src/jalview/gui/SequenceFetcher.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21 import java.util.List;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25
  26 import javax.swing.*;
  27 import javax.swing.tree.DefaultMutableTreeNode;
  28 import javax.swing.tree.MutableTreeNode;
  29 import javax.swing.tree.TreeModel;
  30
  31 import jalview.datamodel.*;
  32 import jalview.io.*;
  33 import jalview.util.DBRefUtils;
  34 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
  35 import jalview.ws.seqfetcher.DbSourceProxy;
  36
  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       public void run()
 145       {
 146         if (getSequenceFetcherSingleton(guiWindow) != null)
 147         {
 148           us.initGui(guiWindow);
 149         }
 150         else
 151         {
 152           javax.swing.SwingUtilities.invokeLater(new Runnable()
 153           {
 154             public void run()
 155             {
 156               JOptionPane
 157                       .showInternalMessageDialog(
 158                               Desktop.desktop,
 159                               "Could not create the sequence fetcher client. Check error logs for details.",
 160                               "Couldn't create SequenceFetcher",
 161                               JOptionPane.ERROR_MESSAGE);
 162             }
 163           });
 164
 165           // raise warning dialog
 166         }
 167       }
 168     });
 169     sf.start();
 170   }
 171
 172   private class DatabaseAuthority extends DefaultMutableTreeNode
 173   {
 174
 175   };
 176
 177   private class DatabaseSource extends DefaultMutableTreeNode
 178   {
 179
 180   };
 181
 182   /**
 183    * called by thread spawned by constructor
 184    *
 185    * @param guiWindow
 186    */
 187   private void initGui(IProgressIndicator guiWindow)
 188   {
 189     this.guiWindow = guiWindow;
 190     if (guiWindow instanceof AlignFrame)
 191     {
 192       alignFrame = (AlignFrame) guiWindow;
 193     }
 194     database = new JDatabaseTree(sfetch);
 195     try
 196     {
 197       jbInit();
 198     } catch (Exception ex)
 199     {
 200       ex.printStackTrace();
 201     }
 202
 203     frame = new JInternalFrame();
 204     frame.setContentPane(this);
 205     if (new jalview.util.Platform().isAMac())
 206     {
 207       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
 208     }
 209     else
 210     {
 211       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
 212     }
 213   }
 214
 215   private String getFrameTitle()
 216   {
 217     return ((alignFrame == null) ? "New " : "Additional ")
 218             + "Sequence Fetcher";
 219   }
 220
 221   private void jbInit() throws Exception
 222   {
 223     this.setLayout(borderLayout2);
 224
 225     database.setFont(JvSwingUtils.getLabelFont());
 226     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
 227     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 228     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 229     jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
 230
 231     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
 232     replacePunctuation
 233             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
 234     replacePunctuation.setText("Replace commas with semi-colons");
 235     ok.setText("OK");
 236     ok.addActionListener(new ActionListener()
 237     {
 238       public void actionPerformed(ActionEvent e)
 239       {
 240         ok_actionPerformed();
 241       }
 242     });
 243     clear.setText("Clear");
 244     clear.addActionListener(new ActionListener()
 245     {
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         clear_actionPerformed();
 249       }
 250     });
 251
 252     example.setText("Example");
 253     example.addActionListener(new ActionListener()
 254     {
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         example_actionPerformed();
 258       }
 259     });
 260     close.setText("Close");
 261     close.addActionListener(new ActionListener()
 262     {
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         close_actionPerformed(e);
 266       }
 267     });
 268     textArea.setFont(JvSwingUtils.getLabelFont());
 269     textArea.setLineWrap(true);
 270     textArea.addKeyListener(new KeyAdapter()
 271     {
 272       public void keyPressed(KeyEvent e)
 273       {
 274         if (e.getKeyCode() == KeyEvent.VK_ENTER)
 275           ok_actionPerformed();
 276       }
 277     });
 278     jPanel3.setLayout(borderLayout1);
 279     borderLayout1.setVgap(5);
 280     jPanel1.add(ok);
 281     jPanel1.add(example);
 282     jPanel1.add(clear);
 283     jPanel1.add(close);
 284     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
 285     jPanel2.setLayout(borderLayout3);
