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