src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.util.*;
  24 import java.util.List;
  25
  26 import java.awt.*;
  27 import java.awt.event.*;
  28
  29 import javax.swing.*;
  30 import javax.swing.tree.DefaultMutableTreeNode;
  31
  32 import com.stevesoft.pat.Regex;
  33
  34 import jalview.datamodel.*;
  35 import jalview.io.*;
  36 import jalview.util.DBRefUtils;
  37 import jalview.util.MessageManager;
  38 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  39 import jalview.ws.seqfetcher.DbSourceProxy;
  40 import java.awt.BorderLayout;
  41
  42 public class SequenceFetcher extends JPanel implements Runnable
  43 {
  44   // ASequenceFetcher sfetch;
  45   JInternalFrame frame;
  46
  47   IProgressIndicator guiWindow;
  48
  49   AlignFrame alignFrame;
  50
  51   StringBuffer result;
  52
  53   final String noDbSelected = "-- Select Database --";
  54
  55   private static jalview.ws.SequenceFetcher sfetch = null;
  56
  57   private static long lastDasSourceRegistry = -3;
  58
  59   private static DasSourceRegistryI dasRegistry = null;
  60
  61   private static boolean _initingFetcher = false;
  62
  63   private static Thread initingThread = null;
  64
  65   /**
  66    * Blocking method that initialises and returns the shared instance of the
  67    * SequenceFetcher client
  68    *
  69    * @param guiWindow
  70    *          - where the initialisation delay message should be shown
  71    * @return the singleton instance of the sequence fetcher client
  72    */
  73   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
  74           final IProgressIndicator guiWindow)
  75   {
  76     if (_initingFetcher && initingThread != null && initingThread.isAlive())
  77     {
  78       if (guiWindow != null)
  79       {
  80         guiWindow.setProgressBar(
  81                 MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
  82                 Thread.currentThread().hashCode());
  83       }
  84       // initting happening on another thread - so wait around to see if it
  85       // finishes.
  86       while (_initingFetcher && initingThread != null
  87               && initingThread.isAlive())
  88       {
  89         try
  90         {
  91           Thread.sleep(10);
  92         } catch (Exception e)
  93         {
  94         }
  95         ;
  96       }
  97       if (guiWindow != null)
  98       {
  99         guiWindow.setProgressBar(
 100                         MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
 101                 Thread.currentThread().hashCode());
 102       }
 103     }
 104     if (sfetch == null
 105             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
 106             || lastDasSourceRegistry != (jalview.bin.Cache
 107                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
 108                     .getDasSourceRegistry().getLocalSourceString())
 109                     .hashCode())
 110     {
 111       _initingFetcher = true;
 112       initingThread = Thread.currentThread();
 113       /**
 114        * give a visual indication that sequence fetcher construction is occuring
 115        */
 116       if (guiWindow != null)
 117       {
 118         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
 119                 Thread.currentThread().hashCode());
 120       }
 121       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
 122       dasRegistry.refreshSources();
 123
 124       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 125       if (guiWindow != null)
 126       {
 127         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
 128                 Thread.currentThread().hashCode());
 129       }
 130       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 131               .getLocalSourceString()).hashCode();
 132       sfetch = sf;
 133       _initingFetcher = false;
 134       initingThread = null;
 135     }
 136     return sfetch;
 137   }
 138
 139   public SequenceFetcher(IProgressIndicator guiIndic)
 140   {
 141     final IProgressIndicator guiWindow = guiIndic;
 142     final SequenceFetcher us = this;
 143     // launch initialiser thread
 144     Thread sf = new Thread(new Runnable()
 145     {
 146
 147       @Override
 148       public void run()
 149       {
 150         if (getSequenceFetcherSingleton(guiWindow) != null)
 151         {
 152           us.initGui(guiWindow);
 153         }
 154         else
 155         {
 156           javax.swing.SwingUtilities.invokeLater(new Runnable()
 157           {
 158             @Override
 159             public void run()
 160             {
 161               JOptionPane
 162                       .showInternalMessageDialog(
 163                               Desktop.desktop,
