src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.Alignment;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.DBRefEntry;
  26 import jalview.datamodel.DBRefSource;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.io.FormatAdapter;
  30 import jalview.io.IdentifyFile;
  31 import jalview.util.DBRefUtils;
  32 import jalview.util.MessageManager;
  33 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  34 import jalview.ws.seqfetcher.DbSourceProxy;
  35
  36 import java.awt.BorderLayout;
  37 import java.awt.Font;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.KeyAdapter;
  41 import java.awt.event.KeyEvent;
  42 import java.util.ArrayList;
  43 import java.util.Arrays;
  44 import java.util.Iterator;
  45 import java.util.List;
  46
  47 import javax.swing.JButton;
  48 import javax.swing.JCheckBox;
  49 import javax.swing.JInternalFrame;
  50 import javax.swing.JLabel;
  51 import javax.swing.JOptionPane;
  52 import javax.swing.JPanel;
  53 import javax.swing.JScrollPane;
  54 import javax.swing.JTextArea;
  55 import javax.swing.SwingConstants;
  56 import javax.swing.tree.DefaultMutableTreeNode;
  57
  58 import com.stevesoft.pat.Regex;
  59
  60 public class SequenceFetcher extends JPanel implements Runnable
  61 {
  62   JLabel dbeg = new JLabel();
  63
  64   JDatabaseTree database;
  65
  66   JButton databaseButt;
  67
  68   JLabel jLabel1 = new JLabel();
  69
  70   JCheckBox replacePunctuation = new JCheckBox();
  71
  72   JButton ok = new JButton();
  73
  74   JButton clear = new JButton();
  75
  76   JButton example = new JButton();
  77
  78   JButton close = new JButton();
  79
  80   JPanel jPanel1 = new JPanel();
  81
  82   JTextArea textArea = new JTextArea();
  83
  84   JScrollPane jScrollPane1 = new JScrollPane();
  85
  86   JPanel jPanel2 = new JPanel();
  87
  88   JPanel jPanel3 = new JPanel();
  89
  90   JPanel jPanel4 = new JPanel();
  91
  92   BorderLayout borderLayout1 = new BorderLayout();
  93
  94   BorderLayout borderLayout2 = new BorderLayout();
  95
  96   BorderLayout borderLayout3 = new BorderLayout();
  97
  98   JInternalFrame frame;
  99
 100   IProgressIndicator guiWindow;
 101
 102   AlignFrame alignFrame;
 103
 104   StringBuffer result;
 105
 106   final String noDbSelected = "-- Select Database --";
 107
 108   private static jalview.ws.SequenceFetcher sfetch = null;
 109
 110   private static long lastDasSourceRegistry = -3;
 111
 112   private static DasSourceRegistryI dasRegistry = null;
 113
 114   private static boolean _initingFetcher = false;
 115
 116   private static Thread initingThread = null;
 117
 118   int x = 0;
 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.setProgressBar(
 135                 MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
 136                 Thread.currentThread().hashCode());
 137       }
 138       // initting happening on another thread - so wait around to see if it
 139       // finishes.
