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
 235             .getString("label.separate_multiple_accession_ids"));
 236
 237     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 238     replacePunctuation
 239             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 240     replacePunctuation.setText(MessageManager
 241             .getString("label.replace_commas_semicolons"));
 242     ok.setText(MessageManager.getString("action.ok"));
 243     ok.addActionListener(new ActionListener()
 244     {
 245       @Override
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         ok_actionPerformed();
 249       }
 250     });
 251     clear.setText(MessageManager.getString("action.clear"));
 252     clear.addActionListener(new ActionListener()
 253     {
 254       @Override
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         clear_actionPerformed();
 258       }
 259     });
 260
 261     example.setText(MessageManager.getString("label.example"));
 262     example.addActionListener(new ActionListener()
 263     {
 264       @Override
 265       public void actionPerformed(ActionEvent e)
 266       {
 267         example_actionPerformed();
 268       }
 269     });
 270     close.setText(MessageManager.getString("action.close"));
 271     close.addActionListener(new ActionListener()
 272     {
 273       @Override
 274       public void actionPerformed(ActionEvent e)
 275       {
 276         close_actionPerformed(e);
 277       }
 278     });
 279     textArea.setFont(JvSwingUtils.getLabelFont());
 280     textArea.setLineWrap(true);
 281     textArea.addKeyListener(new KeyAdapter()
 282     {
 283       @Override
 284       public void keyPressed(KeyEvent e)
 285       {
 286         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 287           ok_actionPerformed();
 288       }
 289     });
 290     jPanel3.setLayout(borderLayout1);
 291     borderLayout1.setVgap(5);
 292     jPanel1.add(ok);
 293     jPanel1.add(example);
 294     jPanel1.add(clear);
 295     jPanel1.add(close);
 296     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 297     jPanel2.setLayout(borderLayout3);
 298     databaseButt = database.getDatabaseSelectorButton();
 299     databaseButt.setFont(JvSwingUtils.getLabelFont());
 300     database.addActionListener(new ActionListener()
 301     {
 302
 303       @Override
 304       public void actionPerformed(ActionEvent e)
 305       {
 306         try
 307         {
 308           databaseButt.setText(database.getSelectedItem()
 309                   + (database.getSelectedSources().size() > 1 ? " (and "
 310                           + database.getSelectedSources().size()
 311                           + " others)" : ""));
 312           String eq = database.getExampleQueries();
 313           dbeg.setText(MessageManager.formatMessage(
 314                   "label.example_query_param", new String[]
 315                   { eq }));
 316           boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
 317           for (DbSourceProxy dbs : database.getSelectedSources())
 318           {
 319             if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
 320             {
 321               enablePunct = false;
 322               break;
 323             }
 324           }
 325           replacePunctuation.setEnabled(enablePunct);
 326
 327         } catch (Exception ex)
 328         {
 329           dbeg.setText("");
 330           replacePunctuation.setEnabled(true);
 331         }
 332         jPanel2.repaint();
 333       }
 334     });
 335     dbeg.setText("");
 336     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 337     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 338     JPanel jPanel2a = new JPanel(new BorderLayout());
 339     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 340     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 341     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 342     // jPanel2.setPreferredSize(new Dimension())
 343     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 344     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 345     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 346     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 347     jScrollPane1.getViewport().add(textArea);
 348
 349   }
 350
 351   protected void example_actionPerformed()
 352   {
 353     DbSourceProxy db = null;
 354     try
 355     {
 356       textArea.setText(database.getExampleQueries());
 357     } catch (Exception ex)
 358     {
 359     }
 360     jPanel3.repaint();
 361   }
 362
 363   protected void clear_actionPerformed()
 364   {
 365     textArea.setText("");
 366     jPanel3.repaint();
 367   }
 368
 369   JLabel dbeg = new JLabel();
 370
 371   JDatabaseTree database;
 372
 373   JButton databaseButt;
 374
 375   JLabel jLabel1 = new JLabel();
 376
 377   JCheckBox replacePunctuation = new JCheckBox();
 378
 379   JButton ok = new JButton();
 380
 381   JButton clear = new JButton();
 382
 383   JButton example = new JButton();
 384
 385   JButton close = new JButton();
 386
 387   JPanel jPanel1 = new JPanel();
 388
 389   JTextArea textArea = new JTextArea();
 390
 391   JScrollPane jScrollPane1 = new JScrollPane();
 392
 393   JPanel jPanel2 = new JPanel();
 394
 395   JPanel jPanel3 = new JPanel();
 396
 397   JPanel jPanel4 = new JPanel();
 398
 399   BorderLayout borderLayout1 = new BorderLayout();
 400
 401   BorderLayout borderLayout2 = new BorderLayout();
 402
 403   BorderLayout borderLayout3 = new BorderLayout();
 404
 405   public void close_actionPerformed(ActionEvent e)
 406   {
 407     try
 408     {
 409       frame.setClosed(true);
 410     } catch (Exception ex)
 411     {
 412     }
 413   }
 414
