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           {
 311             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 312             {
 313               enablePunct = false;
 314               break;
 315             }
 316           }
 317           replacePunctuation.setEnabled(enablePunct);
 318
 319         } catch (Exception ex)
 320         {
 321           dbeg.setText("");
 322           replacePunctuation.setEnabled(true);
 323         }
 324         jPanel2.repaint();
 325       }
 326     });
 327     dbeg.setText("");
 328     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 329     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 330     JPanel jPanel2a = new JPanel(new BorderLayout());
 331     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 332     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 333     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 334     // jPanel2.setPreferredSize(new Dimension())
 335     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 336     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 337     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 338     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 339     jScrollPane1.getViewport().add(textArea);
 340
 341   }
 342
 343   protected void example_actionPerformed()
 344   {
 345     DbSourceProxy db = null;
 346     try
 347     {
 348       textArea.setText(database.getExampleQueries());
 349     } catch (Exception ex)
 350     {
 351     }
 352     jPanel3.repaint();
 353   }
 354
 355   protected void clear_actionPerformed()
 356   {
 357     textArea.setText("");
 358     jPanel3.repaint();
 359   }
 360
 361   JLabel dbeg = new JLabel();
 362
 363   JDatabaseTree database;
 364
 365   JButton databaseButt;
 366
 367   JLabel jLabel1 = new JLabel();
 368
 369   JCheckBox replacePunctuation = new JCheckBox();
 370
 371   JButton ok = new JButton();
 372
 373   JButton clear = new JButton();
 374
 375   JButton example = new JButton();
 376
 377   JButton close = new JButton();
 378
 379   JPanel jPanel1 = new JPanel();
 380
 381   JTextArea textArea = new JTextArea();
 382
 383   JScrollPane jScrollPane1 = new JScrollPane();
 384
 385   JPanel jPanel2 = new JPanel();
 386
 387   JPanel jPanel3 = new JPanel();
 388
 389   JPanel jPanel4 = new JPanel();
 390
 391   BorderLayout borderLayout1 = new BorderLayout();
 392
 393   BorderLayout borderLayout2 = new BorderLayout();
 394
 395   BorderLayout borderLayout3 = new BorderLayout();
 396
 397   public void close_actionPerformed(ActionEvent e)
 398   {
 399     try
 400     {
 401       frame.setClosed(true);
 402     } catch (Exception ex)
 403     {
 404     }
 405   }
 406
 407   public void ok_actionPerformed()
 408   {
 409     database.setEnabled(false);
 410     textArea.setEnabled(false);
 411     ok.setEnabled(false);
 412     close.setEnabled(false);
 413
 414     Thread worker = new Thread(this);
 415     worker.start();
 416   }
 417
 418   private void resetDialog()
 419   {
 420     database.setEnabled(true);
 421     textArea.setEnabled(true);
 422     ok.setEnabled(true);
 423     close.setEnabled(true);
 424   }
 425
 426   @Override
 427   public void run()
 428   {
 429     String error = "";
 430     if (!database.hasSelection())
 431     {
 432       error += "Please select the source database\n";
 433     }
 434     // TODO: make this transformation more configurable
 435     com.stevesoft.pat.Regex empty;
 436     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 437     {
 438       empty = new com.stevesoft.pat.Regex(
 439       // replace commas and spaces with a semicolon
 440               "(\\s|[,; ])+", ";");
 441     }
 442     else
 443     {
 444       // just turn spaces and semicolons into single semicolons
 445       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 446     }
 447     textArea.setText(empty.replaceAll(textArea.getText()));
 448     // see if there's anthing to search with
 449     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 450             .getText()))
 451     {
 452       error += "Please enter a (semi-colon separated list of) database id(s)";
 453     }
 454     if (error.length() > 0)
 455     {
 456       showErrorMessage(error);
 457       resetDialog();
 458       return;
 459     }
 460     // indicate if successive sources should be merged into one alignment.
