src/jalview/gui/SequenceFetcher.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 package jalview.gui;
  22
  23 import jalview.api.FeatureSettingsModelI;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.DBRefEntry;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.util.DBRefUtils;
  29 import jalview.util.MessageManager;
  30 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  31 import jalview.ws.seqfetcher.DbSourceProxy;
  32
  33 import java.awt.BorderLayout;
  34 import java.awt.Font;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.awt.event.KeyAdapter;
  38 import java.awt.event.KeyEvent;
  39 import java.util.ArrayList;
  40 import java.util.Arrays;
  41 import java.util.Iterator;
  42 import java.util.List;
  43
  44 import javax.swing.JButton;
  45 import javax.swing.JCheckBox;
  46 import javax.swing.JInternalFrame;
  47 import javax.swing.JLabel;
  48 import javax.swing.JOptionPane;
  49 import javax.swing.JPanel;
  50 import javax.swing.JScrollPane;
  51 import javax.swing.JTextArea;
  52 import javax.swing.SwingConstants;
  53 import javax.swing.tree.DefaultMutableTreeNode;
  54
  55 public class SequenceFetcher extends JPanel implements Runnable
  56 {
  57   JLabel dbeg = new JLabel();
  58
  59   JDatabaseTree database;
  60
  61   JButton databaseButt;
  62
  63   JLabel jLabel1 = new JLabel();
  64
  65   JCheckBox replacePunctuation = new JCheckBox();
  66
  67   JButton ok = new JButton();
  68
  69   JButton clear = new JButton();
  70
  71   JButton example = new JButton();
  72
  73   JButton close = new JButton();
  74
  75   JPanel jPanel1 = new JPanel();
  76
  77   JTextArea textArea = new JTextArea();
  78
  79   JScrollPane jScrollPane1 = new JScrollPane();
  80
  81   JPanel jPanel2 = new JPanel();
  82
  83   JPanel jPanel3 = new JPanel();
  84
  85   JPanel jPanel4 = new JPanel();
  86
  87   BorderLayout borderLayout1 = new BorderLayout();
  88
  89   BorderLayout borderLayout2 = new BorderLayout();
  90
  91   BorderLayout borderLayout3 = new BorderLayout();
  92
  93   JInternalFrame frame;
  94
  95   IProgressIndicator guiWindow;
  96
  97   AlignFrame alignFrame;
  98
  99   StringBuffer result;
 100
 101   final String noDbSelected = "-- Select Database --";
 102
 103   private static jalview.ws.SequenceFetcher sfetch = null;
 104
 105   private static long lastDasSourceRegistry = -3;
 106
 107   private static DasSourceRegistryI dasRegistry = null;
 108
 109   private static boolean _initingFetcher = false;
 110
 111   private static Thread initingThread = null;
 112
 113   int debounceTrap = 0;
 114
 115   /**
 116    * Blocking method that initialises and returns the shared instance of the
 117    * SequenceFetcher client
 118    *
 119    * @param guiWindow
 120    *          - where the initialisation delay message should be shown
 121    * @return the singleton instance of the sequence fetcher client
 122    */
 123   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
 124           final IProgressIndicator guiWindow)
 125   {
 126     if (_initingFetcher && initingThread != null && initingThread.isAlive())
 127     {
 128       if (guiWindow != null)
 129       {
 130         guiWindow
 131                 .setProgressBar(
 132                         MessageManager
 133                                 .getString("status.waiting_sequence_database_fetchers_init"),
 134                         Thread.currentThread().hashCode());
 135       }
 136       // initting happening on another thread - so wait around to see if it
 137       // finishes.
