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.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   private IProgressIndicator progressIndicator;
 194   public SequenceFetcher(IProgressIndicator guiIndic)
 195   {
 196     this.progressIndicator = guiIndic;
 197     final SequenceFetcher us = this;
 198     // launch initialiser thread
 199     Thread sf = new Thread(new Runnable()
 200     {
 201
 202       @Override
 203       public void run()
 204       {
 205         if (getSequenceFetcherSingleton(progressIndicator) != null)
 206         {
 207           us.initGui(progressIndicator);
 208         }
 209         else
 210         {
 211           javax.swing.SwingUtilities.invokeLater(new Runnable()
 212           {
 213             @Override
 214             public void run()
 215             {
 216               JOptionPane
 217                       .showInternalMessageDialog(
 218                               Desktop.desktop,
 219                               MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
 220                               MessageManager.getString("label.couldnt_create_sequence_fetcher"),
 221                               JOptionPane.ERROR_MESSAGE);
 222             }
 223           });
 224
 225           // raise warning dialog
 226         }
 227       }
 228     });
 229     sf.start();
 230   }
 231
 232   private class DatabaseAuthority extends DefaultMutableTreeNode
 233   {
 234
 235   };
 236
 237   private class DatabaseSource extends DefaultMutableTreeNode
 238   {
 239
 240   };
 241
 242   /**
 243    * called by thread spawned by constructor
 244    *
 245    * @param guiWindow
 246    */
 247   private void initGui(IProgressIndicator guiWindow)
 248   {
 249     this.guiWindow = guiWindow;
 250     if (guiWindow instanceof AlignFrame)
 251     {
 252       alignFrame = (AlignFrame) guiWindow;
 253     }
 254     database = new JDatabaseTree(sfetch);
 255     try
 256     {
 257       jbInit();
 258     } catch (Exception ex)
 259     {
 260       ex.printStackTrace();
 261     }
 262
 263     frame = new JInternalFrame();
 264     frame.setContentPane(this);
 265     if (new jalview.util.Platform().isAMac())
 266     {
 267       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 268     }
 269     else
 270     {
 271       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 272     }
 273   }
 274
 275   private String getFrameTitle()
 276   {
 277     return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
 278   }
 279
 280   private void jbInit() throws Exception
 281   {
 282     this.setLayout(borderLayout2);
 283
 284     database.setFont(JvSwingUtils.getLabelFont());
 285     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 286     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 287     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 288     jLabel1.setText(MessageManager
 289             .getString("label.separate_multiple_accession_ids"));
 290
 291     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 292     replacePunctuation
 293             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 294     replacePunctuation.setText(MessageManager
 295             .getString("label.replace_commas_semicolons"));
 296     ok.setText(MessageManager.getString("action.ok"));
 297     ok.addActionListener(new ActionListener()
 298     {
 299       @Override
 300       public void actionPerformed(ActionEvent e)
 301       {
 302         ok_actionPerformed();
 303       }
 304     });
 305     clear.setText(MessageManager.getString("action.clear"));
 306     clear.addActionListener(new ActionListener()
 307     {
 308       @Override
 309       public void actionPerformed(ActionEvent e)
 310       {
 311         clear_actionPerformed();
 312       }
 313     });
 314
 315     example.setText(MessageManager.getString("label.example"));
 316     example.addActionListener(new ActionListener()
 317     {
 318       @Override
 319       public void actionPerformed(ActionEvent e)
 320       {
 321         example_actionPerformed();
 322       }
 323     });
 324     close.setText(MessageManager.getString("action.close"));
 325     close.addActionListener(new ActionListener()
 326     {
 327       @Override
 328       public void actionPerformed(ActionEvent e)
 329       {
 330         close_actionPerformed(e);
 331       }
 332     });
 333     textArea.setFont(JvSwingUtils.getLabelFont());
 334     textArea.setLineWrap(true);
 335     textArea.addKeyListener(new KeyAdapter()
 336     {
 337       @Override
 338       public void keyPressed(KeyEvent e)
 339       {
 340         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 341         {