 461     boolean addToLast = false;
 462     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 463     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 464     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 465             .iterator();
 466     String[] qries;
 467     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 468             .split(";"));
 469     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 470     int nqueries = qries.length;
 471     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 472     {
 473       if (!en.hasNext() && nextfetch.size() > 0)
 474       {
 475         en = nextfetch.iterator();
 476         nqueries = nextfetch.size();
 477         // save the remaining queries in the original array
 478         qries = nextfetch.toArray(new String[nqueries]);
 479         nextfetch = new ArrayList<String>();
 480       }
 481
 482       DbSourceProxy proxy = proxies.next();
 483       boolean isAliSource = false;
 484       try
 485       {
 486         // update status
 487         guiWindow.setProgressBar("Fetching " + nqueries
 488                 + " sequence queries from " + proxy.getDbName(), Thread
 489                 .currentThread().hashCode());
 490         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 491         if (proxy.getAccessionSeparator() == null)
 492         {
 493           while (en.hasNext())
 494           {
 495             String item = en.next();
 496             try
 497             {
 498               if (aresult != null)
 499               {
 500                 try
 501                 {
 502                   // give the server a chance to breathe
 503                   Thread.sleep(5);
 504                 } catch (Exception e)
 505                 {
 506                   //
 507                 }
 508
 509               }
 510
 511               AlignmentI indres = null;
 512               try
 513               {
 514                 indres = proxy.getSequenceRecords(item);
 515               } catch (OutOfMemoryError oome)
 516               {
 517                 new OOMWarning("fetching " + item + " from "
 518                         + proxy.getDbName(), oome, this);
 519               }
 520               if (indres != null)
 521               {
 522                 aresultq.add(item);
 523                 aresult.add(indres);
 524               }
 525               else
 526               {
 527                 nextfetch.add(item);
 528               }
 529             } catch (Exception e)
 530             {
 531               jalview.bin.Cache.log.info("Error retrieving " + item
 532                       + " from " + proxy.getDbName(), e);
 533               nextfetch.add(item);
 534             }
 535           }
 536         }
 537         else
 538         {
 539           StringBuffer multiacc = new StringBuffer();
 540           ArrayList<String> tosend = new ArrayList<String>();
 541           while (en.hasNext())
 542           {
 543             String nel = en.next();
 544             tosend.add(nel);
 545             multiacc.append(nel);
 546             if (en.hasNext())
 547             {
 548               multiacc.append(proxy.getAccessionSeparator());
 549             }
 550           }
 551           try
 552           {
 553             AlignmentI rslt;
 554             SequenceI[] rs;
 555             List<String> nores = new ArrayList<String>();
 556             rslt = proxy.getSequenceRecords(multiacc.toString());
 557             if (rslt == null || rslt.getHeight() == 0)
 558             {
 559               // no results - pass on all queries to next source
 560               nextfetch.addAll(tosend);
 561             }
 562             else
 563             {
 564               aresultq.add(multiacc.toString());
 565               aresult.add(rslt);
 566
 567               rs = rslt.getSequencesArray();
 568               // search for each query in the dbrefs associated with each
 569               // sequence
 570               // returned.
 571               // ones we do not find will be used to query next source (if any)
 572               for (String q : tosend)
 573               {
 574                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 575                 dbr.setSource(proxy.getDbSource());
 576                 dbr.setVersion(null);
 577                 if (proxy.getAccessionValidator() != null)
 578                 {
 579                   Regex vgr = proxy.getAccessionValidator();
 580                   vgr.search(q);
 581                   if (vgr.numSubs() > 0)
 582                   {
 583                     dbr.setAccessionId(vgr.stringMatched(1));
 584                   }
 585                   else
 586                   {
 587                     dbr.setAccessionId(vgr.stringMatched());
 588                   }
 589                 }
 590                 else
 591                 {
 592                   dbr.setAccessionId(q);
 593                 }
 594                 boolean rfound = false;
 595                 for (int r = 0; r < rs.length; r++)
 596                 {
 597                   if (rs[r] != null
 598                           && (found = DBRefUtils.searchRefs(
 599                                   rs[r].getDBRef(), dbr)) != null
 600                           && found.length > 0)
 601                   {
 602                     rfound = true;
 603                     rs[r] = null;
 604                     continue;
 605                   }
 606                 }
 607                 if (!rfound)
 608                 {
 609                   nextfetch.add(q);
 610                 }
 611               }
 612             }
 613           } catch (OutOfMemoryError oome)
 614           {
 615             new OOMWarning("fetching " + multiacc + " from "
 616                     + database.getSelectedItem(), oome, this);
 617           }
 618         }
 619
 620       } catch (Exception e)
 621       {
 622         showErrorMessage("Error retrieving " + textArea.getText()
 623                 + " from " + database.getSelectedItem());
 624         // error
 625         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 626         System.err.println("Retrieval failed for source ='"
 627                 + database.getSelectedItem() + "' and query\n'"
 628                 + textArea.getText() + "'\n");
 629         e.printStackTrace();
 630       } catch (OutOfMemoryError e)
 631       {
 632         // resets dialog box - so we don't use OOMwarning here.
