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.api.FeatureSettingsModelI;
  24 import jalview.bin.Cache;
  25 import jalview.datamodel.AlignmentI;
  26 import jalview.datamodel.DBRefEntry;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.fts.service.pdb.PDBFTSPanel;
  30 import jalview.fts.service.uniprot.UniprotFTSPanel;
  31 import jalview.io.gff.SequenceOntologyI;
  32 import jalview.util.DBRefUtils;
  33 import jalview.util.MessageManager;
  34 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  35 import jalview.ws.seqfetcher.DbSourceProxy;
  36
  37 import java.awt.BorderLayout;
  38 import java.awt.Font;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.KeyAdapter;
  42 import java.awt.event.KeyEvent;
  43 import java.util.ArrayList;
  44 import java.util.Arrays;
  45 import java.util.Iterator;
  46 import java.util.List;
  47
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JInternalFrame;
  51 import javax.swing.JLabel;
  52 import javax.swing.JOptionPane;
  53 import javax.swing.JPanel;
  54 import javax.swing.JScrollPane;
  55 import javax.swing.JTextArea;
  56 import javax.swing.SwingConstants;
  57 import javax.swing.tree.DefaultMutableTreeNode;
  58
  59 public class SequenceFetcher extends JPanel implements Runnable
  60 {
  61   JLabel dbeg = new JLabel();
  62
  63   JDatabaseTree database;
  64
  65   JButton databaseButt;
  66
  67   JLabel jLabel1 = new JLabel();
  68
  69   JCheckBox replacePunctuation = new JCheckBox();
  70
  71   JButton ok = new JButton();
  72
  73   JButton clear = new JButton();
  74
  75   JButton example = new JButton();
  76
  77   JButton close = new JButton();
  78
  79   JPanel jPanel1 = new JPanel();
  80
  81   JTextArea textArea = new JTextArea();
  82
  83   JScrollPane jScrollPane1 = new JScrollPane();
  84
  85   JPanel jPanel2 = new JPanel();
  86
  87   JPanel jPanel3 = new JPanel();
  88
  89   JPanel jPanel4 = new JPanel();
  90
  91   BorderLayout borderLayout1 = new BorderLayout();
  92
  93   BorderLayout borderLayout2 = new BorderLayout();
  94
  95   BorderLayout borderLayout3 = new BorderLayout();
  96
  97   JInternalFrame frame;
  98
  99   IProgressIndicator guiWindow;
 100
 101   AlignFrame alignFrame;
 102
 103   StringBuffer result;
 104
 105   final String noDbSelected = "-- Select Database --";
 106
 107   private static jalview.ws.SequenceFetcher sfetch = null;
 108
 109   private static long lastDasSourceRegistry = -3;
 110
 111   private static DasSourceRegistryI dasRegistry = null;
 112
 113   private static boolean _initingFetcher = false;
 114
 115   private static Thread initingThread = null;
 116
 117   int debounceTrap = 0;
 118
 119   public JTextArea getTextArea()
 120   {
 121     return textArea;
 122   }
 123
 124   /**
 125    * Blocking method that initialises and returns the shared instance of the
 126    * SequenceFetcher client
 127    *
 128    * @param guiWindow
 129    *          - where the initialisation delay message should be shown
 130    * @return the singleton instance of the sequence fetcher client
 131    */
 132   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
 133           final IProgressIndicator guiWindow)
 134   {
 135     if (_initingFetcher && initingThread != null && initingThread.isAlive())
 136     {
 137       if (guiWindow != null)
 138       {
 139         guiWindow
 140                 .setProgressBar(
 141                         MessageManager
 142                                 .getString("status.waiting_sequence_database_fetchers_init"),
 143                         Thread.currentThread().hashCode());
 144       }
 145       // initting happening on another thread - so wait around to see if it
 146       // finishes.
