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.bin.Cache;
  25 import jalview.datamodel.AlignmentI;
  26 import jalview.datamodel.DBRefEntry;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.fts.service.pdb.PDBFTSPanel;
  30 import jalview.io.gff.SequenceOntologyI;
  31 import jalview.util.DBRefUtils;
  32 import jalview.util.MessageManager;
  33 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  34 import jalview.ws.seqfetcher.DbSourceProxy;
  35
  36 import java.awt.BorderLayout;
  37 import java.awt.Font;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.KeyAdapter;
  41 import java.awt.event.KeyEvent;
  42 import java.util.ArrayList;
  43 import java.util.Arrays;
  44 import java.util.Iterator;
  45 import java.util.List;
  46
  47 import javax.swing.JButton;
  48 import javax.swing.JCheckBox;
  49 import javax.swing.JInternalFrame;
  50 import javax.swing.JLabel;
  51 import javax.swing.JOptionPane;
  52 import javax.swing.JPanel;
  53 import javax.swing.JScrollPane;
  54 import javax.swing.JTextArea;
  55 import javax.swing.SwingConstants;
  56 import javax.swing.tree.DefaultMutableTreeNode;
  57
  58 public class SequenceFetcher extends JPanel implements Runnable
  59 {
  60   JLabel dbeg = new JLabel();
  61
  62   JDatabaseTree database;
  63
  64   JButton databaseButt;
  65
  66   JLabel jLabel1 = new JLabel();
  67
  68   JCheckBox replacePunctuation = new JCheckBox();
  69
  70   JButton ok = new JButton();
  71
  72   JButton clear = new JButton();
  73
  74   JButton example = new JButton();
  75
  76   JButton close = new JButton();
  77
  78   JPanel jPanel1 = new JPanel();
  79
  80   JTextArea textArea = new JTextArea();
  81
  82   JScrollPane jScrollPane1 = new JScrollPane();
  83
  84   JPanel jPanel2 = new JPanel();
  85
  86   JPanel jPanel3 = new JPanel();
  87
  88   JPanel jPanel4 = new JPanel();
  89
  90   BorderLayout borderLayout1 = new BorderLayout();
  91
  92   BorderLayout borderLayout2 = new BorderLayout();
  93
  94   BorderLayout borderLayout3 = new BorderLayout();
  95
  96   JInternalFrame frame;
  97
  98   IProgressIndicator guiWindow;
  99
 100   AlignFrame alignFrame;
 101
 102   StringBuffer result;
 103
 104   final String noDbSelected = "-- Select Database --";
 105
 106   private static jalview.ws.SequenceFetcher sfetch = null;
 107
 108   private static long lastDasSourceRegistry = -3;
 109
 110   private static DasSourceRegistryI dasRegistry = null;
 111
 112   private static boolean _initingFetcher = false;
 113
 114   private static Thread initingThread = null;
 115
 116   int debounceTrap = 0;
 117
 118   public JTextArea getTextArea()
 119   {
 120     return textArea;
 121   }
 122
 123   /**
 124    * Blocking method that initialises and returns the shared instance of the
 125    * SequenceFetcher client
 126    *
 127    * @param guiWindow
 128    *          - where the initialisation delay message should be shown
 129    * @return the singleton instance of the sequence fetcher client
 130    */
 131   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
 132           final IProgressIndicator guiWindow)
 133   {
 134     if (_initingFetcher && initingThread != null && initingThread.isAlive())
 135     {
 136       if (guiWindow != null)
 137       {
 138         guiWindow
 139                 .setProgressBar(
 140                         MessageManager
 141                                 .getString("status.waiting_sequence_database_fetchers_init"),
 142                         Thread.currentThread().hashCode());
 143       }
 144       // initting happening on another thread - so wait around to see if it
 145       // finishes.