 415   public void ok_actionPerformed()
 416   {
 417     databaseButt.setEnabled(false);
 418     example.setEnabled(false);
 419     textArea.setEnabled(false);
 420     ok.setEnabled(false);
 421     close.setEnabled(false);
 422
 423     Thread worker = new Thread(this);
 424     worker.start();
 425   }
 426
 427   private void resetDialog()
 428   {
 429     databaseButt.setEnabled(true);
 430     example.setEnabled(true);
 431     textArea.setEnabled(true);
 432     ok.setEnabled(true);
 433     close.setEnabled(true);
 434   }
 435
 436   @Override
 437   public void run()
 438   {
 439     String error = "";
 440     if (!database.hasSelection())
 441     {
 442       error += "Please select the source database\n";
 443     }
 444     // TODO: make this transformation more configurable
 445     com.stevesoft.pat.Regex empty;
 446     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 447     {
 448       empty = new com.stevesoft.pat.Regex(
 449       // replace commas and spaces with a semicolon
 450               "(\\s|[,; ])+", ";");
 451     }
 452     else
 453     {
 454       // just turn spaces and semicolons into single semicolons
 455       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 456     }
 457     textArea.setText(empty.replaceAll(textArea.getText()));
 458     // see if there's anthing to search with
 459     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 460             .getText()))
 461     {
 462       error += "Please enter a (semi-colon separated list of) database id(s)";
 463     }
 464     if (error.length() > 0)
 465     {
 466       showErrorMessage(error);
 467       resetDialog();
 468       return;
 469     }
 470     // indicate if successive sources should be merged into one alignment.
 471     boolean addToLast = false;
 472     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 473     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 474     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 475             .iterator();
 476     String[] qries;
 477     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 478             .split(";"));
 479     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 480     int nqueries = qries.length;
 481     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 482     {
 483       if (!en.hasNext() && nextfetch.size() > 0)
 484       {
 485         en = nextfetch.iterator();
 486         nqueries = nextfetch.size();
 487         // save the remaining queries in the original array
 488         qries = nextfetch.toArray(new String[nqueries]);
 489         nextfetch = new ArrayList<String>();
 490       }
 491
 492       DbSourceProxy proxy = proxies.next();
 493       boolean isAliSource = false;
 494       try
 495       {
 496         // update status
 497         guiWindow.setProgressBar("Fetching " + nqueries
 498                 + " sequence queries from " + proxy.getDbName(), Thread
 499                 .currentThread().hashCode());
 500         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 501         if (proxy.getAccessionSeparator() == null)
 502         {
 503           while (en.hasNext())
 504           {
 505             String item = en.next();
 506             try
 507             {
 508               if (aresult != null)
 509               {
 510                 try
 511                 {
 512                   // give the server a chance to breathe
 513                   Thread.sleep(5);
 514                 } catch (Exception e)
 515                 {
 516                   //
 517                 }
 518
 519               }
 520
 521               AlignmentI indres = null;
 522               try
 523               {
 524                 indres = proxy.getSequenceRecords(item);
 525               } catch (OutOfMemoryError oome)
 526               {
 527                 new OOMWarning("fetching " + item + " from "
 528                         + proxy.getDbName(), oome, this);
 529               }
 530               if (indres != null)
 531               {
 532                 aresultq.add(item);
 533                 aresult.add(indres);
 534               }
 535               else
 536               {
 537                 nextfetch.add(item);
 538               }
 539             } catch (Exception e)
 540             {
 541               jalview.bin.Cache.log.info("Error retrieving " + item
 542                       + " from " + proxy.getDbName(), e);
 543               nextfetch.add(item);
 544             }
 545           }
 546         }
 547         else
 548         {
 549           StringBuffer multiacc = new StringBuffer();
 550           ArrayList<String> tosend = new ArrayList<String>();
 551           while (en.hasNext())
 552           {
 553             String nel = en.next();
 554             tosend.add(nel);
 555             multiacc.append(nel);
 556             if (en.hasNext())
 557             {
 558               multiacc.append(proxy.getAccessionSeparator());
 559             }
 560           }
 561           try
 562           {
 563             AlignmentI rslt;
 564             SequenceI[] rs;
 565             List<String> nores = new ArrayList<String>();
 566             rslt = proxy.getSequenceRecords(multiacc.toString());
 567             if (rslt == null || rslt.getHeight() == 0)
 568             {
 569               // no results - pass on all queries to next source
 570               nextfetch.addAll(tosend);
 571             }
 572             else
 573             {
 574               aresultq.add(multiacc.toString());
 575               aresult.add(rslt);
 576
 577               rs = rslt.getSequencesArray();
 578               // search for each query in the dbrefs associated with each
 579               // sequence
 580               // returned.
