src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21 import java.util.List;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25
  26 import javax.swing.*;
  27 import javax.swing.tree.DefaultMutableTreeNode;
  28 import javax.swing.tree.MutableTreeNode;
  29 import javax.swing.tree.TreeModel;
  30
  31 import jalview.datamodel.*;
  32 import jalview.io.*;
  33 import jalview.util.DBRefUtils;
  34 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  35 import jalview.ws.seqfetcher.DbSourceProxy;
  36 import jalview.ws.seqfetcher.DbSourceProxyImpl;
  37
  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       public void run()
 146       {
 147         if (getSequenceFetcherSingleton(guiWindow) != null)
 148         {
 149           us.initGui(guiWindow);
 150         }
 151         else
 152         {
 153           javax.swing.SwingUtilities.invokeLater(new Runnable()
 154           {
 155             public void run()
 156             {
 157               JOptionPane
 158                       .showInternalMessageDialog(
 159                               Desktop.desktop,
 160                               "Could not create the sequence fetcher client. Check error logs for details.",
 161                               "Couldn't create SequenceFetcher",
 162                               JOptionPane.ERROR_MESSAGE);
 163             }
 164           });
 165
 166           // raise warning dialog
 167         }
 168       }
 169     });
 170     sf.start();
 171   }
 172
 173   private class DatabaseAuthority extends DefaultMutableTreeNode
 174   {
 175
 176   };
 177
 178   private class DatabaseSource extends DefaultMutableTreeNode
 179   {
 180
 181   };
 182
 183   /**
 184    * called by thread spawned by constructor
 185    *
 186    * @param guiWindow
 187    */
 188   private void initGui(IProgressIndicator guiWindow)
 189   {
 190     this.guiWindow = guiWindow;
 191     if (guiWindow instanceof AlignFrame)
 192     {
 193       alignFrame = (AlignFrame) guiWindow;
 194     }
 195     database = new JDatabaseTree(sfetch);
 196     try
 197     {
 198       jbInit();
 199     } catch (Exception ex)
 200     {
 201       ex.printStackTrace();
 202     }
 203
 204     frame = new JInternalFrame();
 205     frame.setContentPane(this);
 206     if (new jalview.util.Platform().isAMac())
 207     {
 208       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 209     }
 210     else
 211     {
 212       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 213     }
 214   }
 215
 216   private String getFrameTitle()
 217   {
 218     return ((alignFrame == null) ? "New " : "Additional ")
 219             + "Sequence Fetcher";
 220   }
 221
 222   private void jbInit() throws Exception
 223   {
 224     this.setLayout(borderLayout2);
 225
 226     database.setFont(JvSwingUtils.getLabelFont());
 227     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 228     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 229     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 230     jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
 231
 232     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 233     replacePunctuation
 234             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 235     replacePunctuation.setText("Replace commas with semi-colons");
 236     ok.setText("OK");
 237     ok.addActionListener(new ActionListener()
 238     {
 239       public void actionPerformed(ActionEvent e)
 240       {
 241         ok_actionPerformed();
 242       }
 243     });
 244     clear.setText("Clear");
 245     clear.addActionListener(new ActionListener()
 246     {
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         clear_actionPerformed();
 250       }
 251     });
 252
 253     example.setText("Example");
 254     example.addActionListener(new ActionListener()
 255     {
 256       public void actionPerformed(ActionEvent e)
 257       {
 258         example_actionPerformed();
 259       }
 260     });
 261     close.setText("Close");
 262     close.addActionListener(new ActionListener()
 263     {
 264       public void actionPerformed(ActionEvent e)
 265       {
 266         close_actionPerformed(e);
 267       }
 268     });
 269     textArea.setFont(JvSwingUtils.getLabelFont());
 270     textArea.setLineWrap(true);
 271     textArea.addKeyListener(new KeyAdapter()
 272     {
 273       public void keyPressed(KeyEvent e)
 274       {
 275         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 276           ok_actionPerformed();
 277       }
 278     });
 279     jPanel3.setLayout(borderLayout1);
 280     borderLayout1.setVgap(5);
 281     jPanel1.add(ok);
 282     jPanel1.add(example);
 283     jPanel1.add(clear);
 284     jPanel1.add(close);
 285     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 286     jPanel2.setLayout(borderLayout3);
 287     databaseButt = database.getDatabaseSelectorButton();
 288     databaseButt.setFont(JvSwingUtils.getLabelFont());