 342           ok_actionPerformed();
 343         }
 344       }
 345     });
 346     jPanel3.setLayout(borderLayout1);
 347     borderLayout1.setVgap(5);
 348     jPanel1.add(ok);
 349     jPanel1.add(example);
 350     jPanel1.add(clear);
 351     jPanel1.add(close);
 352     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 353     jPanel2.setLayout(borderLayout3);
 354     databaseButt = database.getDatabaseSelectorButton();
 355     databaseButt.setFont(JvSwingUtils.getLabelFont());
 356     database.addActionListener(new ActionListener()
 357     {
 358       @Override
 359       public void actionPerformed(ActionEvent e)
 360       {
 361         debounceTrap++;
 362         String currentSelection = database.getSelectedItem();
 363
 364         if (!currentSelection.equalsIgnoreCase("pdb"))
 365         {
 366             otherSourceAction();
 367         }
 368         if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
 369         {
 370           pdbSourceAction();
 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 pdbSourceAction()
 392   {
 393     databaseButt.setText(database.getSelectedItem());
 394     new PDBSearchPanel(this);
 395     frame.dispose();
 396   }
 397
 398   private void otherSourceAction()
 399   {
 400     try
 401     {
 402       databaseButt.setText(database.getSelectedItem()
 403               + (database.getSelectedSources().size() > 1 ? " (and "
 404                       + database.getSelectedSources().size() + " others)"
 405                       : ""));
 406       String eq = database.getExampleQueries();
 407       dbeg.setText(MessageManager.formatMessage(
 408               "label.example_query_param", new String[]
 409               { eq }));
 410       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 411       for (DbSourceProxy dbs : database.getSelectedSources())
 412       {
 413         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 414         {
 415           enablePunct = false;
 416           break;
 417         }
 418       }
 419       replacePunctuation.setEnabled(enablePunct);
 420
 421     } catch (Exception ex)
 422     {
 423       dbeg.setText("");
 424       replacePunctuation.setEnabled(true);
 425     }
 426     jPanel2.repaint();
 427   }
 428
 429   protected void example_actionPerformed()
 430   {
 431     DbSourceProxy db = null;
 432     try
 433     {
 434       textArea.setText(database.getExampleQueries());
 435     } catch (Exception ex)
 436     {
 437     }
 438     jPanel3.repaint();
 439   }
 440
 441   protected void clear_actionPerformed()
 442   {
 443     textArea.setText("");
 444     jPanel3.repaint();
 445   }
 446
 447
 448
 449   public void close_actionPerformed(ActionEvent e)
 450   {
 451     try
 452     {
 453       frame.setClosed(true);
 454     } catch (Exception ex)
 455     {
 456     }
 457   }
 458
 459   public void ok_actionPerformed()
 460   {
 461     databaseButt.setEnabled(false);
 462     example.setEnabled(false);
 463     textArea.setEnabled(false);
 464     ok.setEnabled(false);
 465     close.setEnabled(false);
 466
 467     Thread worker = new Thread(this);
 468     worker.start();
 469   }
 470
 471   private void resetDialog()
 472   {
 473     databaseButt.setEnabled(true);
 474     example.setEnabled(true);
 475     textArea.setEnabled(true);
 476     ok.setEnabled(true);
 477     close.setEnabled(true);
 478   }
 479
 480   @Override
 481   public void run()
 482   {
 483     String error = "";
 484     if (!database.hasSelection())
 485     {
 486       error += "Please select the source database\n";
 487     }
 488     // TODO: make this transformation more configurable
 489     com.stevesoft.pat.Regex empty;
 490     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 491     {
 492       empty = new com.stevesoft.pat.Regex(
 493       // replace commas and spaces with a semicolon
 494               "(\\s|[,; ])+", ";");
 495     }
 496     else
 497     {
 498       // just turn spaces and semicolons into single semicolons
 499       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 500     }
 501     textArea.setText(empty.replaceAll(textArea.getText()));
 502     // see if there's anthing to search with
 503     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 504             .getText()))
 505     {
 506       error += "Please enter a (semi-colon separated list of) database id(s)";
 507     }
 508     if (error.length() > 0)
 509     {
 510       showErrorMessage(error);
 511       resetDialog();
 512       return;
 513     }
 514     // indicate if successive sources should be merged into one alignment.
