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