src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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.bin.Cache;
  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.util.Platform;
  34 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  35 import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
  36 import jalview.ws.seqfetcher.DbSourceProxy;
  37
  38 import java.awt.BorderLayout;
  39 import java.awt.Font;
  40 import java.awt.event.ActionEvent;
  41 import java.awt.event.ActionListener;
  42 import java.awt.event.KeyAdapter;
  43 import java.awt.event.KeyEvent;
  44 import java.util.ArrayList;
  45 import java.util.Arrays;
  46 import java.util.Iterator;
  47 import java.util.List;
  48
  49 import javax.swing.JButton;
  50 import javax.swing.JCheckBox;
  51 import javax.swing.JInternalFrame;
  52 import javax.swing.JLabel;
  53 import javax.swing.JOptionPane;
  54 import javax.swing.JPanel;
  55 import javax.swing.JScrollPane;
  56 import javax.swing.JTextArea;
  57 import javax.swing.SwingConstants;
  58 import javax.swing.tree.DefaultMutableTreeNode;
  59
  60 import com.stevesoft.pat.Regex;
  61
  62 public class SequenceFetcher extends JPanel implements Runnable
  63 {
  64   JLabel dbeg = new JLabel();
  65
  66   JDatabaseTree database;
  67
  68   JButton databaseButt;
  69
  70   JLabel jLabel1 = new JLabel();
  71
  72   JCheckBox replacePunctuation = new JCheckBox();
  73
  74   JButton ok = new JButton();
  75
  76   JButton clear = new JButton();
  77
  78   JButton example = new JButton();
  79
  80   JButton close = new JButton();
  81
  82   JPanel jPanel1 = new JPanel();
  83
  84   JTextArea textArea = new JTextArea();
  85
  86   JScrollPane jScrollPane1 = new JScrollPane();
  87
  88   JPanel jPanel2 = new JPanel();
  89
  90   JPanel jPanel3 = new JPanel();
  91
  92   JPanel jPanel4 = new JPanel();
  93
  94   BorderLayout borderLayout1 = new BorderLayout();
  95
  96   BorderLayout borderLayout2 = new BorderLayout();
  97
  98   BorderLayout borderLayout3 = new BorderLayout();
  99
 100   JInternalFrame frame;
 101
 102   IProgressIndicator guiWindow;
 103
 104   AlignFrame alignFrame;
 105
 106   StringBuffer result;
 107
 108   final String noDbSelected = "-- Select Database --";
 109
 110   private static jalview.ws.SequenceFetcher sfetch = null;
 111
 112   private static long lastDasSourceRegistry = -3;
 113
 114   private static DasSourceRegistryI dasRegistry = null;
 115
 116   private static boolean _initingFetcher = false;
 117
 118   private static Thread initingThread = null;
 119
 120   int debounceTrap = 0;
 121   /**
 122    * Blocking method that initialises and returns the shared instance of the
 123    * SequenceFetcher client
 124    *
 125    * @param guiWindow
 126    *          - where the initialisation delay message should be shown
 127    * @return the singleton instance of the sequence fetcher client
 128    */
 129   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
 130           final IProgressIndicator guiWindow)
 131   {
 132     if (_initingFetcher && initingThread != null && initingThread.isAlive())
 133     {
 134       if (guiWindow != null)
 135       {
 136         guiWindow.setProgressBar(
 137                 MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
 138                 Thread.currentThread().hashCode());
 139       }
 140       // initting happening on another thread - so wait around to see if it
 141       // finishes.
