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.api.FeatureSettingsModelI;
  24 import jalview.bin.Cache;
  25 import jalview.datamodel.AlignmentI;
  26 import jalview.datamodel.DBRefEntry;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.io.gff.SequenceOntologyI;
  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 public class SequenceFetcher extends JPanel implements Runnable
  58 {
  59   JLabel dbeg = new JLabel();
  60
  61   JDatabaseTree database;
  62
  63   JButton databaseButt;
  64
  65   JLabel jLabel1 = new JLabel();
  66
  67   JCheckBox replacePunctuation = new JCheckBox();
  68
  69   JButton ok = new JButton();
  70
  71   JButton clear = new JButton();
  72
  73   JButton example = new JButton();
  74
  75   JButton close = new JButton();
  76
  77   JPanel jPanel1 = new JPanel();
  78
  79   JTextArea textArea = new JTextArea();
  80
  81   JScrollPane jScrollPane1 = new JScrollPane();
  82
  83   JPanel jPanel2 = new JPanel();
  84
  85   JPanel jPanel3 = new JPanel();
  86
  87   JPanel jPanel4 = new JPanel();
  88
  89   BorderLayout borderLayout1 = new BorderLayout();
  90
  91   BorderLayout borderLayout2 = new BorderLayout();
  92
  93   BorderLayout borderLayout3 = new BorderLayout();
  94
  95   JInternalFrame frame;
  96
  97   IProgressIndicator guiWindow;
  98
  99   AlignFrame alignFrame;
 100
 101   StringBuffer result;
 102
 103   final String noDbSelected = "-- Select Database --";
 104
 105   private static jalview.ws.SequenceFetcher sfetch = null;
 106
 107   private static long lastDasSourceRegistry = -3;
 108
 109   private static DasSourceRegistryI dasRegistry = null;
 110
 111   private static boolean _initingFetcher = false;
 112
 113   private static Thread initingThread = null;
 114
 115   int debounceTrap = 0;
 116
 117   /**
 118    * Blocking method that initialises and returns the shared instance of the
 119    * SequenceFetcher client
 120    *
 121    * @param guiWindow
 122    *          - where the initialisation delay message should be shown
 123    * @return the singleton instance of the sequence fetcher client
 124    */
 125   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
 126           final IProgressIndicator guiWindow)
 127   {
 128     if (_initingFetcher && initingThread != null && initingThread.isAlive())
 129     {
 130       if (guiWindow != null)
 131       {
 132         guiWindow
 133                 .setProgressBar(
 134                         MessageManager
 135                                 .getString("status.waiting_sequence_database_fetchers_init"),
 136                         Thread.currentThread().hashCode());
 137       }
 138       // initting happening on another thread - so wait around to see if it
 139       // finishes.
 140       while (_initingFetcher && initingThread != null
 141               && initingThread.isAlive())
 142       {
 143         try
 144         {
 145           Thread.sleep(10);
 146         } catch (Exception e)
 147         {
 148         }
 149         ;
 150       }
 151       if (guiWindow != null)
 152       {
 153         guiWindow
 154                 .setProgressBar(
 155                         MessageManager
 156                                 .getString("status.waiting_sequence_database_fetchers_init"),
 157                         Thread.currentThread().hashCode());
 158       }
 159     }
 160     if (sfetch == null
 161             || dasRegistry != Cache.getDasSourceRegistry()
 162             || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
 163                     .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
 175                 .getString("status.init_sequence_database_fetchers"),
 176                 Thread.currentThread().hashCode());
 177       }
 178       dasRegistry = Cache.getDasSourceRegistry();
 179       dasRegistry.refreshSources();
 180
 181       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
 182       if (guiWindow != null)
 183       {
 184         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 185       }
 186       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
 187               .getLocalSourceString()).hashCode();
 188       sfetch = sf;
 189       _initingFetcher = false;
 190       initingThread = null;
 191     }
 192     return sfetch;
 193   }
 194
 195   private IProgressIndicator progressIndicator;
 196
 197   public SequenceFetcher(IProgressIndicator guiIndic)
 198   {
 199     this.progressIndicator = guiIndic;
 200     final SequenceFetcher us = this;
 201     // launch initialiser thread
 202     Thread sf = new Thread(new Runnable()
 203     {
 204
 205       @Override
 206       public void run()
 207       {
 208         if (getSequenceFetcherSingleton(progressIndicator) != null)
 209         {
 210           us.initGui(progressIndicator);
 211         }
 212         else
 213         {
