src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   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 jalview.datamodel.Alignment;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.DBRefEntry;
  26 import jalview.datamodel.DBRefSource;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.io.FormatAdapter;
  30 import jalview.io.IdentifyFile;
  31 import jalview.util.DBRefUtils;
  32 import jalview.util.MessageManager;
  33 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  34 import jalview.ws.seqfetcher.DbSourceProxy;
  35
  36 import java.awt.BorderLayout;
  37 import java.awt.Font;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.KeyAdapter;
  41 import java.awt.event.KeyEvent;
  42 import java.util.ArrayList;
  43 import java.util.Arrays;
  44 import java.util.Iterator;
  45 import java.util.List;
  46
  47 import javax.swing.JButton;
  48 import javax.swing.JCheckBox;
  49 import javax.swing.JInternalFrame;
  50 import javax.swing.JLabel;
  51 import javax.swing.JOptionPane;
  52 import javax.swing.JPanel;
  53 import javax.swing.JScrollPane;
  54 import javax.swing.JTextArea;
  55 import javax.swing.SwingConstants;
  56 import javax.swing.tree.DefaultMutableTreeNode;
  57
  58 import com.stevesoft.pat.Regex;
  59
  60 public class SequenceFetcher extends JPanel implements Runnable
  61 {
  62   // ASequenceFetcher sfetch;
  63   JInternalFrame frame;
  64
  65   IProgressIndicator guiWindow;
  66
  67   AlignFrame alignFrame;
  68
  69   StringBuffer result;
  70
  71   final String noDbSelected = "-- Select Database --";
  72
  73   private static jalview.ws.SequenceFetcher sfetch = null;
  74
  75   private static long lastDasSourceRegistry = -3;
  76
  77   private static DasSourceRegistryI dasRegistry = null;
  78
  79   private static boolean _initingFetcher = false;
  80
  81   private static Thread initingThread = null;
  82
  83   /**
  84    * Blocking method that initialises and returns the shared instance of the
  85    * SequenceFetcher client
  86    *
  87    * @param guiWindow
  88    *          - where the initialisation delay message should be shown
  89    * @return the singleton instance of the sequence fetcher client
  90    */
  91   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
  92           final IProgressIndicator guiWindow)
  93   {
  94     if (_initingFetcher && initingThread != null && initingThread.isAlive())
  95     {
  96       if (guiWindow != null)
  97       {
  98         guiWindow.setProgressBar(
  99                 MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
 100                 Thread.currentThread().hashCode());
 101       }
 102       // initting happening on another thread - so wait around to see if it
 103       // finishes.
 104       while (_initingFetcher && initingThread != null
 105               && initingThread.isAlive())
 106       {
 107         try
 108         {
 109           Thread.sleep(10);
 110         } catch (Exception e)
 111         {
 112         }
 113         ;
 114       }
 115       if (guiWindow != null)
 116       {
 117         guiWindow.setProgressBar(
 118                         MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
 119                 Thread.currentThread().hashCode());
 120       }
 121     }
 122     if (sfetch == null
 123             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
 124             || lastDasSourceRegistry != (jalview.bin.Cache
 125                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
 126                     .getDasSourceRegistry().getLocalSourceString())
 127                     .hashCode())
 128     {
 129       _initingFetcher = true;
 130       initingThread = Thread.currentThread();
 131       /**
 132        * give a visual indication that sequence fetcher construction is occuring
 133        */
 134       if (guiWindow != null)
 135       {
 136         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
 137                 Thread.currentThread().hashCode());
 138       }
 139       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
 140       dasRegistry.refreshSources();
 141
 142       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 143       if (guiWindow != null)
 144       {
 145         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
 146                 Thread.currentThread().hashCode());
 147       }
 148       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 149               .getLocalSourceString()).hashCode();
 150       sfetch = sf;
 151       _initingFetcher = false;
 152       initingThread = null;
 153     }
 154     return sfetch;
 155   }
 156
 157   public SequenceFetcher(IProgressIndicator guiIndic)
 158   {
 159     final IProgressIndicator guiWindow = guiIndic;
 160     final SequenceFetcher us = this;
 161     // launch initialiser thread
 162     Thread sf = new Thread(new Runnable()
 163     {
 164
 165       @Override
 166       public void run()