 138       while (_initingFetcher && initingThread != null
 139               && initingThread.isAlive())
 140       {
 141         try
 142         {
 143           Thread.sleep(10);
 144         } catch (Exception e)
 145         {
 146         }
 147         ;
 148       }
 149       if (guiWindow != null)
 150       {
 151         guiWindow
 152                 .setProgressBar(
 153                         MessageManager
 154                                 .getString("status.waiting_sequence_database_fetchers_init"),
 155                         Thread.currentThread().hashCode());
 156       }
 157     }
 158     if (sfetch == null
 159             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
 160             || lastDasSourceRegistry != (jalview.bin.Cache
 161                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
 162                     .getDasSourceRegistry().getLocalSourceString())
 163                     .hashCode())
 164     {
 165       _initingFetcher = true;
 166       initingThread = Thread.currentThread();
 167       /**
 168        * give a visual indication that sequence fetcher construction is occuring
 169        */
 170       if (guiWindow != null)
 171       {
 172         guiWindow.setProgressBar(MessageManager
 173                 .getString("status.init_sequence_database_fetchers"),
 174                 Thread.currentThread().hashCode());
 175       }
 176       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
 177       dasRegistry.refreshSources();
 178
 179       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 180       if (guiWindow != null)
 181       {
 182         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 183       }
 184       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 185               .getLocalSourceString()).hashCode();
 186       sfetch = sf;
 187       _initingFetcher = false;
 188       initingThread = null;
 189     }
 190     return sfetch;
 191   }
 192
 193   private IProgressIndicator progressIndicator;
 194
 195   public SequenceFetcher(IProgressIndicator guiIndic)
 196   {
 197     this.progressIndicator = guiIndic;
 198     final SequenceFetcher us = this;
 199     // launch initialiser thread
 200     Thread sf = new Thread(new Runnable()
 201     {
 202
 203       @Override
 204       public void run()
 205       {
 206         if (getSequenceFetcherSingleton(progressIndicator) != null)
 207         {
 208           us.initGui(progressIndicator);
 209         }
 210         else
 211         {
 212           javax.swing.SwingUtilities.invokeLater(new Runnable()
 213           {
 214             @Override
 215             public void run()
 216             {
 217               JOptionPane
 218                       .showInternalMessageDialog(
 219                               Desktop.desktop,
 220                               MessageManager
 221                                       .getString("warn.couldnt_create_sequence_fetcher_client"),
 222                               MessageManager
 223                                       .getString("label.couldnt_create_sequence_fetcher"),
 224                               JOptionPane.ERROR_MESSAGE);
 225             }
 226           });
 227
 228           // raise warning dialog
 229         }
 230       }
 231     });
 232     sf.start();
 233   }
 234
 235   private class DatabaseAuthority extends DefaultMutableTreeNode
 236   {
 237
 238   };
 239
 240   private class DatabaseSource extends DefaultMutableTreeNode
 241   {
 242
 243   };
 244
 245   /**
 246    * called by thread spawned by constructor
 247    *
 248    * @param guiWindow
 249    */
 250   private void initGui(IProgressIndicator guiWindow)
 251   {
 252     this.guiWindow = guiWindow;
 253     if (guiWindow instanceof AlignFrame)
 254     {
 255       alignFrame = (AlignFrame) guiWindow;
 256     }
 257     database = new JDatabaseTree(sfetch);
 258     try
 259     {
 260       jbInit();
 261     } catch (Exception ex)
 262     {
 263       ex.printStackTrace();
 264     }
 265
 266     frame = new JInternalFrame();
 267     frame.setContentPane(this);
 268     if (new jalview.util.Platform().isAMac())
 269     {
 270       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 271     }
 272     else
 273     {
 274       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 275     }
 276   }
 277
 278   private String getFrameTitle()
 279   {
 280     return ((alignFrame == null) ? MessageManager
 281             .getString("label.new_sequence_fetcher") : MessageManager
 282             .getString("label.additional_sequence_fetcher"));
 283   }
 284
 285   private void jbInit() throws Exception
 286   {
 287     this.setLayout(borderLayout2);
 288
 289     database.setFont(JvSwingUtils.getLabelFont());
 290     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 291     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 292     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 293     jLabel1.setText(MessageManager
 294             .getString("label.separate_multiple_accession_ids"));
 295
 296     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 297     replacePunctuation
 298             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 299     replacePunctuation.setText(MessageManager
 300             .getString("label.replace_commas_semicolons"));
 301     ok.setText(MessageManager.getString("action.ok"));
 302     ok.addActionListener(new ActionListener()
 303     {
 304       @Override