 214           javax.swing.SwingUtilities.invokeLater(new Runnable()
 215           {
 216             @Override
 217             public void run()
 218             {
 219               JOptionPane
 220                       .showInternalMessageDialog(
 221                               Desktop.desktop,
 222                               MessageManager
 223                                       .getString("warn.couldnt_create_sequence_fetcher_client"),
 224                               MessageManager
 225                                       .getString("label.couldnt_create_sequence_fetcher"),
 226                               JOptionPane.ERROR_MESSAGE);
 227             }
 228           });
 229
 230           // raise warning dialog
 231         }
 232       }
 233     });
 234     sf.start();
 235   }
 236
 237   private class DatabaseAuthority extends DefaultMutableTreeNode
 238   {
 239
 240   };
 241
 242   private class DatabaseSource extends DefaultMutableTreeNode
 243   {
 244
 245   };
 246
 247   /**
 248    * called by thread spawned by constructor
 249    *
 250    * @param guiWindow
 251    */
 252   private void initGui(IProgressIndicator guiWindow)
 253   {
 254     this.guiWindow = guiWindow;
 255     if (guiWindow instanceof AlignFrame)
 256     {
 257       alignFrame = (AlignFrame) guiWindow;
 258     }
 259     database = new JDatabaseTree(sfetch);
 260     try
 261     {
 262       jbInit();
 263     } catch (Exception ex)
 264     {
 265       ex.printStackTrace();
 266     }
 267
 268     frame = new JInternalFrame();
 269     frame.setContentPane(this);
 270     if (new jalview.util.Platform().isAMac())
 271     {
 272       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 273     }
 274     else
 275     {
 276       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 277     }
 278   }
 279
 280   private String getFrameTitle()
 281   {
 282     return ((alignFrame == null) ? MessageManager
 283             .getString("label.new_sequence_fetcher") : MessageManager
 284             .getString("label.additional_sequence_fetcher"));
 285   }
 286
 287   private void jbInit() throws Exception
 288   {
 289     this.setLayout(borderLayout2);
 290
 291     database.setFont(JvSwingUtils.getLabelFont());
 292     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 293     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 294     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 295     jLabel1.setText(MessageManager
 296             .getString("label.separate_multiple_accession_ids"));
 297
 298     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 299     replacePunctuation
 300             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 301     replacePunctuation.setText(MessageManager
 302             .getString("label.replace_commas_semicolons"));
 303     ok.setText(MessageManager.getString("action.ok"));
 304     ok.addActionListener(new ActionListener()
 305     {
 306       @Override
 307       public void actionPerformed(ActionEvent e)
 308       {
 309         ok_actionPerformed();
 310       }
 311     });
 312     clear.setText(MessageManager.getString("action.clear"));
 313     clear.addActionListener(new ActionListener()
 314     {
 315       @Override
 316       public void actionPerformed(ActionEvent e)
 317       {
 318         clear_actionPerformed();
 319       }
 320     });
 321
 322     example.setText(MessageManager.getString("label.example"));
 323     example.addActionListener(new ActionListener()
 324     {
 325       @Override
 326       public void actionPerformed(ActionEvent e)
 327       {
 328         example_actionPerformed();
 329       }
 330     });
 331     close.setText(MessageManager.getString("action.close"));
 332     close.addActionListener(new ActionListener()
 333     {
 334       @Override
 335       public void actionPerformed(ActionEvent e)
 336       {
 337         close_actionPerformed(e);
 338       }
 339     });
 340     textArea.setFont(JvSwingUtils.getLabelFont());
 341     textArea.setLineWrap(true);
 342     textArea.addKeyListener(new KeyAdapter()
 343     {
 344       @Override
 345       public void keyPressed(KeyEvent e)
 346       {
 347         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 348         {
 349           ok_actionPerformed();
 350         }
 351       }
 352     });
 353     jPanel3.setLayout(borderLayout1);
 354     borderLayout1.setVgap(5);
 355     jPanel1.add(ok);
 356     jPanel1.add(example);
 357     jPanel1.add(clear);
 358     jPanel1.add(close);
 359     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 360     jPanel2.setLayout(borderLayout3);
 361     databaseButt = database.getDatabaseSelectorButton();
 362     databaseButt.setFont(JvSwingUtils.getLabelFont());
 363     database.addActionListener(new ActionListener()
 364     {
 365       @Override
