JAL-1834 removed quotes around truncated strings with ellipsis
[jalview.git] / 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.datamodel.AlignmentI;
24 import jalview.datamodel.DBRefEntry;
25 import jalview.datamodel.DBRefSource;
26 import jalview.datamodel.SequenceFeature;
27 import jalview.datamodel.SequenceI;
28 import jalview.io.FormatAdapter;
29 import jalview.io.IdentifyFile;
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 import com.stevesoft.pat.Regex;
58
59 public class SequenceFetcher extends JPanel implements Runnable
60 {
61   JLabel dbeg = new JLabel();
62
63   JDatabaseTree database;
64
65   JButton databaseButt;
66
67   JLabel jLabel1 = new JLabel();
68
69   JCheckBox replacePunctuation = new JCheckBox();
70
71   JButton ok = new JButton();
72
73   JButton clear = new JButton();
74
75   JButton example = new JButton();
76
77   JButton close = new JButton();
78
79   JPanel jPanel1 = new JPanel();
80
81   JTextArea textArea = new JTextArea();
82
83   JScrollPane jScrollPane1 = new JScrollPane();
84
85   JPanel jPanel2 = new JPanel();
86
87   JPanel jPanel3 = new JPanel();
88
89   JPanel jPanel4 = new JPanel();
90
91   BorderLayout borderLayout1 = new BorderLayout();
92
93   BorderLayout borderLayout2 = new BorderLayout();
94
95   BorderLayout borderLayout3 = new BorderLayout();
96
97   JInternalFrame frame;
98
99   IProgressIndicator guiWindow;
100
101   AlignFrame alignFrame;
102
103   StringBuffer result;
104
105   final String noDbSelected = "-- Select Database --";
106
107   private static jalview.ws.SequenceFetcher sfetch = null;
108
109   private static long lastDasSourceRegistry = -3;
110
111   private static DasSourceRegistryI dasRegistry = null;
112
113   private static boolean _initingFetcher = false;
114
115   private static Thread initingThread = null;
116
117   int debounceTrap = 0;
118   /**
119    * Blocking method that initialises and returns the shared instance of the
120    * SequenceFetcher client
121    * 
122    * @param guiWindow
123    *          - where the initialisation delay message should be shown
124    * @return the singleton instance of the sequence fetcher client
125    */
126   public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
127           final IProgressIndicator guiWindow)
128   {
129     if (_initingFetcher && initingThread != null && initingThread.isAlive())
130     {
131       if (guiWindow != null)
132       {
133         guiWindow.setProgressBar(
134                 MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
135                 Thread.currentThread().hashCode());
136       }
137       // initting happening on another thread - so wait around to see if it
138       // finishes.
139       while (_initingFetcher && initingThread != null
140               && initingThread.isAlive())
141       {
142         try
143         {
144           Thread.sleep(10);
145         } catch (Exception e)
146         {
147         }
148         ;
149       }
150       if (guiWindow != null)
151       {
152         guiWindow.setProgressBar(
153                         MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
154                 Thread.currentThread().hashCode());
155       }
156     }
157     if (sfetch == null
158             || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
159             || lastDasSourceRegistry != (jalview.bin.Cache
160                     .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
161                     .getDasSourceRegistry().getLocalSourceString())
162                     .hashCode())
163     {
164       _initingFetcher = true;
165       initingThread = Thread.currentThread();
166       /**
167        * give a visual indication that sequence fetcher construction is occuring
168        */
169       if (guiWindow != null)
170       {
171         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
172                 Thread.currentThread().hashCode());
173       }
174       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
175       dasRegistry.refreshSources();
176
177       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
178       if (guiWindow != null)
179       {
180         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
181       }
182       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
183               .getLocalSourceString()).hashCode();
184       sfetch = sf;
185       _initingFetcher = false;
186       initingThread = null;
187     }
188     return sfetch;
189   }
190
191   private IProgressIndicator progressIndicator;
192   public SequenceFetcher(IProgressIndicator guiIndic)
193   {
194     this.progressIndicator = guiIndic;
195     final SequenceFetcher us = this;
196     // launch initialiser thread
197     Thread sf = new Thread(new Runnable()
198     {
199
200       @Override
201       public void run()
202       {
203         if (getSequenceFetcherSingleton(progressIndicator) != null)
204         {
205           us.initGui(progressIndicator);
206         }
207         else
208         {
209           javax.swing.SwingUtilities.invokeLater(new Runnable()
210           {
211             @Override
212             public void run()
213             {
214               JOptionPane
215                       .showInternalMessageDialog(
216                               Desktop.desktop,
217                               MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
218                               MessageManager.getString("label.couldnt_create_sequence_fetcher"),
219                               JOptionPane.ERROR_MESSAGE);
220             }
221           });
222
223           // raise warning dialog
224         }
225       }
226     });
227     sf.start();
228   }
229
230   private class DatabaseAuthority extends DefaultMutableTreeNode
231   {
232
233   };
234
235   private class DatabaseSource extends DefaultMutableTreeNode
236   {
237
238   };
239
240   /**
241    * called by thread spawned by constructor
242    * 
243    * @param guiWindow
244    */
245   private void initGui(IProgressIndicator guiWindow)
246   {
247     this.guiWindow = guiWindow;
248     if (guiWindow instanceof AlignFrame)
249     {