 140       while (_initingFetcher && initingThread != null
 141               && initingThread.isAlive())
 142       {
 143         try
 144         {
 145           Thread.sleep(10);
 146         } catch (Exception e)
 147         {
 148         }
 149         ;
 150       }
 151       if (guiWindow != null)
 152       {
 153         guiWindow.setProgressBar(
 154                         MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
 155                 Thread.currentThread().hashCode());
 156       }
 157     }
 158     if (sfetch == null
 159             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
 160             || lastDasSourceRegistry != (jalview.bin.Cache
 161                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
 162                     .getDasSourceRegistry().getLocalSourceString())
 163                     .hashCode())
 164     {
 165       _initingFetcher = true;
 166       initingThread = Thread.currentThread();
 167       /**
 168        * give a visual indication that sequence fetcher construction is occuring
 169        */
 170       if (guiWindow != null)
 171       {
 172         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
 173                 Thread.currentThread().hashCode());
 174       }
 175       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
 176       dasRegistry.refreshSources();
 177
 178       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 179       if (guiWindow != null)
 180       {
 181         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
 182                 Thread.currentThread().hashCode());
 183       }
 184       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 185               .getLocalSourceString()).hashCode();
 186       sfetch = sf;
 187       _initingFetcher = false;
 188       initingThread = null;
 189     }
 190     return sfetch;
 191   }
 192
 193   public SequenceFetcher(IProgressIndicator guiIndic)
 194   {
 195     final IProgressIndicator guiWindow = guiIndic;
 196     final SequenceFetcher us = this;
 197     // launch initialiser thread
 198     Thread sf = new Thread(new Runnable()
 199     {
 200
 201       @Override
 202       public void run()
 203       {
 204         if (getSequenceFetcherSingleton(guiWindow) != null)
 205         {
 206           us.initGui(guiWindow);
 207         }
 208         else
 209         {
 210           javax.swing.SwingUtilities.invokeLater(new Runnable()
 211           {
 212             @Override
 213             public void run()
 214             {
 215               JOptionPane
 216                       .showInternalMessageDialog(
 217                               Desktop.desktop,
 218                               MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
 219                               MessageManager.getString("label.couldnt_create_sequence_fetcher"),
 220                               JOptionPane.ERROR_MESSAGE);
 221             }
 222           });
 223
 224           // raise warning dialog
 225         }
 226       }
 227     });
 228     sf.start();
 229   }
 230
 231   private class DatabaseAuthority extends DefaultMutableTreeNode
 232   {
 233
 234   };
 235
 236   private class DatabaseSource extends DefaultMutableTreeNode
 237   {
 238
 239   };
 240
 241   /**
 242    * called by thread spawned by constructor
 243    *
 244    * @param guiWindow
 245    */
 246   private void initGui(IProgressIndicator guiWindow)
 247   {
 248     this.guiWindow = guiWindow;
 249     if (guiWindow instanceof AlignFrame)
 250     {
 251       alignFrame = (AlignFrame) guiWindow;
 252     }
 253     database = new JDatabaseTree(sfetch);
 254     try
 255     {
 256       jbInit();
 257     } catch (Exception ex)
 258     {
 259       ex.printStackTrace();
 260     }
 261
 262     frame = new JInternalFrame();
 263     frame.setContentPane(this);
 264     if (new jalview.util.Platform().isAMac())
 265     {
 266       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 267     }
 268     else
 269     {
 270       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 271     }
 272   }
 273
 274   private String getFrameTitle()
 275   {
 276     return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
 277   }
 278
 279   private void jbInit() throws Exception
 280   {
 281     this.setLayout(borderLayout2);
 282
 283     database.setFont(JvSwingUtils.getLabelFont());
 284     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 285     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 286     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 287     jLabel1.setText(MessageManager
 288             .getString("label.separate_multiple_accession_ids"));
 289
 290     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 291     replacePunctuation
 292             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 293     replacePunctuation.setText(MessageManager
 294             .getString("label.replace_commas_semicolons"));
 295     ok.setText(MessageManager.getString("action.ok"));
 296     ok.addActionListener(new ActionListener()
 297     {
 298       @Override
 299       public void actionPerformed(ActionEvent e)
 300       {
 301         ok_actionPerformed();
 302       }
 303     });
 304     clear.setText(MessageManager.getString("action.clear"));
 305     clear.addActionListener(new ActionListener()
 306     {
 307       @Override