 167       {
 168         if (getSequenceFetcherSingleton(guiWindow) != null)
 169         {
 170           us.initGui(guiWindow);
 171         }
 172         else
 173         {
 174           javax.swing.SwingUtilities.invokeLater(new Runnable()
 175           {
 176             @Override
 177             public void run()
 178             {
 179               JOptionPane
 180                       .showInternalMessageDialog(
 181                               Desktop.desktop,
 182                               MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
 183                               MessageManager.getString("label.couldnt_create_sequence_fetcher"),
 184                               JOptionPane.ERROR_MESSAGE);
 185             }
 186           });
 187
 188           // raise warning dialog
 189         }
 190       }
 191     });
 192     sf.start();
 193   }
 194
 195   private class DatabaseAuthority extends DefaultMutableTreeNode
 196   {
 197
 198   };
 199
 200   private class DatabaseSource extends DefaultMutableTreeNode
 201   {
 202
 203   };
 204
 205   /**
 206    * called by thread spawned by constructor
 207    *
 208    * @param guiWindow
 209    */
 210   private void initGui(IProgressIndicator guiWindow)
 211   {
 212     this.guiWindow = guiWindow;
 213     if (guiWindow instanceof AlignFrame)
 214     {
 215       alignFrame = (AlignFrame) guiWindow;
 216     }
 217     database = new JDatabaseTree(sfetch);
 218     try
 219     {
 220       jbInit();
 221     } catch (Exception ex)
 222     {
 223       ex.printStackTrace();
 224     }
 225
 226     frame = new JInternalFrame();
 227     frame.setContentPane(this);
 228     if (new jalview.util.Platform().isAMac())
 229     {
 230       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 231     }
 232     else
 233     {
 234       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 235     }
 236   }
 237
 238   private String getFrameTitle()
 239   {
 240     return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
 241   }
 242
 243   private void jbInit() throws Exception
 244   {
 245     this.setLayout(borderLayout2);
 246
 247     database.setFont(JvSwingUtils.getLabelFont());
 248     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 249     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 250     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 251     jLabel1.setText(MessageManager
 252             .getString("label.separate_multiple_accession_ids"));
 253
 254     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 255     replacePunctuation
 256             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 257     replacePunctuation.setText(MessageManager
 258             .getString("label.replace_commas_semicolons"));
 259     ok.setText(MessageManager.getString("action.ok"));
 260     ok.addActionListener(new ActionListener()
 261     {
 262       @Override
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         ok_actionPerformed();
 266       }
 267     });
 268     clear.setText(MessageManager.getString("action.clear"));
 269     clear.addActionListener(new ActionListener()
 270     {
 271       @Override
 272       public void actionPerformed(ActionEvent e)
 273       {
 274         clear_actionPerformed();
 275       }
 276     });
 277
 278     example.setText(MessageManager.getString("label.example"));
 279     example.addActionListener(new ActionListener()
 280     {
 281       @Override
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         example_actionPerformed();
 285       }
 286     });
 287     close.setText(MessageManager.getString("action.close"));
 288     close.addActionListener(new ActionListener()
 289     {
 290       @Override
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         close_actionPerformed(e);
 294       }
 295     });
 296     textArea.setFont(JvSwingUtils.getLabelFont());
 297     textArea.setLineWrap(true);
 298     textArea.addKeyListener(new KeyAdapter()
 299     {
 300       @Override
 301       public void keyPressed(KeyEvent e)
 302       {
 303         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 304         {
 305           ok_actionPerformed();
 306         }
 307       }
 308     });
 309     jPanel3.setLayout(borderLayout1);
 310     borderLayout1.setVgap(5);
 311     jPanel1.add(ok);
 312     jPanel1.add(example);
 313     jPanel1.add(clear);
 314     jPanel1.add(close);
 315     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 316     jPanel2.setLayout(borderLayout3);
 317     databaseButt = database.getDatabaseSelectorButton();
 318     databaseButt.setFont(JvSwingUtils.getLabelFont());
 319     database.addActionListener(new ActionListener()
 320     {
 321
 322       @Override
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         try
 326         {
 327           databaseButt.setText(database.getSelectedItem()
 328                   + (database.getSelectedSources().size() > 1 ? " (and "