 366       public void actionPerformed(ActionEvent e)
 367       {
 368         debounceTrap++;
 369         String currentSelection = database.getSelectedItem();
 370         if (!currentSelection.equalsIgnoreCase("pdb"))
 371         {
 372           otherSourceAction();
 373         }
 374         if (currentSelection.equalsIgnoreCase("pdb")
 375                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
 376         {
 377           pdbSourceAction();
 378         }
 379         database.action = -1;
 380       }
 381     });
 382
 383     dbeg.setText("");
 384     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 385     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 386     JPanel jPanel2a = new JPanel(new BorderLayout());
 387     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 388     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 389     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 390     // jPanel2.setPreferredSize(new Dimension())
 391     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 392     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 393     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 394     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 395     jScrollPane1.getViewport().add(textArea);
 396
 397   }
 398
 399   private void pdbSourceAction()
 400   {
 401     databaseButt.setText(database.getSelectedItem());
 402     new PDBSearchPanel(this);
 403     frame.dispose();
 404   }
 405
 406   private void otherSourceAction()
 407   {
 408     try
 409     {
 410       databaseButt.setText(database.getSelectedItem()
 411               + (database.getSelectedSources().size() > 1 ? " (and "
 412                       + database.getSelectedSources().size() + " others)"
 413                       : ""));
 414       String eq = database.getExampleQueries();
 415       dbeg.setText(MessageManager.formatMessage(
 416               "label.example_query_param", new String[] { eq }));
 417       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 418       for (DbSourceProxy dbs : database.getSelectedSources())
 419       {
 420         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 421         {
 422           enablePunct = false;
 423           break;
 424         }
 425       }
 426       replacePunctuation.setEnabled(enablePunct);
 427
 428     } catch (Exception ex)
 429     {
 430       dbeg.setText("");
 431       replacePunctuation.setEnabled(true);
 432     }
 433     jPanel2.repaint();
 434   }
 435
 436   protected void example_actionPerformed()
 437   {
 438     DbSourceProxy db = null;
 439     try
 440     {
 441       textArea.setText(database.getExampleQueries());
 442     } catch (Exception ex)
 443     {
 444     }
 445     jPanel3.repaint();
 446   }
 447
 448   protected void clear_actionPerformed()
 449   {
 450     textArea.setText("");
 451     jPanel3.repaint();
 452   }
 453
 454   public void close_actionPerformed(ActionEvent e)
 455   {
 456     try
 457     {
 458       frame.setClosed(true);
 459     } catch (Exception ex)
 460     {
 461     }
 462   }
 463
 464   public void ok_actionPerformed()
 465   {
 466     databaseButt.setEnabled(false);
 467     example.setEnabled(false);
 468     textArea.setEnabled(false);
 469     ok.setEnabled(false);
 470     close.setEnabled(false);
 471
 472     Thread worker = new Thread(this);
 473     worker.start();
 474   }
 475
 476   private void resetDialog()
 477   {
 478     databaseButt.setEnabled(true);
 479     example.setEnabled(true);
 480     textArea.setEnabled(true);
 481     ok.setEnabled(true);
 482     close.setEnabled(true);
 483   }
 484
 485   @Override
 486   public void run()
 487   {
 488     String error = "";
 489     if (!database.hasSelection())
 490     {
 491       error += "Please select the source database\n";
 492     }
 493     // TODO: make this transformation more configurable
 494     com.stevesoft.pat.Regex empty;
 495     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 496     {
 497       empty = new com.stevesoft.pat.Regex(
 498       // replace commas and spaces with a semicolon
 499               "(\\s|[,; ])+", ";");
 500     }
 501     else
 502     {
 503       // just turn spaces and semicolons into single semicolons
 504       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 505     }
 506     textArea.setText(empty.replaceAll(textArea.getText()));
 507     // see if there's anthing to search with
 508     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 509             .getText()))
 510     {
 511       error += "Please enter a (semi-colon separated list of) database id(s)";
 512     }
 513     if (error.length() > 0)
 514     {
 515       showErrorMessage(error);
 516       resetDialog();
 517       return;
 518     }
 519     // TODO: Refactor to GUI independent code and write tests.
