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.fts.service.uniprot.UniprotFTSPanel;
  31 import jalview.io.gff.SequenceOntologyI;
  32 import jalview.util.DBRefUtils;
  33 import jalview.util.MessageManager;
  34 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  35 import jalview.ws.seqfetcher.DbSourceProxy;
  36
  37 import java.awt.BorderLayout;
  38 import java.awt.Font;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.KeyAdapter;
  42 import java.awt.event.KeyEvent;
  43 import java.util.ArrayList;
  44 import java.util.Arrays;
  45 import java.util.Iterator;
  46 import java.util.List;
  47
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JInternalFrame;
  51 import javax.swing.JLabel;
  52 import javax.swing.JOptionPane;
  53 import javax.swing.JPanel;
  54 import javax.swing.JScrollPane;
  55 import javax.swing.JTextArea;
  56 import javax.swing.SwingConstants;
  57 import javax.swing.tree.DefaultMutableTreeNode;
  58
  59 public class SequenceFetcher extends JPanel implements Runnable
  60 {
  61   JLabel dbeg = new JLabel();
  62
  63   JDatabaseTree database;
  64
  65   JButton databaseButt;
  66
  67   JLabel jLabel1 = new JLabel();
  68
  69   JCheckBox replacePunctuation = new JCheckBox();
  70
  71   JButton ok = new JButton();
  72
  73   JButton clear = new JButton();
  74
  75   JButton example = new JButton();
  76
  77   JButton close = new JButton();
  78
  79   JPanel jPanel1 = new JPanel();
  80
  81   JTextArea textArea = new JTextArea();
  82
  83   JScrollPane jScrollPane1 = new JScrollPane();
  84
  85   JPanel jPanel2 = new JPanel();
  86
  87   JPanel jPanel3 = new JPanel();
  88
  89   JPanel jPanel4 = new JPanel();
  90
  91   BorderLayout borderLayout1 = new BorderLayout();
  92
  93   BorderLayout borderLayout2 = new BorderLayout();
  94
  95   BorderLayout borderLayout3 = new BorderLayout();
  96
  97   JInternalFrame frame;
  98
  99   IProgressIndicator guiWindow;
 100
 101   AlignFrame alignFrame;
 102
 103   StringBuffer result;
 104
 105   final String noDbSelected = "-- Select Database --";
 106
 107   private static jalview.ws.SequenceFetcher sfetch = null;
 108
 109   private static long lastDasSourceRegistry = -3;
 110
 111   private static DasSourceRegistryI dasRegistry = null;
 112
 113   private static boolean _initingFetcher = false;
 114
 115   private static Thread initingThread = null;
 116
 117   int debounceTrap = 0;
 118
 119   public JTextArea getTextArea()
 120   {
 121     return textArea;
 122   }
 123
 124   /**
 125    * Blocking method that initialises and returns the shared instance of the
 126    * SequenceFetcher client
 127    *
 128    * @param guiWindow
 129    *          - where the initialisation delay message should be shown
 130    * @return the singleton instance of the sequence fetcher client
 131    */
 132   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
 133           final IProgressIndicator guiWindow)
 134   {
 135     if (_initingFetcher && initingThread != null && initingThread.isAlive())
 136     {
 137       if (guiWindow != null)
 138       {
 139         guiWindow
 140                 .setProgressBar(
 141                         MessageManager
 142                                 .getString("status.waiting_sequence_database_fetchers_init"),
 143                         Thread.currentThread().hashCode());
 144       }
 145       // initting happening on another thread - so wait around to see if it
 146       // finishes.
