialog, or null
 823    */
 824   private StructureViewer sViewer = null;
 825
 826   public void showStructures(boolean waitUntilFinished)
 827   {
 828
 829     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 830
 831     final int preferredHeight = pnl_filter.getHeight();
 832
 833     Runnable viewStruc = new Runnable()
 834     {
 835       @Override
 836       public void run()
 837       {
 838         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
 839                 .getSelectedItem());
 840         String currentView = selectedFilterOpt.getView();
 841         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
 842                 : tbl_local_pdb;
 843
 844         if (currentView == VIEWS_FILTER)
 845         {
 846           int[] selectedRows = restable.getSelectedRows();
 847           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 848           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 849           pdbEntriesToView = data.collectSelectedRows(restable,selectedRows,selectedSeqsToView);
 850
 851           SequenceI[] selectedSeqs = selectedSeqsToView
 852                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 853           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 854                   selectedSeqs);
 855         }
 856         else if (currentView == VIEWS_LOCAL_PDB)
 857         {
 858           int[] selectedRows = tbl_local_pdb.getSelectedRows();
 859           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
 860           int count = 0;
 861           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
 862                   .getModelIndex();
 863           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
 864                   .getModelIndex();
 865           List<SequenceI> selectedSeqsToView = new ArrayList<>();
 866           for (int row : selectedRows)
 867           {
 868             PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb.getModel()).getPDBEntryAt(row).getPdbEntry();
 869
 870             pdbEntriesToView[count++] = pdbEntry;
 871             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
 872                     .getValueAt(row, refSeqColIndex);
 873             selectedSeqsToView.add(selectedSeq);
 874           }
 875           SequenceI[] selectedSeqs = selectedSeqsToView
 876                   .toArray(new SequenceI[selectedSeqsToView.size()]);
 877           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 878                   selectedSeqs);
 879         }
 880         else if (currentView == VIEWS_ENTER_ID)
 881         {
 882           SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
 883                   .getCmb_assSeq().getSelectedItem()).getSequence();
 884           if (userSelectedSeq != null)
 885           {
 886             selectedSequence = userSelectedSeq;
 887           }
 888           String pdbIdStr = txt_search.getText();
 889           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
 890           if (pdbEntry == null)
 891           {
 892             pdbEntry = new PDBEntry();
 893             if (pdbIdStr.split(":").length > 1)
 894             {
 895               pdbEntry.setId(pdbIdStr.split(":")[0]);
 896               pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
 897             }
 898             else
 899             {
 900               pdbEntry.setId(pdbIdStr);
 901             }
 902             pdbEntry.setType(PDBEntry.Type.PDB);
 903             selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
 904           }
 905
 906           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
 907           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
 908                   new SequenceI[]
 909                   { selectedSequence });
 910         }
 911         else if (currentView == VIEWS_FROM_FILE)
 912         {
 913           SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
 914                   .getCmb_assSeq().getSelectedItem()).getSequence();
 915           if (userSelectedSeq != null)
 916           {
 917             selectedSequence = userSelectedSeq;
 918           }
 919           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
 920                   .associatePdbWithSeq(selectedPdbFileName,
 921                           DataSourceType.FILE, selectedSequence, true,
 922                           Desktop.instance);
 923
 924           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
 925                   ap, new SequenceI[]
 926                   { selectedSequence });
 927         }
 928         SwingUtilities.invokeLater(new Runnable()
 929         {
 930           @Override
 931           public void run()
 932           {
 933             closeAction(preferredHeight);
 934             mainFrame.dispose();
 935           }
 936         });
 937       }
 938     };
 939     Thread runner = new Thread(viewStruc);
 940     runner.start();
 941     if (waitUntilFinished)
 942     {
 943       while (sViewer == null ? runner.isAlive()
 944               : (sViewer.sview == null ? true
 945                       : !sViewer.sview.hasMapping()))
 946       {
 947         try
 948         {
 949           Thread.sleep(300);
 950         } catch (InterruptedException ie)
 951         {
 952
 953         }
 954       }
 955     }
 956   }
 957
 958   /**
 959    * Answers a structure viewer (new or existing) configured to superimpose
 960    * added structures or not according to the user's choice
 961    *
 962    * @param ssm
 963    * @return
 964    */
 965   StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
 966   {
 967     Object sv = targetView.getSelectedItem();
 968
 969     return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
 970   }
 971
 972   /**
 973    * Adds PDB structures to a new or existing structure viewer
 974    *
 975    * @param ssm
 976    * @param pdbEntriesToView
 977    * @param alignPanel
 978    * @param sequences
 979    * @return
 980    */
 981   private StructureViewer launchStructureViewer(
 982           StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
 983           final AlignmentPanel alignPanel, SequenceI[] sequences)
 984   {
 985     long progressId = sequences.hashCode();
 986     setProgressBar(MessageManager
 987             .getString("status.launching_3d_structure_viewer"), progressId);
 988     final StructureViewer theViewer = getTargetedStructureViewer(ssm);
 989     boolean superimpose = chk_superpose.isSelected();
 990     theViewer.setSuperpose(superimpose);
 991
 992     /*
 993      * remember user's choice of superimpose or not
 994      */
 995     Cache.setProperty(AUTOSUPERIMPOSE,
 996             Boolean.valueOf(superimpose).toString());
 997
 998     setProgressBar(null, progressId);
 999     if (SiftsSettings.isMapWithSifts())
1000     {
1001       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
1002       int p = 0;
1003       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
1004       // real PDB ID. For moment, we can also safely do this if there is already
1005       // a known mapping between the PDBEntry and the sequence.
