src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22 import java.util.List;
  23
  24 import java.awt.*;
  25 import java.awt.event.*;
  26
  27 import javax.swing.*;
  28 import javax.swing.tree.DefaultMutableTreeNode;
  29
  30 import com.stevesoft.pat.Regex;
  31
  32 import jalview.datamodel.*;
  33 import jalview.io.*;
  34 import jalview.util.DBRefUtils;
  35 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  36 import jalview.ws.seqfetcher.DbSourceProxy;
  37 import java.awt.BorderLayout;
  38
  39 public class SequenceFetcher extends JPanel implements Runnable
  40 {
  41   // ASequenceFetcher sfetch;
  42   JInternalFrame frame;
  43
  44   IProgressIndicator guiWindow;
  45
  46   AlignFrame alignFrame;
  47
  48   StringBuffer result;
  49
  50   final String noDbSelected = "-- Select Database --";
  51
  52   private static jalview.ws.SequenceFetcher sfetch = null;
  53
  54   private static long lastDasSourceRegistry = -3;
  55
  56   private static DasSourceRegistryI dasRegistry = null;
  57
  58   private static boolean _initingFetcher = false;
  59
  60   private static Thread initingThread = null;
  61
  62   /**
  63    * Blocking method that initialises and returns the shared instance of the
  64    * SequenceFetcher client
  65    *
  66    * @param guiWindow
  67    *          - where the initialisation delay message should be shown
  68    * @return the singleton instance of the sequence fetcher client
  69    */
  70   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
  71           final IProgressIndicator guiWindow)
  72   {
  73     if (_initingFetcher && initingThread != null && initingThread.isAlive())
  74     {
  75       if (guiWindow != null)
  76       {
  77         guiWindow.setProgressBar(
  78                 "Waiting for Sequence Database Fetchers to initialise",
  79                 Thread.currentThread().hashCode());
  80       }
  81       // initting happening on another thread - so wait around to see if it
  82       // finishes.
  83       while (_initingFetcher && initingThread != null
  84               && initingThread.isAlive())
  85       {
  86         try
  87         {
  88           Thread.sleep(10);
  89         } catch (Exception e)
  90         {
  91         }
  92         ;
  93       }
  94       if (guiWindow != null)
  95       {
  96         guiWindow.setProgressBar(
  97                 "Waiting for Sequence Database Fetchers to initialise",
  98                 Thread.currentThread().hashCode());
  99       }
 100     }
 101     if (sfetch == null
 102             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
 103             || lastDasSourceRegistry != (jalview.bin.Cache
 104                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
 105                     .getDasSourceRegistry().getLocalSourceString())
 106                     .hashCode())
 107     {
 108       _initingFetcher = true;
 109       initingThread = Thread.currentThread();
 110       /**
 111        * give a visual indication that sequence fetcher construction is occuring
 112        */
 113       if (guiWindow != null)
 114       {
 115         guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
 116                 Thread.currentThread().hashCode());
 117       }
 118       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
 119       dasRegistry.refreshSources();
 120
 121       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 122       if (guiWindow != null)
 123       {
 124         guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
 125                 Thread.currentThread().hashCode());
 126       }
 127       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 128               .getLocalSourceString()).hashCode();
 129       sfetch = sf;
 130       _initingFetcher = false;
 131       initingThread = null;
 132     }
 133     return sfetch;
 134   }
 135
 136   public SequenceFetcher(IProgressIndicator guiIndic)
 137   {
 138     final IProgressIndicator guiWindow = guiIndic;
 139     final SequenceFetcher us = this;
 140     // launch initialiser thread
 141     Thread sf = new Thread(new Runnable()
 142     {
 143
 144       @Override
 145       public void run()
 146       {
 147         if (getSequenceFetcherSingleton(guiWindow) != null)
 148         {
 149           us.initGui(guiWindow);
 150         }
 151         else
 152         {
 153           javax.swing.SwingUtilities.invokeLater(new Runnable()
 154           {
 155             @Override
 156             public void run()
 157             {
 158               JOptionPane
 159                       .showInternalMessageDialog(
 160                               Desktop.desktop,
 161                               "Could not create the sequence fetcher client. Check error logs for details.",
 162                               "Couldn't create SequenceFetcher",
 163                               JOptionPane.ERROR_MESSAGE);
 164             }
 165           });
 166
 167           // raise warning dialog
 168         }
 169       }
 170     });
 171     sf.start();
 172   }
 173
 174   private class DatabaseAuthority extends DefaultMutableTreeNode
 175   {
 176
 177   };
 178
 179   private class DatabaseSource extends DefaultMutableTreeNode
 180   {
 181
 182   };
 183
 184   /**
 185    * called by thread spawned by constructor
 186    *
 187    * @param guiWindow
 188    */
 189   private void initGui(IProgressIndicator guiWindow)
 190   {
 191     this.guiWindow = guiWindow;
 192     if (guiWindow instanceof AlignFrame)
 193     {
 194       alignFrame = (AlignFrame) guiWindow;
 195     }
 196     database = new JDatabaseTree(sfetch);
 197     try