 147       while (_initingFetcher && initingThread != null
 148               && initingThread.isAlive())
 149       {
 150         try
 151         {
 152           Thread.sleep(10);
 153         } catch (Exception e)
 154         {
 155         }
 156         ;
 157       }
 158       if (guiWindow != null)
 159       {
 160         guiWindow
 161                 .setProgressBar(
 162                         MessageManager
 163                                 .getString("status.waiting_sequence_database_fetchers_init"),
 164                         Thread.currentThread().hashCode());
 165       }
 166     }
 167     if (sfetch == null
 168             || dasRegistry != Cache.getDasSourceRegistry()
 169             || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
 170                     .getDasRegistryURL() + Cache
 171                     .getDasSourceRegistry().getLocalSourceString())
 172                     .hashCode())
 173     {
 174       _initingFetcher = true;
 175       initingThread = Thread.currentThread();
 176       /**
 177        * give a visual indication that sequence fetcher construction is occuring
 178        */
 179       if (guiWindow != null)
 180       {
 181         guiWindow.setProgressBar(MessageManager
 182                 .getString("status.init_sequence_database_fetchers"),
 183                 Thread.currentThread().hashCode());
 184       }
 185       dasRegistry = Cache.getDasSourceRegistry();
 186       dasRegistry.refreshSources();
 187
 188       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 189       if (guiWindow != null)
 190       {
 191         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 192       }
 193       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 194               .getLocalSourceString()).hashCode();
 195       sfetch = sf;
 196       _initingFetcher = false;
 197       initingThread = null;
 198     }
 199     return sfetch;
 200   }
 201
 202   private IProgressIndicator progressIndicator;
 203
 204   public SequenceFetcher(IProgressIndicator guiIndic)
 205   {
 206     this.progressIndicator = guiIndic;
 207     final SequenceFetcher us = this;
 208     // launch initialiser thread
 209     Thread sf = new Thread(new Runnable()
 210     {
 211
 212       @Override
 213       public void run()
 214       {
 215         if (getSequenceFetcherSingleton(progressIndicator) != null)
 216         {
 217           us.initGui(progressIndicator);
 218         }
 219         else
 220         {
 221           javax.swing.SwingUtilities.invokeLater(new Runnable()
 222           {
 223             @Override
 224             public void run()
 225             {
 226               JOptionPane
 227                       .showInternalMessageDialog(
 228                               Desktop.desktop,
 229                               MessageManager
 230                                       .getString("warn.couldnt_create_sequence_fetcher_client"),
 231                               MessageManager
 232                                       .getString("label.couldnt_create_sequence_fetcher"),
 233                               JOptionPane.ERROR_MESSAGE);
 234             }
 235           });
 236
 237           // raise warning dialog
 238         }
 239       }
 240     });
 241     sf.start();
 242   }
 243
 244   private class DatabaseAuthority extends DefaultMutableTreeNode
 245   {
 246
 247   };
 248
 249   private class DatabaseSource extends DefaultMutableTreeNode
 250   {
 251
 252   };
 253
 254   /**
 255    * called by thread spawned by constructor
 256    *
 257    * @param guiWindow
 258    */
 259   private void initGui(IProgressIndicator guiWindow)
 260   {
 261     this.guiWindow = guiWindow;
 262     if (guiWindow instanceof AlignFrame)
 263     {
 264       alignFrame = (AlignFrame) guiWindow;
 265     }
 266     database = new JDatabaseTree(sfetch);
 267     try
 268     {
 269       jbInit();
 270     } catch (Exception ex)
 271     {
 272       ex.printStackTrace();
 273     }
 274
 275     frame = new JInternalFrame();
 276     frame.setContentPane(this);
 277     if (new jalview.util.Platform().isAMac())
 278     {
 279       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 280     }
 281     else
 282     {
 283       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 284     }
 285   }
 286
 287   private String getFrameTitle()
 288   {
 289     return ((alignFrame == null) ? MessageManager
 290             .getString("label.new_sequence_fetcher") : MessageManager
 291             .getString("label.additional_sequence_fetcher"));
 292   }
 293
 294   private void jbInit() throws Exception
 295   {
 296     this.setLayout(borderLayout2);
 297
 298     database.setFont(JvSwingUtils.getLabelFont());
 299     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 300     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 301     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 302     jLabel1.setText(MessageManager
 303             .getString("label.separate_multiple_accession_ids"));
 304
 305     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 306     replacePunctuation
 307             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 308     replacePunctuation.setText(MessageManager
 309             .getString("label.replace_commas_semicolons"));
 310     ok.setText(MessageManager.getString("action.ok"));
 311     ok.addActionListener(new ActionListener()
 312     {
 313       @Override
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         ok_actionPerformed();
 317       }
 318     });
 319     clear.setText(MessageManager.getString("action.clear"));