 289     database.addActionListener(new ActionListener()
 290     {
 291
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         try
 295         {
 296           databaseButt.setText(database.getSelectedItem()
 297                   + (database.getSelectedSources().size() > 1 ? " (and "
 298                           + database.getSelectedSources().size()
 299                           + " others)" : ""));
 300           String eq = database.getExampleQueries();
 301           dbeg.setText("Example query: " + eq);
 302           boolean enablePunct=!(eq != null && eq.indexOf(",") > -1);
 303           for (DbSourceProxy dbs:database.getSelectedSources()) {
 304             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 305             {
 306               enablePunct = false;
 307               break;
 308             }
 309           }
 310           replacePunctuation.setEnabled(enablePunct);
 311
 312         } catch (Exception ex)
 313         {
 314           dbeg.setText("");
 315           replacePunctuation.setEnabled(true);
 316         }
 317         jPanel2.repaint();
 318       }
 319     });
 320     dbeg.setText("");
 321     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 322     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 323     JPanel jPanel2a = new JPanel(new BorderLayout());
 324     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 325     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 326     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 327     // jPanel2.setPreferredSize(new Dimension())
 328     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 329     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 330     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 331     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 332     jScrollPane1.getViewport().add(textArea);
 333
 334   }
 335
 336   protected void example_actionPerformed()
 337   {
 338     DbSourceProxy db = null;
 339     try
 340     {
 341       textArea.setText(database.getExampleQueries());
 342     } catch (Exception ex)
 343     {
 344     }
 345     jPanel3.repaint();
 346   }
 347
 348   protected void clear_actionPerformed()
 349   {
 350     textArea.setText("");
 351     jPanel3.repaint();
 352   }
 353
 354   JLabel dbeg = new JLabel();
 355
 356   JDatabaseTree database;
 357
 358   JButton databaseButt;
 359
 360   JLabel jLabel1 = new JLabel();
 361
 362   JCheckBox replacePunctuation = new JCheckBox();
 363
 364   JButton ok = new JButton();
 365
 366   JButton clear = new JButton();
 367
 368   JButton example = new JButton();
 369
 370   JButton close = new JButton();
 371
 372   JPanel jPanel1 = new JPanel();
 373
 374   JTextArea textArea = new JTextArea();
 375
 376   JScrollPane jScrollPane1 = new JScrollPane();
 377
 378   JPanel jPanel2 = new JPanel();
 379
 380   JPanel jPanel3 = new JPanel();
 381
 382   JPanel jPanel4 = new JPanel();
 383
 384   BorderLayout borderLayout1 = new BorderLayout();
 385
 386   BorderLayout borderLayout2 = new BorderLayout();
 387
 388   BorderLayout borderLayout3 = new BorderLayout();
 389
 390   public void close_actionPerformed(ActionEvent e)
 391   {
 392     try
 393     {
 394       frame.setClosed(true);
 395     } catch (Exception ex)
 396     {
 397     }
 398   }
 399
 400   public void ok_actionPerformed()
 401   {
 402     database.setEnabled(false);
 403     textArea.setEnabled(false);
 404     ok.setEnabled(false);
 405     close.setEnabled(false);
 406
 407     Thread worker = new Thread(this);
 408     worker.start();
 409   }
 410
 411   private void resetDialog()
 412   {
 413     database.setEnabled(true);
 414     textArea.setEnabled(true);
 415     ok.setEnabled(true);
 416     close.setEnabled(true);
 417   }
 418
 419   public void run()
 420   {
 421     String error = "";
 422     if (!database.hasSelection())
 423     {
 424       error += "Please select the source database\n";
 425     }
 426     // TODO: make this transformation more configurable
 427     com.stevesoft.pat.Regex empty;
 428     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 429     {
 430       empty = new com.stevesoft.pat.Regex(
 431       // replace commas and spaces with a semicolon
 432               "(\\s|[,; ])+", ";");
 433     }
 434     else
 435     {
 436       // just turn spaces and semicolons into single semicolons
 437       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 438     }
 439     textArea.setText(empty.replaceAll(textArea.getText()));
 440     // see if there's anthing to search with
 441     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 442             .getText()))
 443     {
 444       error += "Please enter a (semi-colon separated list of) database id(s)";
 445     }
 446     if (error.length() > 0)
 447     {
 448       showErrorMessage(error);
 449       resetDialog();
 450       return;
 451     }
 452     // indicate if successive sources should be merged into one alignment.
