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 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                 "Waiting for Sequence Database Fetchers to initialise",
  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                 "Waiting for Sequence Database Fetchers to initialise",
 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("Initialising 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("Initialising 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                               "Could not create the sequence fetcher client. Check error logs for details.",
 165                               "Couldn't create SequenceFetcher",
 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) ? "New " : "Additional ")
 223             + "Sequence Fetcher";
 224   }
 225
 226   private void jbInit() throws Exception
 227   {
 228     this.setLayout(borderLayout2);
 229
 230     database.setFont(JvSwingUtils.getLabelFont());
 231     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 232     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 233     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 234     jLabel1.setText(MessageManager.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.getString("label.replace_commas_semicolons"));
 240     ok.setText(MessageManager.getString("action.ok"));
 241     ok.addActionListener(new ActionListener()
 242     {
 243       @Override
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         ok_actionPerformed();
 247       }
 248     });
 249     clear.setText(MessageManager.getString("action.clear"));
 250     clear.addActionListener(new ActionListener()
 251     {
 252       @Override
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         clear_actionPerformed();
 256       }
 257     });
 258
 259     example.setText(MessageManager.getString("label.example"));
 260     example.addActionListener(new ActionListener()
 261     {
 262       @Override
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         example_actionPerformed();
 266       }
 267     });
 268     close.setText(MessageManager.getString("action.close"));
 269     close.addActionListener(new ActionListener()
 270     {
 271       @Override
 272       public void actionPerformed(ActionEvent e)
 273       {
 274         close_actionPerformed(e);
 275       }
 276     });
 277     textArea.setFont(JvSwingUtils.getLabelFont());
 278     textArea.setLineWrap(true);
 279     textArea.addKeyListener(new KeyAdapter()
 280     {
 281       @Override
 282       public void keyPressed(KeyEvent e)
 283       {
 284         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 285           ok_actionPerformed();
 286       }
 287     });
 288     jPanel3.setLayout(borderLayout1);
 289     borderLayout1.setVgap(5);
 290     jPanel1.add(ok);
 291     jPanel1.add(example);
 292     jPanel1.add(clear);
 293     jPanel1.add(close);
 294     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 295     jPanel2.setLayout(borderLayout3);
 296     databaseButt = database.getDatabaseSelectorButton();
 297     databaseButt.setFont(JvSwingUtils.getLabelFont());
 298     database.addActionListener(new ActionListener()
 299     {
 300
 301       @Override
 302       public void actionPerformed(ActionEvent e)
 303       {
 304         try
 305         {
 306           databaseButt.setText(database.getSelectedItem()
 307                   + (database.getSelectedSources().size() > 1 ? " (and "
 308                           + database.getSelectedSources().size()
 309                           + " others)" : ""));
 310           String eq = database.getExampleQueries();
 311           dbeg.setText(MessageManager.formatMessage("label.example_query_param", new String[]{eq}));
 312           boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 313           for (DbSourceProxy dbs : database.getSelectedSources())
 314           {
 315             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 316             {
 317               enablePunct = false;
 318               break;
 319             }
 320           }
 321           replacePunctuation.setEnabled(enablePunct);
 322
 323         } catch (Exception ex)
 324         {
 325           dbeg.setText("");
 326           replacePunctuation.setEnabled(true);
 327         }
 328         jPanel2.repaint();
 329       }
 330     });
 331     dbeg.setText("");
 332     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 333     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 334     JPanel jPanel2a = new JPanel(new BorderLayout());
 335     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 336     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 337     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 338     // jPanel2.setPreferredSize(new Dimension())
 339     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 340     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 341     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 342     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 343     jScrollPane1.getViewport().add(textArea);
 344
 345   }
 346
 347   protected void example_actionPerformed()
 348   {
 349     DbSourceProxy db = null;
 350     try
 351     {
 352       textArea.setText(database.getExampleQueries());
 353     } catch (Exception ex)
 354     {
 355     }
 356     jPanel3.repaint();
 357   }
 358
 359   protected void clear_actionPerformed()
 360   {
 361     textArea.setText("");
 362     jPanel3.repaint();
 363   }
 364
 365   JLabel dbeg = new JLabel();
 366
 367   JDatabaseTree database;
 368
 369   JButton databaseButt;
 370
 371   JLabel jLabel1 = new JLabel();
 372
 373   JCheckBox replacePunctuation = new JCheckBox();
 374
 375   JButton ok = new JButton();
 376
 377   JButton clear = new JButton();
 378
 379   JButton example = new JButton();
 380
 381   JButton close = new JButton();
 382
 383   JPanel jPanel1 = new JPanel();
 384
 385   JTextArea textArea = new JTextArea();
 386
 387   JScrollPane jScrollPane1 = new JScrollPane();
 388
 389   JPanel jPanel2 = new JPanel();
 390
 391   JPanel jPanel3 = new JPanel();
 392
 393   JPanel jPanel4 = new JPanel();
