src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.datamodel.AlignmentI;
  24 import jalview.datamodel.DBRefEntry;
  25 import jalview.datamodel.SequenceFeature;
  26 import jalview.datamodel.SequenceI;
  27 import jalview.io.FormatAdapter;
  28 import jalview.io.IdentifyFile;
  29 import jalview.util.DBRefUtils;
  30 import jalview.util.MessageManager;
  31 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  32 import jalview.ws.seqfetcher.DbSourceProxy;
  33
  34 import java.awt.BorderLayout;
  35 import java.awt.Font;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.KeyAdapter;
  39 import java.awt.event.KeyEvent;
  40 import java.util.ArrayList;
  41 import java.util.Arrays;
  42 import java.util.Iterator;
  43 import java.util.List;
  44
  45 import javax.swing.JButton;
  46 import javax.swing.JCheckBox;
  47 import javax.swing.JInternalFrame;
  48 import javax.swing.JLabel;
  49 import javax.swing.JOptionPane;
  50 import javax.swing.JPanel;
  51 import javax.swing.JScrollPane;
  52 import javax.swing.JTextArea;
  53 import javax.swing.SwingConstants;
  54 import javax.swing.tree.DefaultMutableTreeNode;
  55
  56 public class SequenceFetcher extends JPanel implements Runnable
  57 {
  58   JLabel dbeg = new JLabel();
  59
  60   JDatabaseTree database;
  61
  62   JButton databaseButt;
  63
  64   JLabel jLabel1 = new JLabel();
  65
  66   JCheckBox replacePunctuation = new JCheckBox();
  67
  68   JButton ok = new JButton();
  69
  70   JButton clear = new JButton();
  71
  72   JButton example = new JButton();
  73
  74   JButton close = new JButton();
  75
  76   JPanel jPanel1 = new JPanel();
  77
  78   JTextArea textArea = new JTextArea();
  79
  80   JScrollPane jScrollPane1 = new JScrollPane();
  81
  82   JPanel jPanel2 = new JPanel();
  83
  84   JPanel jPanel3 = new JPanel();
  85
  86   JPanel jPanel4 = new JPanel();
  87
  88   BorderLayout borderLayout1 = new BorderLayout();
  89
  90   BorderLayout borderLayout2 = new BorderLayout();
  91
  92   BorderLayout borderLayout3 = new BorderLayout();
  93
  94   JInternalFrame frame;
  95
  96   IProgressIndicator guiWindow;
  97
  98   AlignFrame alignFrame;
  99
 100   StringBuffer result;
 101
 102   final String noDbSelected = "-- Select Database --";
 103
 104   private static jalview.ws.SequenceFetcher sfetch = null;
 105
 106   private static long lastDasSourceRegistry = -3;
 107
 108   private static DasSourceRegistryI dasRegistry = null;
 109
 110   private static boolean _initingFetcher = false;
 111
 112   private static Thread initingThread = null;
 113
 114   int debounceTrap = 0;
 115
 116   /**
 117    * Blocking method that initialises and returns the shared instance of the
 118    * SequenceFetcher client
 119    *
 120    * @param guiWindow
 121    *          - where the initialisation delay message should be shown
 122    * @return the singleton instance of the sequence fetcher client
 123    */
 124   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
 125           final IProgressIndicator guiWindow)
 126   {
 127     if (_initingFetcher && initingThread != null && initingThread.isAlive())
 128     {
 129       if (guiWindow != null)
 130       {
 131         guiWindow
 132                 .setProgressBar(
 133                         MessageManager
 134                                 .getString("status.waiting_sequence_database_fetchers_init"),
 135                         Thread.currentThread().hashCode());
 136       }
 137       // initting happening on another thread - so wait around to see if it
 138       // finishes.