 453     boolean addToLast=false;
 454     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 455     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 456     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 457             .iterator();
 458     String[] qries;
 459     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 460             .split(";"));
 461     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 462     int nqueries = qries.length;
 463     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 464     {
 465       if (!en.hasNext() && nextfetch.size() > 0)
 466       {
 467         en = nextfetch.iterator();
 468         nqueries = nextfetch.size();
 469         // save the remaining queries in the original array
 470         qries = nextfetch.toArray(new String[nqueries]);
 471         nextfetch = new ArrayList<String>();
 472       }
 473
 474       DbSourceProxy proxy = proxies.next();
 475       boolean isAliSource = false;
 476       try
 477       {
 478         // update status
 479         guiWindow.setProgressBar("Fetching " + nqueries
 480                 + " sequence queries from " + proxy.getDbName(), Thread
 481                 .currentThread().hashCode());
 482         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 483         if (proxy.getAccessionSeparator() == null)
 484         {
 485           while (en.hasNext())
 486           {
 487             String item = en.next();
 488             try
 489             {
 490               if (aresult != null)
 491               {
 492                 try
 493                 {
 494                   // give the server a chance to breathe
 495                   Thread.sleep(5);
 496                 } catch (Exception e)
 497                 {
 498                   //
 499                 }
 500
 501               }
 502
 503               AlignmentI indres = null;
 504               try
 505               {
 506                 indres = proxy.getSequenceRecords(item);
 507               } catch (OutOfMemoryError oome)
 508               {
 509                 new OOMWarning("fetching " + item + " from "
 510                         + proxy.getDbName(), oome, this);
 511               }
 512               if (indres != null)
 513               {
 514                 aresultq.add(item);
 515                 aresult.add(indres);
 516               }
 517               else
 518               {
 519                 nextfetch.add(item);
 520               }
 521             } catch (Exception e)
 522             {
 523               jalview.bin.Cache.log.info("Error retrieving " + item
 524                       + " from " + proxy.getDbName(), e);
 525               nextfetch.add(item);
 526             }
 527           }
 528         }
 529         else
 530         {
 531           StringBuffer multiacc = new StringBuffer();
 532           ArrayList<String> tosend = new ArrayList<String>();
 533           while (en.hasNext())
 534           {
 535             String nel = en.next();
 536             tosend.add(nel);
 537             multiacc.append(nel);
 538             if (en.hasNext())
 539             {
 540               multiacc.append(proxy.getAccessionSeparator());
 541             }
 542           }
 543           try
 544           {
 545             AlignmentI rslt;
 546             SequenceI[] rs;
 547             List<String> nores = new ArrayList<String>();
 548             rslt = proxy.getSequenceRecords(multiacc.toString());
 549             if (rslt == null || rslt.getHeight() == 0)
 550             {
 551               // no results - pass on all queries to next source
 552               nextfetch.addAll(tosend);
 553             }
 554             else
 555             {
 556               aresultq.add(multiacc.toString());
 557               aresult.add(rslt);
 558
 559               rs = rslt.getSequencesArray();
 560               // search for each query in the dbrefs associated with each
 561               // sequence
 562               // returned.
 563               // ones we do not find will be used to query next source (if any)
 564               for (String q : tosend)
 565               {
 566                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 567                 dbr.setSource(proxy.getDbSource());
 568                 boolean rfound = false;
 569                 for (int r = 0; r < rs.length; r++)
 570                 {
 571                   if (rs[r] != null
 572                           && (found = DBRefUtils.searchRefs(
 573                                   rs[r].getDBRef(), dbr)) != null
 574                           && found.length > 0)
 575                   {
 576                     rfound = true;
 577                     rs[r] = null;
 578                     continue;
 579                   }
 580                 }
 581                 if (!rfound)
 582                 {
 583                   nextfetch.add(q);
 584                 }
 585               }
 586             }
 587           } catch (OutOfMemoryError oome)
 588           {
 589             new OOMWarning("fetching " + multiacc + " from "
 590                     + database.getSelectedItem(), oome, this);
 591           }
 592         }
 593
 594       } catch (Exception e)
 595       {
 596         showErrorMessage("Error retrieving " + textArea.getText()
 597                 + " from " + database.getSelectedItem());
 598         // error
 599         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 600         System.err.println("Retrieval failed for source ='"
 601                 + database.getSelectedItem() + "' and query\n'"
 602                 + textArea.getText() + "'\n");
 603         e.printStackTrace();
 604       } catch (OutOfMemoryError e)
 605       {
 606         // resets dialog box - so we don't use OOMwarning here.