 394
 395   BorderLayout borderLayout1 = new BorderLayout();
 396
 397   BorderLayout borderLayout2 = new BorderLayout();
 398
 399   BorderLayout borderLayout3 = new BorderLayout();
 400
 401   public void close_actionPerformed(ActionEvent e)
 402   {
 403     try
 404     {
 405       frame.setClosed(true);
 406     } catch (Exception ex)
 407     {
 408     }
 409   }
 410
 411   public void ok_actionPerformed()
 412   {
 413     databaseButt.setEnabled(false);
 414     example.setEnabled(false);
 415     textArea.setEnabled(false);
 416     ok.setEnabled(false);
 417     close.setEnabled(false);
 418
 419     Thread worker = new Thread(this);
 420     worker.start();
 421   }
 422
 423   private void resetDialog()
 424   {
 425     databaseButt.setEnabled(true);
 426     example.setEnabled(true);
 427     textArea.setEnabled(true);
 428     ok.setEnabled(true);
 429     close.setEnabled(true);
 430   }
 431
 432   @Override
 433   public void run()
 434   {
 435     String error = "";
 436     if (!database.hasSelection())
 437     {
 438       error += "Please select the source database\n";
 439     }
 440     // TODO: make this transformation more configurable
 441     com.stevesoft.pat.Regex empty;
 442     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 443     {
 444       empty = new com.stevesoft.pat.Regex(
 445       // replace commas and spaces with a semicolon
 446               "(\\s|[,; ])+", ";");
 447     }
 448     else
 449     {
 450       // just turn spaces and semicolons into single semicolons
 451       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 452     }
 453     textArea.setText(empty.replaceAll(textArea.getText()));
 454     // see if there's anthing to search with
 455     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 456             .getText()))
 457     {
 458       error += "Please enter a (semi-colon separated list of) database id(s)";
 459     }
 460     if (error.length() > 0)
 461     {
 462       showErrorMessage(error);
 463       resetDialog();
 464       return;
 465     }
 466     // indicate if successive sources should be merged into one alignment.
 467     boolean addToLast = false;
 468     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 469     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 470     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 471             .iterator();
 472     String[] qries;
 473     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 474             .split(";"));
 475     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 476     int nqueries = qries.length;
 477     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 478     {
 479       if (!en.hasNext() && nextfetch.size() > 0)
 480       {
 481         en = nextfetch.iterator();
 482         nqueries = nextfetch.size();
 483         // save the remaining queries in the original array
 484         qries = nextfetch.toArray(new String[nqueries]);
 485         nextfetch = new ArrayList<String>();
 486       }
 487
 488       DbSourceProxy proxy = proxies.next();
 489       boolean isAliSource = false;
 490       try
 491       {
 492         // update status
 493         guiWindow.setProgressBar("Fetching " + nqueries
 494                 + " sequence queries from " + proxy.getDbName(), Thread
 495                 .currentThread().hashCode());
 496         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 497         if (proxy.getAccessionSeparator() == null)
 498         {
 499           while (en.hasNext())
 500           {
 501             String item = en.next();
 502             try
 503             {
 504               if (aresult != null)
 505               {
 506                 try
 507                 {
 508                   // give the server a chance to breathe
 509                   Thread.sleep(5);
 510                 } catch (Exception e)
 511                 {
 512                   //
 513                 }
 514
 515               }
 516
 517               AlignmentI indres = null;
 518               try
 519               {
 520                 indres = proxy.getSequenceRecords(item);
 521               } catch (OutOfMemoryError oome)
 522               {
 523                 new OOMWarning("fetching " + item + " from "
 524                         + proxy.getDbName(), oome, this);
 525               }
 526               if (indres != null)
 527               {
 528                 aresultq.add(item);
 529                 aresult.add(indres);
 530               }
 531               else
 532               {
 533                 nextfetch.add(item);
 534               }
 535             } catch (Exception e)
 536             {
 537               jalview.bin.Cache.log.info("Error retrieving " + item
 538                       + " from " + proxy.getDbName(), e);
 539               nextfetch.add(item);
 540             }
 541           }
 542         }
 543         else
 544         {
 545           StringBuffer multiacc = new StringBuffer();
 546           ArrayList<String> tosend = new ArrayList<String>();
 547           while (en.hasNext())
 548           {
 549             String nel = en.next();
 550             tosend.add(nel);
 551             multiacc.append(nel);
 552             if (en.hasNext())
 553             {
 554               multiacc.append(proxy.getAccessionSeparator());
 555             }
 556           }
 557           try
 558           {
 559             AlignmentI rslt;
 560             SequenceI[] rs;
 561             List<String> nores = new ArrayList<String>();
 562             rslt = proxy.getSequenceRecords(multiacc.toString());
 563             if (rslt == null || rslt.getHeight() == 0)
 564             {
 565               // no results - pass on all queries to next source
 566               nextfetch.addAll(tosend);
 567             }
 568             else
 569             {
 570               aresultq.add(multiacc.toString());
 571               aresult.add(rslt);
 572
 573               rs = rslt.getSequencesArray();
 574               // search for each query in the dbrefs associated with each
 575               // sequence
 576               // returned.