250       alignFrame = (AlignFrame) guiWindow;
251     }
252     database = new JDatabaseTree(sfetch);
253     try
254     {
255       jbInit();
256     } catch (Exception ex)
257     {
258       ex.printStackTrace();
259     }
260
261     frame = new JInternalFrame();
262     frame.setContentPane(this);
263     if (new jalview.util.Platform().isAMac())
264     {
265       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
266     }
267     else
268     {
269       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
270     }
271   }
272
273   private String getFrameTitle()
274   {
275     return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
276   }
277
278   private void jbInit() throws Exception
279   {
280     this.setLayout(borderLayout2);
281
282     database.setFont(JvSwingUtils.getLabelFont());
283     dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
284     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
285     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
286     jLabel1.setText(MessageManager
287             .getString("label.separate_multiple_accession_ids"));
288
289     replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
290     replacePunctuation
291             .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
292     replacePunctuation.setText(MessageManager
293             .getString("label.replace_commas_semicolons"));
294     ok.setText(MessageManager.getString("action.ok"));
295     ok.addActionListener(new ActionListener()
296     {
297       @Override
298       public void actionPerformed(ActionEvent e)
299       {
300         ok_actionPerformed();
301       }
302     });
303     clear.setText(MessageManager.getString("action.clear"));
304     clear.addActionListener(new ActionListener()
305     {
306       @Override
307       public void actionPerformed(ActionEvent e)
308       {
309         clear_actionPerformed();
310       }
311     });
312
313     example.setText(MessageManager.getString("label.example"));
314     example.addActionListener(new ActionListener()
315     {
316       @Override
317       public void actionPerformed(ActionEvent e)
318       {
319         example_actionPerformed();
320       }
321     });
322     close.setText(MessageManager.getString("action.close"));
323     close.addActionListener(new ActionListener()
324     {
325       @Override
326       public void actionPerformed(ActionEvent e)
327       {
328         close_actionPerformed(e);
329       }
330     });
331     textArea.setFont(JvSwingUtils.getLabelFont());
332     textArea.setLineWrap(true);
333     textArea.addKeyListener(new KeyAdapter()
334     {
335       @Override
336       public void keyPressed(KeyEvent e)
337       {
338         if (e.getKeyCode() == KeyEvent.VK_ENTER)
339         {
340           ok_actionPerformed();
341         }
342       }
343     });
344     jPanel3.setLayout(borderLayout1);
345     borderLayout1.setVgap(5);
346     jPanel1.add(ok);
347     jPanel1.add(example);
348     jPanel1.add(clear);
349     jPanel1.add(close);
350     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
351     jPanel2.setLayout(borderLayout3);
352     databaseButt = database.getDatabaseSelectorButton();
353     databaseButt.setFont(JvSwingUtils.getLabelFont());
354     database.addActionListener(new ActionListener()
355     {
356       @Override
357       public void actionPerformed(ActionEvent e)
358       {
359         debounceTrap++;
360         String currentSelection = database.getSelectedItem();
361         if (!currentSelection.equalsIgnoreCase("pdb"))
362         {
363             otherSourceAction();
364         }
365         if (currentSelection.equalsIgnoreCase("pdb")
366                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
367         {
368           pdbSourceAction();
369         }
370         database.action = -1;
371       }
372     });
373
374     dbeg.setText("");
375     jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
376     jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
377     JPanel jPanel2a = new JPanel(new BorderLayout());
378     jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
379     jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
380     jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
381     // jPanel2.setPreferredSize(new Dimension())
382     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
383     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
384     this.add(jPanel3, java.awt.BorderLayout.CENTER);
385     this.add(jPanel2, java.awt.BorderLayout.NORTH);
386     jScrollPane1.getViewport().add(textArea);
387
388   }
389
390   private void pdbSourceAction()
391   {
392     databaseButt.setText(database.getSelectedItem());
393     new PDBSearchPanel(this);
394     frame.dispose();
395   }
396
397   private void otherSourceAction()
398   {
399     try
400     {
401       databaseButt.setText(database.getSelectedItem()
402               + (database.getSelectedSources().size() > 1 ? " (and "
403                       + database.getSelectedSources().size() + " others)"
404                       : ""));
405       String eq = database.getExampleQueries();
406       dbeg.setText(MessageManager.formatMessage(
407               "label.example_query_param", new String[]
408               { eq }));
409       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
410       for (DbSourceProxy dbs : database.getSelectedSources())
411       {
412         if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
413         {
414           enablePunct = false;
415           break;
416         }
417       }
418       replacePunctuation.setEnabled(enablePunct);
419
420     } catch (Exception ex)
421     {
422       dbeg.setText("");
423       replacePunctuation.setEnabled(true);
424     }
425     jPanel2.repaint();
426   }
427
428   protected void example_actionPerformed()
429   {
430     DbSourceProxy db = null;
431     try
432     {
433       textArea.setText(database.getExampleQueries());
434     } catch (Exception ex)
435     {
436     }
437     jPanel3.repaint();
438   }
439
440   protected void clear_actionPerformed()
441   {
442     textArea.setText("");