 581               // ones we do not find will be used to query next source (if any)
 582               for (String q : tosend)
 583               {
 584                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 585                 dbr.setSource(proxy.getDbSource());
 586                 dbr.setVersion(null);
 587                 if (proxy.getAccessionValidator() != null)
 588                 {
 589                   Regex vgr = proxy.getAccessionValidator();
 590                   vgr.search(q);
 591                   if (vgr.numSubs() > 0)
 592                   {
 593                     dbr.setAccessionId(vgr.stringMatched(1));
 594                   }
 595                   else
 596                   {
 597                     dbr.setAccessionId(vgr.stringMatched());
 598                   }
 599                 }
 600                 else
 601                 {
 602                   dbr.setAccessionId(q);
 603                 }
 604                 boolean rfound = false;
 605                 for (int r = 0; r < rs.length; r++)
 606                 {
 607                   if (rs[r] != null
 608                           && (found = DBRefUtils.searchRefs(
 609                                   rs[r].getDBRef(), dbr)) != null
 610                           && found.length > 0)
 611                   {
 612                     rfound = true;
 613                     rs[r] = null;
 614                     continue;
 615                   }
 616                 }
 617                 if (!rfound)
 618                 {
 619                   nextfetch.add(q);
 620                 }
 621               }
 622             }
 623           } catch (OutOfMemoryError oome)
 624           {
 625             new OOMWarning("fetching " + multiacc + " from "
 626                     + database.getSelectedItem(), oome, this);
 627           }
 628         }
 629
 630       } catch (Exception e)
 631       {
 632         showErrorMessage("Error retrieving " + textArea.getText()
 633                 + " from " + database.getSelectedItem());
 634         // error
 635         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 636         System.err.println("Retrieval failed for source ='"
 637                 + database.getSelectedItem() + "' and query\n'"
 638                 + textArea.getText() + "'\n");
 639         e.printStackTrace();
 640       } catch (OutOfMemoryError e)
 641       {
 642         // resets dialog box - so we don't use OOMwarning here.
 643         showErrorMessage("Out of Memory when retrieving "
 644                 + textArea.getText()
 645                 + " from "
 646                 + database.getSelectedItem()
 647                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 648         e.printStackTrace();
 649       } catch (Error e)
 650       {
 651         showErrorMessage("Serious Error retrieving " + textArea.getText()
 652                 + " from " + database.getSelectedItem());
 653         e.printStackTrace();
 654       }
 655       // Stack results ready for opening in alignment windows
 656       if (aresult != null && aresult.size() > 0)
 657       {
 658         AlignmentI ar = null;
 659         if (isAliSource)
 660         {
 661           addToLast = false;
 662           // new window for each result
 663           while (aresult.size() > 0)
 664           {
 665             presult.add(aresult.remove(0));
 666             presultTitle.add(aresultq.remove(0) + " "
 667                     + getDefaultRetrievalTitle());
 668           }
 669         }
 670         else
 671         {
 672           String titl = null;
 673           if (addToLast && presult.size() > 0)
 674           {
 675             ar = presult.remove(presult.size() - 1);
 676             titl = presultTitle.remove(presultTitle.size() - 1);
 677           }
 678           // concatenate all results in one window
 679           while (aresult.size() > 0)
 680           {
 681             if (ar == null)
 682             {
 683               ar = aresult.remove(0);
 684             }
 685             else
 686             {
 687               ar.append(aresult.remove(0));
 688             }
 689             ;
 690           }
 691           addToLast = true;
 692           presult.add(ar);
 693           presultTitle.add(titl);
 694         }
 695       }
 696       guiWindow.setProgressBar("Finished querying", Thread.currentThread()
 697               .hashCode());
 698     }
 699     guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
 700             : "Processing ..", Thread.currentThread().hashCode());
 701     // process results
 702     while (presult.size() > 0)
 703     {
 704       parseResult(presult.remove(0), presultTitle.remove(0), null);
 705     }
 706     // only remove visual delay after we finished parsing.