 329                           + database.getSelectedSources().size()
 330                           + " others)" : ""));
 331           String eq = database.getExampleQueries();
 332           dbeg.setText(MessageManager.formatMessage(
 333                   "label.example_query_param", new String[]
 334                   { eq }));
 335           boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 336           for (DbSourceProxy dbs : database.getSelectedSources())
 337           {
 338             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 339             {
 340               enablePunct = false;
 341               break;
 342             }
 343           }
 344           replacePunctuation.setEnabled(enablePunct);
 345
 346         } catch (Exception ex)
 347         {
 348           dbeg.setText("");
 349           replacePunctuation.setEnabled(true);
 350         }
 351         jPanel2.repaint();
 352       }
 353     });
 354     dbeg.setText("");
 355     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 356     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 357     JPanel jPanel2a = new JPanel(new BorderLayout());
 358     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 359     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 360     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 361     // jPanel2.setPreferredSize(new Dimension())
 362     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 363     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 364     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 365     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 366     jScrollPane1.getViewport().add(textArea);
 367
 368   }
 369
 370   protected void example_actionPerformed()
 371   {
 372     DbSourceProxy db = null;
 373     try
 374     {
 375       textArea.setText(database.getExampleQueries());
 376     } catch (Exception ex)
 377     {
 378     }
 379     jPanel3.repaint();
 380   }
 381
 382   protected void clear_actionPerformed()
 383   {
 384     textArea.setText("");
 385     jPanel3.repaint();
 386   }
 387
 388   JLabel dbeg = new JLabel();
 389
 390   JDatabaseTree database;
 391
 392   JButton databaseButt;
 393
 394   JLabel jLabel1 = new JLabel();
 395
 396   JCheckBox replacePunctuation = new JCheckBox();
 397
 398   JButton ok = new JButton();
 399
 400   JButton clear = new JButton();
 401
 402   JButton example = new JButton();
 403
 404   JButton close = new JButton();
 405
 406   JPanel jPanel1 = new JPanel();
 407
 408   JTextArea textArea = new JTextArea();
 409
 410   JScrollPane jScrollPane1 = new JScrollPane();
 411
 412   JPanel jPanel2 = new JPanel();
 413
 414   JPanel jPanel3 = new JPanel();
 415
 416   JPanel jPanel4 = new JPanel();
 417
 418   BorderLayout borderLayout1 = new BorderLayout();
 419
 420   BorderLayout borderLayout2 = new BorderLayout();
 421
 422   BorderLayout borderLayout3 = new BorderLayout();
 423
 424   public void close_actionPerformed(ActionEvent e)
 425   {
 426     try
 427     {
 428       frame.setClosed(true);
 429     } catch (Exception ex)
 430     {
 431     }
 432   }
 433
 434   public void ok_actionPerformed()
 435   {
 436     databaseButt.setEnabled(false);
 437     example.setEnabled(false);
 438     textArea.setEnabled(false);
 439     ok.setEnabled(false);
 440     close.setEnabled(false);
 441
 442     Thread worker = new Thread(this);
 443     worker.start();
 444   }
 445
 446   private void resetDialog()
 447   {
 448     databaseButt.setEnabled(true);
 449     example.setEnabled(true);
 450     textArea.setEnabled(true);
 451     ok.setEnabled(true);
 452     close.setEnabled(true);
 453   }
 454
 455   @Override
 456   public void run()
 457   {
 458     String error = "";
 459     if (!database.hasSelection())
 460     {
 461       error += "Please select the source database\n";
 462     }
 463     // TODO: make this transformation more configurable
 464     com.stevesoft.pat.Regex empty;
 465     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 466     {
 467       empty = new com.stevesoft.pat.Regex(
 468       // replace commas and spaces with a semicolon
 469               "(\\s|[,; ])+", ";");
 470     }
 471     else
 472     {
 473       // just turn spaces and semicolons into single semicolons
 474       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 475     }
 476     textArea.setText(empty.replaceAll(textArea.getText()));
 477     // see if there's anthing to search with
 478     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 479             .getText()))
 480     {
 481       error += "Please enter a (semi-colon separated list of) database id(s)";
 482     }
 483     if (error.length() > 0)
 484     {
 485       showErrorMessage(error);
 486       resetDialog();
 487       return;
 488     }
 489     // indicate if successive sources should be merged into one alignment.