 146       while (_initingFetcher && initingThread != null
 147               && initingThread.isAlive())
 148       {
 149         try
 150         {
 151           Thread.sleep(10);
 152         } catch (Exception e)
 153         {
 154         }
 155         ;
 156       }
 157       if (guiWindow != null)
 158       {
 159         guiWindow
 160                 .setProgressBar(
 161                         MessageManager
 162                                 .getString("status.waiting_sequence_database_fetchers_init"),
 163                         Thread.currentThread().hashCode());
 164       }
 165     }
 166     if (sfetch == null
 167             || dasRegistry != Cache.getDasSourceRegistry()
 168             || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
 169                     .getDasRegistryURL() + Cache
 170                     .getDasSourceRegistry().getLocalSourceString())
 171                     .hashCode())
 172     {
 173       _initingFetcher = true;
 174       initingThread = Thread.currentThread();
 175       /**
 176        * give a visual indication that sequence fetcher construction is occuring
 177        */
 178       if (guiWindow != null)
 179       {
 180         guiWindow.setProgressBar(MessageManager
 181                 .getString("status.init_sequence_database_fetchers"),
 182                 Thread.currentThread().hashCode());
 183       }
 184       dasRegistry = Cache.getDasSourceRegistry();
 185       dasRegistry.refreshSources();
 186
 187       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 188       if (guiWindow != null)
 189       {
 190         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 191       }
 192       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 193               .getLocalSourceString()).hashCode();
 194       sfetch = sf;
 195       _initingFetcher = false;
 196       initingThread = null;
 197     }
 198     return sfetch;
 199   }
 200
 201   private IProgressIndicator progressIndicator;
 202
 203   public SequenceFetcher(IProgressIndicator guiIndic)
 204   {
 205     this.progressIndicator = guiIndic;
 206     final SequenceFetcher us = this;
 207     // launch initialiser thread
 208     Thread sf = new Thread(new Runnable()
 209     {
 210
 211       @Override
 212       public void run()
 213       {
 214         if (getSequenceFetcherSingleton(progressIndicator) != null)
 215         {
 216           us.initGui(progressIndicator);
 217         }
 218         else
 219         {
 220           javax.swing.SwingUtilities.invokeLater(new Runnable()
 221           {
 222             @Override
 223             public void run()
 224             {
 225               JOptionPane
 226                       .showInternalMessageDialog(
 227                               Desktop.desktop,
 228                               MessageManager
 229                                       .getString("warn.couldnt_create_sequence_fetcher_client"),
 230                               MessageManager
 231                                       .getString("label.couldnt_create_sequence_fetcher"),
 232                               JOptionPane.ERROR_MESSAGE);
 233             }
 234           });
 235
 236           // raise warning dialog
 237         }
 238       }
 239     });
 240     sf.start();
 241   }
 242
 243   private class DatabaseAuthority extends DefaultMutableTreeNode
 244   {
 245
 246   };
 247
 248   private class DatabaseSource extends DefaultMutableTreeNode
 249   {
 250
 251   };
 252
 253   /**
 254    * called by thread spawned by constructor
 255    *
 256    * @param guiWindow
 257    */
 258   private void initGui(IProgressIndicator guiWindow)
 259   {
 260     this.guiWindow = guiWindow;
 261     if (guiWindow instanceof AlignFrame)
 262     {
 263       alignFrame = (AlignFrame) guiWindow;
 264     }
 265     database = new JDatabaseTree(sfetch);
 266     try
 267     {
 268       jbInit();
 269     } catch (Exception ex)
 270     {
 271       ex.printStackTrace();
 272     }
 273
 274     frame = new JInternalFrame();
 275     frame.setContentPane(this);
 276     if (new jalview.util.Platform().isAMac())
 277     {
 278       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 279     }
 280     else
 281     {
 282       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 283     }
 284   }
 285
 286   private String getFrameTitle()
 287   {
 288     return ((alignFrame == null) ? MessageManager
 289             .getString("label.new_sequence_fetcher") : MessageManager
 290             .getString("label.additional_sequence_fetcher"));
 291   }
 292
 293   private void jbInit() throws Exception
 294   {
 295     this.setLayout(borderLayout2);
 296
 297     database.setFont(JvSwingUtils.getLabelFont());
 298     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 299     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 300     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 301     jLabel1.setText(MessageManager
 302             .getString("label.separate_multiple_accession_ids"));
 303
 304     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 305     replacePunctuation
 306             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 307     replacePunctuation.setText(MessageManager
 308             .getString("label.replace_commas_semicolons"));
 309     ok.setText(MessageManager.getString("action.ok"));
 310     ok.addActionListener(new ActionListener()
 311     {
 312       @Override
 313       public void actionPerformed(ActionEvent e)