 198     {
 199       jbInit();
 200     } catch (Exception ex)
 201     {
 202       ex.printStackTrace();
 203     }
 204
 205     frame = new JInternalFrame();
 206     frame.setContentPane(this);
 207     if (new jalview.util.Platform().isAMac())
 208     {
 209       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 210     }
 211     else
 212     {
 213       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 214     }
 215   }
 216
 217   private String getFrameTitle()
 218   {
 219     return ((alignFrame == null) ? "New " : "Additional ")
 220             + "Sequence Fetcher";
 221   }
 222
 223   private void jbInit() throws Exception
 224   {
 225     this.setLayout(borderLayout2);
 226
 227     database.setFont(JvSwingUtils.getLabelFont());
 228     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 229     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 230     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 231     jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
 232
 233     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 234     replacePunctuation
 235             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 236     replacePunctuation.setText("Replace commas with semi-colons");
 237     ok.setText("OK");
 238     ok.addActionListener(new ActionListener()
 239     {
 240       @Override
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         ok_actionPerformed();
 244       }
 245     });
 246     clear.setText("Clear");
 247     clear.addActionListener(new ActionListener()
 248     {
 249       @Override
 250       public void actionPerformed(ActionEvent e)
 251       {
 252         clear_actionPerformed();
 253       }
 254     });
 255
 256     example.setText("Example");
 257     example.addActionListener(new ActionListener()
 258     {
 259       @Override
 260       public void actionPerformed(ActionEvent e)
 261       {
 262         example_actionPerformed();
 263       }
 264     });
 265     close.setText("Close");
 266     close.addActionListener(new ActionListener()
 267     {
 268       @Override
 269       public void actionPerformed(ActionEvent e)
 270       {
 271         close_actionPerformed(e);
 272       }
 273     });
 274     textArea.setFont(JvSwingUtils.getLabelFont());
 275     textArea.setLineWrap(true);
 276     textArea.addKeyListener(new KeyAdapter()
 277     {
 278       @Override
 279       public void keyPressed(KeyEvent e)
 280       {
 281         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 282           ok_actionPerformed();
 283       }
 284     });
 285     jPanel3.setLayout(borderLayout1);
 286     borderLayout1.setVgap(5);
 287     jPanel1.add(ok);
 288     jPanel1.add(example);
 289     jPanel1.add(clear);
 290     jPanel1.add(close);
 291     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 292     jPanel2.setLayout(borderLayout3);
 293     databaseButt = database.getDatabaseSelectorButton();
 294     databaseButt.setFont(JvSwingUtils.getLabelFont());
 295     database.addActionListener(new ActionListener()
 296     {
 297
 298       @Override
 299       public void actionPerformed(ActionEvent e)
 300       {
 301         try
 302         {
 303           databaseButt.setText(database.getSelectedItem()
 304                   + (database.getSelectedSources().size() > 1 ? " (and "
 305                           + database.getSelectedSources().size()
 306                           + " others)" : ""));
 307           String eq = database.getExampleQueries();
 308           dbeg.setText("Example query: " + eq);
 309           boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 310           for (DbSourceProxy dbs : database.getSelectedSources())
 311           {
 312             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 313             {
 314               enablePunct = false;
 315               break;
 316             }
 317           }
 318           replacePunctuation.setEnabled(enablePunct);
 319
 320         } catch (Exception ex)
 321         {
 322           dbeg.setText("");
 323           replacePunctuation.setEnabled(true);
 324         }
 325         jPanel2.repaint();
 326       }
 327     });
 328     dbeg.setText("");
 329     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 330     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 331     JPanel jPanel2a = new JPanel(new BorderLayout());
 332     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 333     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 334     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 335     // jPanel2.setPreferredSize(new Dimension())
 336     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 337     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 338     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 339     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 340     jScrollPane1.getViewport().add(textArea);
 341
 342   }
 343
 344   protected void example_actionPerformed()
 345   {
 346     DbSourceProxy db = null;
 347     try
 348     {
 349       textArea.setText(database.getExampleQueries());
 350     } catch (Exception ex)
 351     {
 352     }
 353     jPanel3.repaint();
 354   }
 355
 356   protected void clear_actionPerformed()
 357   {
 358     textArea.setText("");
 359     jPanel3.repaint();
 360   }
 361
 362   JLabel dbeg = new JLabel();
 363
 364   JDatabaseTree database;
 365
 366   JButton databaseButt;
 367
 368   JLabel jLabel1 = new JLabel();
 369
 370   JCheckBox replacePunctuation = new JCheckBox();
 371
 372   JButton ok = new JButton();
 373
 374   JButton clear = new JButton();
 375