 139       while (_initingFetcher && initingThread != null
 140               && initingThread.isAlive())
 141       {
 142         try
 143         {
 144           Thread.sleep(10);
 145         } catch (Exception e)
 146         {
 147         }
 148         ;
 149       }
 150       if (guiWindow != null)
 151       {
 152         guiWindow
 153                 .setProgressBar(
 154                         MessageManager
 155                                 .getString("status.waiting_sequence_database_fetchers_init"),
 156                         Thread.currentThread().hashCode());
 157       }
 158     }
 159     if (sfetch == null
 160             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
 161             || lastDasSourceRegistry != (jalview.bin.Cache
 162                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
 163                     .getDasSourceRegistry().getLocalSourceString())
 164                     .hashCode())
 165     {
 166       _initingFetcher = true;
 167       initingThread = Thread.currentThread();
 168       /**
 169        * give a visual indication that sequence fetcher construction is occuring
 170        */
 171       if (guiWindow != null)
 172       {
 173         guiWindow.setProgressBar(MessageManager
 174                 .getString("status.init_sequence_database_fetchers"),
 175                 Thread.currentThread().hashCode());
 176       }
 177       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
 178       dasRegistry.refreshSources();
 179
 180       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 181       if (guiWindow != null)
 182       {
 183         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 184       }
 185       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 186               .getLocalSourceString()).hashCode();
 187       sfetch = sf;
 188       _initingFetcher = false;
 189       initingThread = null;
 190     }
 191     return sfetch;
 192   }
 193
 194   private IProgressIndicator progressIndicator;
 195
 196   public SequenceFetcher(IProgressIndicator guiIndic)
 197   {
 198     this.progressIndicator = guiIndic;
 199     final SequenceFetcher us = this;
 200     // launch initialiser thread
 201     Thread sf = new Thread(new Runnable()
 202     {
 203
 204       @Override
 205       public void run()
 206       {
 207         if (getSequenceFetcherSingleton(progressIndicator) != null)
 208         {
 209           us.initGui(progressIndicator);
 210         }
 211         else
 212         {
 213           javax.swing.SwingUtilities.invokeLater(new Runnable()
 214           {
 215             @Override
 216             public void run()
 217             {
 218               JOptionPane
 219                       .showInternalMessageDialog(
 220                               Desktop.desktop,
 221                               MessageManager
 222                                       .getString("warn.couldnt_create_sequence_fetcher_client"),
 223                               MessageManager
 224                                       .getString("label.couldnt_create_sequence_fetcher"),
 225                               JOptionPane.ERROR_MESSAGE);
 226             }
 227           });
 228
 229           // raise warning dialog
 230         }
 231       }
 232     });
 233     sf.start();
 234   }
 235
 236   private class DatabaseAuthority extends DefaultMutableTreeNode
 237   {
 238
 239   };
 240
 241   private class DatabaseSource extends DefaultMutableTreeNode
 242   {
 243
 244   };
 245
 246   /**
 247    * called by thread spawned by constructor
 248    *
 249    * @param guiWindow
 250    */
 251   private void initGui(IProgressIndicator guiWindow)
 252   {
 253     this.guiWindow = guiWindow;
 254     if (guiWindow instanceof AlignFrame)
 255     {
 256       alignFrame = (AlignFrame) guiWindow;
 257     }
 258     database = new JDatabaseTree(sfetch);
 259     try
 260     {
 261       jbInit();
 262     } catch (Exception ex)
 263     {
 264       ex.printStackTrace();
 265     }
 266
 267     frame = new JInternalFrame();
 268     frame.setContentPane(this);
 269     if (new jalview.util.Platform().isAMac())
 270     {
 271       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 272     }
 273     else
 274     {
 275       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 276     }
 277   }
 278
 279   private String getFrameTitle()
 280   {
 281     return ((alignFrame == null) ? MessageManager
 282             .getString("label.new_sequence_fetcher") : MessageManager
 283             .getString("label.additional_sequence_fetcher"));
 284   }
 285
 286   private void jbInit() throws Exception
 287   {
 288     this.setLayout(borderLayout2);
 289
 290     database.setFont(JvSwingUtils.getLabelFont());
 291     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 292     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 293     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 294     jLabel1.setText(MessageManager
 295             .getString("label.separate_multiple_accession_ids"));
 296
 297     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 298     replacePunctuation
 299             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 300     replacePunctuation.setText(MessageManager
 301             .getString("label.replace_commas_semicolons"));
 302     ok.setText(MessageManager.getString("action.ok"));
 303     ok.addActionListener(new ActionListener()
 304     {
 305       @Override
 306       public void actionPerformed(ActionEvent e)
 307       {
 308         ok_actionPerformed();
 309       }
 310     });
 311     clear.setText(MessageManager.getString("action.clear"));
 312     clear.addActionListener(new ActionListener()
 313     {
 314       @Override
 315       public void actionPerformed(ActionEvent e)
 316       {
 317         clear_actionPerformed();
 318       }
 319     });
 320
 321     example.setText(MessageManager.getString("label.example"));
 322     example.addActionListener(new ActionListener()
 323     {
 324       @Override