 147       while (_initingFetcher && initingThread != null
 148               && initingThread.isAlive())
 149       {
 150         try
 151         {
 152           Thread.sleep(10);
 153         } catch (Exception e)
 154         {
 155         }
 156         ;
 157       }
 158       if (guiWindow != null)
 159       {
 160         guiWindow
 161                 .setProgressBar(
 162                         MessageManager
 163                                 .getString("status.waiting_sequence_database_fetchers_init"),
 164                         Thread.currentThread().hashCode());
 165       }
 166     }
 167     if (sfetch == null
 168             || dasRegistry != Cache.getDasSourceRegistry()
 169             || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
 170                     .getDasRegistryURL() + Cache
 171                     .getDasSourceRegistry().getLocalSourceString())
 172                     .hashCode())
 173     {
 174       _initingFetcher = true;
 175       initingThread = Thread.currentThread();
 176       /**
 177        * give a visual indication that sequence fetcher construction is occuring
 178        */
 179       if (guiWindow != null)
 180       {
 181         guiWindow.setProgressBar(MessageManager
 182                 .getString("status.init_sequence_database_fetchers"),
 183                 Thread.currentThread().hashCode());
 184       }
 185       dasRegistry = Cache.getDasSourceRegistry();
 186       dasRegistry.refreshSources();
 187
 188       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 189       if (guiWindow != null)
 190       {
 191         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 192       }
 193       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 194               .getLocalSourceString()).hashCode();
 195       sfetch = sf;
 196       _initingFetcher = false;
 197       initingThread = null;
 198     }
 199     return sfetch;
 200   }
 201
 202   private IProgressIndicator progressIndicator;
 203
 204   public SequenceFetcher(IProgressIndicator guiIndic)
 205   {
 206     this.progressIndicator = guiIndic;
 207     final SequenceFetcher us = this;
 208     // launch initialiser thread
 209     Thread sf = new Thread(new Runnable()
 210     {
 211
 212       @Override
 213       public void run()
 214       {
 215         if (getSequenceFetcherSingleton(progressIndicator) != null)
 216         {
 217           us.initGui(progressIndicator);
 218         }
 219         else
 220         {
 221           javax.swing.SwingUtilities.invokeLater(new Runnable()
 222           {
 223             @Override
 224             public void run()
 225             {
 226               JOptionPane
 227                       .showInternalMessageDialog(
 228                               Desktop.desktop,
 229                               MessageManager
 230                                       .getString("warn.couldnt_create_sequence_fetcher_client"),
 231                               MessageManager
 232                                       .getString("label.couldnt_create_sequence_fetcher"),
 233                               JOptionPane.ERROR_MESSAGE);
 234             }
 235           });
 236
 237           // raise warning dialog
 238         }
 239       }
 240     });
 241     sf.start();
 242   }
 243
 244   private class DatabaseAuthority extends DefaultMutableTreeNode
 245   {
 246
 247   };
 248
 249   private class DatabaseSource extends DefaultMutableTreeNode
 250   {
 251
 252   };
 253
 254   /**
 255    * called by thread spawned by constructor
 256    *
 257    * @param guiWindow
 258    */
 259   private void initGui(IProgressIndicator guiWindow)
 260   {
 261     this.guiWindow = guiWindow;
 262     if (guiWindow instanceof AlignFrame)
 263     {
 264       alignFrame = (AlignFrame) guiWindow;
 265     }
 266     database = new JDatabaseTree(sfetch);
 267     try
 268     {
 269       jbInit();
 270     } catch (Exception ex)
 271     {
 272       ex.printStackTrace();
 273     }
 274
 275     frame = new JInternalFrame();
 276     frame.setContentPane(this);
 277     if (new jalview.util.Platform().isAMac())
 278     {
 279       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 280     }
 281     else
 282     {
 283       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 284     }
 285   }
 286
 287   private String getFrameTitle()
 288   {
 289     return ((alignFrame == null) ? MessageManager
 290             .getString("label.new_sequence_fetcher") : MessageManager
 291             .getString("label.additional_sequence_fetcher"));
 292   }
 293
 294   private void jbInit() throws Exception
 295   {
 296     this.setLayout(borderLayout2);
 297
 298     database.setFont(JvSwingUtils.getLabelFont());
 299     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 300     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 301     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 302     jLabel1.setText(MessageManager
 303             .getString("label.separate_multiple_accession_ids"));
 304
 305     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 306     replacePunctuation
 307             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 308     replacePunctuation.setText(MessageManager
 309             .getString("label.replace_commas_semicolons"));
 310     ok.setText(MessageManager.getString("action.ok"));
 311     ok.addActionListener(new ActionListener()
 312     {
 313       @Override
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         ok_actionPerformed();
 317       }
 318     });
 319     clear.setText(MessageManager.getString("action.clear"));