 376   JButton example = new JButton();
 377
 378   JButton close = new JButton();
 379
 380   JPanel jPanel1 = new JPanel();
 381
 382   JTextArea textArea = new JTextArea();
 383
 384   JScrollPane jScrollPane1 = new JScrollPane();
 385
 386   JPanel jPanel2 = new JPanel();
 387
 388   JPanel jPanel3 = new JPanel();
 389
 390   JPanel jPanel4 = new JPanel();
 391
 392   BorderLayout borderLayout1 = new BorderLayout();
 393
 394   BorderLayout borderLayout2 = new BorderLayout();
 395
 396   BorderLayout borderLayout3 = new BorderLayout();
 397
 398   public void close_actionPerformed(ActionEvent e)
 399   {
 400     try
 401     {
 402       frame.setClosed(true);
 403     } catch (Exception ex)
 404     {
 405     }
 406   }
 407
 408   public void ok_actionPerformed()
 409   {
 410     databaseButt.setEnabled(false);
 411     example.setEnabled(false);
 412     textArea.setEnabled(false);
 413     ok.setEnabled(false);
 414     close.setEnabled(false);
 415
 416     Thread worker = new Thread(this);
 417     worker.start();
 418   }
 419
 420   private void resetDialog()
 421   {
 422     databaseButt.setEnabled(true);
 423     example.setEnabled(true);
 424     textArea.setEnabled(true);
 425     ok.setEnabled(true);
 426     close.setEnabled(true);
 427   }
 428
 429   @Override
 430   public void run()
 431   {
 432     String error = "";
 433     if (!database.hasSelection())
 434     {
 435       error += "Please select the source database\n";
 436     }
 437     // TODO: make this transformation more configurable
 438     com.stevesoft.pat.Regex empty;
 439     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 440     {
 441       empty = new com.stevesoft.pat.Regex(
 442       // replace commas and spaces with a semicolon
 443               "(\\s|[,; ])+", ";");
 444     }
 445     else
 446     {
 447       // just turn spaces and semicolons into single semicolons
 448       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 449     }
 450     textArea.setText(empty.replaceAll(textArea.getText()));
 451     // see if there's anthing to search with
 452     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 453             .getText()))
 454     {
 455       error += "Please enter a (semi-colon separated list of) database id(s)";
 456     }
 457     if (error.length() > 0)
 458     {
 459       showErrorMessage(error);
 460       resetDialog();
 461       return;
 462     }
 463     // indicate if successive sources should be merged into one alignment.
 464     boolean addToLast = false;
 465     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 466     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 467     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 468             .iterator();
 469     String[] qries;
 470     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 471             .split(";"));
 472     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 473     int nqueries = qries.length;
 474     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 475     {
 476       if (!en.hasNext() && nextfetch.size() > 0)
 477       {
 478         en = nextfetch.iterator();
 479         nqueries = nextfetch.size();
 480         // save the remaining queries in the original array
 481         qries = nextfetch.toArray(new String[nqueries]);
 482         nextfetch = new ArrayList<String>();
 483       }
 484
 485       DbSourceProxy proxy = proxies.next();
 486       boolean isAliSource = false;
 487       try
 488       {
 489         // update status
 490         guiWindow.setProgressBar("Fetching " + nqueries
 491                 + " sequence queries from " + proxy.getDbName(), Thread
 492                 .currentThread().hashCode());
 493         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 494         if (proxy.getAccessionSeparator() == null)
 495         {
 496           while (en.hasNext())
 497           {
 498             String item = en.next();
 499             try
 500             {
 501               if (aresult != null)
 502               {
 503                 try
 504                 {
 505                   // give the server a chance to breathe
 506                   Thread.sleep(5);
 507                 } catch (Exception e)
 508                 {
 509                   //
 510                 }
 511
 512               }
 513
 514               AlignmentI indres = null;
 515               try
 516               {
 517                 indres = proxy.getSequenceRecords(item);
 518               } catch (OutOfMemoryError oome)
 519               {
 520                 new OOMWarning("fetching " + item + " from "
 521                         + proxy.getDbName(), oome, this);
 522               }
 523               if (indres != null)
 524               {
 525                 aresultq.add(item);
 526                 aresult.add(indres);
 527               }
 528               else
 529               {
 530                 nextfetch.add(item);
 531               }
 532             } catch (Exception e)
 533             {
 534               jalview.bin.Cache.log.info("Error retrieving " + item
 535                       + " from " + proxy.getDbName(), e);
 536               nextfetch.add(item);
 537             }
 538           }
 539         }
 540         else
 541         {
 542           StringBuffer multiacc = new StringBuffer();
 543           ArrayList<String> tosend = new ArrayList<String>();
 544           while (en.hasNext())
 545           {
 546             String nel = en.next();
 547             tosend.add(nel);
 548             multiacc.append(nel);
 549             if (en.hasNext())
 550             {
 551               multiacc.append(proxy.getAccessionSeparator());