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         example_actionPerformed();
 328       }
 329     });
 330     close.setText(MessageManager.getString("action.close"));
 331     close.addActionListener(new ActionListener()
 332     {
 333       @Override
 334       public void actionPerformed(ActionEvent e)
 335       {
 336         close_actionPerformed(e);
 337       }
 338     });
 339     textArea.setFont(JvSwingUtils.getLabelFont());
 340     textArea.setLineWrap(true);
 341     textArea.addKeyListener(new KeyAdapter()
 342     {
 343       @Override
 344       public void keyPressed(KeyEvent e)
 345       {
 346         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 347         {
 348           ok_actionPerformed();
 349         }
 350       }
 351     });
 352     jPanel3.setLayout(borderLayout1);
 353     borderLayout1.setVgap(5);
 354     jPanel1.add(ok);
 355     jPanel1.add(example);
 356     jPanel1.add(clear);
 357     jPanel1.add(close);
 358     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 359     jPanel2.setLayout(borderLayout3);
 360     databaseButt = database.getDatabaseSelectorButton();
 361     databaseButt.setFont(JvSwingUtils.getLabelFont());
 362     database.addActionListener(new ActionListener()
 363     {
 364       @Override
 365       public void actionPerformed(ActionEvent e)
 366       {
 367         debounceTrap++;
 368         String currentSelection = database.getSelectedItem();
 369         if (!currentSelection.equalsIgnoreCase("pdb"))
 370         {
 371           otherSourceAction();
 372         }
 373         if (currentSelection.equalsIgnoreCase("pdb")
 374                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
 375         {
 376           pdbSourceAction();
 377         }
 378         database.action = -1;
 379       }
 380     });
 381
 382     dbeg.setText("");
 383     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 384     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 385     JPanel jPanel2a = new JPanel(new BorderLayout());
 386     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 387     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 388     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 389     // jPanel2.setPreferredSize(new Dimension())
 390     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 391     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 392     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 393     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 394     jScrollPane1.getViewport().add(textArea);
 395
 396   }
 397
 398   private void pdbSourceAction()
 399   {
 400     databaseButt.setText(database.getSelectedItem());
 401     new PDBSearchPanel(this);
 402     frame.dispose();
 403   }
 404
 405   private void otherSourceAction()
 406   {
 407     try
 408     {
 409       databaseButt.setText(database.getSelectedItem()
 410               + (database.getSelectedSources().size() > 1 ? " (and "
 411                       + database.getSelectedSources().size() + " others)"
 412                       : ""));
 413       String eq = database.getExampleQueries();
 414       dbeg.setText(MessageManager.formatMessage(
 415               "label.example_query_param", new String[] { eq }));
 416       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 417       for (DbSourceProxy dbs : database.getSelectedSources())
 418       {
 419         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 420         {
 421           enablePunct = false;
 422           break;
 423         }
 424       }
 425       replacePunctuation.setEnabled(enablePunct);
 426
 427     } catch (Exception ex)
 428     {
 429       dbeg.setText("");
 430       replacePunctuation.setEnabled(true);
 431     }
 432     jPanel2.repaint();
 433   }
 434
 435   protected void example_actionPerformed()
 436   {
 437     DbSourceProxy db = null;
 438     try
 439     {
 440       textArea.setText(database.getExampleQueries());
 441     } catch (Exception ex)
 442     {
 443     }
 444     jPanel3.repaint();
 445   }
 446
 447   protected void clear_actionPerformed()
 448   {
 449     textArea.setText("");
 450     jPanel3.repaint();
 451   }
 452
 453   public void close_actionPerformed(ActionEvent e)
 454   {
 455     try
 456     {
 457       frame.setClosed(true);
 458     } catch (Exception ex)
 459     {
 460     }
 461   }
 462
 463   public void ok_actionPerformed()
 464   {
 465     databaseButt.setEnabled(false);
 466     example.setEnabled(false);
 467     textArea.setEnabled(false);
 468     ok.setEnabled(false);
 469     close.setEnabled(false);
 470
 471     Thread worker = new Thread(this);
 472     worker.start();
 473   }
 474
 475   private void resetDialog()
 476   {
 477     databaseButt.setEnabled(true);
 478     example.setEnabled(true);
 479     textArea.setEnabled(true);
 480     ok.setEnabled(true);
 481     close.setEnabled(true);
 482   }
 483
 484   @Override
 485   public void run()
 486   {
 487     String error = "";
 488     if (!database.hasSelection())
 489     {
 490       error += "Please select the source database\n";
 491     }
 492     // TODO: make this transformation more configurable
 493     com.stevesoft.pat.Regex empty;
 494     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 495     {
 496       empty = new com.stevesoft.pat.Regex(
 497       // replace commas and spaces with a semicolon
 498               "(\\s|[,; ])+", ";");
 499     }
 500     else
 501     {
 502       // just turn spaces and semicolons into single semicolons
 503       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 504     }
 505     textArea.setText(empty.replaceAll(textArea.getText()));
 506     // see if there's anthing to search with
 507     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 508             .getText()))
 509     {
 510       error += "Please enter a (semi-colon separated list of) database id(s)";
 511     }
 512     if (error.length() > 0)
 513     {
 514       showErrorMessage(error);
 515       resetDialog();
 516       return;
 517     }
 518     // TODO: Refactor to GUI independent code and write tests.