 305       public void actionPerformed(ActionEvent e)
 306       {
 307         ok_actionPerformed();
 308       }
 309     });
 310     clear.setText(MessageManager.getString("action.clear"));
 311     clear.addActionListener(new ActionListener()
 312     {
 313       @Override
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         clear_actionPerformed();
 317       }
 318     });
 319
 320     example.setText(MessageManager.getString("label.example"));
 321     example.addActionListener(new ActionListener()
 322     {
 323       @Override
 324       public void actionPerformed(ActionEvent e)
 325       {
 326         example_actionPerformed();
 327       }
 328     });
 329     close.setText(MessageManager.getString("action.close"));
 330     close.addActionListener(new ActionListener()
 331     {
 332       @Override
 333       public void actionPerformed(ActionEvent e)
 334       {
 335         close_actionPerformed(e);
 336       }
 337     });
 338     textArea.setFont(JvSwingUtils.getLabelFont());
 339     textArea.setLineWrap(true);
 340     textArea.addKeyListener(new KeyAdapter()
 341     {
 342       @Override
 343       public void keyPressed(KeyEvent e)
 344       {
 345         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 346         {
 347           ok_actionPerformed();
 348         }
 349       }
 350     });
 351     jPanel3.setLayout(borderLayout1);
 352     borderLayout1.setVgap(5);
 353     jPanel1.add(ok);
 354     jPanel1.add(example);
 355     jPanel1.add(clear);
 356     jPanel1.add(close);
 357     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 358     jPanel2.setLayout(borderLayout3);
 359     databaseButt = database.getDatabaseSelectorButton();
 360     databaseButt.setFont(JvSwingUtils.getLabelFont());
 361     database.addActionListener(new ActionListener()
 362     {
 363       @Override
 364       public void actionPerformed(ActionEvent e)
 365       {
 366         debounceTrap++;
 367         String currentSelection = database.getSelectedItem();
 368         if (!currentSelection.equalsIgnoreCase("pdb"))
 369         {
 370           otherSourceAction();
 371         }
 372         if (currentSelection.equalsIgnoreCase("pdb")
 373                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
 374         {
 375           pdbSourceAction();
 376         }
 377         database.action = -1;
 378       }
 379     });
 380
 381     dbeg.setText("");
 382     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 383     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 384     JPanel jPanel2a = new JPanel(new BorderLayout());
 385     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 386     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 387     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 388     // jPanel2.setPreferredSize(new Dimension())
 389     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 390     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 391     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 392     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 393     jScrollPane1.getViewport().add(textArea);
 394
 395   }
 396
 397   private void pdbSourceAction()
 398   {
 399     databaseButt.setText(database.getSelectedItem());
 400     new PDBSearchPanel(this);
 401     frame.dispose();
 402   }
 403
 404   private void otherSourceAction()
 405   {
 406     try
 407     {
 408       databaseButt.setText(database.getSelectedItem()
 409               + (database.getSelectedSources().size() > 1 ? " (and "
 410                       + database.getSelectedSources().size() + " others)"
 411                       : ""));
 412       String eq = database.getExampleQueries();
 413       dbeg.setText(MessageManager.formatMessage(
 414               "label.example_query_param", new String[] { eq }));
 415       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 416       for (DbSourceProxy dbs : database.getSelectedSources())
 417       {
 418         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 419         {
 420           enablePunct = false;
 421           break;
 422         }
 423       }
 424       replacePunctuation.setEnabled(enablePunct);
 425
 426     } catch (Exception ex)
 427     {
 428       dbeg.setText("");
 429       replacePunctuation.setEnabled(true);
 430     }
 431     jPanel2.repaint();
 432   }
 433
 434   protected void example_actionPerformed()
 435   {
 436     DbSourceProxy db = null;
 437     try
 438     {
 439       textArea.setText(database.getExampleQueries());
 440     } catch (Exception ex)
 441     {
 442     }
 443     jPanel3.repaint();
 444   }
 445
 446   protected void clear_actionPerformed()
 447   {
 448     textArea.setText("");
 449     jPanel3.repaint();
 450   }
 451
 452   public void close_actionPerformed(ActionEvent e)
 453   {
 454     try
 455     {
 456       frame.setClosed(true);
 457     } catch (Exception ex)
 458     {
 459     }
 460   }
 461
 462   public void ok_actionPerformed()
 463   {
 464     databaseButt.setEnabled(false);
 465     example.setEnabled(false);
 466     textArea.setEnabled(false);
 467     ok.setEnabled(false);
 468     close.setEnabled(false);
 469
 470     Thread worker = new Thread(this);
 471     worker.start();
 472   }
 473
 474   private void resetDialog()
 475   {
 476     databaseButt.setEnabled(true);
 477     example.setEnabled(true);
 478     textArea.setEnabled(true);
 479     ok.setEnabled(true);
 480     close.setEnabled(true);
 481   }
 482
 483   @Override
 484   public void run()