 633         showErrorMessage("Out of Memory when retrieving "
 634                 + textArea.getText()
 635                 + " from "
 636                 + database.getSelectedItem()
 637                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 638         e.printStackTrace();
 639       } catch (Error e)
 640       {
 641         showErrorMessage("Serious Error retrieving " + textArea.getText()
 642                 + " from " + database.getSelectedItem());
 643         e.printStackTrace();
 644       }
 645       // Stack results ready for opening in alignment windows
 646       if (aresult != null && aresult.size() > 0)
 647       {
 648         AlignmentI ar = null;
 649         if (isAliSource)
 650         {
 651           addToLast = false;
 652           // new window for each result
 653           while (aresult.size() > 0)
 654           {
 655             presult.add(aresult.remove(0));
 656             presultTitle.add(aresultq.remove(0) + " "
 657                     + getDefaultRetrievalTitle());
 658           }
 659         }
 660         else
 661         {
 662           String titl = null;
 663           if (addToLast && presult.size() > 0)
 664           {
 665             ar = presult.remove(presult.size() - 1);
 666             titl = presultTitle.remove(presultTitle.size() - 1);
 667           }
 668           // concatenate all results in one window
 669           while (aresult.size() > 0)
 670           {
 671             if (ar == null)
 672             {
 673               ar = aresult.remove(0);
 674             }
 675             else
 676             {
 677               ar.append(aresult.remove(0));
 678             }
 679             ;
 680           }
 681           addToLast = true;
 682           presult.add(ar);
 683           presultTitle.add(titl);
 684         }
 685       }
 686       guiWindow.setProgressBar("Finished querying", Thread.currentThread()
 687               .hashCode());
 688     }
 689     guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
 690             : "Processing ..", Thread.currentThread().hashCode());
 691     // process results
 692     while (presult.size() > 0)
 693     {
 694       parseResult(presult.remove(0), presultTitle.remove(0), null);
 695     }
 696     // only remove visual delay after we finished parsing.
 697     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 698     if (nextfetch.size() > 0)
 699     {
 700       StringBuffer sb = new StringBuffer();
 701       sb.append("Didn't retrieve the following "
 702               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 703                       + " queries") + ": \n");
 704       int l = sb.length(), lr = 0;
 705       for (String s : nextfetch)
 706       {
 707         if (l != sb.length())
 708         {
 709           sb.append("; ");
 710         }
 711         if (lr - sb.length() > 40)
 712         {
 713           sb.append("\n");
 714         }
 715         sb.append(s);
 716       }
 717       showErrorMessage(sb.toString());
 718     }
 719     resetDialog();
 720   }
 721
 722   AlignmentI parseResult(String result, String title)
 723   {
 724     String format = new IdentifyFile().Identify(result, "Paste");
 725     Alignment sequences = null;
 726     if (FormatAdapter.isValidFormat(format))
 727     {
 728       sequences = null;
 729       try
 730       {
 731         sequences = new FormatAdapter().readFile(result.toString(),
 732                 "Paste", format);
 733       } catch (Exception ex)
 734       {
 735       }
 736
 737       if (sequences != null)
 738       {
 739         return parseResult(sequences, title, format);
 740       }
 741     }
 742     else
 743     {
 744       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 745               + database.getSelectedItem());
 746     }
 747
 748     return null;
 749   }
 750
 751   /**
 752    *
 753    * @return a standard title for any results retrieved using the currently
 754    *         selected source and settings
 755    */
 756   public String getDefaultRetrievalTitle()
 757   {
 758     return "Retrieved from " + database.getSelectedItem();
 759   }
 760
 761   AlignmentI parseResult(AlignmentI al, String title,
 762           String currentFileFormat)
 763   {
 764
 765     if (al != null && al.getHeight() > 0)
 766     {
 767       if (alignFrame == null)
 768       {
 769         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 770                 AlignFrame.DEFAULT_HEIGHT);
 771         if (currentFileFormat != null)
 772         {
 773           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 774           // FORMAT FOR
 775           // NON-FormatAdapter Sourced
 776           // Alignments?
 777         }
 778
 779         if (title == null)
 780         {
 781           title = getDefaultRetrievalTitle();
 782         }
 783         SequenceFeature[] sfs = null;
 784         List<SequenceI> alsqs;
 785         synchronized (alsqs = al.getSequences())
 786         {
 787           for (SequenceI sq : alsqs)
 788           {
 789             if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
 790             {
 791               if (sfs.length > 0)
 792               {
 793                 af.setShowSeqFeatures(true);
 794                 break;
 795               }
 796             }
 797
 798           }
 799         }
 800         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 801                 AlignFrame.DEFAULT_HEIGHT);
 802
 803         af.statusBar.setText("Successfully pasted alignment file");
 804
 805         try
 806         {
 807           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 808                   false));
 809         } catch (Exception ex)
 810         {
 811         }
 812       }
 813       else
 814       {
 815         for (int i = 0; i < al.getHeight(); i++)
 816         {
 817           alignFrame.viewport.getAlignment().addSequence(
 818                   al.getSequenceAt(i)); // this
 819           // also
 820           // creates
 821           // dataset
 822           // sequence
 823           // entries
 824         }
 825         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 826                 .getHeight());
 827         alignFrame.viewport.getAlignment().getWidth();
 828         alignFrame.viewport.firePropertyChange("alignment", null,
 829                 alignFrame.viewport.getAlignment().getSequences());
 830       }
 831     }
 832     return al;
 833   }
 834
 835   void showErrorMessage(final String error)
 836   {
 837     resetDialog();
 838     javax.swing.SwingUtilities.invokeLater(new Runnable()
 839     {
 840       @Override
 841       public void run()
 842       {
 843         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 844                 "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
 845       }
 846     });
 847   }
 848 }