 320     clear.addActionListener(new ActionListener()
 321     {
 322       @Override
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         clear_actionPerformed();
 326       }
 327     });
 328
 329     example.setText(MessageManager.getString("label.example"));
 330     example.addActionListener(new ActionListener()
 331     {
 332       @Override
 333       public void actionPerformed(ActionEvent e)
 334       {
 335         example_actionPerformed();
 336       }
 337     });
 338     close.setText(MessageManager.getString("action.close"));
 339     close.addActionListener(new ActionListener()
 340     {
 341       @Override
 342       public void actionPerformed(ActionEvent e)
 343       {
 344         close_actionPerformed(e);
 345       }
 346     });
 347     textArea.setFont(JvSwingUtils.getLabelFont());
 348     textArea.setLineWrap(true);
 349     textArea.addKeyListener(new KeyAdapter()
 350     {
 351       @Override
 352       public void keyPressed(KeyEvent e)
 353       {
 354         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 355         {
 356           ok_actionPerformed();
 357         }
 358       }
 359     });
 360     jPanel3.setLayout(borderLayout1);
 361     borderLayout1.setVgap(5);
 362     jPanel1.add(ok);
 363     jPanel1.add(example);
 364     jPanel1.add(clear);
 365     jPanel1.add(close);
 366     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 367     jPanel2.setLayout(borderLayout3);
 368     databaseButt = database.getDatabaseSelectorButton();
 369     databaseButt.setFont(JvSwingUtils.getLabelFont());
 370     database.addActionListener(new ActionListener()
 371     {
 372       @Override
 373       public void actionPerformed(ActionEvent e)
 374       {
 375         debounceTrap++;
 376         String currentSelection = database.getSelectedItem();
 377
 378         if (currentSelection.equalsIgnoreCase("pdb")
 379                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
 380         {
 381           pdbSourceAction();
 382         }
 383         // else if (currentSelection.equalsIgnoreCase("uniprot")
 384         // && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) ==
 385         // 0)))
 386         // {
 387         // uniprotSourceAction();
 388         // }
 389         else
 390         {
 391           otherSourceAction();
 392         }
 393         database.action = -1;
 394       }
 395     });
 396
 397     dbeg.setText("");
 398     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 399     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 400     JPanel jPanel2a = new JPanel(new BorderLayout());
 401     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 402     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 403     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 404     // jPanel2.setPreferredSize(new Dimension())
 405     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 406     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 407     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 408     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 409     jScrollPane1.getViewport().add(textArea);
 410
 411   }
 412
 413   private void pdbSourceAction()
 414   {
 415     databaseButt.setText(database.getSelectedItem());
 416     new PDBFTSPanel(this);
 417     frame.dispose();
 418   }
 419
 420   private void uniprotSourceAction()
 421   {
 422     databaseButt.setText(database.getSelectedItem());
 423     new UniprotFTSPanel(this);
 424     frame.dispose();
 425   }
 426   private void otherSourceAction()
 427   {
 428     try
 429     {
 430       databaseButt.setText(database.getSelectedItem()
 431               + (database.getSelectedSources().size() > 1 ? " (and "
 432                       + database.getSelectedSources().size() + " others)"
 433                       : ""));
 434       String eq = database.getExampleQueries();
 435       dbeg.setText(MessageManager.formatMessage(
 436               "label.example_query_param", new String[] { eq }));
 437       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 438       for (DbSourceProxy dbs : database.getSelectedSources())
 439       {
 440         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 441         {
 442           enablePunct = false;
 443           break;
 444         }
 445       }
 446       replacePunctuation.setEnabled(enablePunct);
 447
 448     } catch (Exception ex)
 449     {
 450       dbeg.setText("");
 451       replacePunctuation.setEnabled(true);
 452     }
 453     jPanel2.repaint();
 454   }
 455
 456   protected void example_actionPerformed()
 457   {
 458     DbSourceProxy db = null;
 459     try
 460     {
 461       textArea.setText(database.getExampleQueries());
 462     } catch (Exception ex)
 463     {
 464     }
 465     jPanel3.repaint();
 466   }
 467
 468   protected void clear_actionPerformed()
 469   {
 470     textArea.setText("");
 471     jPanel3.repaint();
 472   }
 473
 474   public void close_actionPerformed(ActionEvent e)
 475   {
 476     try
 477     {
 478       frame.setClosed(true);
 479     } catch (Exception ex)
 480     {
 481     }
 482   }
 483
 484   public void ok_actionPerformed()
 485   {
 486     databaseButt.setEnabled(false);
 487     example.setEnabled(false);
 488     textArea.setEnabled(false);
 489     ok.setEnabled(false);
 490     close.setEnabled(false);
 491
 492     Thread worker = new Thread(this);
 493     worker.start();
 494   }
 495
 496   private void resetDialog()
 497   {
 498     databaseButt.setEnabled(true);
 499     example.setEnabled(true);
 500     textArea.setEnabled(true);