 552             }
 553           }
 554           try
 555           {
 556             AlignmentI rslt;
 557             SequenceI[] rs;
 558             List<String> nores = new ArrayList<String>();
 559             rslt = proxy.getSequenceRecords(multiacc.toString());
 560             if (rslt == null || rslt.getHeight() == 0)
 561             {
 562               // no results - pass on all queries to next source
 563               nextfetch.addAll(tosend);
 564             }
 565             else
 566             {
 567               aresultq.add(multiacc.toString());
 568               aresult.add(rslt);
 569
 570               rs = rslt.getSequencesArray();
 571               // search for each query in the dbrefs associated with each
 572               // sequence
 573               // returned.
 574               // ones we do not find will be used to query next source (if any)
 575               for (String q : tosend)
 576               {
 577                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 578                 dbr.setSource(proxy.getDbSource());
 579                 dbr.setVersion(null);
 580                 if (proxy.getAccessionValidator() != null)
 581                 {
 582                   Regex vgr = proxy.getAccessionValidator();
 583                   vgr.search(q);
 584                   if (vgr.numSubs() > 0)
 585                   {
 586                     dbr.setAccessionId(vgr.stringMatched(1));
 587                   }
 588                   else
 589                   {
 590                     dbr.setAccessionId(vgr.stringMatched());
 591                   }
 592                 }
 593                 else
 594                 {
 595                   dbr.setAccessionId(q);
 596                 }
 597                 boolean rfound = false;
 598                 for (int r = 0; r < rs.length; r++)
 599                 {
 600                   if (rs[r] != null
 601                           && (found = DBRefUtils.searchRefs(
 602                                   rs[r].getDBRef(), dbr)) != null
 603                           && found.length > 0)
 604                   {
 605                     rfound = true;
 606                     rs[r] = null;
 607                     continue;
 608                   }
 609                 }
 610                 if (!rfound)
 611                 {
 612                   nextfetch.add(q);
 613                 }
 614               }
 615             }
 616           } catch (OutOfMemoryError oome)
 617           {
 618             new OOMWarning("fetching " + multiacc + " from "
 619                     + database.getSelectedItem(), oome, this);
 620           }
 621         }
 622
 623       } catch (Exception e)
 624       {
 625         showErrorMessage("Error retrieving " + textArea.getText()
 626                 + " from " + database.getSelectedItem());
 627         // error
 628         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 629         System.err.println("Retrieval failed for source ='"
 630                 + database.getSelectedItem() + "' and query\n'"
 631                 + textArea.getText() + "'\n");
 632         e.printStackTrace();
 633       } catch (OutOfMemoryError e)
 634       {
 635         // resets dialog box - so we don't use OOMwarning here.
 636         showErrorMessage("Out of Memory when retrieving "
 637                 + textArea.getText()
 638                 + " from "
 639                 + database.getSelectedItem()
 640                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 641         e.printStackTrace();
 642       } catch (Error e)
 643       {
 644         showErrorMessage("Serious Error retrieving " + textArea.getText()
 645                 + " from " + database.getSelectedItem());
 646         e.printStackTrace();
 647       }
 648       // Stack results ready for opening in alignment windows
 649       if (aresult != null && aresult.size() > 0)
 650       {
 651         AlignmentI ar = null;
 652         if (isAliSource)
 653         {
 654           addToLast = false;
 655           // new window for each result
 656           while (aresult.size() > 0)
 657           {
 658             presult.add(aresult.remove(0));
 659             presultTitle.add(aresultq.remove(0) + " "
 660                     + getDefaultRetrievalTitle());
 661           }
 662         }
 663         else
 664         {
 665           String titl = null;
 666           if (addToLast && presult.size() > 0)
 667           {
 668             ar = presult.remove(presult.size() - 1);
 669             titl = presultTitle.remove(presultTitle.size() - 1);
 670           }
 671           // concatenate all results in one window
 672           while (aresult.size() > 0)
 673           {
 674             if (ar == null)
 675             {
 676               ar = aresult.remove(0);
 677             }
 678             else
 679             {
 680               ar.append(aresult.remove(0));
 681             }
 682             ;
 683           }
 684           addToLast = true;
 685           presult.add(ar);
 686           presultTitle.add(titl);
 687         }
 688       }
 689       guiWindow.setProgressBar("Finished querying", Thread.currentThread()
 690               .hashCode());
 691     }
 692     guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
 693             : "Processing ..", Thread.currentThread().hashCode());
 694     // process results
 695     while (presult.size() > 0)
 696     {
 697       parseResult(presult.remove(0), presultTitle.remove(0), null);
 698     }
 699     // only remove visual delay after we finished parsing.
