src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22 import java.util.List;
  23
  24 import java.awt.*;
  25 import java.awt.event.*;
  26
  27 import javax.swing.*;
  28 import javax.swing.tree.DefaultMutableTreeNode;
  29
  30 import com.stevesoft.pat.Regex;
  31
  32 import jalview.datamodel.*;
  33 import jalview.io.*;
  34 import jalview.util.DBRefUtils;
  35 import jalview.util.MessageManager;
  36 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  37 import jalview.ws.seqfetcher.DbSourceProxy;
  38 import java.awt.BorderLayout;
  39
  40 public class SequenceFetcher extends JPanel implements Runnable
  41 {
  42   // ASequenceFetcher sfetch;
  43   JInternalFrame frame;
  44
  45   IProgressIndicator guiWindow;
  46
  47   AlignFrame alignFrame;
  48
  49   StringBuffer result;
  50
  51   final String noDbSelected = "-- Select Database --";
  52
  53   private static jalview.ws.SequenceFetcher sfetch = null;
  54
  55   private static long lastDasSourceRegistry = -3;
  56
  57   private static DasSourceRegistryI dasRegistry = null;
  58
  59   private static boolean _initingFetcher = false;
  60
  61   private static Thread initingThread = null;
  62
  63   /**
  64    * Blocking method that initialises and returns the shared instance of the
  65    * SequenceFetcher client
  66    *
  67    * @param guiWindow
  68    *          - where the initialisation delay message should be shown
  69    * @return the singleton instance of the sequence fetcher client
  70    */
  71   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
  72           final IProgressIndicator guiWindow)
  73   {
  74     if (_initingFetcher && initingThread != null && initingThread.isAlive())
  75     {
  76       if (guiWindow != null)
  77       {
  78         guiWindow.setProgressBar(
  79                 "Waiting for Sequence Database Fetchers to initialise",
  80                 Thread.currentThread().hashCode());
  81       }
  82       // initting happening on another thread - so wait around to see if it
  83       // finishes.
  84       while (_initingFetcher && initingThread != null
  85               && initingThread.isAlive())
  86       {
  87         try
  88         {
  89           Thread.sleep(10);
  90         } catch (Exception e)
  91         {
  92         }
  93         ;
  94       }
  95       if (guiWindow != null)
  96       {
  97         guiWindow.setProgressBar(
  98                 "Waiting for Sequence Database Fetchers to initialise",
  99                 Thread.currentThread().hashCode());
 100       }
 101     }
 102     if (sfetch == null
 103             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
 104             || lastDasSourceRegistry != (jalview.bin.Cache
 105                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
 106                     .getDasSourceRegistry().getLocalSourceString())
 107                     .hashCode())
 108     {
 109       _initingFetcher = true;
 110       initingThread = Thread.currentThread();
 111       /**
 112        * give a visual indication that sequence fetcher construction is occuring
 113        */
 114       if (guiWindow != null)
 115       {
 116         guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
 117                 Thread.currentThread().hashCode());
 118       }
 119       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
 120       dasRegistry.refreshSources();
 121
 122       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 123       if (guiWindow != null)
 124       {
 125         guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
 126                 Thread.currentThread().hashCode());
 127       }
 128       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 129               .getLocalSourceString()).hashCode();
 130       sfetch = sf;
 131       _initingFetcher = false;
 132       initingThread = null;
 133     }
 134     return sfetch;
 135   }
 136
 137   public SequenceFetcher(IProgressIndicator guiIndic)
 138   {
 139     final IProgressIndicator guiWindow = guiIndic;
 140     final SequenceFetcher us = this;
 141     // launch initialiser thread
 142     Thread sf = new Thread(new Runnable()
 143     {
 144
 145       @Override
 146       public void run()
 147       {
 148         if (getSequenceFetcherSingleton(guiWindow) != null)
 149         {
 150           us.initGui(guiWindow);
 151         }
 152         else
 153         {
 154           javax.swing.SwingUtilities.invokeLater(new Runnable()
 155           {
 156             @Override
 157             public void run()
 158             {
 159               JOptionPane
 160                       .showInternalMessageDialog(
 161                               Desktop.desktop,