 314       {
 315         ok_actionPerformed();
 316       }
 317     });
 318     clear.setText(MessageManager.getString("action.clear"));
 319     clear.addActionListener(new ActionListener()
 320     {
 321       @Override
 322       public void actionPerformed(ActionEvent e)
 323       {
 324         clear_actionPerformed();
 325       }
 326     });
 327
 328     example.setText(MessageManager.getString("label.example"));
 329     example.addActionListener(new ActionListener()
 330     {
 331       @Override
 332       public void actionPerformed(ActionEvent e)
 333       {
 334         example_actionPerformed();
 335       }
 336     });
 337     close.setText(MessageManager.getString("action.close"));
 338     close.addActionListener(new ActionListener()
 339     {
 340       @Override
 341       public void actionPerformed(ActionEvent e)
 342       {
 343         close_actionPerformed(e);
 344       }
 345     });
 346     textArea.setFont(JvSwingUtils.getLabelFont());
 347     textArea.setLineWrap(true);
 348     textArea.addKeyListener(new KeyAdapter()
 349     {
 350       @Override
 351       public void keyPressed(KeyEvent e)
 352       {
 353         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 354         {
 355           ok_actionPerformed();
 356         }
 357       }
 358     });
 359     jPanel3.setLayout(borderLayout1);
 360     borderLayout1.setVgap(5);
 361     jPanel1.add(ok);
 362     jPanel1.add(example);
 363     jPanel1.add(clear);
 364     jPanel1.add(close);
 365     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 366     jPanel2.setLayout(borderLayout3);
 367     databaseButt = database.getDatabaseSelectorButton();
 368     databaseButt.setFont(JvSwingUtils.getLabelFont());
 369     database.addActionListener(new ActionListener()
 370     {
 371       @Override
 372       public void actionPerformed(ActionEvent e)
 373       {
 374         debounceTrap++;
 375         String currentSelection = database.getSelectedItem();
 376         if (!currentSelection.equalsIgnoreCase("pdb"))
 377         {
 378           otherSourceAction();
 379         }
 380         if (currentSelection.equalsIgnoreCase("pdb")
 381                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
 382         {
 383           pdbSourceAction();
 384         }
 385         database.action = -1;
 386       }
 387     });
 388
 389     dbeg.setText("");
 390     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 391     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 392     JPanel jPanel2a = new JPanel(new BorderLayout());
 393     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 394     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 395     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 396     // jPanel2.setPreferredSize(new Dimension())
 397     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 398     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 399     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 400     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 401     jScrollPane1.getViewport().add(textArea);
 402
 403   }
 404
 405   private void pdbSourceAction()
 406   {
 407     databaseButt.setText(database.getSelectedItem());
 408     new PDBFTSPanel(this);
 409     frame.dispose();
 410   }
 411
 412   private void otherSourceAction()
 413   {
 414     try
 415     {
 416       databaseButt.setText(database.getSelectedItem()
 417               + (database.getSelectedSources().size() > 1 ? " (and "
 418                       + database.getSelectedSources().size() + " others)"
 419                       : ""));
 420       String eq = database.getExampleQueries();
 421       dbeg.setText(MessageManager.formatMessage(
 422               "label.example_query_param", new String[] { eq }));
 423       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 424       for (DbSourceProxy dbs : database.getSelectedSources())
 425       {
 426         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 427         {
 428           enablePunct = false;
 429           break;
 430         }
 431       }
 432       replacePunctuation.setEnabled(enablePunct);
 433
 434     } catch (Exception ex)
 435     {
 436       dbeg.setText("");
 437       replacePunctuation.setEnabled(true);
 438     }
 439     jPanel2.repaint();
 440   }
 441
 442   protected void example_actionPerformed()
 443   {
 444     DbSourceProxy db = null;
 445     try
 446     {
 447       textArea.setText(database.getExampleQueries());
 448     } catch (Exception ex)
 449     {
 450     }
 451     jPanel3.repaint();
 452   }
 453
 454   protected void clear_actionPerformed()
 455   {
 456     textArea.setText("");
 457     jPanel3.repaint();
 458   }
 459
 460   public void close_actionPerformed(ActionEvent e)
 461   {
 462     try
 463     {
 464       frame.setClosed(true);
 465     } catch (Exception ex)
 466     {
 467     }
 468   }
 469
 470   public void ok_actionPerformed()
 471   {
 472     databaseButt.setEnabled(false);
 473     example.setEnabled(false);
 474     textArea.setEnabled(false);
 475     ok.setEnabled(false);
 476     close.setEnabled(false);
 477
 478     Thread worker = new Thread(this);
 479     worker.start();
 480   }
 481
 482   private void resetDialog()
 483   {
 484     databaseButt.setEnabled(true);
 485     example.setEnabled(true);
 486     textArea.setEnabled(true);
 487     ok.setEnabled(true);
 488     close.setEnabled(true);
 489   }
 490
 491   @Override
 492   public void run()
 493   {