 142       while (_initingFetcher && initingThread != null
 143               && initingThread.isAlive())
 144       {
 145         try
 146         {
 147           Thread.sleep(10);
 148         } catch (Exception e)
 149         {
 150         }
 151         ;
 152       }
 153       if (guiWindow != null)
 154       {
 155         guiWindow.setProgressBar(
 156                         MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
 157                 Thread.currentThread().hashCode());
 158       }
 159     }
 160     if (sfetch == null
 161             || dasRegistry != Cache.getDasSourceRegistry()
 162             || lastDasSourceRegistry != (Cache
 163                     .getDasSourceRegistry().getDasRegistryURL() + Cache
 164                     .getDasSourceRegistry().getLocalSourceString())
 165                     .hashCode())
 166     {
 167       _initingFetcher = true;
 168       initingThread = Thread.currentThread();
 169       /**
 170        * give a visual indication that sequence fetcher construction is occuring
 171        */
 172       if (guiWindow != null)
 173       {
 174         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
 175                 Thread.currentThread().hashCode());
 176       }
 177       dasRegistry = Cache.getDasSourceRegistry();
 178       dasRegistry.refreshSources();
 179
 180       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 181       if (guiWindow != null)
 182       {
 183         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 184       }
 185       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 186               .getLocalSourceString()).hashCode();
 187       sfetch = sf;
 188       _initingFetcher = false;
 189       initingThread = null;
 190     }
 191     return sfetch;
 192   }
 193
 194   private IProgressIndicator progressIndicator;
 195   public SequenceFetcher(IProgressIndicator guiIndic)
 196   {
 197     this.progressIndicator = guiIndic;
 198     final SequenceFetcher us = this;
 199     // launch initialiser thread
 200     Thread sf = new Thread(new Runnable()
 201     {
 202
 203       @Override
 204       public void run()
 205       {
 206         if (getSequenceFetcherSingleton(progressIndicator) != null)
 207         {
 208           us.initGui(progressIndicator);
 209         }
 210         else
 211         {
 212           javax.swing.SwingUtilities.invokeLater(new Runnable()
 213           {
 214             @Override
 215             public void run()
 216             {
 217               JOptionPane
 218                       .showInternalMessageDialog(
 219                               Desktop.desktop,
 220                               MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
 221                               MessageManager.getString("label.couldnt_create_sequence_fetcher"),
 222                               JOptionPane.ERROR_MESSAGE);
 223             }
 224           });
 225
 226           // raise warning dialog
 227         }
 228       }
 229     });
 230     sf.start();
 231   }
 232
 233   private class DatabaseAuthority extends DefaultMutableTreeNode
 234   {
 235
 236   };
 237
 238   private class DatabaseSource extends DefaultMutableTreeNode
 239   {
 240
 241   };
 242
 243   /**
 244    * called by thread spawned by constructor
 245    *
 246    * @param guiWindow
 247    */
 248   private void initGui(IProgressIndicator guiWindow)
 249   {
 250     this.guiWindow = guiWindow;
 251     if (guiWindow instanceof AlignFrame)
 252     {
 253       alignFrame = (AlignFrame) guiWindow;
 254     }
 255     database = new JDatabaseTree(sfetch);
 256     try
 257     {
 258       jbInit();
 259     } catch (Exception ex)
 260     {
 261       ex.printStackTrace();
 262     }
 263
 264     frame = new JInternalFrame();
 265     frame.setContentPane(this);
 266     if (Platform.isAMac())
 267     {
 268       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 269     }
 270     else
 271     {
 272       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 273     }
 274   }
 275
 276   private String getFrameTitle()
 277   {
 278     return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
 279   }
 280
 281   private void jbInit() throws Exception
 282   {
 283     this.setLayout(borderLayout2);
 284
 285     database.setFont(JvSwingUtils.getLabelFont());
 286     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 287     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 288     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 289     jLabel1.setText(MessageManager
 290             .getString("label.separate_multiple_accession_ids"));
 291
 292     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 293     replacePunctuation
 294             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 295     replacePunctuation.setText(MessageManager
 296             .getString("label.replace_commas_semicolons"));
 297     ok.setText(MessageManager.getString("action.ok"));
 298     ok.addActionListener(new ActionListener()
 299     {
 300       @Override
 301       public void actionPerformed(ActionEvent e)
 302       {
 303         ok_actionPerformed();
 304       }
 305     });