 515     boolean addToLast = false;
 516     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 517     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 518     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 519             .iterator();
 520     String[] qries;
 521     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 522             .split(";"));
 523     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 524     int nqueries = qries.length;
 525     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 526     {
 527       if (!en.hasNext() && nextfetch.size() > 0)
 528       {
 529         en = nextfetch.iterator();
 530         nqueries = nextfetch.size();
 531         // save the remaining queries in the original array
 532         qries = nextfetch.toArray(new String[nqueries]);
 533         nextfetch = new ArrayList<String>();
 534       }
 535
 536       DbSourceProxy proxy = proxies.next();
 537       boolean isAliSource = false;
 538       try
 539       {
 540         // update status
 541         guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
 542                 .currentThread().hashCode());
 543         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 544         if (proxy.getAccessionSeparator() == null)
 545         {
 546           while (en.hasNext())
 547           {
 548             String item = en.next();
 549             try
 550             {
 551               if (aresult != null)
 552               {
 553                 try
 554                 {
 555                   // give the server a chance to breathe
 556                   Thread.sleep(5);
 557                 } catch (Exception e)
 558                 {
 559                   //
 560                 }
 561
 562               }
 563
 564               AlignmentI indres = null;
 565               try
 566               {
 567                 indres = proxy.getSequenceRecords(item);
 568               } catch (OutOfMemoryError oome)
 569               {
 570                 new OOMWarning("fetching " + item + " from "
 571                         + proxy.getDbName(), oome, this);
 572               }
 573               if (indres != null)
 574               {
 575                 aresultq.add(item);
 576                 aresult.add(indres);
 577               }
 578               else
 579               {
 580                 nextfetch.add(item);
 581               }
 582             } catch (Exception e)
 583             {
 584               jalview.bin.Cache.log.info("Error retrieving " + item
 585                       + " from " + proxy.getDbName(), e);
 586               nextfetch.add(item);
 587             }
 588           }
 589         }
 590         else
 591         {
 592           StringBuffer multiacc = new StringBuffer();
 593           ArrayList<String> tosend = new ArrayList<String>();
 594           while (en.hasNext())
 595           {
 596             String nel = en.next();
 597             tosend.add(nel);
 598             multiacc.append(nel);
 599             if (en.hasNext())
 600             {
 601               multiacc.append(proxy.getAccessionSeparator());
 602             }
 603           }
 604           try
 605           {
 606             AlignmentI rslt;
 607             SequenceI[] rs;
 608             List<String> nores = new ArrayList<String>();
 609             rslt = proxy.getSequenceRecords(multiacc.toString());
 610             if (rslt == null || rslt.getHeight() == 0)
 611             {
 612               // no results - pass on all queries to next source
 613               nextfetch.addAll(tosend);
 614             }
 615             else
 616             {
 617               aresultq.add(multiacc.toString());
 618               aresult.add(rslt);
 619
 620               rs = rslt.getSequencesArray();
 621               // search for each query in the dbrefs associated with each
 622               // sequence
 623               // returned.
 624               // ones we do not find will be used to query next source (if any)
 625               for (String q : tosend)
 626               {
 627                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 628                 dbr.setSource(proxy.getDbSource());
 629                 dbr.setVersion(null);
 630                 if (proxy.getAccessionValidator() != null)
 631                 {
 632                   Regex vgr = proxy.getAccessionValidator();
 633                   vgr.search(q);
 634                   if (vgr.numSubs() > 0)
 635                   {
 636                     dbr.setAccessionId(vgr.stringMatched(1));
 637                   }
 638                   else
 639                   {
 640                     dbr.setAccessionId(vgr.stringMatched());
 641                   }
 642                 }
 643                 else
 644                 {
 645                   dbr.setAccessionId(q);
 646                 }
 647                 boolean rfound = false;
 648                 for (int r = 0; r < rs.length; r++)
 649                 {
 650                   if (rs[r] != null
 651                           && (found = DBRefUtils.searchRefs(
 652                                   rs[r].getDBRef(), dbr)) != null
 653                           && found.length > 0)
 654                   {
 655                     rfound = true;
 656                     rs[r] = null;
 657                     continue;
 658                   }
 659                 }
 660                 if (!rfound)
 661                 {
 662                   nextfetch.add(q);
 663                 }
 664               }
 665             }
 666           } catch (OutOfMemoryError oome)
 667           {
 668             new OOMWarning("fetching " + multiacc + " from "
 669                     + database.getSelectedItem(), oome, this);
 670           }
 671         }
 672
 673       } catch (Exception e)
 674       {
 675         showErrorMessage("Error retrieving " + textArea.getText()
 676                 + " from " + database.getSelectedItem());
 677         // error
 678         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 679         System.err.println("Retrieval failed for source ='"
 680                 + database.getSelectedItem() + "' and query\n'"
 681                 + textArea.getText() + "'\n");
 682         e.printStackTrace();
 683       } catch (OutOfMemoryError e)
 684       {
 685         // resets dialog box - so we don't use OOMwarning here.
 686         showErrorMessage("Out of Memory when retrieving "
 687                 + textArea.getText()
 688                 + " from "
 689                 + database.getSelectedItem()
 690                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 691         e.printStackTrace();
 692       } catch (Error e)
 693       {
 694         showErrorMessage("Serious Error retrieving " + textArea.getText()
 695                 + " from " + database.getSelectedItem());
 696         e.printStackTrace();
 697       }
 698       // Stack results ready for opening in alignment windows
 699       if (aresult != null && aresult.size() > 0)
 700       {
 701         AlignmentI ar = null;
 702         if (isAliSource)
 703         {
 704           addToLast = false;
 705           // new window for each result
 706           while (aresult.size() > 0)
 707           {
 708             presult.add(aresult.remove(0));
 709             presultTitle.add(aresultq.remove(0) + " "
 710                     + getDefaultRetrievalTitle());
 711           }
 712         }
 713         else
 714         {
 715           String titl = null;
 716           if (addToLast && presult.size() > 0)
 717           {
 718             ar = presult.remove(presult.size() - 1);
 719             titl = presultTitle.remove(presultTitle.size() - 1);
 720           }
 721           // concatenate all results in one window
 722           while (aresult.size() > 0)
 723           {
 724             if (ar == null)
 725             {
 726               ar = aresult.remove(0);
 727             }
 728             else
 729             {
 730               ar.append(aresult.remove(0));
 731             }
 732             ;
 733           }
 734           addToLast = true;
 735           presult.add(ar);
 736           presultTitle.add(titl);
 737         }
 738       }
 739       guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
 740               .hashCode());
 741     }
 742     guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
 743             : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
 744     // process results
 745     while (presult.size() > 0)
 746     {
 747       parseResult(presult.remove(0), presultTitle.remove(0), null);
 748     }
 749     // only remove visual delay after we finished parsing.