 494     String error = "";
 495     if (!database.hasSelection())
 496     {
 497       error += "Please select the source database\n";
 498     }
 499     // TODO: make this transformation more configurable
 500     com.stevesoft.pat.Regex empty;
 501     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 502     {
 503       empty = new com.stevesoft.pat.Regex(
 504       // replace commas and spaces with a semicolon
 505               "(\\s|[,; ])+", ";");
 506     }
 507     else
 508     {
 509       // just turn spaces and semicolons into single semicolons
 510       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 511     }
 512     textArea.setText(empty.replaceAll(textArea.getText()));
 513     // see if there's anthing to search with
 514     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 515             .getText()))
 516     {
 517       error += "Please enter a (semi-colon separated list of) database id(s)";
 518     }
 519     if (error.length() > 0)
 520     {
 521       showErrorMessage(error);
 522       resetDialog();
 523       return;
 524     }
 525     // TODO: Refactor to GUI independent code and write tests.
 526     // indicate if successive sources should be merged into one alignment.
 527     boolean addToLast = false;
 528     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 529     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 530     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 531             .iterator();
 532     String[] qries;
 533     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 534             .split(";"));
 535     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 536     int nqueries = qries.length;
 537
 538     FeatureSettingsModelI preferredFeatureColours = null;
 539     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 540     {
 541       if (!en.hasNext() && nextfetch.size() > 0)
 542       {
 543         en = nextfetch.iterator();
 544         nqueries = nextfetch.size();
 545         // save the remaining queries in the original array
 546         qries = nextfetch.toArray(new String[nqueries]);
 547         nextfetch = new ArrayList<String>();
 548       }
 549
 550       DbSourceProxy proxy = proxies.next();
 551       boolean isAliSource = false;
 552       try
 553       {
 554         // update status
 555         guiWindow
 556                 .setProgressBar(MessageManager.formatMessage(
 557                         "status.fetching_sequence_queries_from",
 558                         new String[] {
 559                             Integer.valueOf(nqueries).toString(),
 560                             proxy.getDbName() }), Thread.currentThread()
 561                         .hashCode());
 562         isAliSource = proxy.isAlignmentSource();
 563         if (proxy.getMaximumQueryCount() == 1)
 564         {
 565           while (en.hasNext())
 566           {
 567             String item = en.next();
 568             try
 569             {
 570               if (aresult != null)
 571               {
 572                 try
 573                 {
 574                   // give the server a chance to breathe
 575                   Thread.sleep(5);
 576                 } catch (Exception e)
 577                 {
 578                   //
 579                 }
 580
 581               }
 582
 583               AlignmentI indres = null;
 584               try
 585               {
 586                 indres = proxy.getSequenceRecords(item);
 587               } catch (OutOfMemoryError oome)
 588               {
 589                 new OOMWarning("fetching " + item + " from "
 590                         + proxy.getDbName(), oome, this);
 591               }
 592               if (indres != null)
 593               {
 594                 aresultq.add(item);
 595                 aresult.add(indres);
 596               }
 597               else
 598               {
 599                 nextfetch.add(item);
 600               }
 601             } catch (Exception e)
 602             {
 603               Cache.log.info(
 604                       "Error retrieving " + item
 605                       + " from " + proxy.getDbName(), e);
 606               nextfetch.add(item);
 607             }
 608           }
 609         }
 610         else
 611         {
 612           StringBuffer multiacc = new StringBuffer();
 613           ArrayList<String> tosend = new ArrayList<String>();
 614           while (en.hasNext())
 615           {
 616             String nel = en.next();
 617             tosend.add(nel);
 618             multiacc.append(nel);
 619             if (en.hasNext())
 620             {
 621               multiacc.append(proxy.getAccessionSeparator());
 622             }
 623           }
 624           try
 625           {
 626             AlignmentI rslt;
 627             SequenceI[] rs;
 628             List<String> nores = new ArrayList<String>();
 629             rslt = proxy.getSequenceRecords(multiacc.toString());
 630             if (rslt == null || rslt.getHeight() == 0)
 631             {
 632               // no results - pass on all queries to next source
 633               nextfetch.addAll(tosend);
 634             }
 635             else
 636             {
 637               aresultq.add(multiacc.toString());
 638               aresult.add(rslt);
 639
 640               rs = rslt.getSequencesArray();
 641               // search for each query in the dbrefs associated with each
 642               // sequence
 643               // returned.
