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 debounceTrap = 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         debounceTrap++;
 361         String currentSelection = database.getSelectedItem();
 362
 363         if (!currentSelection.equalsIgnoreCase("pdb"))
 364         {
 365             otherSourceAction();
 366         }
 367         if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
 368         {
 369           pdbSourceAction();
 370         }
 371
 372       }
 373     });
 374     dbeg.setText("");
 375     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 376     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 377     JPanel jPanel2a = new JPanel(new BorderLayout());
 378     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 379     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 380     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 381     // jPanel2.setPreferredSize(new Dimension())
 382     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 383     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 384     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 385     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 386     jScrollPane1.getViewport().add(textArea);
 387
 388   }
 389
 390   private void pdbSourceAction()
 391   {
 392     databaseButt.setText(database.getSelectedItem());
 393     new EBIFetchPanel(this);
 394     frame.dispose();
 395   }
 396
 397   private void otherSourceAction()
 398   {
 399     try
 400     {
 401       databaseButt.setText(database.getSelectedItem()
 402               + (database.getSelectedSources().size() > 1 ? " (and "
 403                       + database.getSelectedSources().size() + " others)"
 404                       : ""));
 405       String eq = database.getExampleQueries();
 406       dbeg.setText(MessageManager.formatMessage(
 407               "label.example_query_param", new String[]
 408               { eq }));
 409       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 410       for (DbSourceProxy dbs : database.getSelectedSources())
 411       {
 412         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 413         {
 414           enablePunct = false;
 415           break;
 416         }
 417       }
 418       replacePunctuation.setEnabled(enablePunct);
 419
 420     } catch (Exception ex)
 421     {
 422       dbeg.setText("");
 423       replacePunctuation.setEnabled(true);
 424     }
 425     jPanel2.repaint();
 426   }
 427
 428   protected void example_actionPerformed()
 429   {
 430     DbSourceProxy db = null;
 431     try
 432     {
 433       textArea.setText(database.getExampleQueries());
 434     } catch (Exception ex)
 435     {
 436     }
 437     jPanel3.repaint();
 438   }
 439
 440   protected void clear_actionPerformed()
 441   {
 442     textArea.setText("");
 443     jPanel3.repaint();
 444   }
 445
 446
 447
 448   public void close_actionPerformed(ActionEvent e)
 449   {
 450     try
 451     {
 452       frame.setClosed(true);
 453     } catch (Exception ex)
 454     {
 455     }
 456   }
 457
 458   public void ok_actionPerformed()
 459   {
 460     databaseButt.setEnabled(false);
 461     example.setEnabled(false);
 462     textArea.setEnabled(false);
 463     ok.setEnabled(false);
 464     close.setEnabled(false);
 465
 466     Thread worker = new Thread(this);
 467     worker.start();
 468   }
 469
 470   private void resetDialog()
 471   {
 472     databaseButt.setEnabled(true);
 473     example.setEnabled(true);
 474     textArea.setEnabled(true);
 475     ok.setEnabled(true);
 476     close.setEnabled(true);
 477   }
 478
 479   @Override
 480   public void run()
 481   {
 482     String error = "";
 483     if (!database.hasSelection())
 484     {
 485       error += "Please select the source database\n";
 486     }
 487     // TODO: make this transformation more configurable
 488     com.stevesoft.pat.Regex empty;
 489     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 490     {
 491       empty = new com.stevesoft.pat.Regex(
 492       // replace commas and spaces with a semicolon
 493               "(\\s|[,; ])+", ";");
 494     }
 495     else
 496     {
 497       // just turn spaces and semicolons into single semicolons
 498       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 499     }
 500     textArea.setText(empty.replaceAll(textArea.getText()));
 501     // see if there's anthing to search with
 502     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 503             .getText()))
 504     {
 505       error += "Please enter a (semi-colon separated list of) database id(s)";
 506     }
 507     if (error.length() > 0)
 508     {
 509       showErrorMessage(error);
 510       resetDialog();
 511       return;
 512     }
 513     // indicate if successive sources should be merged into one alignment.