 577               // ones we do not find will be used to query next source (if any)
 578               for (String q : tosend)
 579               {
 580                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 581                 dbr.setSource(proxy.getDbSource());
 582                 dbr.setVersion(null);
 583                 if (proxy.getAccessionValidator() != null)
 584                 {
 585                   Regex vgr = proxy.getAccessionValidator();
 586                   vgr.search(q);
 587                   if (vgr.numSubs() > 0)
 588                   {
 589                     dbr.setAccessionId(vgr.stringMatched(1));
 590                   }
 591                   else
 592                   {
 593                     dbr.setAccessionId(vgr.stringMatched());
 594                   }
 595                 }
 596                 else
 597                 {
 598                   dbr.setAccessionId(q);
 599                 }
 600                 boolean rfound = false;
 601                 for (int r = 0; r < rs.length; r++)
 602                 {
 603                   if (rs[r] != null
 604                           && (found = DBRefUtils.searchRefs(
 605                                   rs[r].getDBRef(), dbr)) != null
 606                           && found.length > 0)
 607                   {
 608                     rfound = true;
 609                     rs[r] = null;
 610                     continue;
 611                   }
 612                 }
 613                 if (!rfound)
 614                 {
 615                   nextfetch.add(q);
 616                 }
 617               }
 618             }
 619           } catch (OutOfMemoryError oome)
 620           {
 621             new OOMWarning("fetching " + multiacc + " from "
 622                     + database.getSelectedItem(), oome, this);
 623           }
 624         }
 625
 626       } catch (Exception e)
 627       {
 628         showErrorMessage("Error retrieving " + textArea.getText()
 629                 + " from " + database.getSelectedItem());
 630         // error
 631         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 632         System.err.println("Retrieval failed for source ='"
 633                 + database.getSelectedItem() + "' and query\n'"
 634                 + textArea.getText() + "'\n");
 635         e.printStackTrace();
 636       } catch (OutOfMemoryError e)
 637       {
 638         // resets dialog box - so we don't use OOMwarning here.
 639         showErrorMessage("Out of Memory when retrieving "
 640                 + textArea.getText()
 641                 + " from "
 642                 + database.getSelectedItem()
 643                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 644         e.printStackTrace();
 645       } catch (Error e)
 646       {
 647         showErrorMessage("Serious Error retrieving " + textArea.getText()
 648                 + " from " + database.getSelectedItem());
 649         e.printStackTrace();
 650       }
 651       // Stack results ready for opening in alignment windows
 652       if (aresult != null && aresult.size() > 0)
 653       {
 654         AlignmentI ar = null;
 655         if (isAliSource)
 656         {
 657           addToLast = false;
 658           // new window for each result
 659           while (aresult.size() > 0)
 660           {
 661             presult.add(aresult.remove(0));
 662             presultTitle.add(aresultq.remove(0) + " "
 663                     + getDefaultRetrievalTitle());
 664           }
 665         }
 666         else
 667         {
 668           String titl = null;
 669           if (addToLast && presult.size() > 0)
 670           {
 671             ar = presult.remove(presult.size() - 1);
 672             titl = presultTitle.remove(presultTitle.size() - 1);
 673           }
 674           // concatenate all results in one window
 675           while (aresult.size() > 0)
 676           {
 677             if (ar == null)
 678             {
 679               ar = aresult.remove(0);
 680             }
 681             else
 682             {
 683               ar.append(aresult.remove(0));
 684             }
 685             ;
 686           }
 687           addToLast = true;
 688           presult.add(ar);
 689           presultTitle.add(titl);
 690         }
 691       }
 692       guiWindow.setProgressBar("Finished querying", Thread.currentThread()
 693               .hashCode());
 694     }
 695     guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
 696             : "Processing ..", Thread.currentThread().hashCode());
 697     // process results
 698     while (presult.size() > 0)
 699     {
 700       parseResult(presult.remove(0), presultTitle.remove(0), null);
 701     }
 702     // only remove visual delay after we finished parsing.