 162                               "Could not create the sequence fetcher client. Check error logs for details.",
 163                               "Couldn't create SequenceFetcher",
 164                               JOptionPane.ERROR_MESSAGE);
 165             }
 166           });
 167
 168           // raise warning dialog
 169         }
 170       }
 171     });
 172     sf.start();
 173   }
 174
 175   private class DatabaseAuthority extends DefaultMutableTreeNode
 176   {
 177
 178   };
 179
 180   private class DatabaseSource extends DefaultMutableTreeNode
 181   {
 182
 183   };
 184
 185   /**
 186    * called by thread spawned by constructor
 187    *
 188    * @param guiWindow
 189    */
 190   private void initGui(IProgressIndicator guiWindow)
 191   {
 192     this.guiWindow = guiWindow;
 193     if (guiWindow instanceof AlignFrame)
 194     {
 195       alignFrame = (AlignFrame) guiWindow;
 196     }
 197     database = new JDatabaseTree(sfetch);
 198     try
 199     {
 200       jbInit();
 201     } catch (Exception ex)
 202     {
 203       ex.printStackTrace();
 204     }
 205
 206     frame = new JInternalFrame();
 207     frame.setContentPane(this);
 208     if (new jalview.util.Platform().isAMac())
 209     {
 210       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 211     }
 212     else
 213     {
 214       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 215     }
 216   }
 217
 218   private String getFrameTitle()
 219   {
 220     return ((alignFrame == null) ? "New " : "Additional ")
 221             + "Sequence Fetcher";
 222   }
 223
 224   private void jbInit() throws Exception
 225   {
 226     this.setLayout(borderLayout2);
 227
 228     database.setFont(JvSwingUtils.getLabelFont());
 229     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 230     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 231     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 232     jLabel1.setText(MessageManager.getString("label.separate_multiple_accession_ids"));
 233
 234     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 235     replacePunctuation
 236             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 237     replacePunctuation.setText(MessageManager.getString("label.replace_commas_semicolons"));
 238     ok.setText(MessageManager.getString("action.ok"));
 239     ok.addActionListener(new ActionListener()
 240     {
 241       @Override
 242       public void actionPerformed(ActionEvent e)
 243       {
 244         ok_actionPerformed();
 245       }
 246     });
 247     clear.setText(MessageManager.getString("action.clear"));
 248     clear.addActionListener(new ActionListener()
 249     {
 250       @Override
 251       public void actionPerformed(ActionEvent e)
 252       {
 253         clear_actionPerformed();
 254       }
 255     });
 256
 257     example.setText(MessageManager.getString("label.example"));
 258     example.addActionListener(new ActionListener()
 259     {
 260       @Override
 261       public void actionPerformed(ActionEvent e)
 262       {
 263         example_actionPerformed();
 264       }
 265     });
 266     close.setText(MessageManager.getString("action.close"));
 267     close.addActionListener(new ActionListener()
 268     {
 269       @Override
 270       public void actionPerformed(ActionEvent e)
 271       {
 272         close_actionPerformed(e);
 273       }
 274     });
 275     textArea.setFont(JvSwingUtils.getLabelFont());
 276     textArea.setLineWrap(true);
 277     textArea.addKeyListener(new KeyAdapter()
 278     {
 279       @Override
 280       public void keyPressed(KeyEvent e)
 281       {
 282         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 283           ok_actionPerformed();
 284       }
 285     });
 286     jPanel3.setLayout(borderLayout1);
 287     borderLayout1.setVgap(5);
 288     jPanel1.add(ok);
 289     jPanel1.add(example);
 290     jPanel1.add(clear);
 291     jPanel1.add(close);
 292     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 293     jPanel2.setLayout(borderLayout3);
 294     databaseButt = database.getDatabaseSelectorButton();
 295     databaseButt.setFont(JvSwingUtils.getLabelFont());
 296     database.addActionListener(new ActionListener()
 297     {
 298
 299       @Override
 300       public void actionPerformed(ActionEvent e)
 301       {
 302         try
 303         {
 304           databaseButt.setText(database.getSelectedItem()
 305                   + (database.getSelectedSources().size() > 1 ? " (and "
 306                           + database.getSelectedSources().size()
 307                           + " others)" : ""));
 308           String eq = database.getExampleQueries();