 501     ok.setEnabled(true);
 502     close.setEnabled(true);
 503   }
 504
 505   @Override
 506   public void run()
 507   {
 508     String error = "";
 509     if (!database.hasSelection())
 510     {
 511       error += "Please select the source database\n";
 512     }
 513     // TODO: make this transformation more configurable
 514     com.stevesoft.pat.Regex empty;
 515     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 516     {
 517       empty = new com.stevesoft.pat.Regex(
 518       // replace commas and spaces with a semicolon
 519               "(\\s|[,; ])+", ";");
 520     }
 521     else
 522     {
 523       // just turn spaces and semicolons into single semicolons
 524       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 525     }
 526     textArea.setText(empty.replaceAll(textArea.getText()));
 527     // see if there's anthing to search with
 528     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 529             .getText()))
 530     {
 531       error += "Please enter a (semi-colon separated list of) database id(s)";
 532     }
 533     if (error.length() > 0)
 534     {
 535       showErrorMessage(error);
 536       resetDialog();
 537       return;
 538     }
 539     // TODO: Refactor to GUI independent code and write tests.
 540     // indicate if successive sources should be merged into one alignment.
 541     boolean addToLast = false;
 542     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 543     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 544     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 545             .iterator();
 546     String[] qries;
 547     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 548             .split(";"));
 549     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 550     int nqueries = qries.length;
 551
 552     FeatureSettingsModelI preferredFeatureColours = null;
 553     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 554     {
 555       if (!en.hasNext() && nextfetch.size() > 0)
 556       {
 557         en = nextfetch.iterator();
 558         nqueries = nextfetch.size();
 559         // save the remaining queries in the original array
 560         qries = nextfetch.toArray(new String[nqueries]);
 561         nextfetch = new ArrayList<String>();
 562       }
 563
 564       DbSourceProxy proxy = proxies.next();
 565       boolean isAliSource = false;
 566       try
 567       {
 568         // update status
 569         guiWindow
 570                 .setProgressBar(MessageManager.formatMessage(
 571                         "status.fetching_sequence_queries_from",
 572                         new String[] {
 573                             Integer.valueOf(nqueries).toString(),
 574                             proxy.getDbName() }), Thread.currentThread()
 575                         .hashCode());
 576         isAliSource = proxy.isAlignmentSource();
 577         if (proxy.getMaximumQueryCount() == 1)
 578         {
 579           while (en.hasNext())
 580           {
 581             String item = en.next();
 582             try
 583             {
 584               if (aresult != null)
 585               {
 586                 try
 587                 {
 588                   // give the server a chance to breathe
 589                   Thread.sleep(5);
 590                 } catch (Exception e)
 591                 {
 592                   //
 593                 }
 594
 595               }
 596
 597               AlignmentI indres = null;
 598               try
 599               {
 600                 indres = proxy.getSequenceRecords(item);
 601               } catch (OutOfMemoryError oome)
 602               {
 603                 new OOMWarning("fetching " + item + " from "
 604                         + proxy.getDbName(), oome, this);
 605               }
 606               if (indres != null)
 607               {
 608                 aresultq.add(item);
 609                 aresult.add(indres);
 610               }
 611               else
 612               {
 613                 nextfetch.add(item);
 614               }
 615             } catch (Exception e)
 616             {
 617               Cache.log.info(
 618                       "Error retrieving " + item
 619                       + " from " + proxy.getDbName(), e);
 620               nextfetch.add(item);
 621             }
 622           }
 623         }
 624         else
 625         {
 626           StringBuffer multiacc = new StringBuffer();
 627           ArrayList<String> tosend = new ArrayList<String>();
 628           while (en.hasNext())
 629           {
 630             String nel = en.next();
 631             tosend.add(nel);
 632             multiacc.append(nel);
 633             if (en.hasNext())
 634             {
 635               multiacc.append(proxy.getAccessionSeparator());
 636             }
 637           }
 638           try
 639           {
 640             AlignmentI rslt;
 641             SequenceI[] rs;
 642             List<String> nores = new ArrayList<String>();
 643             rslt = proxy.getSequenceRecords(multiacc.toString());
 644             if (rslt == null || rslt.getHeight() == 0)
 645             {
 646               // no results - pass on all queries to next source
 647               nextfetch.addAll(tosend);
 648             }
 649             else
 650             {
 651               aresultq.add(multiacc.toString());
 652               aresult.add(rslt);
 653
 654               rs = rslt.getSequencesArray();
 655               // search for each query in the dbrefs associated with each
 656               // sequence
 657               // returned.