 644               // ones we do not find will be used to query next source (if any)
 645               for (String q : tosend)
 646               {
 647                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 648                 dbr.setSource(proxy.getDbSource());
 649                 dbr.setVersion(null);
 650                 String accId = proxy.getAccessionIdFromQuery(q);
 651                 dbr.setAccessionId(accId);
 652                 boolean rfound = false;
 653                 for (int r = 0; r < rs.length; r++)
 654                 {
 655                   if (rs[r] != null)
 656                   {
 657                     found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
 658                     if (found != null && found.length > 0)
 659                     {
 660                       rfound = true;
 661                       rs[r] = null;
 662                     }
 663                   }
 664                 }
 665                 if (!rfound)
 666                 {
 667                   nextfetch.add(q);
 668                 }
 669               }
 670             }
 671           } catch (OutOfMemoryError oome)
 672           {
 673             new OOMWarning("fetching " + multiacc + " from "
 674                     + database.getSelectedItem(), oome, this);
 675           }
 676         }
 677
 678       } catch (Exception e)
 679       {
 680         showErrorMessage("Error retrieving " + textArea.getText()
 681                 + " from " + database.getSelectedItem());
 682         // error
 683         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 684         System.err.println("Retrieval failed for source ='"
 685                 + database.getSelectedItem() + "' and query\n'"
 686                 + textArea.getText() + "'\n");
 687         e.printStackTrace();
 688       } catch (OutOfMemoryError e)
 689       {
 690         // resets dialog box - so we don't use OOMwarning here.
 691         showErrorMessage("Out of Memory when retrieving "
 692                 + textArea.getText()
 693                 + " from "
 694                 + database.getSelectedItem()
 695                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 696         e.printStackTrace();
 697       } catch (Error e)
 698       {
 699         showErrorMessage("Serious Error retrieving " + textArea.getText()
 700                 + " from " + database.getSelectedItem());
 701         e.printStackTrace();
 702       }
 703       // Stack results ready for opening in alignment windows
 704       if (aresult != null && aresult.size() > 0)
 705       {
 706         FeatureSettingsModelI proxyColourScheme = proxy
 707                 .getFeatureColourScheme();
 708         if (proxyColourScheme != null)
 709         {
 710           preferredFeatureColours = proxyColourScheme;
 711         }
 712
 713         AlignmentI ar = null;
 714         if (isAliSource)
 715         {
 716           addToLast = false;
 717           // new window for each result
 718           while (aresult.size() > 0)
 719           {
 720             presult.add(aresult.remove(0));
 721             presultTitle.add(aresultq.remove(0) + " "
 722                     + getDefaultRetrievalTitle());
 723           }
 724         }
 725         else
 726         {
 727           String titl = null;
 728           if (addToLast && presult.size() > 0)
 729           {
 730             ar = presult.remove(presult.size() - 1);
 731             titl = presultTitle.remove(presultTitle.size() - 1);
 732           }
 733           // concatenate all results in one window
 734           while (aresult.size() > 0)
 735           {
 736             if (ar == null)
 737             {
 738               ar = aresult.remove(0);
 739             }
 740             else
 741             {
 742               ar.append(aresult.remove(0));
 743             }
 744             ;
 745           }
 746           addToLast = true;
 747           presult.add(ar);
 748           presultTitle.add(titl);
 749         }
 750       }
 751       guiWindow.setProgressBar(MessageManager
 752               .getString("status.finshed_querying"), Thread.currentThread()
 753               .hashCode());
 754     }
 755     guiWindow.setProgressBar(
 756             (presult.size() > 0) ? MessageManager
 757                     .getString("status.parsing_results") : MessageManager
 758                     .getString("status.processing"), Thread.currentThread()
 759                     .hashCode());
 760     // process results
 761     while (presult.size() > 0)
 762     {
 763       parseResult(presult.remove(0), presultTitle.remove(0), null,
 764               preferredFeatureColours);
 765     }
 766     // only remove visual delay after we finished parsing.