 490     boolean addToLast = false;
 491     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 492     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 493     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 494             .iterator();
 495     String[] qries;
 496     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 497             .split(";"));
 498     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 499     int nqueries = qries.length;
 500     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 501     {
 502       if (!en.hasNext() && nextfetch.size() > 0)
 503       {
 504         en = nextfetch.iterator();
 505         nqueries = nextfetch.size();
 506         // save the remaining queries in the original array
 507         qries = nextfetch.toArray(new String[nqueries]);
 508         nextfetch = new ArrayList<String>();
 509       }
 510
 511       DbSourceProxy proxy = proxies.next();
 512       boolean isAliSource = false;
 513       try
 514       {
 515         // update status
 516         guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
 517                 .currentThread().hashCode());
 518         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 519         if (proxy.getAccessionSeparator() == null)
 520         {
 521           while (en.hasNext())
 522           {
 523             String item = en.next();
 524             try
 525             {
 526               if (aresult != null)
 527               {
 528                 try
 529                 {
 530                   // give the server a chance to breathe
 531                   Thread.sleep(5);
 532                 } catch (Exception e)
 533                 {
 534                   //
 535                 }
 536
 537               }
 538
 539               AlignmentI indres = null;
 540               try
 541               {
 542                 indres = proxy.getSequenceRecords(item);
 543               } catch (OutOfMemoryError oome)
 544               {
 545                 new OOMWarning("fetching " + item + " from "
 546                         + proxy.getDbName(), oome, this);
 547               }
 548               if (indres != null)
 549               {
 550                 aresultq.add(item);
 551                 aresult.add(indres);
 552               }
 553               else
 554               {
 555                 nextfetch.add(item);
 556               }
 557             } catch (Exception e)
 558             {
 559               jalview.bin.Cache.log.info("Error retrieving " + item
 560                       + " from " + proxy.getDbName(), e);
 561               nextfetch.add(item);
 562             }
 563           }
 564         }
 565         else
 566         {
 567           StringBuffer multiacc = new StringBuffer();
 568           ArrayList<String> tosend = new ArrayList<String>();
 569           while (en.hasNext())
 570           {
 571             String nel = en.next();
 572             tosend.add(nel);
 573             multiacc.append(nel);
 574             if (en.hasNext())
 575             {
 576               multiacc.append(proxy.getAccessionSeparator());
 577             }
 578           }
 579           try
 580           {
 581             AlignmentI rslt;
 582             SequenceI[] rs;
 583             List<String> nores = new ArrayList<String>();
 584             rslt = proxy.getSequenceRecords(multiacc.toString());
 585             if (rslt == null || rslt.getHeight() == 0)
 586             {
 587               // no results - pass on all queries to next source
 588               nextfetch.addAll(tosend);
 589             }
 590             else
 591             {
 592               aresultq.add(multiacc.toString());
 593               aresult.add(rslt);
 594
 595               rs = rslt.getSequencesArray();
 596               // search for each query in the dbrefs associated with each
 597               // sequence
 598               // returned.
