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