 607         showErrorMessage("Out of Memory when retrieving "
 608                 + textArea.getText()
 609                 + " from "
 610                 + database.getSelectedItem()
 611                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 612         e.printStackTrace();
 613       } catch (Error e)
 614       {
 615         showErrorMessage("Serious Error retrieving " + textArea.getText()
 616                 + " from " + database.getSelectedItem());
 617         e.printStackTrace();
 618       }
 619       // Stack results ready for opening in alignment windows
 620       if (aresult != null && aresult.size() > 0)
 621       {
 622         AlignmentI ar = null;
 623         if (isAliSource)
 624         {
 625           addToLast=false;
 626           // new window for each result
 627           while (aresult.size() > 0)
 628           {
 629             presult.add(aresult.remove(0));
 630             presultTitle.add(aresultq.remove(0) + " "
 631                     + getDefaultRetrievalTitle());
 632           }
 633         }
 634         else
 635         {
 636           String titl=null;
 637           if (addToLast && presult.size()>0)
 638           {
 639             ar=presult.remove(presult.size()-1);
 640             titl=presultTitle.remove(presultTitle.size()-1);
 641           }
 642           // concatenate all results in one window
 643           while (aresult.size() > 0)
 644           {
 645             if (ar == null)
 646             {
 647               ar = aresult.remove(0);
 648             }
 649             else
 650             {
 651               ar.append(aresult.remove(0));
 652             }
 653             ;
 654           }
 655           addToLast=true;
 656           presult.add(ar);
 657           presultTitle.add(titl);
 658         }
 659       }
 660       guiWindow.setProgressBar("Finished querying", Thread.currentThread().hashCode());
 661     }
 662     guiWindow.setProgressBar((presult.size()>0) ? "Parsing results.":"Processing ..", Thread.currentThread().hashCode());
 663     // process results
 664     while (presult.size() > 0)
 665     {
 666       parseResult(presult.remove(0), presultTitle.remove(0), null);
 667     }
 668     // only remove visual delay after we finished parsing.
 669     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 670     if (nextfetch.size() > 0)
 671     {
 672       StringBuffer sb = new StringBuffer();
 673       sb.append("Didn't retrieve the following "
 674               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 675                       + " queries") + ": \n");
 676       int l = sb.length(),lr=0;
 677       for (String s : nextfetch)
 678       {
 679         if (l != sb.length())
 680         {
 681           sb.append("; ");
 682         }
 683         if (lr-sb.length()>40)
 684         {
 685           sb.append("\n");
 686         }
 687         sb.append(s);
 688       }
 689       showErrorMessage(sb.toString());
 690     }
 691     resetDialog();
 692   }
 693
 694   AlignmentI parseResult(String result, String title)
 695   {
 696     String format = new IdentifyFile().Identify(result, "Paste");
 697     Alignment sequences = null;
 698     if (FormatAdapter.isValidFormat(format))
 699     {
 700       sequences = null;
 701       try
 702       {
 703         sequences = new FormatAdapter().readFile(result.toString(),
 704                 "Paste", format);
 705       } catch (Exception ex)
 706       {
 707       }
 708
 709       if (sequences != null)
 710       {
 711         return parseResult(sequences, title, format);
 712       }
 713     }
 714     else
 715     {
 716       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 717               + database.getSelectedItem());
 718     }
 719
 720     return null;
 721   }
 722
 723   /**
 724    *
 725    * @return a standard title for any results retrieved using the currently
 726    *         selected source and settings
 727    */
 728   public String getDefaultRetrievalTitle()
 729   {
 730     return "Retrieved from " + database.getSelectedItem();
 731   }
 732
 733   AlignmentI parseResult(AlignmentI al, String title,
 734           String currentFileFormat)
 735   {
 736
 737     if (al != null && al.getHeight() > 0)
 738     {
 739       if (alignFrame == null)
 740       {
 741         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 742                 AlignFrame.DEFAULT_HEIGHT);
 743         if (currentFileFormat != null)
 744         {
 745           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 746           // FORMAT FOR
 747           // NON-FormatAdapter Sourced
 748           // Alignments?
 749         }
 750
 751         if (title == null)
 752         {
 753           title = getDefaultRetrievalTitle();
 754         }
 755         SequenceFeature[] sfs = null;
 756         for (Enumeration sq = al.getSequences().elements(); sq
 757                 .hasMoreElements();)
 758         {
 759           if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
 760                   .getSequenceFeatures()) != null)
 761           {
 762             if (sfs.length > 0)
 763             {
 764               af.setShowSeqFeatures(true);
 765               break;
 766             }
 767           }
 768
 769         }
 770         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 771                 AlignFrame.DEFAULT_HEIGHT);
 772
 773         af.statusBar.setText("Successfully pasted alignment file");
 774
 775         try
 776         {
 777           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 778                   false));
 779         } catch (Exception ex)
 780         {
 781         }
 782       }
 783       else
 784       {
 785         for (int i = 0; i < al.getHeight(); i++)
 786         {
 787           alignFrame.viewport.getAlignment().addSequence(
 788                   al.getSequenceAt(i)); // this
 789           // also
 790           // creates
 791           // dataset
 792           // sequence
 793           // entries
 794         }
 795         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 796                 .getHeight());
 797         alignFrame.viewport.getAlignment().getWidth();
 798         alignFrame.viewport.firePropertyChange("alignment", null,
 799                 alignFrame.viewport.getAlignment().getSequences());
 800       }
 801     }
 802     return al;
 803   }
 804
 805   void showErrorMessage(final String error)
 806   {
 807     resetDialog();
 808     javax.swing.SwingUtilities.invokeLater(new Runnable()
 809     {
 810       public void run()
 811       {
 812         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 813                 "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
 814       }
 815     });
 816   }
 817 }