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