 306     clear.setText(MessageManager.getString("action.clear"));
 307     clear.addActionListener(new ActionListener()
 308     {
 309       @Override
 310       public void actionPerformed(ActionEvent e)
 311       {
 312         clear_actionPerformed();
 313       }
 314     });
 315
 316     example.setText(MessageManager.getString("label.example"));
 317     example.addActionListener(new ActionListener()
 318     {
 319       @Override
 320       public void actionPerformed(ActionEvent e)
 321       {
 322         example_actionPerformed();
 323       }
 324     });
 325     close.setText(MessageManager.getString("action.close"));
 326     close.addActionListener(new ActionListener()
 327     {
 328       @Override
 329       public void actionPerformed(ActionEvent e)
 330       {
 331         close_actionPerformed(e);
 332       }
 333     });
 334     textArea.setFont(JvSwingUtils.getLabelFont());
 335     textArea.setLineWrap(true);
 336     textArea.addKeyListener(new KeyAdapter()
 337     {
 338       @Override
 339       public void keyPressed(KeyEvent e)
 340       {
 341         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 342         {
 343           ok_actionPerformed();
 344         }
 345       }
 346     });
 347     jPanel3.setLayout(borderLayout1);
 348     borderLayout1.setVgap(5);
 349     jPanel1.add(ok);
 350     jPanel1.add(example);
 351     jPanel1.add(clear);
 352     jPanel1.add(close);
 353     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 354     jPanel2.setLayout(borderLayout3);
 355     databaseButt = database.getDatabaseSelectorButton();
 356     databaseButt.setFont(JvSwingUtils.getLabelFont());
 357     database.addActionListener(new ActionListener()
 358     {
 359       @Override
 360       public void actionPerformed(ActionEvent e)
 361       {
 362         debounceTrap++;
 363         String currentSelection = database.getSelectedItem();
 364
 365         if (!currentSelection.equalsIgnoreCase("pdb"))
 366         {
 367             otherSourceAction();
 368         }
 369         if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
 370         {
 371           pdbSourceAction();
 372         }
 373
 374       }
 375     });
 376     dbeg.setText("");
 377     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 378     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 379     JPanel jPanel2a = new JPanel(new BorderLayout());
 380     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 381     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 382     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 383     // jPanel2.setPreferredSize(new Dimension())
 384     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 385     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 386     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 387     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 388     jScrollPane1.getViewport().add(textArea);
 389
 390   }
 391
 392   private void pdbSourceAction()
 393   {
 394     databaseButt.setText(database.getSelectedItem());
 395     new PDBSearchPanel(this);
 396     frame.dispose();
 397   }
 398
 399   private void otherSourceAction()
 400   {
 401     try
 402     {
 403       databaseButt.setText(database.getSelectedItem()
 404               + (database.getSelectedSources().size() > 1 ? " (and "
 405                       + database.getSelectedSources().size() + " others)"
 406                       : ""));
 407       String eq = database.getExampleQueries();
 408       dbeg.setText(MessageManager.formatMessage(
 409               "label.example_query_param", new String[]
 410               { eq }));
 411       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 412       for (DbSourceProxy dbs : database.getSelectedSources())
 413       {
 414         if (dbs instanceof DasSequenceSource)
 415         {
 416           enablePunct = false;
 417           break;
 418         }
 419       }
 420       replacePunctuation.setEnabled(enablePunct);
 421
 422     } catch (Exception ex)
 423     {
 424       dbeg.setText("");
 425       replacePunctuation.setEnabled(true);
 426     }
 427     jPanel2.repaint();
 428   }
 429
 430   protected void example_actionPerformed()
 431   {
 432     DbSourceProxy db = null;
 433     try
 434     {
 435       textArea.setText(database.getExampleQueries());
 436     } catch (Exception ex)
 437     {
 438     }
 439     jPanel3.repaint();
 440   }
 441
 442   protected void clear_actionPerformed()
 443   {
 444     textArea.setText("");
 445     jPanel3.repaint();
 446   }
 447
 448
 449
 450   public void close_actionPerformed(ActionEvent e)
 451   {
 452     try
 453     {
 454       frame.setClosed(true);
 455     } catch (Exception ex)
 456     {
 457     }
 458   }
 459
 460   public void ok_actionPerformed()
 461   {
 462     databaseButt.setEnabled(false);
 463     example.setEnabled(false);
 464     textArea.setEnabled(false);
 465     ok.setEnabled(false);
 466     close.setEnabled(false);
 467
 468     Thread worker = new Thread(this);
 469     worker.start();
 470   }
 471
 472   private void resetDialog()
 473   {
 474     databaseButt.setEnabled(true);
 475     example.setEnabled(true);