 707     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 708     if (nextfetch.size() > 0)
 709     {
 710       StringBuffer sb = new StringBuffer();
 711       sb.append("Didn't retrieve the following "
 712               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 713                       + " queries") + ": \n");
 714       int l = sb.length(), lr = 0;
 715       for (String s : nextfetch)
 716       {
 717         if (l != sb.length())
 718         {
 719           sb.append("; ");
 720         }
 721         if (lr - sb.length() > 40)
 722         {
 723           sb.append("\n");
 724         }
 725         sb.append(s);
 726       }
 727       showErrorMessage(sb.toString());
 728     }
 729     resetDialog();
 730   }
 731
 732   AlignmentI parseResult(String result, String title)
 733   {
 734     String format = new IdentifyFile().Identify(result, "Paste");
 735     Alignment sequences = null;
 736     if (FormatAdapter.isValidFormat(format))
 737     {
 738       sequences = null;
 739       try
 740       {
 741         sequences = new FormatAdapter().readFile(result.toString(),
 742                 "Paste", format);
 743       } catch (Exception ex)
 744       {
 745       }
 746
 747       if (sequences != null)
 748       {
 749         return parseResult(sequences, title, format);
 750       }
 751     }
 752     else
 753     {
 754       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 755               + database.getSelectedItem());
 756     }
 757
 758     return null;
 759   }
 760
 761   /**
 762    *
 763    * @return a standard title for any results retrieved using the currently
 764    *         selected source and settings
 765    */
 766   public String getDefaultRetrievalTitle()
 767   {
 768     return "Retrieved from " + database.getSelectedItem();
 769   }
 770
 771   AlignmentI parseResult(AlignmentI al, String title,
 772           String currentFileFormat)
 773   {
 774
 775     if (al != null && al.getHeight() > 0)
 776     {
 777       if (alignFrame == null)
 778       {
 779         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 780                 AlignFrame.DEFAULT_HEIGHT);
 781         if (currentFileFormat != null)
 782         {
 783           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 784           // FORMAT FOR
 785           // NON-FormatAdapter Sourced
 786           // Alignments?
 787         }
 788
 789         if (title == null)
 790         {
 791           title = getDefaultRetrievalTitle();
 792         }
 793         SequenceFeature[] sfs = null;
 794         List<SequenceI> alsqs;
 795         synchronized (alsqs = al.getSequences())
 796         {
 797           for (SequenceI sq : alsqs)
 798           {
 799             if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
 800             {
 801               if (sfs.length > 0)
 802               {
 803                 af.setShowSeqFeatures(true);
 804                 break;
 805               }
 806             }
 807
 808           }
 809         }
 810         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 811                 AlignFrame.DEFAULT_HEIGHT);
 812
 813         af.statusBar.setText(MessageManager
 814                 .getString("label.successfully_pasted_alignment_file"));
 815
 816         try
 817         {
 818           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 819                   false));
 820         } catch (Exception ex)
 821         {
 822         }
 823       }
 824       else
 825       {
 826         for (int i = 0; i < al.getHeight(); i++)
 827         {
 828           alignFrame.viewport.getAlignment().addSequence(
 829                   al.getSequenceAt(i)); // this
 830           // also
 831           // creates
 832           // dataset
 833           // sequence
 834           // entries
 835         }
 836         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 837                 .getHeight());
 838         alignFrame.viewport.getAlignment().getWidth();
 839         alignFrame.viewport.firePropertyChange("alignment", null,
 840                 alignFrame.viewport.getAlignment().getSequences());
 841       }
 842     }
 843     return al;
 844   }
 845
 846   void showErrorMessage(final String error)
 847   {
 848     resetDialog();
 849     javax.swing.SwingUtilities.invokeLater(new Runnable()
 850     {
 851       @Override
 852       public void run()
 853       {
 854         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 855                 MessageManager.getString("label.error_retrieving_data"),
 856                 JOptionPane.WARNING_MESSAGE);
 857       }
 858     });
 859   }
 860 }