1006       for (SequenceI seq : sequences)
1007       {
1008         PDBEntry pdbe = pdbEntriesToView[p++];
1009         if (pdbe != null && pdbe.getFile() != null)
1010         {
1011           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
1012           if (smm != null && smm.length > 0)
1013           {
1014             for (StructureMapping sm : smm)
1015             {
1016               if (sm.getSequence() == seq)
1017               {
1018                 continue;
1019               }
1020             }
1021           }
1022         }
1023         if (seq.getPrimaryDBRefs().isEmpty())
1024         {
1025           seqsWithoutSourceDBRef.add(seq);
1026           continue;
1027         }
1028       }
1029       if (!seqsWithoutSourceDBRef.isEmpty())
1030       {
1031         int y = seqsWithoutSourceDBRef.size();
1032         setProgressBar(MessageManager.formatMessage(
1033                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
1034                 y), progressId);
1035         SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
1036                 .toArray(new SequenceI[y]);
1037         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
1038         dbRefFetcher.fetchDBRefs(true);
1039
1040         setProgressBar("Fetch complete.", progressId); // todo i18n
1041       }
1042     }
1043     if (pdbEntriesToView.length > 1)
1044     {
1045       setProgressBar(
1046               MessageManager.getString(
1047                       "status.fetching_3d_structures_for_selected_entries"),
1048               progressId);
1049       theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
1050     }
1051     else
1052     {
1053       setProgressBar(MessageManager.formatMessage(
1054               "status.fetching_3d_structures_for",
1055               pdbEntriesToView[0].getId()), progressId);
1056       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
1057     }
1058     setProgressBar(null, progressId);
1059     // remember the last viewer we used...
1060     lastTargetedView = theViewer;
1061     return theViewer;
1062   }
1063
1064   /**
1065    * Populates the combo-box used in associating manually fetched structures to
1066    * a unique sequence when more than one sequence selection is made.
1067    */
1068   @Override
1069   protected void populateCmbAssociateSeqOptions(
1070           JComboBox<AssociateSeqOptions> cmb_assSeq,
1071           JLabel lbl_associateSeq)
1072   {
1073     cmb_assSeq.removeAllItems();
1074     cmb_assSeq.addItem(
1075             new AssociateSeqOptions("-Select Associated Seq-", null));
1076     lbl_associateSeq.setVisible(false);
1077     if (selectedSequences.length > 1)
1078     {
1079       for (SequenceI seq : selectedSequences)
1080       {
1081         cmb_assSeq.addItem(new AssociateSeqOptions(seq));
1082       }
1083     }
1084     else
1085     {
1086       String seqName = selectedSequence.getDisplayId(false);
1087       seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
1088       lbl_associateSeq.setText(seqName);
1089       lbl_associateSeq.setVisible(true);
1090       cmb_assSeq.setVisible(false);
1091     }
1092   }
1093
1094   protected boolean isStructuresDiscovered()
1095   {
1096     return discoveredStructuresSet != null
1097             && !discoveredStructuresSet.isEmpty();
1098   }
1099
1100   protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
1101                                // this.
1102   // Doing a search for "1" or "1c" is valuable?
1103   // Those work but are enormously slow.