 286     databaseButt = database.getDatabaseSelectorButton();
 287     databaseButt.setFont(JvSwingUtils.getLabelFont());
 288     database.addActionListener(new ActionListener()
 289     {
 290
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         DbSourceProxy db = null;
 294         try
 295         {
 296           databaseButt.setText(database.getSelectedItem()
 297                   + (database.getSelectedSources().size() > 1 ? " (and "
 298                           + database.getSelectedSources().size()
 299                           + " others)" : ""));
 300           String eq = database.getExampleQueries();
 301           dbeg.setText("Example query: " + eq);
 302           replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
 303         } catch (Exception ex)
 304         {
 305           dbeg.setText("");
 306           replacePunctuation.setEnabled(true);
 307         }
 308         jPanel2.repaint();
 309       }
 310     });
 311     dbeg.setText("");
 312     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
 313     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
 314     JPanel jPanel2a = new JPanel(new BorderLayout());
 315     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
 316     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
 317     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
 318     // jPanel2.setPreferredSize(new Dimension())
 319     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
 320     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 321     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 322     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 323     jScrollPane1.getViewport().add(textArea);
 324
 325   }
 326
 327   protected void example_actionPerformed()
 328   {
 329     DbSourceProxy db = null;
 330     try
 331     {
 332       textArea.setText(database.getExampleQueries());
 333     } catch (Exception ex)
 334     {
 335     }
 336     jPanel3.repaint();
 337   }
 338
 339   protected void clear_actionPerformed()
 340   {
 341     textArea.setText("");
 342     jPanel3.repaint();
 343   }
 344
 345   JLabel dbeg = new JLabel();
 346
 347   JDatabaseTree database;
 348
 349   JButton databaseButt;
 350
 351   JLabel jLabel1 = new JLabel();
 352
 353   JCheckBox replacePunctuation = new JCheckBox();
 354
 355   JButton ok = new JButton();
 356
 357   JButton clear = new JButton();
 358
 359   JButton example = new JButton();
 360
 361   JButton close = new JButton();
 362
 363   JPanel jPanel1 = new JPanel();
 364
 365   JTextArea textArea = new JTextArea();
 366
 367   JScrollPane jScrollPane1 = new JScrollPane();
 368
 369   JPanel jPanel2 = new JPanel();
 370
 371   JPanel jPanel3 = new JPanel();
 372
 373   JPanel jPanel4 = new JPanel();
 374
 375   BorderLayout borderLayout1 = new BorderLayout();
 376
 377   BorderLayout borderLayout2 = new BorderLayout();
 378
 379   BorderLayout borderLayout3 = new BorderLayout();
 380
 381   public void close_actionPerformed(ActionEvent e)
 382   {
 383     try
 384     {
 385       frame.setClosed(true);
 386     } catch (Exception ex)
 387     {
 388     }
 389   }
 390
 391   public void ok_actionPerformed()
 392   {
 393     database.setEnabled(false);
 394     textArea.setEnabled(false);
 395     ok.setEnabled(false);
 396     close.setEnabled(false);
 397
 398     Thread worker = new Thread(this);
 399     worker.start();
 400   }
 401
 402   private void resetDialog()
 403   {
 404     database.setEnabled(true);
 405     textArea.setEnabled(true);
 406     ok.setEnabled(true);
 407     close.setEnabled(true);
 408   }
 409
 410   public void run()
 411   {
 412     String error = "";
 413     if (!database.hasSelection())
 414     {
 415       error += "Please select the source database\n";
 416     }
 417     // TODO: make this transformation more configurable
 418     com.stevesoft.pat.Regex empty;
 419     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
 420     {
 421       empty = new com.stevesoft.pat.Regex(
 422       // replace commas and spaces with a semicolon
 423               "(\\s|[,; ])+", ";");
 424     }
 425     else
 426     {
 427       // just turn spaces and semicolons into single semicolons
 428       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
 429     }
 430     textArea.setText(empty.replaceAll(textArea.getText()));
 431     // see if there's anthing to search with
 432     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
 433             .getText()))
 434     {
 435       error += "Please enter a (semi-colon separated list of) database id(s)";
 436     }
 437     if (error.length() > 0)
 438     {
 439       showErrorMessage(error);
 440       resetDialog();
 441       return;
 442     }
 443     // indicate if successive sources should be merged into one alignment.