 520     // indicate if successive sources should be merged into one alignment.
 521     boolean addToLast = false;
 522     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 523     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 524     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 525             .iterator();
 526     String[] qries;
 527     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 528             .split(";"));
 529     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 530     int nqueries = qries.length;
 531
 532     FeatureSettingsModelI preferredFeatureColours = null;
 533     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 534     {
 535       if (!en.hasNext() && nextfetch.size() > 0)
 536       {
 537         en = nextfetch.iterator();
 538         nqueries = nextfetch.size();
 539         // save the remaining queries in the original array
 540         qries = nextfetch.toArray(new String[nqueries]);
 541         nextfetch = new ArrayList<String>();
 542       }
 543
 544       DbSourceProxy proxy = proxies.next();
 545       boolean isAliSource = false;
 546       try
 547       {
 548         // update status
 549         guiWindow
 550                 .setProgressBar(MessageManager.formatMessage(
 551                         "status.fetching_sequence_queries_from",
 552                         new String[] {
 553                             Integer.valueOf(nqueries).toString(),
 554                             proxy.getDbName() }), Thread.currentThread()
 555                         .hashCode());
 556         isAliSource = proxy.isAlignmentSource();
 557         if (proxy.getMaximumQueryCount() == 1)
 558         {
 559           while (en.hasNext())
 560           {
 561             String item = en.next();
 562             try
 563             {
 564               if (aresult != null)
 565               {
 566                 try
 567                 {
 568                   // give the server a chance to breathe
 569                   Thread.sleep(5);
 570                 } catch (Exception e)
 571                 {
 572                   //
 573                 }
 574
 575               }
 576
 577               AlignmentI indres = null;
 578               try
 579               {
 580                 indres = proxy.getSequenceRecords(item);
 581               } catch (OutOfMemoryError oome)
 582               {
 583                 new OOMWarning("fetching " + item + " from "
 584                         + proxy.getDbName(), oome, this);
 585               }
 586               if (indres != null)
 587               {
 588                 aresultq.add(item);
 589                 aresult.add(indres);
 590               }
 591               else
 592               {
 593                 nextfetch.add(item);
 594               }
 595             } catch (Exception e)
 596             {
 597               Cache.log.info(
 598                       "Error retrieving " + item
 599                       + " from " + proxy.getDbName(), e);
 600               nextfetch.add(item);
 601             }
 602           }
 603         }
 604         else
 605         {
 606           StringBuffer multiacc = new StringBuffer();
 607           ArrayList<String> tosend = new ArrayList<String>();
 608           while (en.hasNext())
 609           {
 610             String nel = en.next();
 611             tosend.add(nel);
 612             multiacc.append(nel);
 613             if (en.hasNext())
 614             {
 615               multiacc.append(proxy.getAccessionSeparator());
 616             }
 617           }
 618           try
 619           {
 620             AlignmentI rslt;
 621             SequenceI[] rs;
 622             List<String> nores = new ArrayList<String>();
 623             rslt = proxy.getSequenceRecords(multiacc.toString());
 624             if (rslt == null || rslt.getHeight() == 0)
 625             {
 626               // no results - pass on all queries to next source
 627               nextfetch.addAll(tosend);
 628             }
 629             else
 630             {
 631               aresultq.add(multiacc.toString());
 632               aresult.add(rslt);
 633
 634               rs = rslt.getSequencesArray();
 635               // search for each query in the dbrefs associated with each
 636               // sequence
 637               // returned.