 309           dbeg.setText(MessageManager.formatMessage("label.example_query_param", new String[]{eq}));
 310           boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 311           for (DbSourceProxy dbs : database.getSelectedSources())
 312           {
 313             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 314             {
 315               enablePunct = false;
 316               break;
 317             }
 318           }
 319           replacePunctuation.setEnabled(enablePunct);
 320
 321         } catch (Exception ex)
 322         {
 323           dbeg.setText("");
 324           replacePunctuation.setEnabled(true);
 325         }
 326         jPanel2.repaint();
 327       }
 328     });
 329     dbeg.setText("");
 330     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 331     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 332     JPanel jPanel2a = new JPanel(new BorderLayout());
 333     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 334     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 335     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 336     // jPanel2.setPreferredSize(new Dimension())
 337     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 338     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 339     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 340     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 341     jScrollPane1.getViewport().add(textArea);
 342
 343   }
 344
 345   protected void example_actionPerformed()
 346   {
 347     DbSourceProxy db = null;
 348     try
 349     {
 350       textArea.setText(database.getExampleQueries());
 351     } catch (Exception ex)
 352     {
 353     }
 354     jPanel3.repaint();
 355   }
 356
 357   protected void clear_actionPerformed()
 358   {
 359     textArea.setText("");
 360     jPanel3.repaint();
 361   }
 362
 363   JLabel dbeg = new JLabel();
 364
 365   JDatabaseTree database;
 366
 367   JButton databaseButt;
 368
 369   JLabel jLabel1 = new JLabel();
 370
 371   JCheckBox replacePunctuation = new JCheckBox();
 372
 373   JButton ok = new JButton();
 374
 375   JButton clear = new JButton();
 376
 377   JButton example = new JButton();
 378
 379   JButton close = new JButton();
 380
 381   JPanel jPanel1 = new JPanel();
 382
 383   JTextArea textArea = new JTextArea();
 384
 385   JScrollPane jScrollPane1 = new JScrollPane();
 386
 387   JPanel jPanel2 = new JPanel();
 388
 389   JPanel jPanel3 = new JPanel();
 390
 391   JPanel jPanel4 = new JPanel();
 392
 393   BorderLayout borderLayout1 = new BorderLayout();
 394
 395   BorderLayout borderLayout2 = new BorderLayout();
 396
 397   BorderLayout borderLayout3 = new BorderLayout();
 398
 399   public void close_actionPerformed(ActionEvent e)
 400   {
 401     try
 402     {
 403       frame.setClosed(true);
 404     } catch (Exception ex)
 405     {
 406     }
 407   }
 408
 409   public void ok_actionPerformed()
 410   {
 411     databaseButt.setEnabled(false);
 412     example.setEnabled(false);
 413     textArea.setEnabled(false);
 414     ok.setEnabled(false);
 415     close.setEnabled(false);
 416
 417     Thread worker = new Thread(this);
 418     worker.start();
 419   }
 420
 421   private void resetDialog()
 422   {
 423     databaseButt.setEnabled(true);
 424     example.setEnabled(true);
 425     textArea.setEnabled(true);
 426     ok.setEnabled(true);
 427     close.setEnabled(true);
 428   }
 429
 430   @Override
 431   public void run()
 432   {
 433     String error = "";
 434     if (!database.hasSelection())
 435     {
 436       error += "Please select the source database\n";
 437     }
 438     // TODO: make this transformation more configurable
 439     com.stevesoft.pat.Regex empty;
 440     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 441     {
 442       empty = new com.stevesoft.pat.Regex(
 443       // replace commas and spaces with a semicolon
 444               "(\\s|[,; ])+", ";");
 445     }
 446     else
 447     {
 448       // just turn spaces and semicolons into single semicolons
 449       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 450     }
 451     textArea.setText(empty.replaceAll(textArea.getText()));
 452     // see if there's anthing to search with
 453     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 454             .getText()))
 455     {
 456       error += "Please enter a (semi-colon separated list of) database id(s)";
 457     }
 458     if (error.length() > 0)
 459     {
 460       showErrorMessage(error);
 461       resetDialog();
 462       return;
 463     }
 464     // indicate if successive sources should be merged into one alignment.