 444     boolean addToLast=false;
 445     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
 446     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
 447     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
 448             .iterator();
 449     String[] qries;
 450     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
 451             .split(";"));
 452     Iterator<String> en = Arrays.asList(new String[0]).iterator();
 453     int nqueries = qries.length;
 454     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
 455     {
 456       if (!en.hasNext() && nextfetch.size() > 0)
 457       {
 458         en = nextfetch.iterator();
 459         nqueries = nextfetch.size();
 460         // save the remaining queries in the original array
 461         qries = nextfetch.toArray(new String[nqueries]);
 462         nextfetch = new ArrayList<String>();
 463       }
 464
 465       DbSourceProxy proxy = proxies.next();
 466       boolean isAliSource = false;
 467       try
 468       {
 469         // update status
 470         guiWindow.setProgressBar("Fetching " + nqueries
 471                 + " sequence queries from " + proxy.getDbName(), Thread
 472                 .currentThread().hashCode());
 473         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
 474         if (proxy.getAccessionSeparator() == null)
 475         {
 476           while (en.hasNext())
 477           {
 478             String item = en.next();
 479             try
 480             {
 481               if (aresult != null)
 482               {
 483                 try
 484                 {
 485                   // give the server a chance to breathe
 486                   Thread.sleep(5);
 487                 } catch (Exception e)
 488                 {
 489                   //
 490                 }
 491
 492               }
 493
 494               AlignmentI indres = null;
 495               try
 496               {
 497                 indres = proxy.getSequenceRecords(item);
 498               } catch (OutOfMemoryError oome)
 499               {
 500                 new OOMWarning("fetching " + item + " from "
 501                         + proxy.getDbName(), oome, this);
 502               }
 503               if (indres != null)
 504               {
 505                 aresultq.add(item);
 506                 aresult.add(indres);
 507               }
 508               else
 509               {
 510                 nextfetch.add(item);
 511               }
 512             } catch (Exception e)
 513             {
 514               jalview.bin.Cache.log.info("Error retrieving " + item
 515                       + " from " + proxy.getDbName(), e);
 516               nextfetch.add(item);
 517             }
 518           }
 519         }
 520         else
 521         {
 522           StringBuffer multiacc = new StringBuffer();
 523           ArrayList<String> tosend = new ArrayList<String>();
 524           while (en.hasNext())
 525           {
 526             String nel = en.next();
 527             tosend.add(nel);
 528             multiacc.append(nel);
 529             if (en.hasNext())
 530             {
 531               multiacc.append(proxy.getAccessionSeparator());
 532             }
 533           }
 534           try
 535           {
 536             AlignmentI rslt;
 537             SequenceI[] rs;
 538             List<String> nores = new ArrayList<String>();
 539             rslt = proxy.getSequenceRecords(multiacc.toString());
 540             if (rslt == null || rslt.getHeight() == 0)
 541             {
 542               // no results - pass on all queries to next source
 543               nextfetch.addAll(tosend);
 544             }
 545             else
 546             {
 547               aresultq.add(multiacc.toString());
 548               aresult.add(rslt);
 549
 550               rs = rslt.getSequencesArray();
 551               // search for each query in the dbrefs associated with each
 552               // sequence
 553               // returned.
 554               // ones we do not find will be used to query next source (if any)
 555               for (String q : tosend)
 556               {
 557                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
 558                 dbr.setSource(proxy.getDbSource());
 559                 boolean rfound = false;
 560                 for (int r = 0; r < rs.length; r++)
 561                 {
 562                   if (rs[r] != null
 563                           && (found = DBRefUtils.searchRefs(
 564                                   rs[r].getDBRef(), dbr)) != null
 565                           && found.length > 0)
 566                   {
 567                     rfound = true;
 568                     rs[r] = null;
 569                     continue;
 570                   }
 571                 }
 572                 if (!rfound)
 573                 {
 574                   nextfetch.add(q);
 575                 }
 576               }
 577             }
 578           } catch (OutOfMemoryError oome)
 579           {
 580             new OOMWarning("fetching " + multiacc + " from "
 581                     + database.getSelectedItem(), oome, this);
 582           }
 583         }
 584
 585       } catch (Exception e)
 586       {
 587         showErrorMessage("Error retrieving " + textArea.getText()
 588                 + " from " + database.getSelectedItem());
 589         // error
 590         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
 591         System.err.println("Retrieval failed for source ='"
 592                 + database.getSelectedItem() + "' and query\n'"
 593                 + textArea.getText() + "'\n");
 594         e.printStackTrace();
 595       } catch (OutOfMemoryError e)
 596       {
 597         // resets dialog box - so we don't use OOMwarning here.
 598         showErrorMessage("Out of Memory when retrieving "
 599                 + textArea.getText()
 600                 + " from "
 601                 + database.getSelectedItem()
 602                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
 603         e.printStackTrace();
 604       } catch (Error e)
 605       {
 606         showErrorMessage("Serious Error retrieving " + textArea.getText()
 607                 + " from " + database.getSelectedItem());
 608         e.printStackTrace();
 609       }
 610       // Stack results ready for opening in alignment windows
 611       if (aresult != null && aresult.size() > 0)
 612       {
 613         AlignmentI ar = null;
 614         if (isAliSource)
 615         {
 616           addToLast=false;
 617           // new window for each result
 618           while (aresult.size() > 0)
 619           {
 620             presult.add(aresult.remove(0));
 621             presultTitle.add(aresultq.remove(0) + " "
 622                     + getDefaultRetrievalTitle());
 623           }
 624         }
 625         else
 626         {
 627           String titl=null;
 628           if (addToLast && presult.size()>0)
 629           {
 630             ar=presult.remove(presult.size()-1);
 631             titl=presultTitle.remove(presultTitle.size()-1);
 632           }
 633           // concatenate all results in one window
 634           while (aresult.size() > 0)
 635           {
 636             if (ar == null)
 637             {
 638               ar = aresult.remove(0);
 639             }
 640             else
 641             {
 642               ar.append(aresult.remove(0));
 643             }
 644             ;
 645           }
 646           addToLast=true;
 647           presult.add(ar);
 648           presultTitle.add(titl);
 649         }
 650       }
 651       guiWindow.setProgressBar("Finished querying", Thread.currentThread().hashCode());
 652     }
 653     guiWindow.setProgressBar((presult.size()>0) ? "Parsing results.":"Processing ..", Thread.currentThread().hashCode());
 654     // process results
 655     while (presult.size() > 0)
 656     {
 657       parseResult(presult.remove(0), presultTitle.remove(0), null);
 658     }
 659     // only remove visual delay after we finished parsing.