 638               // ones we do not find will be used to query next source (if any)
 639               for (String q : tosend)
 640               {
 641                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 642                 dbr.setSource(proxy.getDbSource());
 643                 dbr.setVersion(null);
 644                 String accId = proxy.getAccessionIdFromQuery(q);
 645                 dbr.setAccessionId(accId);
 646                 boolean rfound = false;
 647                 for (int r = 0; r < rs.length; r++)
 648                 {
 649                   if (rs[r] != null)
 650                   {
 651                     found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
 652                     if (found != null && found.length > 0)
 653                     {
 654                       rfound = true;
 655                       rs[r] = null;
 656                     }
 657                   }
 658                 }
 659                 if (!rfound)
 660                 {
 661                   nextfetch.add(q);
 662                 }
 663               }
 664             }
 665           } catch (OutOfMemoryError oome)
 666           {
 667             new OOMWarning("fetching " + multiacc + " from "
 668                     + database.getSelectedItem(), oome, this);
 669           }
 670         }
 671
 672       } catch (Exception e)
 673       {
 674         showErrorMessage("Error retrieving " + textArea.getText()
 675                 + " from " + database.getSelectedItem());
 676         // error
 677         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 678         System.err.println("Retrieval failed for source ='"
 679                 + database.getSelectedItem() + "' and query\n'"
 680                 + textArea.getText() + "'\n");
 681         e.printStackTrace();
 682       } catch (OutOfMemoryError e)
 683       {
 684         // resets dialog box - so we don't use OOMwarning here.
 685         showErrorMessage("Out of Memory when retrieving "
 686                 + textArea.getText()
 687                 + " from "
 688                 + database.getSelectedItem()
 689                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 690         e.printStackTrace();
 691       } catch (Error e)
 692       {
 693         showErrorMessage("Serious Error retrieving " + textArea.getText()
 694                 + " from " + database.getSelectedItem());
 695         e.printStackTrace();
 696       }
 697       // Stack results ready for opening in alignment windows
 698       if (aresult != null && aresult.size() > 0)
 699       {
 700         FeatureSettingsModelI proxyColourScheme = proxy
 701                 .getFeatureColourScheme();
 702         if (proxyColourScheme != null)
 703         {
 704           preferredFeatureColours = proxyColourScheme;
 705         }
 706
 707         AlignmentI ar = null;
 708         if (isAliSource)
 709         {
 710           addToLast = false;
 711           // new window for each result
 712           while (aresult.size() > 0)
 713           {
 714             presult.add(aresult.remove(0));
 715             presultTitle.add(aresultq.remove(0) + " "
 716                     + getDefaultRetrievalTitle());
 717           }
 718         }
 719         else
 720         {
 721           String titl = null;
 722           if (addToLast && presult.size() > 0)
 723           {
 724             ar = presult.remove(presult.size() - 1);
 725             titl = presultTitle.remove(presultTitle.size() - 1);
 726           }
 727           // concatenate all results in one window
 728           while (aresult.size() > 0)
 729           {
 730             if (ar == null)
 731             {
 732               ar = aresult.remove(0);
 733             }
 734             else
 735             {
 736               ar.append(aresult.remove(0));
 737             }
 738             ;
 739           }
 740           addToLast = true;
 741           presult.add(ar);
 742           presultTitle.add(titl);
 743         }
 744       }
 745       guiWindow.setProgressBar(MessageManager
 746               .getString("status.finshed_querying"), Thread.currentThread()
 747               .hashCode());
 748     }
 749     guiWindow.setProgressBar(
 750             (presult.size() > 0) ? MessageManager
 751                     .getString("status.parsing_results") : MessageManager
 752                     .getString("status.processing"), Thread.currentThread()
 753                     .hashCode());
 754     // process results
 755     while (presult.size() > 0)
 756     {
 757       parseResult(presult.remove(0), presultTitle.remove(0), null,
 758               preferredFeatureColours);
 759     }
 760     // only remove visual delay after we finished parsing.