 599               // ones we do not find will be used to query next source (if any)
 600               for (String q : tosend)
 601               {
 602                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 603                 dbr.setSource(proxy.getDbSource());
 604                 dbr.setVersion(null);
 605                 if (proxy.getAccessionValidator() != null)
 606                 {
 607                   Regex vgr = proxy.getAccessionValidator();
 608                   vgr.search(q);
 609                   if (vgr.numSubs() > 0)
 610                   {
 611                     dbr.setAccessionId(vgr.stringMatched(1));
 612                   }
 613                   else
 614                   {
 615                     dbr.setAccessionId(vgr.stringMatched());
 616                   }
 617                 }
 618                 else
 619                 {
 620                   dbr.setAccessionId(q);
 621                 }
 622                 boolean rfound = false;
 623                 for (int r = 0; r < rs.length; r++)
 624                 {
 625                   if (rs[r] != null
 626                           && (found = DBRefUtils.searchRefs(
 627                                   rs[r].getDBRef(), dbr)) != null
 628                           && found.length > 0)
 629                   {
 630                     rfound = true;
 631                     rs[r] = null;
 632                     continue;
 633                   }
 634                 }
 635                 if (!rfound)
 636                 {
 637                   nextfetch.add(q);
 638                 }
 639               }
 640             }
 641           } catch (OutOfMemoryError oome)
 642           {
 643             new OOMWarning("fetching " + multiacc + " from "
 644                     + database.getSelectedItem(), oome, this);
 645           }
 646         }
 647
 648       } catch (Exception e)
 649       {
 650         showErrorMessage("Error retrieving " + textArea.getText()
 651                 + " from " + database.getSelectedItem());
 652         // error
 653         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 654         System.err.println("Retrieval failed for source ='"
 655                 + database.getSelectedItem() + "' and query\n'"
 656                 + textArea.getText() + "'\n");
 657         e.printStackTrace();
 658       } catch (OutOfMemoryError e)
 659       {
 660         // resets dialog box - so we don't use OOMwarning here.
 661         showErrorMessage("Out of Memory when retrieving "
 662                 + textArea.getText()
 663                 + " from "
 664                 + database.getSelectedItem()
 665                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 666         e.printStackTrace();
 667       } catch (Error e)
 668       {
 669         showErrorMessage("Serious Error retrieving " + textArea.getText()
 670                 + " from " + database.getSelectedItem());
 671         e.printStackTrace();
 672       }
 673       // Stack results ready for opening in alignment windows
 674       if (aresult != null && aresult.size() > 0)
 675       {
 676         AlignmentI ar = null;
 677         if (isAliSource)
 678         {
 679           addToLast = false;
 680           // new window for each result
 681           while (aresult.size() > 0)
 682           {
 683             presult.add(aresult.remove(0));
 684             presultTitle.add(aresultq.remove(0) + " "
 685                     + getDefaultRetrievalTitle());
 686           }
 687         }
 688         else
 689         {
 690           String titl = null;
 691           if (addToLast && presult.size() > 0)
 692           {
 693             ar = presult.remove(presult.size() - 1);
 694             titl = presultTitle.remove(presultTitle.size() - 1);
 695           }
 696           // concatenate all results in one window
 697           while (aresult.size() > 0)
 698           {
 699             if (ar == null)
 700             {
 701               ar = aresult.remove(0);
 702             }
 703             else
 704             {
 705               ar.append(aresult.remove(0));
 706             }
 707             ;
 708           }
 709           addToLast = true;
 710           presult.add(ar);
 711           presultTitle.add(titl);
 712         }
 713       }
 714       guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
 715               .hashCode());
 716     }
 717     guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
 718             : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
 719     // process results
 720     while (presult.size() > 0)
 721     {
 722       parseResult(presult.remove(0), presultTitle.remove(0), null);
 723     }
 724     // only remove visual delay after we finished parsing.