 476     textArea.setEnabled(true);
 477     ok.setEnabled(true);
 478     close.setEnabled(true);
 479   }
 480
 481   @Override
 482   public void run()
 483   {
 484     String error = "";
 485     if (!database.hasSelection())
 486     {
 487       error += "Please select the source database\n";
 488     }
 489     // TODO: make this transformation more configurable
 490     Regex empty;
 491     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 492     {
 493       empty = new Regex(
 494       // replace commas and spaces with a semicolon
 495               "(\\s|[,; ])+", ";");
 496     }
 497     else
 498     {
 499       // just turn spaces and semicolons into single semicolons
 500       empty = new Regex("(\\s|[; ])+", ";");
 501     }
 502     textArea.setText(empty.replaceAll(textArea.getText()));
 503     // see if there's anthing to search with
 504     if (!new Regex("[A-Za-z0-9_.]").search(textArea
 505             .getText()))
 506     {
 507       error += "Please enter a (semi-colon separated list of) database id(s)";
 508     }
 509     if (error.length() > 0)
 510     {
 511       showErrorMessage(error);
 512       resetDialog();
 513       return;
 514     }
 515     // indicate if successive sources should be merged into one alignment.
 516     boolean addToLast = false;
 517     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 518     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 519     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 520             .iterator();
 521     String[] qries;
 522     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 523             .split(";"));
 524     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 525     int nqueries = qries.length;
 526     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 527     {
 528       if (!en.hasNext() && nextfetch.size() > 0)
 529       {
 530         en = nextfetch.iterator();
 531         nqueries = nextfetch.size();
 532         // save the remaining queries in the original array
 533         qries = nextfetch.toArray(new String[nqueries]);
 534         nextfetch = new ArrayList<String>();
 535       }
 536
 537       DbSourceProxy proxy = proxies.next();
 538       boolean isAliSource = false;
 539       try
 540       {
 541         // update status
 542         guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
 543                 .currentThread().hashCode());
 544         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 545         if (proxy.getAccessionSeparator() == null)
 546         {
 547           while (en.hasNext())
 548           {
 549             String item = en.next();
 550             try
 551             {
 552               if (aresult != null)
 553               {
 554                 try
 555                 {
 556                   // give the server a chance to breathe
 557                   Thread.sleep(5);
 558                 } catch (Exception e)
 559                 {
 560                   //
 561                 }
 562
 563               }
 564
 565               AlignmentI indres = null;
 566               try
 567               {
 568                 indres = proxy.getSequenceRecords(item);
 569               } catch (OutOfMemoryError oome)
 570               {
 571                 new OOMWarning("fetching " + item + " from "
 572                         + proxy.getDbName(), oome, this);
 573               }
 574               if (indres != null)
 575               {
 576                 aresultq.add(item);
 577                 aresult.add(indres);
 578               }
 579               else
 580               {
 581                 nextfetch.add(item);
 582               }
 583             } catch (Exception e)
 584             {
 585               Cache.log.info("Error retrieving " + item
 586                       + " from " + proxy.getDbName(), e);
 587               nextfetch.add(item);
 588             }
 589           }
 590         }
 591         else
 592         {
 593           StringBuffer multiacc = new StringBuffer();
 594           ArrayList<String> tosend = new ArrayList<String>();
 595           while (en.hasNext())
 596           {
 597             String nel = en.next();
 598             tosend.add(nel);
 599             multiacc.append(nel);
 600             if (en.hasNext())
 601             {
 602               multiacc.append(proxy.getAccessionSeparator());
 603             }
 604           }
 605           try
 606           {
 607             AlignmentI rslt;
 608             SequenceI[] rs;
 609             List<String> nores = new ArrayList<String>();
 610             rslt = proxy.getSequenceRecords(multiacc.toString());
 611             if (rslt == null || rslt.getHeight() == 0)
 612             {
 613               // no results - pass on all queries to next source
 614               nextfetch.addAll(tosend);
 615             }
 616             else
 617             {
 618               aresultq.add(multiacc.toString());
 619               aresult.add(rslt);
 620
 621               rs = rslt.getSequencesArray();
 622               // search for each query in the dbrefs associated with each
 623               // sequence
 624               // returned.
