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