 320     clear.addActionListener(new ActionListener()
 321     {
 322       @Override
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         clear_actionPerformed();
 326       }
 327     });
 328
 329     example.setText(MessageManager.getString("label.example"));
 330     example.addActionListener(new ActionListener()
 331     {
 332       @Override
 333       public void actionPerformed(ActionEvent e)
 334       {
 335         example_actionPerformed();
 336       }
 337     });
 338     close.setText(MessageManager.getString("action.close"));
 339     close.addActionListener(new ActionListener()
 340     {
 341       @Override
 342       public void actionPerformed(ActionEvent e)
 343       {
 344         close_actionPerformed(e);
 345       }
 346     });
 347     textArea.setFont(JvSwingUtils.getLabelFont());
 348     textArea.setLineWrap(true);
 349     textArea.addKeyListener(new KeyAdapter()
 350     {
 351       @Override
 352       public void keyPressed(KeyEvent e)
 353       {
 354         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 355         {
 356           ok_actionPerformed();
 357         }
 358       }
 359     });
 360     jPanel3.setLayout(borderLayout1);
 361     borderLayout1.setVgap(5);
 362     jPanel1.add(ok);
 363     jPanel1.add(example);
 364     jPanel1.add(clear);
 365     jPanel1.add(close);
 366     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 367     jPanel2.setLayout(borderLayout3);
 368     databaseButt = database.getDatabaseSelectorButton();
 369     databaseButt.setFont(JvSwingUtils.getLabelFont());
 370     database.addActionListener(new ActionListener()
 371     {
 372       @Override
 373       public void actionPerformed(ActionEvent e)
 374       {
 375         debounceTrap++;
 376         String currentSelection = database.getSelectedItem();
 377
 378         if (currentSelection.equalsIgnoreCase("pdb")
 379                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
 380         {
 381           pdbSourceAction();
 382         }
 383         else if (currentSelection.equalsIgnoreCase("uniprot")
 384                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
 385         {
 386           uniprotSourceAction();
 387         }
 388         else
 389         {
 390           otherSourceAction();
 391         }
 392         database.action = -1;
 393       }
 394     });
 395
 396     dbeg.setText("");
 397     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 398     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 399     JPanel jPanel2a = new JPanel(new BorderLayout());
 400     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 401     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 402     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 403     // jPanel2.setPreferredSize(new Dimension())
 404     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 405     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 406     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 407     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 408     jScrollPane1.getViewport().add(textArea);
 409
 410   }
 411
 412   private void pdbSourceAction()
 413   {
 414     databaseButt.setText(database.getSelectedItem());
 415     new PDBFTSPanel(this);
 416     frame.dispose();
 417   }
 418
 419   private void uniprotSourceAction()
 420   {
 421     databaseButt.setText(database.getSelectedItem());
 422     new UniprotFTSPanel(this);
 423     frame.dispose();
 424   }
 425   private void otherSourceAction()
 426   {
 427     try
 428     {
 429       databaseButt.setText(database.getSelectedItem()
 430               + (database.getSelectedSources().size() > 1 ? " (and "
 431                       + database.getSelectedSources().size() + " others)"
 432                       : ""));
 433       String eq = database.getExampleQueries();
 434       dbeg.setText(MessageManager.formatMessage(
 435               "label.example_query_param", new String[] { eq }));
 436       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 437       for (DbSourceProxy dbs : database.getSelectedSources())
 438       {
 439         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 440         {
 441           enablePunct = false;
 442           break;
 443         }
 444       }
 445       replacePunctuation.setEnabled(enablePunct);
 446
 447     } catch (Exception ex)
 448     {
 449       dbeg.setText("");
 450       replacePunctuation.setEnabled(true);
 451     }
 452     jPanel2.repaint();
 453   }
 454
 455   protected void example_actionPerformed()
 456   {
 457     DbSourceProxy db = null;
 458     try
 459     {
 460       textArea.setText(database.getExampleQueries());
 461     } catch (Exception ex)
 462     {
 463     }
 464     jPanel3.repaint();
 465   }
 466
 467   protected void clear_actionPerformed()
 468   {
 469     textArea.setText("");
 470     jPanel3.repaint();
 471   }
 472
 473   public void close_actionPerformed(ActionEvent e)
 474   {
 475     try
 476     {
 477       frame.setClosed(true);
 478     } catch (Exception ex)
 479     {
 480     }
 481   }
 482
 483   public void ok_actionPerformed()
 484   {
 485     databaseButt.setEnabled(false);
 486     example.setEnabled(false);
 487     textArea.setEnabled(false);
 488     ok.setEnabled(false);
 489     close.setEnabled(false);
 490
 491     Thread worker = new Thread(this);
 492     worker.start();
 493   }
 494
 495   private void resetDialog()
 496   {
 497     databaseButt.setEnabled(true);
 498     example.setEnabled(true);
 499     textArea.setEnabled(true);
 500     ok.setEnabled(true);