 308       public void actionPerformed(ActionEvent e)
 309       {
 310         clear_actionPerformed();
 311       }
 312     });
 313
 314     example.setText(MessageManager.getString("label.example"));
 315     example.addActionListener(new ActionListener()
 316     {
 317       @Override
 318       public void actionPerformed(ActionEvent e)
 319       {
 320         example_actionPerformed();
 321       }
 322     });
 323     close.setText(MessageManager.getString("action.close"));
 324     close.addActionListener(new ActionListener()
 325     {
 326       @Override
 327       public void actionPerformed(ActionEvent e)
 328       {
 329         close_actionPerformed(e);
 330       }
 331     });
 332     textArea.setFont(JvSwingUtils.getLabelFont());
 333     textArea.setLineWrap(true);
 334     textArea.addKeyListener(new KeyAdapter()
 335     {
 336       @Override
 337       public void keyPressed(KeyEvent e)
 338       {
 339         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 340         {
 341           ok_actionPerformed();
 342         }
 343       }
 344     });
 345     jPanel3.setLayout(borderLayout1);
 346     borderLayout1.setVgap(5);
 347     jPanel1.add(ok);
 348     jPanel1.add(example);
 349     jPanel1.add(clear);
 350     jPanel1.add(close);
 351     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 352     jPanel2.setLayout(borderLayout3);
 353     databaseButt = database.getDatabaseSelectorButton();
 354     databaseButt.setFont(JvSwingUtils.getLabelFont());
 355     database.addActionListener(new ActionListener()
 356     {
 357       @Override
 358       public void actionPerformed(ActionEvent e)
 359       {
 360         x++;
 361         String currentSelection = database.getSelectedItem();
 362
 363         if (!currentSelection.equalsIgnoreCase("pdb"))
 364         {
 365             otherSourceAction();
 366         }
 367         if (currentSelection.equalsIgnoreCase("pdb") && ((x % 2) == 0))
 368         {
 369           frame.dispose();
 370           new EBIFetchPanel();
 371         }
 372
 373       }
 374     });
 375     dbeg.setText("");
 376     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 377     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 378     JPanel jPanel2a = new JPanel(new BorderLayout());
 379     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 380     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 381     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 382     // jPanel2.setPreferredSize(new Dimension())
 383     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 384     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 385     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 386     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 387     jScrollPane1.getViewport().add(textArea);
 388
 389   }
 390
 391   private void hideX()
 392   {
 393     this.setVisible(false);
 394   }
 395   private void otherSourceAction()
 396   {
 397     try
 398     {
 399       databaseButt.setText(database.getSelectedItem()
 400               + (database.getSelectedSources().size() > 1 ? " (and "
 401                       + database.getSelectedSources().size() + " others)"
 402                       : ""));
 403       String eq = database.getExampleQueries();
 404       dbeg.setText(MessageManager.formatMessage(
 405               "label.example_query_param", new String[]
 406               { eq }));
 407       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 408       for (DbSourceProxy dbs : database.getSelectedSources())
 409       {
 410         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 411         {
 412           enablePunct = false;
 413           break;
 414         }
 415       }
 416       replacePunctuation.setEnabled(enablePunct);
 417
 418     } catch (Exception ex)
 419     {
 420       dbeg.setText("");
 421       replacePunctuation.setEnabled(true);
 422     }
 423     jPanel2.repaint();
 424   }
 425
 426   protected void example_actionPerformed()
 427   {
 428     DbSourceProxy db = null;
 429     try
 430     {
 431       textArea.setText(database.getExampleQueries());
 432     } catch (Exception ex)
 433     {
 434     }
 435     jPanel3.repaint();
 436   }
 437
 438   protected void clear_actionPerformed()
 439   {
 440     textArea.setText("");
 441     jPanel3.repaint();
 442   }
 443
 444
 445
 446   public void close_actionPerformed(ActionEvent e)
 447   {
 448     try
 449     {
 450       frame.setClosed(true);
 451     } catch (Exception ex)
 452     {
 453     }
 454   }
 455
 456   public void ok_actionPerformed()
 457   {
 458     databaseButt.setEnabled(false);
 459     example.setEnabled(false);
 460     textArea.setEnabled(false);
 461     ok.setEnabled(false);
 462     close.setEnabled(false);
 463
 464     Thread worker = new Thread(this);
 465     worker.start();
 466   }
 467
 468   private void resetDialog()
 469   {
 470     databaseButt.setEnabled(true);
 471     example.setEnabled(true);
 472     textArea.setEnabled(true);
 473     ok.setEnabled(true);
 474     close.setEnabled(true);
 475   }
 476
 477   @Override
 478   public void run()
 479   {
 480     String error = "";
 481     if (!database.hasSelection())
 482     {
 483       error += "Please select the source database\n";
 484     }
 485     // TODO: make this transformation more configurable
 486     com.stevesoft.pat.Regex empty;