 514     boolean addToLast = false;
 515     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 516     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 517     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 518             .iterator();
 519     String[] qries;
 520     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 521             .split(";"));
 522     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 523     int nqueries = qries.length;
 524     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 525     {
 526       if (!en.hasNext() && nextfetch.size() > 0)
 527       {
 528         en = nextfetch.iterator();
 529         nqueries = nextfetch.size();
 530         // save the remaining queries in the original array
 531         qries = nextfetch.toArray(new String[nqueries]);
 532         nextfetch = new ArrayList<String>();
 533       }
 534
 535       DbSourceProxy proxy = proxies.next();
 536       boolean isAliSource = false;
 537       try
 538       {
 539         // update status
 540         guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
 541                 .currentThread().hashCode());
 542         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 543         if (proxy.getAccessionSeparator() == null)
 544         {
 545           while (en.hasNext())
 546           {
 547             String item = en.next();
 548             try
 549             {
 550               if (aresult != null)
 551               {
 552                 try
 553                 {
 554                   // give the server a chance to breathe
 555                   Thread.sleep(5);
 556                 } catch (Exception e)
 557                 {
 558                   //
 559                 }
 560
 561               }
 562
 563               AlignmentI indres = null;
 564               try
 565               {
 566                 indres = proxy.getSequenceRecords(item);
 567               } catch (OutOfMemoryError oome)
 568               {
 569                 new OOMWarning("fetching " + item + " from "
 570                         + proxy.getDbName(), oome, this);
 571               }
 572               if (indres != null)
 573               {
 574                 aresultq.add(item);
 575                 aresult.add(indres);
 576               }
 577               else
 578               {
 579                 nextfetch.add(item);
 580               }
 581             } catch (Exception e)
 582             {
 583               jalview.bin.Cache.log.info("Error retrieving " + item
 584                       + " from " + proxy.getDbName(), e);
 585               nextfetch.add(item);
 586             }
 587           }
 588         }
 589         else
 590         {
 591           StringBuffer multiacc = new StringBuffer();
 592           ArrayList<String> tosend = new ArrayList<String>();
 593           while (en.hasNext())
 594           {
 595             String nel = en.next();
 596             tosend.add(nel);
 597             multiacc.append(nel);
 598             if (en.hasNext())
 599             {
 600               multiacc.append(proxy.getAccessionSeparator());
 601             }
 602           }
 603           try
 604           {
 605             AlignmentI rslt;
 606             SequenceI[] rs;
 607             List<String> nores = new ArrayList<String>();
 608             rslt = proxy.getSequenceRecords(multiacc.toString());
 609             if (rslt == null || rslt.getHeight() == 0)
 610             {
 611               // no results - pass on all queries to next source
 612               nextfetch.addAll(tosend);
 613             }
 614             else
 615             {
 616               aresultq.add(multiacc.toString());
 617               aresult.add(rslt);
 618
 619               rs = rslt.getSequencesArray();
 620               // search for each query in the dbrefs associated with each
 621               // sequence
 622               // returned.
 623               // ones we do not find will be used to query next source (if any)
 624               for (String q : tosend)
 625               {
 626                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 627                 dbr.setSource(proxy.getDbSource());
 628                 dbr.setVersion(null);
 629                 if (proxy.getAccessionValidator() != null)
 630                 {
 631                   Regex vgr = proxy.getAccessionValidator();
 632                   vgr.search(q);
 633                   if (vgr.numSubs() > 0)
 634                   {
 635                     dbr.setAccessionId(vgr.stringMatched(1));
 636                   }
 637                   else
 638                   {
 639                     dbr.setAccessionId(vgr.stringMatched());
 640                   }
 641                 }
 642                 else
 643                 {
 644                   dbr.setAccessionId(q);
 645                 }
 646                 boolean rfound = false;
 647                 for (int r = 0; r < rs.length; r++)
 648                 {
 649                   if (rs[r] != null
 650                           && (found = DBRefUtils.searchRefs(
 651                                   rs[r].getDBRef(), dbr)) != null
 652                           && found.length > 0)
 653                   {
 654                     rfound = true;
 655                     rs[r] = null;
 656                     continue;
 657                   }
 658                 }
 659                 if (!rfound)
 660                 {
 661                   nextfetch.add(q);
 662                 }
 663               }
 664             }
 665           } catch (OutOfMemoryError oome)
 666           {
 667             new OOMWarning("fetching " + multiacc + " from "
 668                     + database.getSelectedItem(), oome, this);
 669           }
 670         }
 671
 672       } catch (Exception e)
 673       {
 674         showErrorMessage("Error retrieving " + textArea.getText()
 675                 + " from " + database.getSelectedItem());
 676         // error
 677         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 678         System.err.println("Retrieval failed for source ='"
 679                 + database.getSelectedItem() + "' and query\n'"
 680                 + textArea.getText() + "'\n");
 681         e.printStackTrace();
 682       } catch (OutOfMemoryError e)
 683       {
 684         // resets dialog box - so we don't use OOMwarning here.