 501     close.setEnabled(true);
 502   }
 503
 504   @Override
 505   public void run()
 506   {
 507     String error = "";
 508     if (!database.hasSelection())
 509     {
 510       error += "Please select the source database\n";
 511     }
 512     // TODO: make this transformation more configurable
 513     com.stevesoft.pat.Regex empty;
 514     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 515     {
 516       empty = new com.stevesoft.pat.Regex(
 517       // replace commas and spaces with a semicolon
 518               "(\\s|[,; ])+", ";");
 519     }
 520     else
 521     {
 522       // just turn spaces and semicolons into single semicolons
 523       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 524     }
 525     textArea.setText(empty.replaceAll(textArea.getText()));
 526     // see if there's anthing to search with
 527     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 528             .getText()))
 529     {
 530       error += "Please enter a (semi-colon separated list of) database id(s)";
 531     }
 532     if (error.length() > 0)
 533     {
 534       showErrorMessage(error);
 535       resetDialog();
 536       return;
 537     }
 538     // TODO: Refactor to GUI independent code and write tests.
 539     // indicate if successive sources should be merged into one alignment.
 540     boolean addToLast = false;
 541     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 542     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 543     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 544             .iterator();
 545     String[] qries;
 546     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 547             .split(";"));
 548     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 549     int nqueries = qries.length;
 550
 551     FeatureSettingsModelI preferredFeatureColours = null;
 552     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 553     {
 554       if (!en.hasNext() && nextfetch.size() > 0)
 555       {
 556         en = nextfetch.iterator();
 557         nqueries = nextfetch.size();
 558         // save the remaining queries in the original array
 559         qries = nextfetch.toArray(new String[nqueries]);
 560         nextfetch = new ArrayList<String>();
 561       }
 562
 563       DbSourceProxy proxy = proxies.next();
 564       boolean isAliSource = false;
 565       try
 566       {
 567         // update status
 568         guiWindow
 569                 .setProgressBar(MessageManager.formatMessage(
 570                         "status.fetching_sequence_queries_from",
 571                         new String[] {
 572                             Integer.valueOf(nqueries).toString(),
 573                             proxy.getDbName() }), Thread.currentThread()
 574                         .hashCode());
 575         isAliSource = proxy.isAlignmentSource();
 576         if (proxy.getMaximumQueryCount() == 1)
 577         {
 578           while (en.hasNext())
 579           {
 580             String item = en.next();
 581             try
 582             {
 583               if (aresult != null)
 584               {
 585                 try
 586                 {
 587                   // give the server a chance to breathe
 588                   Thread.sleep(5);
 589                 } catch (Exception e)
 590                 {
 591                   //
 592                 }
 593
 594               }
 595
 596               AlignmentI indres = null;
 597               try
 598               {
 599                 indres = proxy.getSequenceRecords(item);
 600               } catch (OutOfMemoryError oome)
 601               {
 602                 new OOMWarning("fetching " + item + " from "
 603                         + proxy.getDbName(), oome, this);
 604               }
 605               if (indres != null)
 606               {
 607                 aresultq.add(item);
 608                 aresult.add(indres);
 609               }
 610               else
 611               {
 612                 nextfetch.add(item);
 613               }
 614             } catch (Exception e)
 615             {
 616               Cache.log.info(
 617                       "Error retrieving " + item
 618                       + " from " + proxy.getDbName(), e);
 619               nextfetch.add(item);
 620             }
 621           }
 622         }
 623         else
 624         {
 625           StringBuffer multiacc = new StringBuffer();
 626           ArrayList<String> tosend = new ArrayList<String>();
 627           while (en.hasNext())
 628           {
 629             String nel = en.next();
 630             tosend.add(nel);
 631             multiacc.append(nel);
 632             if (en.hasNext())
 633             {
 634               multiacc.append(proxy.getAccessionSeparator());
 635             }
 636           }
 637           try
 638           {
 639             AlignmentI rslt;
 640             SequenceI[] rs;
 641             List<String> nores = new ArrayList<String>();
 642             rslt = proxy.getSequenceRecords(multiacc.toString());
 643             if (rslt == null || rslt.getHeight() == 0)
 644             {
 645               // no results - pass on all queries to next source
 646               nextfetch.addAll(tosend);
 647             }
 648             else
 649             {
 650               aresultq.add(multiacc.toString());
 651               aresult.add(rslt);
 652
 653               rs = rslt.getSequencesArray();
 654               // search for each query in the dbrefs associated with each
 655               // sequence
 656               // returned.