 487     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 488     {
 489       empty = new com.stevesoft.pat.Regex(
 490       // replace commas and spaces with a semicolon
 491               "(\\s|[,; ])+", ";");
 492     }
 493     else
 494     {
 495       // just turn spaces and semicolons into single semicolons
 496       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 497     }
 498     textArea.setText(empty.replaceAll(textArea.getText()));
 499     // see if there's anthing to search with
 500     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 501             .getText()))
 502     {
 503       error += "Please enter a (semi-colon separated list of) database id(s)";
 504     }
 505     if (error.length() > 0)
 506     {
 507       showErrorMessage(error);
 508       resetDialog();
 509       return;
 510     }
 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                 if (proxy.getAccessionValidator() != null)
 628                 {
 629                   Regex vgr = proxy.getAccessionValidator();
 630                   vgr.search(q);
 631                   if (vgr.numSubs() > 0)
 632                   {
 633                     dbr.setAccessionId(vgr.stringMatched(1));
 634                   }
 635                   else
 636                   {
 637                     dbr.setAccessionId(vgr.stringMatched());
 638                   }
 639                 }
 640                 else
 641                 {
 642                   dbr.setAccessionId(q);
 643                 }
 644                 boolean rfound = false;
 645                 for (int r = 0; r < rs.length; r++)
 646                 {
 647                   if (rs[r] != null
 648                           && (found = DBRefUtils.searchRefs(
 649                                   rs[r].getDBRef(), dbr)) != null
 650                           && found.length > 0)
 651                   {
 652                     rfound = true;
 653                     rs[r] = null;
 654                     continue;
 655                   }
 656                 }
 657                 if (!rfound)
 658                 {
 659                   nextfetch.add(q);
 660                 }
 661               }
 662             }
 663           } catch (OutOfMemoryError oome)
 664           {
 665             new OOMWarning("fetching " + multiacc + " from "
 666                     + database.getSelectedItem(), oome, this);
 667           }
 668         }
 669
 670       } catch (Exception e)
 671       {
 672         showErrorMessage("Error retrieving " + textArea.getText()
 673                 + " from " + database.getSelectedItem());
 674         // error
 675         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 676         System.err.println("Retrieval failed for source ='"
 677                 + database.getSelectedItem() + "' and query\n'"
 678                 + textArea.getText() + "'\n");
 679         e.printStackTrace();
 680       } catch (OutOfMemoryError e)
 681       {
 682         // resets dialog box - so we don't use OOMwarning here.
 683         showErrorMessage("Out of Memory when retrieving "
 684                 + textArea.getText()
 685                 + " from "
 686                 + database.getSelectedItem()
 687                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 688         e.printStackTrace();
 689       } catch (Error e)
 690       {
 691         showErrorMessage("Serious Error retrieving " + textArea.getText()
 692                 + " from " + database.getSelectedItem());
 693         e.printStackTrace();
 694       }
 695       // Stack results ready for opening in alignment windows
 696       if (aresult != null && aresult.size() > 0)
 697       {
 698         AlignmentI ar = null;
 699         if (isAliSource)
 700         {
 701           addToLast = false;
 702           // new window for each result
 703           while (aresult.size() > 0)
 704           {
 705             presult.add(aresult.remove(0));
 706             presultTitle.add(aresultq.remove(0) + " "
 707                     + getDefaultRetrievalTitle());
 708           }
 709         }
 710         else
 711         {
 712           String titl = null;
 713           if (addToLast && presult.size() > 0)
 714           {
 715             ar = presult.remove(presult.size() - 1);
 716             titl = presultTitle.remove(presultTitle.size() - 1);
 717           }
 718           // concatenate all results in one window
 719           while (aresult.size() > 0)
 720           {
 721             if (ar == null)
 722             {
 723               ar = aresult.remove(0);
 724             }
 725             else
 726             {
 727               ar.append(aresult.remove(0));
 728             }
 729             ;
 730           }
 731           addToLast = true;
 732           presult.add(ar);
 733           presultTitle.add(titl);
 734         }
 735       }
 736       guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
 737               .hashCode());
 738     }
 739     guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
 740             : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
 741     // process results
 742     while (presult.size() > 0)
 743     {
 744       parseResult(presult.remove(0), presultTitle.remove(0), null);
 745     }
 746     // only remove visual delay after we finished parsing.