 519     // indicate if successive sources should be merged into one alignment.
 520     boolean addToLast = false;
 521     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 522     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 523     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 524             .iterator();
 525     String[] qries;
 526     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 527             .split(";"));
 528     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 529     int nqueries = qries.length;
 530     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 531     {
 532       if (!en.hasNext() && nextfetch.size() > 0)
 533       {
 534         en = nextfetch.iterator();
 535         nqueries = nextfetch.size();
 536         // save the remaining queries in the original array
 537         qries = nextfetch.toArray(new String[nqueries]);
 538         nextfetch = new ArrayList<String>();
 539       }
 540
 541       DbSourceProxy proxy = proxies.next();
 542       boolean isAliSource = false;
 543       try
 544       {
 545         // update status
 546         guiWindow
 547                 .setProgressBar(MessageManager.formatMessage(
 548                         "status.fetching_sequence_queries_from",
 549                         new String[] {
 550                             Integer.valueOf(nqueries).toString(),
 551                             proxy.getDbName() }), Thread.currentThread()
 552                         .hashCode());
 553         isAliSource = proxy.isAlignmentSource();
 554         if (proxy.getAccessionSeparator() == null)
 555         {
 556           while (en.hasNext())
 557           {
 558             String item = en.next();
 559             try
 560             {
 561               if (aresult != null)
 562               {
 563                 try
 564                 {
 565                   // give the server a chance to breathe
 566                   Thread.sleep(5);
 567                 } catch (Exception e)
 568                 {
 569                   //
 570                 }
 571
 572               }
 573
 574               AlignmentI indres = null;
 575               try
 576               {
 577                 indres = proxy.getSequenceRecords(item);
 578               } catch (OutOfMemoryError oome)
 579               {
 580                 new OOMWarning("fetching " + item + " from "
 581                         + proxy.getDbName(), oome, this);
 582               }
 583               if (indres != null)
 584               {
 585                 aresultq.add(item);
 586                 aresult.add(indres);
 587               }
 588               else
 589               {
 590                 nextfetch.add(item);
 591               }
 592             } catch (Exception e)
 593             {
 594               jalview.bin.Cache.log.info("Error retrieving " + item
 595                       + " from " + proxy.getDbName(), e);
 596               nextfetch.add(item);
 597             }
 598           }
 599         }
 600         else
 601         {
 602           StringBuffer multiacc = new StringBuffer();
 603           ArrayList<String> tosend = new ArrayList<String>();
 604           while (en.hasNext())
 605           {
 606             String nel = en.next();
 607             tosend.add(nel);
 608             multiacc.append(nel);
 609             if (en.hasNext())
 610             {
 611               multiacc.append(proxy.getAccessionSeparator());
 612             }
 613           }
 614           try
 615           {
 616             AlignmentI rslt;
 617             SequenceI[] rs;
 618             List<String> nores = new ArrayList<String>();
 619             rslt = proxy.getSequenceRecords(multiacc.toString());
 620             if (rslt == null || rslt.getHeight() == 0)
 621             {
 622               // no results - pass on all queries to next source
 623               nextfetch.addAll(tosend);
 624             }
 625             else
 626             {
 627               aresultq.add(multiacc.toString());
 628               aresult.add(rslt);
 629
 630               rs = rslt.getSequencesArray();
 631               // search for each query in the dbrefs associated with each
 632               // sequence
 633               // returned.