 164                               MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
 165                               MessageManager.getString("label.couldnt_create_sequence_fetcher"),
 166                               JOptionPane.ERROR_MESSAGE);
 167             }
 168           });
 169
 170           // raise warning dialog
 171         }
 172       }
 173     });
 174     sf.start();
 175   }
 176
 177   private class DatabaseAuthority extends DefaultMutableTreeNode
 178   {
 179
 180   };
 181
 182   private class DatabaseSource extends DefaultMutableTreeNode
 183   {
 184
 185   };
 186
 187   /**
 188    * called by thread spawned by constructor
 189    *
 190    * @param guiWindow
 191    */
 192   private void initGui(IProgressIndicator guiWindow)
 193   {
 194     this.guiWindow = guiWindow;
 195     if (guiWindow instanceof AlignFrame)
 196     {
 197       alignFrame = (AlignFrame) guiWindow;
 198     }
 199     database = new JDatabaseTree(sfetch);
 200     try
 201     {
 202       jbInit();
 203     } catch (Exception ex)
 204     {
 205       ex.printStackTrace();
 206     }
 207
 208     frame = new JInternalFrame();
 209     frame.setContentPane(this);
 210     if (new jalview.util.Platform().isAMac())
 211     {
 212       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 213     }
 214     else
 215     {
 216       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 217     }
 218   }
 219
 220   private String getFrameTitle()
 221   {
 222     return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
 223   }
 224
 225   private void jbInit() throws Exception
 226   {
 227     this.setLayout(borderLayout2);
 228
 229     database.setFont(JvSwingUtils.getLabelFont());
 230     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 231     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 232     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 233     jLabel1.setText(MessageManager
 234             .getString("label.separate_multiple_accession_ids"));
 235
 236     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 237     replacePunctuation
 238             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 239     replacePunctuation.setText(MessageManager
 240             .getString("label.replace_commas_semicolons"));
 241     ok.setText(MessageManager.getString("action.ok"));
 242     ok.addActionListener(new ActionListener()
 243     {
 244       @Override
 245       public void actionPerformed(ActionEvent e)
 246       {
 247         ok_actionPerformed();
 248       }
 249     });
 250     clear.setText(MessageManager.getString("action.clear"));
 251     clear.addActionListener(new ActionListener()
 252     {
 253       @Override
 254       public void actionPerformed(ActionEvent e)
 255       {
 256         clear_actionPerformed();
 257       }
 258     });
 259
 260     example.setText(MessageManager.getString("label.example"));
 261     example.addActionListener(new ActionListener()
 262     {
 263       @Override
 264       public void actionPerformed(ActionEvent e)
 265       {
 266         example_actionPerformed();
 267       }
 268     });
 269     close.setText(MessageManager.getString("action.close"));
 270     close.addActionListener(new ActionListener()
 271     {
 272       @Override
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         close_actionPerformed(e);
 276       }
 277     });
 278     textArea.setFont(JvSwingUtils.getLabelFont());
 279     textArea.setLineWrap(true);
 280     textArea.addKeyListener(new KeyAdapter()
 281     {
 282       @Override
 283       public void keyPressed(KeyEvent e)
 284       {
 285         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 286           ok_actionPerformed();
 287       }
 288     });
 289     jPanel3.setLayout(borderLayout1);
 290     borderLayout1.setVgap(5);
 291     jPanel1.add(ok);
 292     jPanel1.add(example);
 293     jPanel1.add(clear);
 294     jPanel1.add(close);
 295     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 296     jPanel2.setLayout(borderLayout3);
 297     databaseButt = database.getDatabaseSelectorButton();
 298     databaseButt.setFont(JvSwingUtils.getLabelFont());
 299     database.addActionListener(new ActionListener()
 300     {
 301
 302       @Override
 303       public void actionPerformed(ActionEvent e)
 304       {
 305         try
 306         {
 307           databaseButt.setText(database.getSelectedItem()
 308                   + (database.getSelectedSources().size() > 1 ? " (and "
 309                           + database.getSelectedSources().size()
 310                           + " others)" : ""));
 311           String eq = database.getExampleQueries();