 767     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 768     if (nextfetch.size() > 0)
 769     {
 770       StringBuffer sb = new StringBuffer();
 771       sb.append("Didn't retrieve the following "
 772               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 773                       + " queries") + ": \n");
 774       int l = sb.length(), lr = 0;
 775       for (String s : nextfetch)
 776       {
 777         if (l != sb.length())
 778         {
 779           sb.append("; ");
 780         }
 781         if (lr - sb.length() > 40)
 782         {
 783           sb.append("\n");
 784         }
 785         sb.append(s);
 786       }
 787       showErrorMessage(sb.toString());
 788     }
 789     resetDialog();
 790   }
 791
 792   /**
 793    *
 794    * @return a standard title for any results retrieved using the currently
 795    *         selected source and settings
 796    */
 797   public String getDefaultRetrievalTitle()
 798   {
 799     return "Retrieved from " + database.getSelectedItem();
 800   }
 801
 802   AlignmentI parseResult(AlignmentI al, String title,
 803           String currentFileFormat,
 804           FeatureSettingsModelI preferredFeatureColours)
 805   {
 806
 807     if (al != null && al.getHeight() > 0)
 808     {
 809       if (title == null)
 810       {
 811         title = getDefaultRetrievalTitle();
 812       }
 813       if (alignFrame == null)
 814       {
 815         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 816                 AlignFrame.DEFAULT_HEIGHT);
 817         if (currentFileFormat != null)
 818         {
 819           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 820           // FORMAT FOR
 821           // NON-FormatAdapter Sourced
 822           // Alignments?
 823         }
 824
 825         SequenceFeature[] sfs = null;
 826         List<SequenceI> alsqs;
 827         synchronized (alsqs = al.getSequences())
 828         {
 829           for (SequenceI sq : alsqs)
 830           {
 831             if ((sfs = sq.getSequenceFeatures()) != null)
 832             {
 833               if (sfs.length > 0)
 834               {
 835                 af.setShowSeqFeatures(true);
 836                 break;
 837               }
 838             }
 839
 840           }
 841         }
 842
 843         if (preferredFeatureColours != null)
 844         {
 845           af.getViewport().applyFeaturesStyle(preferredFeatureColours);
 846         }
 847         if (Cache.getDefault("HIDE_INTRONS", true))
 848         {
 849           hideIntronsIfPresent(af);
 850         }
 851
 852         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 853                 AlignFrame.DEFAULT_HEIGHT);
 854
 855         af.statusBar.setText(MessageManager
 856                 .getString("label.successfully_pasted_alignment_file"));
 857
 858         try
 859         {
 860           af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
 861                   false));
 862         } catch (Exception ex)
 863         {
 864         }
 865       }
 866       else
 867       {
 868         alignFrame.viewport.addAlignment(al, title);
 869       }
 870     }
 871     return al;
 872   }
 873
 874   /**
 875    * Hide columns not containing 'exon' features, provided there are exon
 876    * features on the alignment
 877    *
 878    * @param af
 879    */
 880   public void hideIntronsIfPresent(AlignFrame af)
 881   {
 882     boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
 883             false,
 884             SequenceOntologyI.EXON);
 885     if (hasExons)
 886     {
 887       af.avc.markColumnsContainingFeatures(true, false, true,
 888               SequenceOntologyI.EXON);
 889       af.getViewport().hideSelectedColumns();
 890     }
 891   }
 892
 893   void showErrorMessage(final String error)
 894   {
 895     resetDialog();
 896     javax.swing.SwingUtilities.invokeLater(new Runnable()
 897     {
 898       @Override
 899       public void run()
 900       {
 901         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 902                 MessageManager.getString("label.error_retrieving_data"),
 903                 JOptionPane.WARNING_MESSAGE);
 904       }
 905     });
 906   }
 907
 908   public IProgressIndicator getProgressIndicator()
 909   {
 910     return progressIndicator;
 911   }
 912
 913   public void setProgressIndicator(IProgressIndicator progressIndicator)
 914   {
 915     this.progressIndicator = progressIndicator;
 916   }
 917 }