 658               // ones we do not find will be used to query next source (if any)
 659               for (String q : tosend)
 660               {
 661                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 662                 dbr.setSource(proxy.getDbSource());
 663                 dbr.setVersion(null);
 664                 String accId = proxy.getAccessionIdFromQuery(q);
 665                 dbr.setAccessionId(accId);
 666                 boolean rfound = false;
 667                 for (int r = 0; r < rs.length; r++)
 668                 {
 669                   if (rs[r] != null)
 670                   {
 671                     found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
 672                     if (found != null && found.length > 0)
 673                     {
 674                       rfound = true;
 675                       rs[r] = null;
 676                     }
 677                   }
 678                 }
 679                 if (!rfound)
 680                 {
 681                   nextfetch.add(q);
 682                 }
 683               }
 684             }
 685           } catch (OutOfMemoryError oome)
 686           {
 687             new OOMWarning("fetching " + multiacc + " from "
 688                     + database.getSelectedItem(), oome, this);
 689           }
 690         }
 691
 692       } catch (Exception e)
 693       {
 694         showErrorMessage("Error retrieving " + textArea.getText()
 695                 + " from " + database.getSelectedItem());
 696         // error
 697         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 698         System.err.println("Retrieval failed for source ='"
 699                 + database.getSelectedItem() + "' and query\n'"
 700                 + textArea.getText() + "'\n");
 701         e.printStackTrace();
 702       } catch (OutOfMemoryError e)
 703       {
 704         // resets dialog box - so we don't use OOMwarning here.
 705         showErrorMessage("Out of Memory when retrieving "
 706                 + textArea.getText()
 707                 + " from "
 708                 + database.getSelectedItem()
 709                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 710         e.printStackTrace();
 711       } catch (Error e)
 712       {
 713         showErrorMessage("Serious Error retrieving " + textArea.getText()
 714                 + " from " + database.getSelectedItem());
 715         e.printStackTrace();
 716       }
 717       // Stack results ready for opening in alignment windows
 718       if (aresult != null && aresult.size() > 0)
 719       {
 720         FeatureSettingsModelI proxyColourScheme = proxy
 721                 .getFeatureColourScheme();
 722         if (proxyColourScheme != null)
 723         {
 724           preferredFeatureColours = proxyColourScheme;
 725         }
 726
 727         AlignmentI ar = null;
 728         if (isAliSource)
 729         {
 730           addToLast = false;
 731           // new window for each result
 732           while (aresult.size() > 0)
 733           {
 734             presult.add(aresult.remove(0));
 735             presultTitle.add(aresultq.remove(0) + " "
 736                     + getDefaultRetrievalTitle());
 737           }
 738         }
 739         else
 740         {
 741           String titl = null;
 742           if (addToLast && presult.size() > 0)
 743           {
 744             ar = presult.remove(presult.size() - 1);
 745             titl = presultTitle.remove(presultTitle.size() - 1);
 746           }
 747           // concatenate all results in one window
 748           while (aresult.size() > 0)
 749           {
 750             if (ar == null)
 751             {
 752               ar = aresult.remove(0);
 753             }
 754             else
 755             {
 756               ar.append(aresult.remove(0));
 757             }
 758             ;
 759           }
 760           addToLast = true;
 761           presult.add(ar);
 762           presultTitle.add(titl);
 763         }
 764       }
 765       guiWindow.setProgressBar(MessageManager
 766               .getString("status.finshed_querying"), Thread.currentThread()
 767               .hashCode());
 768     }
 769     guiWindow.setProgressBar(
 770             (presult.size() > 0) ? MessageManager
 771                     .getString("status.parsing_results") : MessageManager
 772                     .getString("status.processing"), Thread.currentThread()
 773                     .hashCode());
 774     // process results
 775     while (presult.size() > 0)
 776     {
 777       parseResult(presult.remove(0), presultTitle.remove(0), null,
 778               preferredFeatureColours);
 779     }
 780     // only remove visual delay after we finished parsing.