 485   {
 486     String error = "";
 487     if (!database.hasSelection())
 488     {
 489       error += "Please select the source database\n";
 490     }
 491     // TODO: make this transformation more configurable
 492     com.stevesoft.pat.Regex empty;
 493     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 494     {
 495       empty = new com.stevesoft.pat.Regex(
 496       // replace commas and spaces with a semicolon
 497               "(\\s|[,; ])+", ";");
 498     }
 499     else
 500     {
 501       // just turn spaces and semicolons into single semicolons
 502       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 503     }
 504     textArea.setText(empty.replaceAll(textArea.getText()));
 505     // see if there's anthing to search with
 506     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 507             .getText()))
 508     {
 509       error += "Please enter a (semi-colon separated list of) database id(s)";
 510     }
 511     if (error.length() > 0)
 512     {
 513       showErrorMessage(error);
 514       resetDialog();
 515       return;
 516     }
 517     // TODO: Refactor to GUI independent code and write tests.
 518     // indicate if successive sources should be merged into one alignment.
 519     boolean addToLast = false;
 520     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 521     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 522     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 523             .iterator();
 524     String[] qries;
 525     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 526             .split(";"));
 527     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 528     int nqueries = qries.length;
 529
 530     FeatureSettingsModelI preferredFeatureColours = null;
 531     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 532     {
 533       if (!en.hasNext() && nextfetch.size() > 0)
 534       {
 535         en = nextfetch.iterator();
 536         nqueries = nextfetch.size();
 537         // save the remaining queries in the original array
 538         qries = nextfetch.toArray(new String[nqueries]);
 539         nextfetch = new ArrayList<String>();
 540       }
 541
 542       DbSourceProxy proxy = proxies.next();
 543       boolean isAliSource = false;
 544       try
 545       {
 546         // update status
 547         guiWindow
 548                 .setProgressBar(MessageManager.formatMessage(
 549                         "status.fetching_sequence_queries_from",
 550                         new String[] {
 551                             Integer.valueOf(nqueries).toString(),
 552                             proxy.getDbName() }), Thread.currentThread()
 553                         .hashCode());
 554         isAliSource = proxy.isAlignmentSource();
 555         if (proxy.getAccessionSeparator() == null)
 556         {
 557           while (en.hasNext())
 558           {
 559             String item = en.next();
 560             try
 561             {
 562               if (aresult != null)
 563               {
 564                 try
 565                 {
 566                   // give the server a chance to breathe
 567                   Thread.sleep(5);
 568                 } catch (Exception e)
 569                 {
 570                   //
 571                 }
 572
 573               }
 574
 575               AlignmentI indres = null;
 576               try
 577               {
 578                 indres = proxy.getSequenceRecords(item);
 579               } catch (OutOfMemoryError oome)
 580               {
 581                 new OOMWarning("fetching " + item + " from "
 582                         + proxy.getDbName(), oome, this);
 583               }
 584               if (indres != null)
 585               {
 586                 aresultq.add(item);
 587                 aresult.add(indres);
 588               }
 589               else
 590               {
 591                 nextfetch.add(item);
 592               }
 593             } catch (Exception e)
 594             {
 595               jalview.bin.Cache.log.info("Error retrieving " + item
 596                       + " from " + proxy.getDbName(), e);
 597               nextfetch.add(item);
 598             }
 599           }
 600         }
 601         else
 602         {
 603           StringBuffer multiacc = new StringBuffer();
 604           ArrayList<String> tosend = new ArrayList<String>();
 605           while (en.hasNext())
 606           {
 607             String nel = en.next();
 608             tosend.add(nel);
 609             multiacc.append(nel);
 610             if (en.hasNext())
 611             {
 612               multiacc.append(proxy.getAccessionSeparator());
 613             }
 614           }
 615           try
 616           {
 617             AlignmentI rslt;
 618             SequenceI[] rs;
 619             List<String> nores = new ArrayList<String>();
 620             rslt = proxy.getSequenceRecords(multiacc.toString());
 621             if (rslt == null || rslt.getHeight() == 0)
 622             {
 623               // no results - pass on all queries to next source
 624               nextfetch.addAll(tosend);
 625             }
 626             else
 627             {
 628               aresultq.add(multiacc.toString());
 629               aresult.add(rslt);
 630
 631               rs = rslt.getSequencesArray();
 632               // search for each query in the dbrefs associated with each
 633               // sequence
 634               // returned.