 465     boolean addToLast = false;
 466     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 467     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 468     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 469             .iterator();
 470     String[] qries;
 471     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 472             .split(";"));
 473     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 474     int nqueries = qries.length;
 475     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 476     {
 477       if (!en.hasNext() && nextfetch.size() > 0)
 478       {
 479         en = nextfetch.iterator();
 480         nqueries = nextfetch.size();
 481         // save the remaining queries in the original array
 482         qries = nextfetch.toArray(new String[nqueries]);
 483         nextfetch = new ArrayList<String>();
 484       }
 485
 486       DbSourceProxy proxy = proxies.next();
 487       boolean isAliSource = false;
 488       try
 489       {
 490         // update status
 491         guiWindow.setProgressBar("Fetching " + nqueries
 492                 + " sequence queries from " + proxy.getDbName(), Thread
 493                 .currentThread().hashCode());
 494         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 495         if (proxy.getAccessionSeparator() == null)
 496         {
 497           while (en.hasNext())
 498           {
 499             String item = en.next();
 500             try
 501             {
 502               if (aresult != null)
 503               {
 504                 try
 505                 {
 506                   // give the server a chance to breathe
 507                   Thread.sleep(5);
 508                 } catch (Exception e)
 509                 {
 510                   //
 511                 }
 512
 513               }
 514
 515               AlignmentI indres = null;
 516               try
 517               {
 518                 indres = proxy.getSequenceRecords(item);
 519               } catch (OutOfMemoryError oome)
 520               {
 521                 new OOMWarning("fetching " + item + " from "
 522                         + proxy.getDbName(), oome, this);
 523               }
 524               if (indres != null)
 525               {
 526                 aresultq.add(item);
 527                 aresult.add(indres);
 528               }
 529               else
 530               {
 531                 nextfetch.add(item);
 532               }
 533             } catch (Exception e)
 534             {
 535               jalview.bin.Cache.log.info("Error retrieving " + item
 536                       + " from " + proxy.getDbName(), e);
 537               nextfetch.add(item);
 538             }
 539           }
 540         }
 541         else
 542         {
 543           StringBuffer multiacc = new StringBuffer();
 544           ArrayList<String> tosend = new ArrayList<String>();
 545           while (en.hasNext())
 546           {
 547             String nel = en.next();
 548             tosend.add(nel);
 549             multiacc.append(nel);
 550             if (en.hasNext())
 551             {
 552               multiacc.append(proxy.getAccessionSeparator());
 553             }
 554           }
 555           try
 556           {
 557             AlignmentI rslt;
 558             SequenceI[] rs;
 559             List<String> nores = new ArrayList<String>();
 560             rslt = proxy.getSequenceRecords(multiacc.toString());
 561             if (rslt == null || rslt.getHeight() == 0)
 562             {
 563               // no results - pass on all queries to next source
 564               nextfetch.addAll(tosend);
 565             }
 566             else
 567             {
 568               aresultq.add(multiacc.toString());
 569               aresult.add(rslt);
 570
 571               rs = rslt.getSequencesArray();
 572               // search for each query in the dbrefs associated with each
 573               // sequence
 574               // returned.