 700     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 701     if (nextfetch.size() > 0)
 702     {
 703       StringBuffer sb = new StringBuffer();
 704       sb.append("Didn't retrieve the following "
 705               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 706                       + " queries") + ": \n");
 707       int l = sb.length(), lr = 0;
 708       for (String s : nextfetch)
 709       {
 710         if (l != sb.length())
 711         {
 712           sb.append("; ");
 713         }
 714         if (lr - sb.length() > 40)
 715         {
 716           sb.append("\n");
 717         }
 718         sb.append(s);
 719       }
 720       showErrorMessage(sb.toString());
 721     }
 722     resetDialog();
 723   }
 724
 725   AlignmentI parseResult(String result, String title)
 726   {
 727     String format = new IdentifyFile().Identify(result, "Paste");
 728     Alignment sequences = null;
 729     if (FormatAdapter.isValidFormat(format))
 730     {
 731       sequences = null;
 732       try
 733       {
 734         sequences = new FormatAdapter().readFile(result.toString(),
 735                 "Paste", format);
 736       } catch (Exception ex)
 737       {
 738       }
 739
 740       if (sequences != null)
 741       {
 742         return parseResult(sequences, title, format);
 743       }
 744     }
 745     else
 746     {
 747       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 748               + database.getSelectedItem());
 749     }
 750
 751     return null;
 752   }
 753
 754   /**
 755    *
 756    * @return a standard title for any results retrieved using the currently
 757    *         selected source and settings
 758    */
 759   public String getDefaultRetrievalTitle()
 760   {
 761     return "Retrieved from " + database.getSelectedItem();
 762   }
 763
 764   AlignmentI parseResult(AlignmentI al, String title,
 765           String currentFileFormat)
 766   {
 767
 768     if (al != null && al.getHeight() > 0)
 769     {
 770       if (alignFrame == null)
 771       {
 772         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 773                 AlignFrame.DEFAULT_HEIGHT);
 774         if (currentFileFormat != null)
 775         {
 776           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 777           // FORMAT FOR
 778           // NON-FormatAdapter Sourced
 779           // Alignments?
 780         }
 781
 782         if (title == null)
 783         {
 784           title = getDefaultRetrievalTitle();
 785         }
 786         SequenceFeature[] sfs = null;
 787         List<SequenceI> alsqs;
 788         synchronized (alsqs = al.getSequences())
 789         {
 790           for (SequenceI sq : alsqs)
 791           {
 792             if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
 793             {
 794               if (sfs.length > 0)
 795               {
 796                 af.setShowSeqFeatures(true);
 797                 break;
 798               }
 799             }
 800
 801           }
 802         }
 803         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 804                 AlignFrame.DEFAULT_HEIGHT);
 805
 806         af.statusBar.setText("Successfully pasted alignment file");
 807
 808         try
 809         {
 810           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 811                   false));
 812         } catch (Exception ex)
 813         {
 814         }
 815       }
 816       else
 817       {
 818         for (int i = 0; i < al.getHeight(); i++)
 819         {
 820           alignFrame.viewport.getAlignment().addSequence(
 821                   al.getSequenceAt(i)); // this
 822           // also
 823           // creates
 824           // dataset
 825           // sequence
 826           // entries
 827         }
 828         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 829                 .getHeight());
 830         alignFrame.viewport.getAlignment().getWidth();
 831         alignFrame.viewport.firePropertyChange("alignment", null,
 832                 alignFrame.viewport.getAlignment().getSequences());
 833       }
 834     }
 835     return al;
 836   }
 837
 838   void showErrorMessage(final String error)
 839   {
 840     resetDialog();
 841     javax.swing.SwingUtilities.invokeLater(new Runnable()
 842     {
 843       @Override
 844       public void run()
 845       {
 846         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 847                 "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
 848       }
 849     });
 850   }
 851 }