 635               // ones we do not find will be used to query next source (if any)
 636               for (String q : tosend)
 637               {
 638                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 639                 dbr.setSource(proxy.getDbSource());
 640                 dbr.setVersion(null);
 641                 String accId = proxy.getAccessionIdFromQuery(q);
 642                 dbr.setAccessionId(accId);
 643                 boolean rfound = false;
 644                 for (int r = 0; r < rs.length; r++)
 645                 {
 646                   if (rs[r] != null)
 647                   {
 648                     found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
 649                     if (found != null && found.length > 0)
 650                     {
 651                       rfound = true;
 652                       rs[r] = null;
 653                     }
 654                   }
 655                 }
 656                 if (!rfound)
 657                 {
 658                   nextfetch.add(q);
 659                 }
 660               }
 661             }
 662           } catch (OutOfMemoryError oome)
 663           {
 664             new OOMWarning("fetching " + multiacc + " from "
 665                     + database.getSelectedItem(), oome, this);
 666           }
 667         }
 668
 669       } catch (Exception e)
 670       {
 671         showErrorMessage("Error retrieving " + textArea.getText()
 672                 + " from " + database.getSelectedItem());
 673         // error
 674         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 675         System.err.println("Retrieval failed for source ='"
 676                 + database.getSelectedItem() + "' and query\n'"
 677                 + textArea.getText() + "'\n");
 678         e.printStackTrace();
 679       } catch (OutOfMemoryError e)
 680       {
 681         // resets dialog box - so we don't use OOMwarning here.
 682         showErrorMessage("Out of Memory when retrieving "
 683                 + textArea.getText()
 684                 + " from "
 685                 + database.getSelectedItem()
 686                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 687         e.printStackTrace();
 688       } catch (Error e)
 689       {
 690         showErrorMessage("Serious Error retrieving " + textArea.getText()
 691                 + " from " + database.getSelectedItem());
 692         e.printStackTrace();
 693       }
 694       // Stack results ready for opening in alignment windows
 695       if (aresult != null && aresult.size() > 0)
 696       {
 697         FeatureSettingsModelI proxyColourScheme = proxy
 698                 .getFeatureColourScheme();
 699         if (proxyColourScheme != null)
 700         {
 701           preferredFeatureColours = proxyColourScheme;
 702         }
 703
 704         AlignmentI ar = null;
 705         if (isAliSource)
 706         {
 707           addToLast = false;
 708           // new window for each result
 709           while (aresult.size() > 0)
 710           {
 711             presult.add(aresult.remove(0));
 712             presultTitle.add(aresultq.remove(0) + " "
 713                     + getDefaultRetrievalTitle());
 714           }
 715         }
 716         else
 717         {
 718           String titl = null;
 719           if (addToLast && presult.size() > 0)
 720           {
 721             ar = presult.remove(presult.size() - 1);
 722             titl = presultTitle.remove(presultTitle.size() - 1);
 723           }
 724           // concatenate all results in one window
 725           while (aresult.size() > 0)
 726           {
 727             if (ar == null)
 728             {
 729               ar = aresult.remove(0);
 730             }
 731             else
 732             {
 733               ar.append(aresult.remove(0));
 734             }
 735             ;
 736           }
 737           addToLast = true;
 738           presult.add(ar);
 739           presultTitle.add(titl);
 740         }
 741       }
 742       guiWindow.setProgressBar(MessageManager
 743               .getString("status.finshed_querying"), Thread.currentThread()
 744               .hashCode());
 745     }
 746     guiWindow.setProgressBar(
 747             (presult.size() > 0) ? MessageManager
 748                     .getString("status.parsing_results") : MessageManager
 749                     .getString("status.processing"), Thread.currentThread()
 750                     .hashCode());
 751     // process results
 752     while (presult.size() > 0)
 753     {
 754       parseResult(presult.remove(0), presultTitle.remove(0), null,
 755               preferredFeatureColours);
 756     }
 757     // only remove visual delay after we finished parsing.
