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