 575               // ones we do not find will be used to query next source (if any)
 576               for (String q : tosend)
 577               {
 578                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 579                 dbr.setSource(proxy.getDbSource());
 580                 dbr.setVersion(null);
 581                 if (proxy.getAccessionValidator() != null)
 582                 {
 583                   Regex vgr = proxy.getAccessionValidator();
 584                   vgr.search(q);
 585                   if (vgr.numSubs() > 0)
 586                   {
 587                     dbr.setAccessionId(vgr.stringMatched(1));
 588                   }
 589                   else
 590                   {
 591                     dbr.setAccessionId(vgr.stringMatched());
 592                   }
 593                 }
 594                 else
 595                 {
 596                   dbr.setAccessionId(q);
 597                 }
 598                 boolean rfound = false;
 599                 for (int r = 0; r < rs.length; r++)
 600                 {
 601                   if (rs[r] != null
 602                           && (found = DBRefUtils.searchRefs(
 603                                   rs[r].getDBRef(), dbr)) != null
 604                           && found.length > 0)
 605                   {
 606                     rfound = true;
 607                     rs[r] = null;
 608                     continue;
 609                   }
 610                 }
 611                 if (!rfound)
 612                 {
 613                   nextfetch.add(q);
 614                 }
 615               }
 616             }
 617           } catch (OutOfMemoryError oome)
 618           {
 619             new OOMWarning("fetching " + multiacc + " from "
 620                     + database.getSelectedItem(), oome, this);
 621           }
 622         }
 623
 624       } catch (Exception e)
 625       {
 626         showErrorMessage("Error retrieving " + textArea.getText()
 627                 + " from " + database.getSelectedItem());
 628         // error
 629         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 630         System.err.println("Retrieval failed for source ='"
 631                 + database.getSelectedItem() + "' and query\n'"
 632                 + textArea.getText() + "'\n");
 633         e.printStackTrace();
 634       } catch (OutOfMemoryError e)
 635       {
 636         // resets dialog box - so we don't use OOMwarning here.
 637         showErrorMessage("Out of Memory when retrieving "
 638                 + textArea.getText()
 639                 + " from "
 640                 + database.getSelectedItem()
 641                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 642         e.printStackTrace();
 643       } catch (Error e)
 644       {
 645         showErrorMessage("Serious Error retrieving " + textArea.getText()
 646                 + " from " + database.getSelectedItem());
 647         e.printStackTrace();
 648       }
 649       // Stack results ready for opening in alignment windows
 650       if (aresult != null && aresult.size() > 0)
 651       {
 652         AlignmentI ar = null;
 653         if (isAliSource)
 654         {
 655           addToLast = false;
 656           // new window for each result
 657           while (aresult.size() > 0)
 658           {
 659             presult.add(aresult.remove(0));
 660             presultTitle.add(aresultq.remove(0) + " "
 661                     + getDefaultRetrievalTitle());
 662           }
 663         }
 664         else
 665         {
 666           String titl = null;
 667           if (addToLast && presult.size() > 0)
 668           {
 669             ar = presult.remove(presult.size() - 1);
 670             titl = presultTitle.remove(presultTitle.size() - 1);
 671           }
 672           // concatenate all results in one window
 673           while (aresult.size() > 0)
 674           {
 675             if (ar == null)
 676             {
 677               ar = aresult.remove(0);
 678             }
 679             else
 680             {
 681               ar.append(aresult.remove(0));
 682             }
 683             ;
 684           }
 685           addToLast = true;
 686           presult.add(ar);
 687           presultTitle.add(titl);
 688         }
 689       }
 690       guiWindow.setProgressBar("Finished querying", Thread.currentThread()
 691               .hashCode());
 692     }
 693     guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
 694             : "Processing ..", Thread.currentThread().hashCode());
 695     // process results
 696     while (presult.size() > 0)
 697     {
 698       parseResult(presult.remove(0), presultTitle.remove(0), null);
 699     }
 700     // only remove visual delay after we finished parsing.