 660     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
 661     if (nextfetch.size() > 0)
 662     {
 663       StringBuffer sb = new StringBuffer();
 664       sb.append("Didn't retrieve the following "
 665               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
 666                       + " queries") + ": \n");
 667       int l = sb.length(),lr=0;
 668       for (String s : nextfetch)
 669       {
 670         if (l != sb.length())
 671         {
 672           sb.append("; ");
 673         }
 674         if (lr-sb.length()>40)
 675         {
 676           sb.append("\n");
 677         }
 678         sb.append(s);
 679       }
 680       showErrorMessage(sb.toString());
 681     }
 682     resetDialog();
 683   }
 684
 685   AlignmentI parseResult(String result, String title)
 686   {
 687     String format = new IdentifyFile().Identify(result, "Paste");
 688     Alignment sequences = null;
 689     if (FormatAdapter.isValidFormat(format))
 690     {
 691       sequences = null;
 692       try
 693       {
 694         sequences = new FormatAdapter().readFile(result.toString(),
 695                 "Paste", format);
 696       } catch (Exception ex)
 697       {
 698       }
 699
 700       if (sequences != null)
 701       {
 702         return parseResult(sequences, title, format);
 703       }
 704     }
 705     else
 706     {
 707       showErrorMessage("Error retrieving " + textArea.getText() + " from "
 708               + database.getSelectedItem());
 709     }
 710
 711     return null;
 712   }
 713
 714   /**
 715    *
 716    * @return a standard title for any results retrieved using the currently
 717    *         selected source and settings
 718    */
 719   public String getDefaultRetrievalTitle()
 720   {
 721     return "Retrieved from " + database.getSelectedItem();
 722   }
 723
 724   AlignmentI parseResult(AlignmentI al, String title,
 725           String currentFileFormat)
 726   {
 727
 728     if (al != null && al.getHeight() > 0)
 729     {
 730       if (alignFrame == null)
 731       {
 732         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
 733                 AlignFrame.DEFAULT_HEIGHT);
 734         if (currentFileFormat != null)
 735         {
 736           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
 737           // FORMAT FOR
 738           // NON-FormatAdapter Sourced
 739           // Alignments?
 740         }
 741
 742         if (title == null)
 743         {
 744           title = getDefaultRetrievalTitle();
 745         }
 746         SequenceFeature[] sfs = null;
 747         for (Enumeration sq = al.getSequences().elements(); sq
 748                 .hasMoreElements();)
 749         {
 750           if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
 751                   .getSequenceFeatures()) != null)
 752           {
 753             if (sfs.length > 0)
 754             {
 755               af.setShowSeqFeatures(true);
 756               break;
 757             }
 758           }
 759
 760         }
 761         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
 762                 AlignFrame.DEFAULT_HEIGHT);
 763
 764         af.statusBar.setText("Successfully pasted alignment file");
 765
 766         try
 767         {
 768           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
 769                   false));
 770         } catch (Exception ex)
 771         {
 772         }
 773       }
 774       else
 775       {
 776         for (int i = 0; i < al.getHeight(); i++)
 777         {
 778           alignFrame.viewport.getAlignment().addSequence(
 779                   al.getSequenceAt(i)); // this
 780           // also
 781           // creates
 782           // dataset
 783           // sequence
 784           // entries
 785         }
 786         alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
 787                 .getHeight());
 788         alignFrame.viewport.getAlignment().getWidth();
 789         alignFrame.viewport.firePropertyChange("alignment", null,
 790                 alignFrame.viewport.getAlignment().getSequences());
 791       }
 792     }
 793     return al;
 794   }
 795
 796   void showErrorMessage(final String error)
 797   {
 798     resetDialog();
 799     javax.swing.SwingUtilities.invokeLater(new Runnable()
 800     {
 801       public void run()
 802       {
 803         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
 804                 "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
 805       }
 806     });
 807   }
 808 }