 747     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 748     if (nextfetch.size() > 0)
 749     {
 750       StringBuffer sb = new StringBuffer();
 751       sb.append("Didn't retrieve the following "
 752               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 753                       + " queries") + ": \n");
 754       int l = sb.length(), lr = 0;
 755       for (String s : nextfetch)
 756       {
 757         if (l != sb.length())
 758         {
 759           sb.append("; ");
 760         }
 761         if (lr - sb.length() > 40)
 762         {
 763           sb.append("\n");
 764         }
 765         sb.append(s);
 766       }
 767       showErrorMessage(sb.toString());
 768     }
 769     resetDialog();
 770   }
 771
 772   AlignmentI parseResult(String result, String title)
 773   {
 774     String format = new IdentifyFile().Identify(result, "Paste");
 775     Alignment sequences = null;
 776     if (FormatAdapter.isValidFormat(format))
 777     {
 778       sequences = null;
 779       try
 780       {
 781         sequences = new FormatAdapter().readFile(result.toString(),
 782                 "Paste", format);
 783       } catch (Exception ex)
 784       {
 785       }
 786
 787       if (sequences != null)
 788       {
 789         return parseResult(sequences, title, format);
 790       }
 791     }
 792     else
 793     {
 794       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 795               + database.getSelectedItem());
 796     }
 797
 798     return null;
 799   }
 800
 801   /**
 802    *
 803    * @return a standard title for any results retrieved using the currently
 804    *         selected source and settings
 805    */
 806   public String getDefaultRetrievalTitle()
 807   {
 808     return "Retrieved from " + database.getSelectedItem();
 809   }
 810
 811   AlignmentI parseResult(AlignmentI al, String title,
 812           String currentFileFormat)
 813   {
 814
 815     if (al != null && al.getHeight() > 0)
 816     {
 817       if (alignFrame == null)
 818       {
 819         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 820                 AlignFrame.DEFAULT_HEIGHT);
 821         if (currentFileFormat != null)
 822         {
 823           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 824           // FORMAT FOR
 825           // NON-FormatAdapter Sourced
 826           // Alignments?
 827         }
 828
 829         if (title == null)
 830         {
 831           title = getDefaultRetrievalTitle();
 832         }
 833         SequenceFeature[] sfs = null;
 834         List<SequenceI> alsqs;
 835         synchronized (alsqs = al.getSequences())
 836         {
 837           for (SequenceI sq : alsqs)
 838           {
 839             if ((sfs = sq.getSequenceFeatures()) != null)
 840             {
 841               if (sfs.length > 0)
 842               {
 843                 af.setShowSeqFeatures(true);
 844                 break;
 845               }
 846             }
 847
 848           }
 849         }
 850         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 851                 AlignFrame.DEFAULT_HEIGHT);
 852
 853         af.statusBar.setText(MessageManager
 854                 .getString("label.successfully_pasted_alignment_file"));
 855
 856         try
 857         {
 858           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 859                   false));
 860         } catch (Exception ex)
 861         {
 862         }
 863       }
 864       else
 865       {
 866         for (int i = 0; i < al.getHeight(); i++)
 867         {
 868           alignFrame.viewport.getAlignment().addSequence(
 869                   al.getSequenceAt(i)); // this
 870           // also
 871           // creates
 872           // dataset
 873           // sequence
 874           // entries
 875         }
 876         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 877                 .getHeight());
 878         alignFrame.viewport.getAlignment().getWidth();
 879         alignFrame.viewport.firePropertyChange("alignment", null,
 880                 alignFrame.viewport.getAlignment().getSequences());
 881       }
 882     }
 883     return al;
 884   }
 885
 886   void showErrorMessage(final String error)
 887   {
 888     resetDialog();
 889     javax.swing.SwingUtilities.invokeLater(new Runnable()
 890     {
 891       @Override
 892       public void run()
 893       {
 894         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 895                 MessageManager.getString("label.error_retrieving_data"),
 896                 JOptionPane.WARNING_MESSAGE);
 897       }
 898     });
 899   }
 900 }