 312           dbeg.setText(MessageManager.formatMessage(
 313                   "label.example_query_param", new String[]
 314                   { eq }));
 315           boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 316           for (DbSourceProxy dbs : database.getSelectedSources())
 317           {
 318             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 319             {
 320               enablePunct = false;
 321               break;
 322             }
 323           }
 324           replacePunctuation.setEnabled(enablePunct);
 325
 326         } catch (Exception ex)
 327         {
 328           dbeg.setText("");
 329           replacePunctuation.setEnabled(true);
 330         }
 331         jPanel2.repaint();
 332       }
 333     });
 334     dbeg.setText("");
 335     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 336     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 337     JPanel jPanel2a = new JPanel(new BorderLayout());
 338     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 339     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 340     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 341     // jPanel2.setPreferredSize(new Dimension())
 342     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 343     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 344     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 345     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 346     jScrollPane1.getViewport().add(textArea);
 347
 348   }
 349
 350   protected void example_actionPerformed()
 351   {
 352     DbSourceProxy db = null;
 353     try
 354     {
 355       textArea.setText(database.getExampleQueries());
 356     } catch (Exception ex)
 357     {
 358     }
 359     jPanel3.repaint();
 360   }
 361
 362   protected void clear_actionPerformed()
 363   {
 364     textArea.setText("");
 365     jPanel3.repaint();
 366   }
 367
 368   JLabel dbeg = new JLabel();
 369
 370   JDatabaseTree database;
 371
 372   JButton databaseButt;
 373
 374   JLabel jLabel1 = new JLabel();
 375
 376   JCheckBox replacePunctuation = new JCheckBox();
 377
 378   JButton ok = new JButton();
 379
 380   JButton clear = new JButton();
 381
 382   JButton example = new JButton();
 383
 384   JButton close = new JButton();
 385
 386   JPanel jPanel1 = new JPanel();
 387
 388   JTextArea textArea = new JTextArea();
 389
 390   JScrollPane jScrollPane1 = new JScrollPane();
 391
 392   JPanel jPanel2 = new JPanel();
 393
 394   JPanel jPanel3 = new JPanel();
 395
 396   JPanel jPanel4 = new JPanel();
 397
 398   BorderLayout borderLayout1 = new BorderLayout();
 399
 400   BorderLayout borderLayout2 = new BorderLayout();
 401
 402   BorderLayout borderLayout3 = new BorderLayout();
 403
 404   public void close_actionPerformed(ActionEvent e)
 405   {
 406     try
 407     {
 408       frame.setClosed(true);
 409     } catch (Exception ex)
 410     {
 411     }
 412   }
 413
 414   public void ok_actionPerformed()
 415   {
 416     databaseButt.setEnabled(false);
 417     example.setEnabled(false);
 418     textArea.setEnabled(false);
 419     ok.setEnabled(false);
 420     close.setEnabled(false);
 421
 422     Thread worker = new Thread(this);
 423     worker.start();
 424   }
 425
 426   private void resetDialog()
 427   {
 428     databaseButt.setEnabled(true);
 429     example.setEnabled(true);
 430     textArea.setEnabled(true);
 431     ok.setEnabled(true);
 432     close.setEnabled(true);
 433   }
 434
 435   @Override
 436   public void run()
 437   {
 438     String error = "";
 439     if (!database.hasSelection())
 440     {
 441       error += "Please select the source database\n";
 442     }
 443     // TODO: make this transformation more configurable
 444     com.stevesoft.pat.Regex empty;
 445     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 446     {
 447       empty = new com.stevesoft.pat.Regex(
 448       // replace commas and spaces with a semicolon
 449               "(\\s|[,; ])+", ";");
 450     }
 451     else
 452     {
 453       // just turn spaces and semicolons into single semicolons
 454       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 455     }
 456     textArea.setText(empty.replaceAll(textArea.getText()));
 457     // see if there's anthing to search with
 458     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 459             .getText()))
 460     {
 461       error += "Please enter a (semi-colon separated list of) database id(s)";
 462     }
 463     if (error.length() > 0)
 464     {
 465       showErrorMessage(error);
 466       resetDialog();
 467       return;
 468     }
 469     // indicate if successive sources should be merged into one alignment.