 685         showErrorMessage("Out of Memory when retrieving "
 686                 + textArea.getText()
 687                 + " from "
 688                 + database.getSelectedItem()
 689                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 690         e.printStackTrace();
 691       } catch (Error e)
 692       {
 693         showErrorMessage("Serious Error retrieving " + textArea.getText()
 694                 + " from " + database.getSelectedItem());
 695         e.printStackTrace();
 696       }
 697       // Stack results ready for opening in alignment windows
 698       if (aresult != null && aresult.size() > 0)
 699       {
 700         AlignmentI ar = null;
 701         if (isAliSource)
 702         {
 703           addToLast = false;
 704           // new window for each result
 705           while (aresult.size() > 0)
 706           {
 707             presult.add(aresult.remove(0));
 708             presultTitle.add(aresultq.remove(0) + " "
 709                     + getDefaultRetrievalTitle());
 710           }
 711         }
 712         else
 713         {
 714           String titl = null;
 715           if (addToLast && presult.size() > 0)
 716           {
 717             ar = presult.remove(presult.size() - 1);
 718             titl = presultTitle.remove(presultTitle.size() - 1);
 719           }
 720           // concatenate all results in one window
 721           while (aresult.size() > 0)
 722           {
 723             if (ar == null)
 724             {
 725               ar = aresult.remove(0);
 726             }
 727             else
 728             {
 729               ar.append(aresult.remove(0));
 730             }
 731             ;
 732           }
 733           addToLast = true;
 734           presult.add(ar);
 735           presultTitle.add(titl);
 736         }
 737       }
 738       guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
 739               .hashCode());
 740     }
 741     guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
 742             : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
 743     // process results
 744     while (presult.size() > 0)
 745     {
 746       parseResult(presult.remove(0), presultTitle.remove(0), null);
 747     }
 748     // only remove visual delay after we finished parsing.
 749     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 750     if (nextfetch.size() > 0)
 751     {
 752       StringBuffer sb = new StringBuffer();
 753       sb.append("Didn't retrieve the following "
 754               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 755                       + " queries") + ": \n");
 756       int l = sb.length(), lr = 0;
 757       for (String s : nextfetch)
 758       {
 759         if (l != sb.length())
 760         {
 761           sb.append("; ");
 762         }
 763         if (lr - sb.length() > 40)
 764         {
 765           sb.append("\n");
 766         }
 767         sb.append(s);
 768       }
 769       showErrorMessage(sb.toString());
 770     }
 771     resetDialog();
 772   }
 773
 774   AlignmentI parseResult(String result, String title)
 775   {
 776     String format = new IdentifyFile().Identify(result, "Paste");
 777     Alignment sequences = null;
 778     if (FormatAdapter.isValidFormat(format))
 779     {
 780       sequences = null;
 781       try
 782       {
 783         sequences = new FormatAdapter().readFile(result.toString(),
 784                 "Paste", format);
 785       } catch (Exception ex)
 786       {
 787       }
 788
 789       if (sequences != null)
 790       {
 791         return parseResult(sequences, title, format);
 792       }
 793     }
 794     else
 795     {
 796       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 797               + database.getSelectedItem());
 798     }
 799
 800     return null;
 801   }
 802
 803   /**
 804    *
 805    * @return a standard title for any results retrieved using the currently
 806    *         selected source and settings
 807    */
 808   public String getDefaultRetrievalTitle()
 809   {
 810     return "Retrieved from " + database.getSelectedItem();
 811   }
 812
 813   AlignmentI parseResult(AlignmentI al, String title,
 814           String currentFileFormat)
 815   {
 816
 817     if (al != null && al.getHeight() > 0)
 818     {
 819       if (alignFrame == null)
 820       {
 821         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 822                 AlignFrame.DEFAULT_HEIGHT);
 823         if (currentFileFormat != null)
 824         {
 825           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 826           // FORMAT FOR
 827           // NON-FormatAdapter Sourced
 828           // Alignments?
 829         }
 830
 831         if (title == null)
 832         {
 833           title = getDefaultRetrievalTitle();
 834         }
 835         SequenceFeature[] sfs = null;
 836         List<SequenceI> alsqs;
 837         synchronized (alsqs = al.getSequences())
 838         {
 839           for (SequenceI sq : alsqs)
 840           {
 841             if ((sfs = sq.getSequenceFeatures()) != null)
 842             {
 843               if (sfs.length > 0)
 844               {
 845                 af.setShowSeqFeatures(true);
 846                 break;
 847               }
 848             }
 849
 850           }
 851         }
 852         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 853                 AlignFrame.DEFAULT_HEIGHT);
 854
 855         af.statusBar.setText(MessageManager
 856                 .getString("label.successfully_pasted_alignment_file"));
 857
 858         try
 859         {
 860           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 861                   false));
 862         } catch (Exception ex)
 863         {
 864         }
 865       }
 866       else
 867       {
 868         for (int i = 0; i < al.getHeight(); i++)
 869         {
 870           alignFrame.viewport.getAlignment().addSequence(
 871                   al.getSequenceAt(i)); // this
 872           // also
 873           // creates
 874           // dataset
 875           // sequence
 876           // entries
 877         }
 878         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 879                 .getHeight());
 880         alignFrame.viewport.getAlignment().getWidth();
 881         alignFrame.viewport.firePropertyChange("alignment", null,
 882                 alignFrame.viewport.getAlignment().getSequences());
 883       }
 884     }
 885     return al;
 886   }
 887
 888   void showErrorMessage(final String error)
 889   {
 890     resetDialog();
 891     javax.swing.SwingUtilities.invokeLater(new Runnable()
 892     {
 893       @Override
 894       public void run()
 895       {
 896         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 897                 MessageManager.getString("label.error_retrieving_data"),
 898                 JOptionPane.WARNING_MESSAGE);
 899       }
 900     });
 901   }
 902 }