 657               // ones we do not find will be used to query next source (if any)
 658               for (String q : tosend)
 659               {
 660                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 661                 dbr.setSource(proxy.getDbSource());
 662                 dbr.setVersion(null);
 663                 String accId = proxy.getAccessionIdFromQuery(q);
 664                 dbr.setAccessionId(accId);
 665                 boolean rfound = false;
 666                 for (int r = 0; r < rs.length; r++)
 667                 {
 668                   if (rs[r] != null)
 669                   {
 670                     found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
 671                     if (found != null && found.length > 0)
 672                     {
 673                       rfound = true;
 674                       rs[r] = null;
 675                     }
 676                   }
 677                 }
 678                 if (!rfound)
 679                 {
 680                   nextfetch.add(q);
 681                 }
 682               }
 683             }
 684           } catch (OutOfMemoryError oome)
 685           {
 686             new OOMWarning("fetching " + multiacc + " from "
 687                     + database.getSelectedItem(), oome, this);
 688           }
 689         }
 690
 691       } catch (Exception e)
 692       {
 693         showErrorMessage("Error retrieving " + textArea.getText()
 694                 + " from " + database.getSelectedItem());
 695         // error
 696         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 697         System.err.println("Retrieval failed for source ='"
 698                 + database.getSelectedItem() + "' and query\n'"
 699                 + textArea.getText() + "'\n");
 700         e.printStackTrace();
 701       } catch (OutOfMemoryError e)
 702       {
 703         // resets dialog box - so we don't use OOMwarning here.
 704         showErrorMessage("Out of Memory when retrieving "
 705                 + textArea.getText()
 706                 + " from "
 707                 + database.getSelectedItem()
 708                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 709         e.printStackTrace();
 710       } catch (Error e)
 711       {
 712         showErrorMessage("Serious Error retrieving " + textArea.getText()
 713                 + " from " + database.getSelectedItem());
 714         e.printStackTrace();
 715       }
 716       // Stack results ready for opening in alignment windows
 717       if (aresult != null && aresult.size() > 0)
 718       {
 719         FeatureSettingsModelI proxyColourScheme = proxy
 720                 .getFeatureColourScheme();
 721         if (proxyColourScheme != null)
 722         {
 723           preferredFeatureColours = proxyColourScheme;
 724         }
 725
 726         AlignmentI ar = null;
 727         if (isAliSource)
 728         {
 729           addToLast = false;
 730           // new window for each result
 731           while (aresult.size() > 0)
 732           {
 733             presult.add(aresult.remove(0));
 734             presultTitle.add(aresultq.remove(0) + " "
 735                     + getDefaultRetrievalTitle());
 736           }
 737         }
 738         else
 739         {
 740           String titl = null;
 741           if (addToLast && presult.size() > 0)
 742           {
 743             ar = presult.remove(presult.size() - 1);
 744             titl = presultTitle.remove(presultTitle.size() - 1);
 745           }
 746           // concatenate all results in one window
 747           while (aresult.size() > 0)
 748           {
 749             if (ar == null)
 750             {
 751               ar = aresult.remove(0);
 752             }
 753             else
 754             {
 755               ar.append(aresult.remove(0));
 756             }
 757             ;
 758           }
 759           addToLast = true;
 760           presult.add(ar);
 761           presultTitle.add(titl);
 762         }
 763       }
 764       guiWindow.setProgressBar(MessageManager
 765               .getString("status.finshed_querying"), Thread.currentThread()
 766               .hashCode());
 767     }
 768     guiWindow.setProgressBar(
 769             (presult.size() > 0) ? MessageManager
 770                     .getString("status.parsing_results") : MessageManager
 771                     .getString("status.processing"), Thread.currentThread()
 772                     .hashCode());
 773     // process results
 774     while (presult.size() > 0)
 775     {
 776       parseResult(presult.remove(0), presultTitle.remove(0), null,
 777               preferredFeatureColours);
 778     }
 779     // only remove visual delay after we finished parsing.