 470     boolean addToLast = false;
 471     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 472     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 473     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 474             .iterator();
 475     String[] qries;
 476     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 477             .split(";"));
 478     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 479     int nqueries = qries.length;
 480     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 481     {
 482       if (!en.hasNext() && nextfetch.size() > 0)
 483       {
 484         en = nextfetch.iterator();
 485         nqueries = nextfetch.size();
 486         // save the remaining queries in the original array
 487         qries = nextfetch.toArray(new String[nqueries]);
 488         nextfetch = new ArrayList<String>();
 489       }
 490
 491       DbSourceProxy proxy = proxies.next();
 492       boolean isAliSource = false;
 493       try
 494       {
 495         // update status
 496         guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
 497                 .currentThread().hashCode());
 498         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 499         if (proxy.getAccessionSeparator() == null)
 500         {
 501           while (en.hasNext())
 502           {
 503             String item = en.next();
 504             try
 505             {
 506               if (aresult != null)
 507               {
 508                 try
 509                 {
 510                   // give the server a chance to breathe
 511                   Thread.sleep(5);
 512                 } catch (Exception e)
 513                 {
 514                   //
 515                 }
 516
 517               }
 518
 519               AlignmentI indres = null;
 520               try
 521               {
 522                 indres = proxy.getSequenceRecords(item);
 523               } catch (OutOfMemoryError oome)
 524               {
 525                 new OOMWarning("fetching " + item + " from "
 526                         + proxy.getDbName(), oome, this);
 527               }
 528               if (indres != null)
 529               {
 530                 aresultq.add(item);
 531                 aresult.add(indres);
 532               }
 533               else
 534               {
 535                 nextfetch.add(item);
 536               }
 537             } catch (Exception e)
 538             {
 539               jalview.bin.Cache.log.info("Error retrieving " + item
 540                       + " from " + proxy.getDbName(), e);
 541               nextfetch.add(item);
 542             }
 543           }
 544         }
 545         else
 546         {
 547           StringBuffer multiacc = new StringBuffer();
 548           ArrayList<String> tosend = new ArrayList<String>();
 549           while (en.hasNext())
 550           {
 551             String nel = en.next();
 552             tosend.add(nel);
 553             multiacc.append(nel);
 554             if (en.hasNext())
 555             {
 556               multiacc.append(proxy.getAccessionSeparator());
 557             }
 558           }
 559           try
 560           {
 561             AlignmentI rslt;
 562             SequenceI[] rs;
 563             List<String> nores = new ArrayList<String>();
 564             rslt = proxy.getSequenceRecords(multiacc.toString());
 565             if (rslt == null || rslt.getHeight() == 0)
 566             {
 567               // no results - pass on all queries to next source
 568               nextfetch.addAll(tosend);
 569             }
 570             else
 571             {
 572               aresultq.add(multiacc.toString());
 573               aresult.add(rslt);
 574
 575               rs = rslt.getSequencesArray();
 576               // search for each query in the dbrefs associated with each
 577               // sequence
 578               // returned.