 634               // ones we do not find will be used to query next source (if any)
 635               for (String q : tosend)
 636               {
 637                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 638                 dbr.setSource(proxy.getDbSource());
 639                 dbr.setVersion(null);
 640                 String accId = proxy.getAccessionIdFromQuery(q);
 641                 dbr.setAccessionId(accId);
 642                 boolean rfound = false;
 643                 for (int r = 0; r < rs.length; r++)
 644                 {
 645                   if (rs[r] != null
 646                           && (found = DBRefUtils.searchRefs(
 647                                   rs[r].getDBRefs(), dbr)) != null
 648                           && found.length > 0)
 649                   {
 650                     rfound = true;
 651                     rs[r] = null;
 652                     continue;
 653                   }
 654                 }
 655                 if (!rfound)
 656                 {
 657                   nextfetch.add(q);
 658                 }
 659               }
 660             }
 661           } catch (OutOfMemoryError oome)
 662           {
 663             new OOMWarning("fetching " + multiacc + " from "
 664                     + database.getSelectedItem(), oome, this);
 665           }
 666         }
 667
 668       } catch (Exception e)
 669       {
 670         showErrorMessage("Error retrieving " + textArea.getText()
 671                 + " from " + database.getSelectedItem());
 672         // error
 673         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 674         System.err.println("Retrieval failed for source ='"
 675                 + database.getSelectedItem() + "' and query\n'"
 676                 + textArea.getText() + "'\n");
 677         e.printStackTrace();
 678       } catch (OutOfMemoryError e)
 679       {
 680         // resets dialog box - so we don't use OOMwarning here.
 681         showErrorMessage("Out of Memory when retrieving "
 682                 + textArea.getText()
 683                 + " from "
 684                 + database.getSelectedItem()
 685                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 686         e.printStackTrace();
 687       } catch (Error e)
 688       {
 689         showErrorMessage("Serious Error retrieving " + textArea.getText()
 690                 + " from " + database.getSelectedItem());
 691         e.printStackTrace();
 692       }
 693       // Stack results ready for opening in alignment windows
 694       if (aresult != null && aresult.size() > 0)
 695       {
 696         AlignmentI ar = null;
 697         if (isAliSource)
 698         {
 699           addToLast = false;
 700           // new window for each result
 701           while (aresult.size() > 0)
 702           {
 703             presult.add(aresult.remove(0));
 704             presultTitle.add(aresultq.remove(0) + " "
 705                     + getDefaultRetrievalTitle());
 706           }
 707         }
 708         else
 709         {
 710           String titl = null;
 711           if (addToLast && presult.size() > 0)
 712           {
 713             ar = presult.remove(presult.size() - 1);
 714             titl = presultTitle.remove(presultTitle.size() - 1);
 715           }
 716           // concatenate all results in one window
 717           while (aresult.size() > 0)
 718           {
 719             if (ar == null)
 720             {
 721               ar = aresult.remove(0);
 722             }
 723             else
 724             {
 725               ar.append(aresult.remove(0));
 726             }
 727             ;
 728           }
 729           addToLast = true;
 730           presult.add(ar);
 731           presultTitle.add(titl);
 732         }
 733       }
 734       guiWindow.setProgressBar(MessageManager
 735               .getString("status.finshed_querying"), Thread.currentThread()
 736               .hashCode());
 737     }
 738     guiWindow.setProgressBar(
 739             (presult.size() > 0) ? MessageManager
 740                     .getString("status.parsing_results") : MessageManager
 741                     .getString("status.processing"), Thread.currentThread()
 742                     .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     AlignmentI 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 (title == null)
 820       {
 821         title = getDefaultRetrievalTitle();
 822       }
 823       if (alignFrame == null)
 824       {
 825         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 826                 AlignFrame.DEFAULT_HEIGHT);
 827         if (currentFileFormat != null)
 828         {
 829           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 830           // FORMAT FOR
 831           // NON-FormatAdapter Sourced
 832           // Alignments?
 833         }
 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         alignFrame.viewport.addAlignment(al, title);
 869       }
 870     }
 871     return al;
 872   }
 873
 874   void showErrorMessage(final String error)
 875   {
 876     resetDialog();
 877     javax.swing.SwingUtilities.invokeLater(new Runnable()
 878     {
 879       @Override
 880       public void run()
 881       {
 882         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 883                 MessageManager.getString("label.error_retrieving_data"),
 884                 JOptionPane.WARNING_MESSAGE);
 885       }
 886     });
 887   }
 888
 889   public IProgressIndicator getProgressIndicator()
 890   {
 891     return progressIndicator;
 892   }
 893
 894   public void setProgressIndicator(IProgressIndicator progressIndicator)
 895   {
 896     this.progressIndicator = progressIndicator;
 897   }
 898 }