 780     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 781     if (nextfetch.size() > 0)
 782     {
 783       StringBuffer sb = new StringBuffer();
 784       sb.append("Didn't retrieve the following "
 785               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 786                       + " queries") + ": \n");
 787       int l = sb.length(), lr = 0;
 788       for (String s : nextfetch)
 789       {
 790         if (l != sb.length())
 791         {
 792           sb.append("; ");
 793         }
 794         if (lr - sb.length() > 40)
 795         {
 796           sb.append("\n");
 797         }
 798         sb.append(s);
 799       }
 800       showErrorMessage(sb.toString());
 801     }
 802     resetDialog();
 803   }
 804
 805   /**
 806    *
 807    * @return a standard title for any results retrieved using the currently
 808    *         selected source and settings
 809    */
 810   public String getDefaultRetrievalTitle()
 811   {
 812     return "Retrieved from " + database.getSelectedItem();
 813   }
 814
 815   AlignmentI parseResult(AlignmentI al, String title,
 816           String currentFileFormat,
 817           FeatureSettingsModelI preferredFeatureColours)
 818   {
 819
 820     if (al != null && al.getHeight() > 0)
 821     {
 822       if (title == null)
 823       {
 824         title = getDefaultRetrievalTitle();
 825       }
 826       if (alignFrame == null)
 827       {
 828         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 829                 AlignFrame.DEFAULT_HEIGHT);
 830         if (currentFileFormat != null)
 831         {
 832           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 833           // FORMAT FOR
 834           // NON-FormatAdapter Sourced
 835           // Alignments?
 836         }
 837
 838         SequenceFeature[] sfs = null;
 839         List<SequenceI> alsqs;
 840         synchronized (alsqs = al.getSequences())
 841         {
 842           for (SequenceI sq : alsqs)
 843           {
 844             if ((sfs = sq.getSequenceFeatures()) != null)
 845             {
 846               if (sfs.length > 0)
 847               {
 848                 af.setShowSeqFeatures(true);
 849                 break;
 850               }
 851             }
 852
 853           }
 854         }
 855
 856         if (preferredFeatureColours != null)
 857         {
 858           af.getViewport().applyFeaturesStyle(preferredFeatureColours);
 859         }
 860         if (Cache.getDefault("HIDE_INTRONS", true))
 861         {
 862           hideIntronsIfPresent(af);
 863         }
 864
 865         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 866                 AlignFrame.DEFAULT_HEIGHT);
 867
 868         af.statusBar.setText(MessageManager
 869                 .getString("label.successfully_pasted_alignment_file"));
 870
 871         try
 872         {
 873           af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
 874                   false));
 875         } catch (Exception ex)
 876         {
 877         }
 878       }
 879       else
 880       {
 881         alignFrame.viewport.addAlignment(al, title);
 882       }
 883     }
 884     return al;
 885   }
 886
 887   /**
 888    * Hide columns not containing 'exon' features, provided there are exon
 889    * features on the alignment
 890    *
 891    * @param af
 892    */
 893   public void hideIntronsIfPresent(AlignFrame af)
 894   {
 895     boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
 896             false,
 897             SequenceOntologyI.EXON);
 898     if (hasExons)
 899     {
 900       af.avc.markColumnsContainingFeatures(true, false, true,
 901               SequenceOntologyI.EXON);
 902       af.getViewport().hideSelectedColumns();
 903     }
 904   }
 905
 906   void showErrorMessage(final String error)
 907   {
 908     resetDialog();
 909     javax.swing.SwingUtilities.invokeLater(new Runnable()
 910     {
 911       @Override
 912       public void run()
 913       {
 914         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 915                 MessageManager.getString("label.error_retrieving_data"),
 916                 JOptionPane.WARNING_MESSAGE);
 917       }
 918     });
 919   }
 920
 921   public IProgressIndicator getProgressIndicator()
 922   {
 923     return progressIndicator;
 924   }
 925
 926   public void setProgressIndicator(IProgressIndicator progressIndicator)
 927   {
 928     this.progressIndicator = progressIndicator;
 929   }
 930 }