 701     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 702     if (nextfetch.size() > 0)
 703     {
 704       StringBuffer sb = new StringBuffer();
 705       sb.append("Didn't retrieve the following "
 706               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 707                       + " queries") + ": \n");
 708       int l = sb.length(), lr = 0;
 709       for (String s : nextfetch)
 710       {
 711         if (l != sb.length())
 712         {
 713           sb.append("; ");
 714         }
 715         if (lr - sb.length() > 40)
 716         {
 717           sb.append("\n");
 718         }
 719         sb.append(s);
 720       }
 721       showErrorMessage(sb.toString());
 722     }
 723     resetDialog();
 724   }
 725
 726   AlignmentI parseResult(String result, String title)
 727   {
 728     String format = new IdentifyFile().Identify(result, "Paste");
 729     Alignment sequences = null;
 730     if (FormatAdapter.isValidFormat(format))
 731     {
 732       sequences = null;
 733       try
 734       {
 735         sequences = new FormatAdapter().readFile(result.toString(),
 736                 "Paste", format);
 737       } catch (Exception ex)
 738       {
 739       }
 740
 741       if (sequences != null)
 742       {
 743         return parseResult(sequences, title, format);
 744       }
 745     }
 746     else
 747     {
 748       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 749               + database.getSelectedItem());
 750     }
 751
 752     return null;
 753   }
 754
 755   /**
 756    *
 757    * @return a standard title for any results retrieved using the currently
 758    *         selected source and settings
 759    */
 760   public String getDefaultRetrievalTitle()
 761   {
 762     return "Retrieved from " + database.getSelectedItem();
 763   }
 764
 765   AlignmentI parseResult(AlignmentI al, String title,
 766           String currentFileFormat)
 767   {
 768
 769     if (al != null && al.getHeight() > 0)
 770     {
 771       if (alignFrame == null)
 772       {
 773         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 774                 AlignFrame.DEFAULT_HEIGHT);
 775         if (currentFileFormat != null)
 776         {
 777           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 778           // FORMAT FOR
 779           // NON-FormatAdapter Sourced
 780           // Alignments?
 781         }
 782
 783         if (title == null)
 784         {
 785           title = getDefaultRetrievalTitle();
 786         }
 787         SequenceFeature[] sfs = null;
 788         List<SequenceI> alsqs;
 789         synchronized (alsqs = al.getSequences())
 790         {
 791           for (SequenceI sq : alsqs)
 792           {
 793             if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
 794             {
 795               if (sfs.length > 0)
 796               {
 797                 af.setShowSeqFeatures(true);
 798                 break;
 799               }
 800             }
 801
 802           }
 803         }
 804         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 805                 AlignFrame.DEFAULT_HEIGHT);
 806
 807         af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
 808
 809         try
 810         {
 811           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 812                   false));
 813         } catch (Exception ex)
 814         {
 815         }
 816       }
 817       else
 818       {
 819         for (int i = 0; i < al.getHeight(); i++)
 820         {
 821           alignFrame.viewport.getAlignment().addSequence(
 822                   al.getSequenceAt(i)); // this
 823           // also
 824           // creates
 825           // dataset
 826           // sequence
 827           // entries
 828         }
 829         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 830                 .getHeight());
 831         alignFrame.viewport.getAlignment().getWidth();
 832         alignFrame.viewport.firePropertyChange("alignment", null,
 833                 alignFrame.viewport.getAlignment().getSequences());
 834       }
 835     }
 836     return al;
 837   }
 838
 839   void showErrorMessage(final String error)
 840   {
 841     resetDialog();
 842     javax.swing.SwingUtilities.invokeLater(new Runnable()
 843     {
 844       @Override
 845       public void run()
 846       {
 847         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 848                 MessageManager.getString("label.error_retrieving_data"), JOptionPane.WARNING_MESSAGE);
 849       }
 850     });
 851   }
 852 }