 625               // ones we do not find will be used to query next source (if any)
 626               for (String q : tosend)
 627               {
 628                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 629                 dbr.setSource(proxy.getDbSource());
 630                 dbr.setVersion(null);
 631                 if (proxy.getAccessionValidator() != null)
 632                 {
 633                   Regex vgr = proxy.getAccessionValidator();
 634                   vgr.search(q);
 635                   if (vgr.numSubs() > 0)
 636                   {
 637                     dbr.setAccessionId(vgr.stringMatched(1));
 638                   }
 639                   else
 640                   {
 641                     dbr.setAccessionId(vgr.stringMatched());
 642                   }
 643                 }
 644                 else
 645                 {
 646                   dbr.setAccessionId(q);
 647                 }
 648                 boolean rfound = false;
 649                 for (int r = 0; r < rs.length; r++)
 650                 {
 651                   if (rs[r] != null
 652                           && (found = DBRefUtils.searchRefs(
 653                                   rs[r].getDBRef(), dbr)) != null
 654                           && found.length > 0)
 655                   {
 656                     rfound = true;
 657                     rs[r] = null;
 658                     continue;
 659                   }
 660                 }
 661                 if (!rfound)
 662                 {
 663                   nextfetch.add(q);
 664                 }
 665               }
 666             }
 667           } catch (OutOfMemoryError oome)
 668           {
 669             new OOMWarning("fetching " + multiacc + " from "
 670                     + database.getSelectedItem(), oome, this);
 671           }
 672         }
 673
 674       } catch (Exception e)
 675       {
 676         showErrorMessage("Error retrieving " + textArea.getText()
 677                 + " from " + database.getSelectedItem());
 678         // error
 679         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 680         System.err.println("Retrieval failed for source ='"
 681                 + database.getSelectedItem() + "' and query\n'"
 682                 + textArea.getText() + "'\n");
 683         e.printStackTrace();
 684       } catch (OutOfMemoryError e)
 685       {
 686         // resets dialog box - so we don't use OOMwarning here.
 687         showErrorMessage("Out of Memory when retrieving "
 688                 + textArea.getText()
 689                 + " from "
 690                 + database.getSelectedItem()
 691                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 692         e.printStackTrace();
 693       } catch (Error e)
 694       {
 695         showErrorMessage("Serious Error retrieving " + textArea.getText()
 696                 + " from " + database.getSelectedItem());
 697         e.printStackTrace();
 698       }
 699       // Stack results ready for opening in alignment windows
 700       if (aresult != null && aresult.size() > 0)
 701       {
 702         AlignmentI ar = null;
 703         if (isAliSource)
 704         {
 705           addToLast = false;
 706           // new window for each result
 707           while (aresult.size() > 0)
 708           {
 709             presult.add(aresult.remove(0));
 710             presultTitle.add(aresultq.remove(0) + " "
 711                     + getDefaultRetrievalTitle());
 712           }
 713         }
 714         else
 715         {
 716           String titl = null;
 717           if (addToLast && presult.size() > 0)
 718           {
 719             ar = presult.remove(presult.size() - 1);
 720             titl = presultTitle.remove(presultTitle.size() - 1);
 721           }
 722           // concatenate all results in one window
 723           while (aresult.size() > 0)
 724           {
 725             if (ar == null)
 726             {
 727               ar = aresult.remove(0);
 728             }
 729             else
 730             {
 731               ar.append(aresult.remove(0));
 732             }
 733             ;
 734           }
 735           addToLast = true;
 736           presult.add(ar);
 737           presultTitle.add(titl);
 738         }
 739       }
 740       guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
 741               .hashCode());
 742     }
 743     guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
 744             : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
 745     // process results
 746     while (presult.size() > 0)
 747     {
 748       parseResult(presult.remove(0), presultTitle.remove(0), null);
 749     }
 750     // only remove visual delay after we finished parsing.