 761     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 762     if (nextfetch.size() > 0)
 763     {
 764       StringBuffer sb = new StringBuffer();
 765       sb.append("Didn't retrieve the following "
 766               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 767                       + " queries") + ": \n");
 768       int l = sb.length(), lr = 0;
 769       for (String s : nextfetch)
 770       {
 771         if (l != sb.length())
 772         {
 773           sb.append("; ");
 774         }
 775         if (lr - sb.length() > 40)
 776         {
 777           sb.append("\n");
 778         }
 779         sb.append(s);
 780       }
 781       showErrorMessage(sb.toString());
 782     }
 783     resetDialog();
 784   }
 785
 786   /**
 787    *
 788    * @return a standard title for any results retrieved using the currently
 789    *         selected source and settings
 790    */
 791   public String getDefaultRetrievalTitle()
 792   {
 793     return "Retrieved from " + database.getSelectedItem();
 794   }
 795
 796   AlignmentI parseResult(AlignmentI al, String title,
 797           String currentFileFormat,
 798           FeatureSettingsModelI preferredFeatureColours)
 799   {
 800
 801     if (al != null && al.getHeight() > 0)
 802     {
 803       if (title == null)
 804       {
 805         title = getDefaultRetrievalTitle();
 806       }
 807       if (alignFrame == null)
 808       {
 809         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 810                 AlignFrame.DEFAULT_HEIGHT);
 811         if (currentFileFormat != null)
 812         {
 813           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 814           // FORMAT FOR
 815           // NON-FormatAdapter Sourced
 816           // Alignments?
 817         }
 818
 819         SequenceFeature[] sfs = null;
 820         List<SequenceI> alsqs;
 821         synchronized (alsqs = al.getSequences())
 822         {
 823           for (SequenceI sq : alsqs)
 824           {
 825             if ((sfs = sq.getSequenceFeatures()) != null)
 826             {
 827               if (sfs.length > 0)
 828               {
 829                 af.setShowSeqFeatures(true);
 830                 break;
 831               }
 832             }
 833
 834           }
 835         }
 836
 837         if (preferredFeatureColours != null)
 838         {
 839           af.getViewport().applyFeaturesStyle(preferredFeatureColours);
 840         }
 841         if (Cache.getDefault("HIDE_INTRONS", true))
 842         {
 843           hideIntronsIfPresent(af);
 844         }
 845
 846         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 847                 AlignFrame.DEFAULT_HEIGHT);
 848
 849         af.statusBar.setText(MessageManager
 850                 .getString("label.successfully_pasted_alignment_file"));
 851
 852         try
 853         {
 854           af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
 855                   false));
 856         } catch (Exception ex)
 857         {
 858         }
 859       }
 860       else
 861       {
 862         alignFrame.viewport.addAlignment(al, title);
 863       }
 864     }
 865     return al;
 866   }
 867
 868   /**
 869    * Hide columns not containing 'exon' features, provided there are exon
 870    * features on the alignment
 871    *
 872    * @param af
 873    */
 874   public void hideIntronsIfPresent(AlignFrame af)
 875   {
 876     boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
 877             false,
 878             SequenceOntologyI.EXON);
 879     if (hasExons)
 880     {
 881       af.avc.markColumnsContainingFeatures(true, false, true,
 882               SequenceOntologyI.EXON);
 883       af.getViewport().hideSelectedColumns();
 884     }
 885   }
 886
 887   void showErrorMessage(final String error)
 888   {
 889     resetDialog();
 890     javax.swing.SwingUtilities.invokeLater(new Runnable()
 891     {
 892       @Override
 893       public void run()
 894       {
 895         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 896                 MessageManager.getString("label.error_retrieving_data"),
 897                 JOptionPane.WARNING_MESSAGE);
 898       }
 899     });
 900   }
 901
 902   public IProgressIndicator getProgressIndicator()
 903   {
 904     return progressIndicator;
 905   }
 906
 907   public void setProgressIndicator(IProgressIndicator progressIndicator)
 908   {
 909     this.progressIndicator = progressIndicator;
 910   }
 911 }