 579               // ones we do not find will be used to query next source (if any)
 580               for (String q : tosend)
 581               {
 582                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 583                 dbr.setSource(proxy.getDbSource());
 584                 dbr.setVersion(null);
 585                 if (proxy.getAccessionValidator() != null)
 586                 {
 587                   Regex vgr = proxy.getAccessionValidator();
 588                   vgr.search(q);
 589                   if (vgr.numSubs() > 0)
 590                   {
 591                     dbr.setAccessionId(vgr.stringMatched(1));
 592                   }
 593                   else
 594                   {
 595                     dbr.setAccessionId(vgr.stringMatched());
 596                   }
 597                 }
 598                 else
 599                 {
 600                   dbr.setAccessionId(q);
 601                 }
 602                 boolean rfound = false;
 603                 for (int r = 0; r < rs.length; r++)
 604                 {
 605                   if (rs[r] != null
 606                           && (found = DBRefUtils.searchRefs(
 607                                   rs[r].getDBRef(), dbr)) != null
 608                           && found.length > 0)
 609                   {
 610                     rfound = true;
 611                     rs[r] = null;
 612                     continue;
 613                   }
 614                 }
 615                 if (!rfound)
 616                 {
 617                   nextfetch.add(q);
 618                 }
 619               }
 620             }
 621           } catch (OutOfMemoryError oome)
 622           {
 623             new OOMWarning("fetching " + multiacc + " from "
 624                     + database.getSelectedItem(), oome, this);
 625           }
 626         }
 627
 628       } catch (Exception e)
 629       {
 630         showErrorMessage("Error retrieving " + textArea.getText()
 631                 + " from " + database.getSelectedItem());
 632         // error
 633         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 634         System.err.println("Retrieval failed for source ='"
 635                 + database.getSelectedItem() + "' and query\n'"
 636                 + textArea.getText() + "'\n");
 637         e.printStackTrace();
 638       } catch (OutOfMemoryError e)
 639       {
 640         // resets dialog box - so we don't use OOMwarning here.
 641         showErrorMessage("Out of Memory when retrieving "
 642                 + textArea.getText()
 643                 + " from "
 644                 + database.getSelectedItem()
 645                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 646         e.printStackTrace();
 647       } catch (Error e)
 648       {
 649         showErrorMessage("Serious Error retrieving " + textArea.getText()
 650                 + " from " + database.getSelectedItem());
 651         e.printStackTrace();
 652       }
 653       // Stack results ready for opening in alignment windows
 654       if (aresult != null && aresult.size() > 0)
 655       {
 656         AlignmentI ar = null;
 657         if (isAliSource)
 658         {
 659           addToLast = false;
 660           // new window for each result
 661           while (aresult.size() > 0)
 662           {
 663             presult.add(aresult.remove(0));
 664             presultTitle.add(aresultq.remove(0) + " "
 665                     + getDefaultRetrievalTitle());
 666           }
 667         }
 668         else
 669         {
 670           String titl = null;
 671           if (addToLast && presult.size() > 0)
 672           {
 673             ar = presult.remove(presult.size() - 1);
 674             titl = presultTitle.remove(presultTitle.size() - 1);
 675           }
 676           // concatenate all results in one window
 677           while (aresult.size() > 0)
 678           {
 679             if (ar == null)
 680             {
 681               ar = aresult.remove(0);
 682             }
 683             else
 684             {
 685               ar.append(aresult.remove(0));
 686             }
 687             ;
 688           }
 689           addToLast = true;
 690           presult.add(ar);
 691           presultTitle.add(titl);
 692         }
 693       }
 694       guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
 695               .hashCode());
 696     }
 697     guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
 698             : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
 699     // process results
 700     while (presult.size() > 0)
 701     {
 702       parseResult(presult.remove(0), presultTitle.remove(0), null);
 703     }
 704     // only remove visual delay after we finished parsing.