 751     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 752     if (nextfetch.size() > 0)
 753     {
 754       StringBuffer sb = new StringBuffer();
 755       sb.append("Didn't retrieve the following "
 756               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 757                       + " queries") + ": \n");
 758       int l = sb.length(), lr = 0;
 759       for (String s : nextfetch)
 760       {
 761         if (l != sb.length())
 762         {
 763           sb.append("; ");
 764         }
 765         if (lr - sb.length() > 40)
 766         {
 767           sb.append("\n");
 768         }
 769         sb.append(s);
 770       }
 771       showErrorMessage(sb.toString());
 772     }
 773     resetDialog();
 774   }
 775
 776   AlignmentI parseResult(String result, String title)
 777   {
 778     String format = new IdentifyFile().Identify(result, "Paste");
 779     AlignmentI sequences = null;
 780     if (FormatAdapter.isValidFormat(format))
 781     {
 782       sequences = null;
 783       try
 784       {
 785         sequences = new FormatAdapter().readFile(result.toString(),
 786                 "Paste", format);
 787       } catch (Exception ex)
 788       {
 789       }
 790
 791       if (sequences != null)
 792       {
 793         return parseResult(sequences, title, format);
 794       }
 795     }
 796     else
 797     {
 798       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 799               + database.getSelectedItem());
 800     }
 801
 802     return null;
 803   }
 804
 805   /**
 806    *
 807    * @return a standard title for any results retrieved using the currently
 808    *         selected source and settings
 809    */
 810   public String getDefaultRetrievalTitle()
 811   {
 812     return "Retrieved from " + database.getSelectedItem();
 813   }
 814
 815   AlignmentI parseResult(AlignmentI al, String title,
 816           String currentFileFormat)
 817   {
 818
 819     if (al != null && al.getHeight() > 0)
 820     {
 821       if (title == null)
 822       {
 823         title = getDefaultRetrievalTitle();
 824       }
 825       if (alignFrame == null)
 826       {
 827         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 828                 AlignFrame.DEFAULT_HEIGHT);
 829         if (currentFileFormat != null)
 830         {
 831           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 832           // FORMAT FOR
 833           // NON-FormatAdapter Sourced
 834           // Alignments?
 835         }
 836
 837         SequenceFeature[] sfs = null;
 838         List<SequenceI> alsqs;
 839         synchronized (alsqs = al.getSequences())
 840         {
 841           for (SequenceI sq : alsqs)
 842           {
 843             if ((sfs = sq.getSequenceFeatures()) != null)
 844             {
 845               if (sfs.length > 0)
 846               {
 847                 af.setShowSeqFeatures(true);
 848                 break;
 849               }
 850             }
 851
 852           }
 853         }
 854         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 855                 AlignFrame.DEFAULT_HEIGHT);
 856
 857         af.statusBar.setText(MessageManager
 858                 .getString("label.successfully_pasted_alignment_file"));
 859
 860         try
 861         {
 862           af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
 863                   false));
 864         } catch (Exception ex)
 865         {
 866         }
 867       }
 868       else
 869       {
 870         alignFrame.viewport.addAlignment(al, title);
 871       }
 872     }
 873     return al;
 874   }
 875
 876   void showErrorMessage(final String error)
 877   {
 878     resetDialog();
 879     javax.swing.SwingUtilities.invokeLater(new Runnable()
 880     {
 881       @Override
 882       public void run()
 883       {
 884         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 885                 MessageManager.getString("label.error_retrieving_data"),
 886                 JOptionPane.WARNING_MESSAGE);
 887       }
 888     });
 889   }
 890
 891   public IProgressIndicator getProgressIndicator()
 892   {
 893     return progressIndicator;
 894   }
 895
 896   public void setProgressIndicator(IProgressIndicator progressIndicator)
 897   {
 898     this.progressIndicator = progressIndicator;
 899   }
 900 }