 703     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 704     if (nextfetch.size() > 0)
 705     {
 706       StringBuffer sb = new StringBuffer();
 707       sb.append("Didn't retrieve the following "
 708               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 709                       + " queries") + ": \n");
 710       int l = sb.length(), lr = 0;
 711       for (String s : nextfetch)
 712       {
 713         if (l != sb.length())
 714         {
 715           sb.append("; ");
 716         }
 717         if (lr - sb.length() > 40)
 718         {
 719           sb.append("\n");
 720         }
 721         sb.append(s);
 722       }
 723       showErrorMessage(sb.toString());
 724     }
 725     resetDialog();
 726   }
 727
 728   AlignmentI parseResult(String result, String title)
 729   {
 730     String format = new IdentifyFile().Identify(result, "Paste");
 731     Alignment sequences = null;
 732     if (FormatAdapter.isValidFormat(format))
 733     {
 734       sequences = null;
 735       try
 736       {
 737         sequences = new FormatAdapter().readFile(result.toString(),
 738                 "Paste", format);
 739       } catch (Exception ex)
 740       {
 741       }
 742
 743       if (sequences != null)
 744       {
 745         return parseResult(sequences, title, format);
 746       }
 747     }
 748     else
 749     {
 750       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 751               + database.getSelectedItem());
 752     }
 753
 754     return null;
 755   }
 756
 757   /**
 758    *
 759    * @return a standard title for any results retrieved using the currently
 760    *         selected source and settings
 761    */
 762   public String getDefaultRetrievalTitle()
 763   {
 764     return "Retrieved from " + database.getSelectedItem();
 765   }
 766
 767   AlignmentI parseResult(AlignmentI al, String title,
 768           String currentFileFormat)
 769   {
 770
 771     if (al != null && al.getHeight() > 0)
 772     {
 773       if (alignFrame == null)
 774       {
 775         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 776                 AlignFrame.DEFAULT_HEIGHT);
 777         if (currentFileFormat != null)
 778         {
 779           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 780           // FORMAT FOR
 781           // NON-FormatAdapter Sourced
 782           // Alignments?
 783         }
 784
 785         if (title == null)
 786         {
 787           title = getDefaultRetrievalTitle();
 788         }
 789         SequenceFeature[] sfs = null;
 790         List<SequenceI> alsqs;
 791         synchronized (alsqs = al.getSequences())
 792         {
 793           for (SequenceI sq : alsqs)
 794           {
 795             if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
 796             {
 797               if (sfs.length > 0)
 798               {
 799                 af.setShowSeqFeatures(true);
 800                 break;
 801               }
 802             }
 803
 804           }
 805         }
 806         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 807                 AlignFrame.DEFAULT_HEIGHT);
 808
 809         af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
 810
 811         try
 812         {
 813           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 814                   false));
 815         } catch (Exception ex)
 816         {
 817         }
 818       }
 819       else
 820       {
 821         for (int i = 0; i < al.getHeight(); i++)
 822         {
 823           alignFrame.viewport.getAlignment().addSequence(
 824                   al.getSequenceAt(i)); // this
 825           // also
 826           // creates
 827           // dataset
 828           // sequence
 829           // entries
 830         }
 831         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 832                 .getHeight());
 833         alignFrame.viewport.getAlignment().getWidth();
 834         alignFrame.viewport.firePropertyChange("alignment", null,
 835                 alignFrame.viewport.getAlignment().getSequences());
 836       }
 837     }
 838     return al;
 839   }
 840
 841   void showErrorMessage(final String error)
 842   {
 843     resetDialog();
 844     javax.swing.SwingUtilities.invokeLater(new Runnable()
 845     {
 846       @Override
 847       public void run()
 848       {
 849         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 850                 MessageManager.getString("label.error_retrieving_data"), JOptionPane.WARNING_MESSAGE);
 851       }
 852     });
 853   }
 854 }