 781     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 782     if (nextfetch.size() > 0)
 783     {
 784       StringBuffer sb = new StringBuffer();
 785       sb.append("Didn't retrieve the following "
 786               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 787                       + " queries") + ": \n");
 788       int l = sb.length(), lr = 0;
 789       for (String s : nextfetch)
 790       {
 791         if (l != sb.length())
 792         {
 793           sb.append("; ");
 794         }
 795         if (lr - sb.length() > 40)
 796         {
 797           sb.append("\n");
 798         }
 799         sb.append(s);
 800       }
 801       showErrorMessage(sb.toString());
 802     }
 803     resetDialog();
 804   }
 805
 806   /**
 807    *
 808    * @return a standard title for any results retrieved using the currently
 809    *         selected source and settings
 810    */
 811   public String getDefaultRetrievalTitle()
 812   {
 813     return "Retrieved from " + database.getSelectedItem();
 814   }
 815
 816   AlignmentI parseResult(AlignmentI al, String title,
 817           String currentFileFormat,
 818           FeatureSettingsModelI preferredFeatureColours)
 819   {
 820
 821     if (al != null && al.getHeight() > 0)
 822     {
 823       if (title == null)
 824       {
 825         title = getDefaultRetrievalTitle();
 826       }
 827       if (alignFrame == null)
 828       {
 829         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 830                 AlignFrame.DEFAULT_HEIGHT);
 831         if (currentFileFormat != null)
 832         {
 833           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 834           // FORMAT FOR
 835           // NON-FormatAdapter Sourced
 836           // Alignments?
 837         }
 838
 839         SequenceFeature[] sfs = null;
 840         List<SequenceI> alsqs;
 841         synchronized (alsqs = al.getSequences())
 842         {
 843           for (SequenceI sq : alsqs)
 844           {
 845             if ((sfs = sq.getSequenceFeatures()) != null)
 846             {
 847               if (sfs.length > 0)
 848               {
 849                 af.setShowSeqFeatures(true);
 850                 break;
 851               }
 852             }
 853
 854           }
 855         }
 856
 857         if (preferredFeatureColours != null)
 858         {
 859           af.getViewport().applyFeaturesStyle(preferredFeatureColours);
 860         }
 861         if (Cache.getDefault("HIDE_INTRONS", true))
 862         {
 863           hideIntronsIfPresent(af);
 864         }
 865
 866         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 867                 AlignFrame.DEFAULT_HEIGHT);
 868
 869         af.statusBar.setText(MessageManager
 870                 .getString("label.successfully_pasted_alignment_file"));
 871
 872         try
 873         {
 874           af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
 875                   false));
 876         } catch (Exception ex)
 877         {
 878         }
 879       }
 880       else
 881       {
 882         alignFrame.viewport.addAlignment(al, title);
 883       }
 884     }
 885     return al;
 886   }
 887
 888   /**
 889    * Hide columns not containing 'exon' features, provided there are exon
 890    * features on the alignment
 891    *
 892    * @param af
 893    */
 894   public void hideIntronsIfPresent(AlignFrame af)
 895   {
 896     boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
 897             false,
 898             SequenceOntologyI.EXON);
 899     if (hasExons)
 900     {
 901       af.avc.markColumnsContainingFeatures(true, false, true,
 902               SequenceOntologyI.EXON);
 903       af.getViewport().hideSelectedColumns();
 904     }
 905   }
 906
 907   void showErrorMessage(final String error)
 908   {
 909     resetDialog();
 910     javax.swing.SwingUtilities.invokeLater(new Runnable()
 911     {
 912       @Override
 913       public void run()
 914       {
 915         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 916                 MessageManager.getString("label.error_retrieving_data"),
 917                 JOptionPane.WARNING_MESSAGE);
 918       }
 919     });
 920   }
 921
 922   public IProgressIndicator getProgressIndicator()
 923   {
 924     return progressIndicator;
 925   }
 926
 927   public void setProgressIndicator(IProgressIndicator progressIndicator)
 928   {
 929     this.progressIndicator = progressIndicator;
 930   }
 931 }