 705     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 706     if (nextfetch.size() > 0)
 707     {
 708       StringBuffer sb = new StringBuffer();
 709       sb.append("Didn't retrieve the following "
 710               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 711                       + " queries") + ": \n");
 712       int l = sb.length(), lr = 0;
 713       for (String s : nextfetch)
 714       {
 715         if (l != sb.length())
 716         {
 717           sb.append("; ");
 718         }
 719         if (lr - sb.length() > 40)
 720         {
 721           sb.append("\n");
 722         }
 723         sb.append(s);
 724       }
 725       showErrorMessage(sb.toString());
 726     }
 727     resetDialog();
 728   }
 729
 730   AlignmentI parseResult(String result, String title)
 731   {
 732     String format = new IdentifyFile().Identify(result, "Paste");
 733     Alignment sequences = null;
 734     if (FormatAdapter.isValidFormat(format))
 735     {
 736       sequences = null;
 737       try
 738       {
 739         sequences = new FormatAdapter().readFile(result.toString(),
 740                 "Paste", format);
 741       } catch (Exception ex)
 742       {
 743       }
 744
 745       if (sequences != null)
 746       {
 747         return parseResult(sequences, title, format);
 748       }
 749     }
 750     else
 751     {
 752       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 753               + database.getSelectedItem());
 754     }
 755
 756     return null;
 757   }
 758
 759   /**
 760    *
 761    * @return a standard title for any results retrieved using the currently
 762    *         selected source and settings
 763    */
 764   public String getDefaultRetrievalTitle()
 765   {
 766     return "Retrieved from " + database.getSelectedItem();
 767   }
 768
 769   AlignmentI parseResult(AlignmentI al, String title,
 770           String currentFileFormat)
 771   {
 772
 773     if (al != null && al.getHeight() > 0)
 774     {
 775       if (alignFrame == null)
 776       {
 777         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 778                 AlignFrame.DEFAULT_HEIGHT);
 779         if (currentFileFormat != null)
 780         {
 781           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 782           // FORMAT FOR
 783           // NON-FormatAdapter Sourced
 784           // Alignments?
 785         }
 786
 787         if (title == null)
 788         {
 789           title = getDefaultRetrievalTitle();
 790         }
 791         SequenceFeature[] sfs = null;
 792         List<SequenceI> alsqs;
 793         synchronized (alsqs = al.getSequences())
 794         {
 795           for (SequenceI sq : alsqs)
 796           {
 797             if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
 798             {
 799               if (sfs.length > 0)
 800               {
 801                 af.setShowSeqFeatures(true);
 802                 break;
 803               }
 804             }
 805
 806           }
 807         }
 808         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 809                 AlignFrame.DEFAULT_HEIGHT);
 810
 811         af.statusBar.setText(MessageManager
 812                 .getString("label.successfully_pasted_alignment_file"));
 813
 814         try
 815         {
 816           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 817                   false));
 818         } catch (Exception ex)
 819         {
 820         }
 821       }
 822       else
 823       {
 824         for (int i = 0; i < al.getHeight(); i++)
 825         {
 826           alignFrame.viewport.getAlignment().addSequence(
 827                   al.getSequenceAt(i)); // this
 828           // also
 829           // creates
 830           // dataset
 831           // sequence
 832           // entries
 833         }
 834         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 835                 .getHeight());
 836         alignFrame.viewport.getAlignment().getWidth();
 837         alignFrame.viewport.firePropertyChange("alignment", null,
 838                 alignFrame.viewport.getAlignment().getSequences());
 839       }
 840     }
 841     return al;
 842   }
 843
 844   void showErrorMessage(final String error)
 845   {
 846     resetDialog();
 847     javax.swing.SwingUtilities.invokeLater(new Runnable()
 848     {
 849       @Override
 850       public void run()
 851       {
 852         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 853                 MessageManager.getString("label.error_retrieving_data"),
 854                 JOptionPane.WARNING_MESSAGE);
 855       }
 856     });
 857   }
 858 }