 725     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 726     if (nextfetch.size() > 0)
 727     {
 728       StringBuffer sb = new StringBuffer();
 729       sb.append("Didn't retrieve the following "
 730               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 731                       + " queries") + ": \n");
 732       int l = sb.length(), lr = 0;
 733       for (String s : nextfetch)
 734       {
 735         if (l != sb.length())
 736         {
 737           sb.append("; ");
 738         }
 739         if (lr - sb.length() > 40)
 740         {
 741           sb.append("\n");
 742         }
 743         sb.append(s);
 744       }
 745       showErrorMessage(sb.toString());
 746     }
 747     resetDialog();
 748   }
 749
 750   AlignmentI parseResult(String result, String title)
 751   {
 752     String format = new IdentifyFile().Identify(result, "Paste");
 753     Alignment sequences = null;
 754     if (FormatAdapter.isValidFormat(format))
 755     {
 756       sequences = null;
 757       try
 758       {
 759         sequences = new FormatAdapter().readFile(result.toString(),
 760                 "Paste", format);
 761       } catch (Exception ex)
 762       {
 763       }
 764
 765       if (sequences != null)
 766       {
 767         return parseResult(sequences, title, format);
 768       }
 769     }
 770     else
 771     {
 772       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 773               + database.getSelectedItem());
 774     }
 775
 776     return null;
 777   }
 778
 779   /**
 780    *
 781    * @return a standard title for any results retrieved using the currently
 782    *         selected source and settings
 783    */
 784   public String getDefaultRetrievalTitle()
 785   {
 786     return "Retrieved from " + database.getSelectedItem();
 787   }
 788
 789   AlignmentI parseResult(AlignmentI al, String title,
 790           String currentFileFormat)
 791   {
 792
 793     if (al != null && al.getHeight() > 0)
 794     {
 795       if (alignFrame == null)
 796       {
 797         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 798                 AlignFrame.DEFAULT_HEIGHT);
 799         if (currentFileFormat != null)
 800         {
 801           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 802           // FORMAT FOR
 803           // NON-FormatAdapter Sourced
 804           // Alignments?
 805         }
 806
 807         if (title == null)
 808         {
 809           title = getDefaultRetrievalTitle();
 810         }
 811         SequenceFeature[] sfs = null;
 812         List<SequenceI> alsqs;
 813         synchronized (alsqs = al.getSequences())
 814         {
 815           for (SequenceI sq : alsqs)
 816           {
 817             if ((sfs = sq.getSequenceFeatures()) != null)
 818             {
 819               if (sfs.length > 0)
 820               {
 821                 af.setShowSeqFeatures(true);
 822                 break;
 823               }
 824             }
 825
 826           }
 827         }
 828         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 829                 AlignFrame.DEFAULT_HEIGHT);
 830
 831         af.statusBar.setText(MessageManager
 832                 .getString("label.successfully_pasted_alignment_file"));
 833
 834         try
 835         {
 836           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 837                   false));
 838         } catch (Exception ex)
 839         {
 840         }
 841       }
 842       else
 843       {
 844         for (int i = 0; i < al.getHeight(); i++)
 845         {
 846           alignFrame.viewport.getAlignment().addSequence(
 847                   al.getSequenceAt(i)); // this
 848           // also
 849           // creates
 850           // dataset
 851           // sequence
 852           // entries
 853         }
 854         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 855                 .getHeight());
 856         alignFrame.viewport.getAlignment().getWidth();
 857         alignFrame.viewport.firePropertyChange("alignment", null,
 858                 alignFrame.viewport.getAlignment().getSequences());
 859       }
 860     }
 861     return al;
 862   }
 863
 864   void showErrorMessage(final String error)
 865   {
 866     resetDialog();
 867     javax.swing.SwingUtilities.invokeLater(new Runnable()
 868     {
 869       @Override
 870       public void run()
 871       {
 872         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 873                 MessageManager.getString("label.error_retrieving_data"),
 874                 JOptionPane.WARNING_MESSAGE);
 875       }
 876     });
 877   }
 878 }