 750     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 751     if (nextfetch.size() > 0)
 752     {
 753       StringBuffer sb = new StringBuffer();
 754       sb.append("Didn't retrieve the following "
 755               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 756                       + " queries") + ": \n");
 757       int l = sb.length(), lr = 0;
 758       for (String s : nextfetch)
 759       {
 760         if (l != sb.length())
 761         {
 762           sb.append("; ");
 763         }
 764         if (lr - sb.length() > 40)
 765         {
 766           sb.append("\n");
 767         }
 768         sb.append(s);
 769       }
 770       showErrorMessage(sb.toString());
 771     }
 772     resetDialog();
 773   }
 774
 775   AlignmentI parseResult(String result, String title)
 776   {
 777     String format = new IdentifyFile().Identify(result, "Paste");
 778     Alignment sequences = null;
 779     if (FormatAdapter.isValidFormat(format))
 780     {
 781       sequences = null;
 782       try
 783       {
 784         sequences = new FormatAdapter().readFile(result.toString(),
 785                 "Paste", format);
 786       } catch (Exception ex)
 787       {
 788       }
 789
 790       if (sequences != null)
 791       {
 792         return parseResult(sequences, title, format);
 793       }
 794     }
 795     else
 796     {
 797       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 798               + database.getSelectedItem());
 799     }
 800
 801     return null;
 802   }
 803
 804   /**
 805    *
 806    * @return a standard title for any results retrieved using the currently
 807    *         selected source and settings
 808    */
 809   public String getDefaultRetrievalTitle()
 810   {
 811     return "Retrieved from " + database.getSelectedItem();
 812   }
 813
 814   AlignmentI parseResult(AlignmentI al, String title,
 815           String currentFileFormat)
 816   {
 817
 818     if (al != null && al.getHeight() > 0)
 819     {
 820       if (title == null)
 821       {
 822         title = getDefaultRetrievalTitle();
 823       }
 824       if (alignFrame == null)
 825       {
 826         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 827                 AlignFrame.DEFAULT_HEIGHT);
 828         if (currentFileFormat != null)
 829         {
 830           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 831           // FORMAT FOR
 832           // NON-FormatAdapter Sourced
 833           // Alignments?
 834         }
 835
 836         SequenceFeature[] sfs = null;
 837         List<SequenceI> alsqs;
 838         synchronized (alsqs = al.getSequences())
 839         {
 840           for (SequenceI sq : alsqs)
 841           {
 842             if ((sfs = sq.getSequenceFeatures()) != null)
 843             {
 844               if (sfs.length > 0)
 845               {
 846                 af.setShowSeqFeatures(true);
 847                 break;
 848               }
 849             }
 850
 851           }
 852         }
 853         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 854                 AlignFrame.DEFAULT_HEIGHT);
 855
 856         af.statusBar.setText(MessageManager
 857                 .getString("label.successfully_pasted_alignment_file"));
 858
 859         try
 860         {
 861           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 862                   false));
 863         } catch (Exception ex)
 864         {
 865         }
 866       }
 867       else
 868       {
 869         alignFrame.viewport.addAlignment(al, title);
 870       }
 871     }
 872     return al;
 873   }
 874
 875   void showErrorMessage(final String error)
 876   {
 877     resetDialog();
 878     javax.swing.SwingUtilities.invokeLater(new Runnable()
 879     {
 880       @Override
 881       public void run()
 882       {
 883         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 884                 MessageManager.getString("label.error_retrieving_data"),
 885                 JOptionPane.WARNING_MESSAGE);
 886       }
 887     });
 888   }
 889
 890   public IProgressIndicator getProgressIndicator()
 891   {
 892     return progressIndicator;
 893   }
 894
 895   public void setProgressIndicator(IProgressIndicator progressIndicator)
 896   {
 897     this.progressIndicator = progressIndicator;
 898   }
 899 }