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