1104
1105   @Override
1106   protected void txt_search_ActionPerformed()
1107   {
1108     String text = txt_search.getText().trim();
1109     if (text.length() >= PDB_ID_MIN)
1110       new Thread()
1111       {
1112
1113         @Override
1114         public void run()
1115         {
1116           errorWarning.setLength(0);
1117           isValidPBDEntry = false;
1118           if (text.length() > 0)
1119           {
1120             // TODO move this pdb id search into the PDB specific
1121             // FTSSearchEngine
1122             // for moment, it will work fine as is because it is self-contained
1123             String searchTerm = text.toLowerCase();
1124             searchTerm = searchTerm.split(":")[0];
1125             // System.out.println(">>>>> search term : " + searchTerm);
1126             List<FTSDataColumnI> wantedFields = new ArrayList<>();
1127             FTSRestRequest pdbRequest = new FTSRestRequest();
1128             pdbRequest.setAllowEmptySeq(false);
1129             pdbRequest.setResponseSize(1);
1130             pdbRequest.setFieldToSearchBy("(pdb_id:");
1131             pdbRequest.setWantedFields(wantedFields);
1132             pdbRequest.setSearchTerm(searchTerm + ")");
1133             pdbRequest.setAssociatedSequence(selectedSequence);
1134             FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
1135             wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
1136             FTSRestResponse resultList;
1137             try
1138             {
1139               resultList = pdbRestClient.executeRequest(pdbRequest);
1140             } catch (Exception e)
1141             {
1142               errorWarning.append(e.getMessage());
1143               return;
1144             } finally
1145             {
1146               validateSelections();
1147             }
1148             if (resultList.getSearchSummary() != null
1149                     && resultList.getSearchSummary().size() > 0)
1150             {
1151               isValidPBDEntry = true;
1152             }
1153           }
1154           validateSelections();
1155         }
1156       }.start();
1157   }
1158
1159   @Override
1160   protected void tabRefresh()
1161   {
1162     if (selectedSequences != null)
1163     {
1164       Thread refreshThread = new Thread(new Runnable()
1165       {
1166         @Override
1167         public void run()
1168         {
1169           fetchStructuresMetaData();
1170           //populateFilterComboBox(true, cachedPDBExists);
1171
1172           filterResultSet(
1173                   ((FilterOption) cmb_filterOption.getSelectedItem())
1174                           .getValue());
1175         }
1176       });
1177       refreshThread.start();
1178     }
1179   }
1180
1181   public class PDBEntryTableModel extends AbstractTableModel
1182   {
1183     String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
1184         "File" };
1185
1186     private List<CachedPDB> pdbEntries;
1187
1188     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
1189     {
1190       this.pdbEntries = new ArrayList<>(pdbEntries);
1191     }
1192
1193     @Override
1194     public String getColumnName(int columnIndex)
1195     {
1196       return columns[columnIndex];
1197     }
1198
1199     @Override
1200     public int getRowCount()
1201     {
1202       return pdbEntries.size();
1203     }
1204
1205     @Override
1206     public int getColumnCount()
1207     {
1208       return columns.length;
1209     }
1210
1211     @Override
1212     public boolean isCellEditable(int row, int column)
1213     {
1214       return false;
1215     }
1216
1217     @Override
1218     public Object getValueAt(int rowIndex, int columnIndex)
1219     {
1220       Object value = "??";
1221       CachedPDB entry = pdbEntries.get(rowIndex);
1222       switch (columnIndex)
1223       {
1224       case 0:
1225         value = entry.getSequence();
1226         break;
1227       case 1:
1228         value = entry.getQualifiedId();
1229         break;
1230       case 2:
1231         value = entry.getPdbEntry().getChainCode() == null ? "_"
1232                 : entry.getPdbEntry().getChainCode();
1233         break;
1234       case 3:
1235         value = entry.getPdbEntry().getType();
1236         break;
1237       case 4:
1238         value = entry.getPdbEntry().getFile();
1239         break;
1240       }
1241       return value;
1242     }
1243
1244     @Override
1245     public Class<?> getColumnClass(int columnIndex)
1246     {
1247       return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
1248     }
1249
1250     public CachedPDB getPDBEntryAt(int row)
1251     {
1252       return pdbEntries.get(row);
1253     }
1254
1255   }
1256
1257   private class CachedPDB
1258   {
1259     private SequenceI sequence;
1260
1261     private PDBEntry pdbEntry;
1262
1263     public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
1264     {
1265       this.sequence = sequence;
1266       this.pdbEntry = pdbEntry;
1267     }
1268
1269     public String getQualifiedId()
1270     {
1271       if (pdbEntry.hasProvider())
1272       {
1273         return pdbEntry.getProvider()+":"+pdbEntry.getId();
1274       }
1275       return pdbEntry.toString();
1276     }
1277
1278     public SequenceI getSequence()
1279     {
1280       return sequence;
1281     }
1282
1283     public PDBEntry getPdbEntry()
1284     {
1285       return pdbEntry;
1286     }
1287
1288   }
1289
1290   private IProgressIndicator progressBar;
1291
1292   @Override
1293   public void setProgressBar(String message, long id)
1294   {
1295     progressBar.setProgressBar(message, id);
1296   }
1297
1298   @Override
1299   public void registerHandler(long id, IProgressIndicatorHandler handler)
1300   {
1301     progressBar.registerHandler(id, handler);
1302   }
1303
1304   @Override
1305   public boolean operationInProgress()
1306   {
1307     return progressBar.operationInProgress();
1308   }
1309
1310   public JalviewStructureDisplayI getOpenedStructureViewer()
1311   {
1312     return sViewer == null ? null : sViewer.sview;
1313   }
1314
1315   @Override
1316   protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs)
1317   {
1318     data.setDocFieldPrefs(newPrefs);
1319
1320   }
1321 }