 758     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 759     if (nextfetch.size() > 0)
 760     {
 761       StringBuffer sb = new StringBuffer();
 762       sb.append("Didn't retrieve the following "
 763               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 764                       + " queries") + ": \n");
 765       int l = sb.length(), lr = 0;
 766       for (String s : nextfetch)
 767       {
 768         if (l != sb.length())
 769         {
 770           sb.append("; ");
 771         }
 772         if (lr - sb.length() > 40)
 773         {
 774           sb.append("\n");
 775         }
 776         sb.append(s);
 777       }
 778       showErrorMessage(sb.toString());
 779     }
 780     resetDialog();
 781   }
 782
 783   /**
 784    *
 785    * @return a standard title for any results retrieved using the currently
 786    *         selected source and settings
 787    */
 788   public String getDefaultRetrievalTitle()
 789   {
 790     return "Retrieved from " + database.getSelectedItem();
 791   }
 792
 793   AlignmentI parseResult(AlignmentI al, String title,
 794           String currentFileFormat,
 795           FeatureSettingsModelI preferredFeatureColours)
 796   {
 797
 798     if (al != null && al.getHeight() > 0)
 799     {
 800       if (title == null)
 801       {
 802         title = getDefaultRetrievalTitle();
 803       }
 804       if (alignFrame == null)
 805       {
 806         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 807                 AlignFrame.DEFAULT_HEIGHT);
 808         if (currentFileFormat != null)
 809         {
 810           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 811           // FORMAT FOR
 812           // NON-FormatAdapter Sourced
 813           // Alignments?
 814         }
 815
 816         SequenceFeature[] sfs = null;
 817         List<SequenceI> alsqs;
 818         synchronized (alsqs = al.getSequences())
 819         {
 820           for (SequenceI sq : alsqs)
 821           {
 822             if ((sfs = sq.getSequenceFeatures()) != null)
 823             {
 824               if (sfs.length > 0)
 825               {
 826                 af.setShowSeqFeatures(true);
 827                 break;
 828               }
 829             }
 830
 831           }
 832         }
 833
 834         if (preferredFeatureColours != null)
 835         {
 836           af.viewport.applyFeaturesStyle(preferredFeatureColours);
 837         }
 838         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 839                 AlignFrame.DEFAULT_HEIGHT);
 840
 841         af.statusBar.setText(MessageManager
 842                 .getString("label.successfully_pasted_alignment_file"));
 843
 844         try
 845         {
 846           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 847                   false));
 848         } catch (Exception ex)
 849         {
 850         }
 851       }
 852       else
 853       {
 854         alignFrame.viewport.addAlignment(al, title);
 855       }
 856     }
 857     return al;
 858   }
 859
 860   void showErrorMessage(final String error)
 861   {
 862     resetDialog();
 863     javax.swing.SwingUtilities.invokeLater(new Runnable()
 864     {
 865       @Override
 866       public void run()
 867       {
 868         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 869                 MessageManager.getString("label.error_retrieving_data"),
 870                 JOptionPane.WARNING_MESSAGE);
 871       }
 872     });
 873   }
 874
 875   public IProgressIndicator getProgressIndicator()
 876   {
 877     return progressIndicator;
 878   }
 879
 880   public void setProgressIndicator(IProgressIndicator progressIndicator)
 881   {
 882     this.progressIndicator = progressIndicator;
 883   }
 884 }