443     jPanel3.repaint();
444   }
445
446
447
448   public void close_actionPerformed(ActionEvent e)
449   {
450     try
451     {
452       frame.setClosed(true);
453     } catch (Exception ex)
454     {
455     }
456   }
457
458   public void ok_actionPerformed()
459   {
460     databaseButt.setEnabled(false);
461     example.setEnabled(false);
462     textArea.setEnabled(false);
463     ok.setEnabled(false);
464     close.setEnabled(false);
465
466     Thread worker = new Thread(this);
467     worker.start();
468   }
469
470   private void resetDialog()
471   {
472     databaseButt.setEnabled(true);
473     example.setEnabled(true);
474     textArea.setEnabled(true);
475     ok.setEnabled(true);
476     close.setEnabled(true);
477   }
478
479   @Override
480   public void run()
481   {
482     String error = "";
483     if (!database.hasSelection())
484     {
485       error += "Please select the source database\n";
486     }
487     // TODO: make this transformation more configurable
488     com.stevesoft.pat.Regex empty;
489     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
490     {
491       empty = new com.stevesoft.pat.Regex(
492       // replace commas and spaces with a semicolon
493               "(\\s|[,; ])+", ";");
494     }
495     else
496     {
497       // just turn spaces and semicolons into single semicolons
498       empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
499     }
500     textArea.setText(empty.replaceAll(textArea.getText()));
501     // see if there's anthing to search with
502     if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
503             .getText()))
504     {
505       error += "Please enter a (semi-colon separated list of) database id(s)";
506     }
507     if (error.length() > 0)
508     {
509       showErrorMessage(error);
510       resetDialog();
511       return;
512     }
513     // indicate if successive sources should be merged into one alignment.
514     boolean addToLast = false;
515     ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
516     ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
517     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
518             .iterator();
519     String[] qries;
520     List<String> nextfetch = Arrays.asList(qries = textArea.getText()
521             .split(";"));
522     Iterator<String> en = Arrays.asList(new String[0]).iterator();
523     int nqueries = qries.length;
524     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
525     {
526       if (!en.hasNext() && nextfetch.size() > 0)
527       {
528         en = nextfetch.iterator();
529         nqueries = nextfetch.size();
530         // save the remaining queries in the original array
531         qries = nextfetch.toArray(new String[nqueries]);
532         nextfetch = new ArrayList<String>();
533       }
534
535       DbSourceProxy proxy = proxies.next();
536       boolean isAliSource = false;
537       try
538       {
539         // update status
540         guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
541                 .currentThread().hashCode());
542         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
543         if (proxy.getAccessionSeparator() == null)
544         {
545           while (en.hasNext())
546           {
547             String item = en.next();
548             try
549             {
550               if (aresult != null)
551               {
552                 try
553                 {
554                   // give the server a chance to breathe
555                   Thread.sleep(5);
556                 } catch (Exception e)
557                 {
558                   //
559                 }
560
561               }
562
563               AlignmentI indres = null;
564               try
565               {
566                 indres = proxy.getSequenceRecords(item);
567               } catch (OutOfMemoryError oome)
568               {
569                 new OOMWarning("fetching " + item + " from "
570                         + proxy.getDbName(), oome, this);
571               }
572               if (indres != null)
573               {
574                 aresultq.add(item);
575                 aresult.add(indres);
576               }
577               else
578               {
579                 nextfetch.add(item);
580               }
581             } catch (Exception e)
582             {
583               jalview.bin.Cache.log.info("Error retrieving " + item
584                       + " from " + proxy.getDbName(), e);
585               nextfetch.add(item);
586             }
587           }
588         }
589         else
590         {
591           StringBuffer multiacc = new StringBuffer();
592           ArrayList<String> tosend = new ArrayList<String>();
593           while (en.hasNext())
594           {
595             String nel = en.next();
596             tosend.add(nel);
597             multiacc.append(nel);
598             if (en.hasNext())
599             {
600               multiacc.append(proxy.getAccessionSeparator());
601             }
602           }
603           try
604           {
605             AlignmentI rslt;
606             SequenceI[] rs;
607             List<String> nores = new ArrayList<String>();
608             rslt = proxy.getSequenceRecords(multiacc.toString());
609             if (rslt == null || rslt.getHeight() == 0)
610             {
611               // no results - pass on all queries to next source
612               nextfetch.addAll(tosend);
613             }
614             else
615             {
616               aresultq.add(multiacc.toString());
617               aresult.add(rslt);
618
619               rs = rslt.getSequencesArray();
620               // search for each query in the dbrefs associated with each
621               // sequence
622               // returned.
623               // ones we do not find will be used to query next source (if any)
624               for (String q : tosend)
625               {
626                 DBRefEntry dbr = new DBRefEntry(), found[] = null;
627                 dbr.setSource(proxy.getDbSource());
628                 dbr.setVersion(null);
629                 if (proxy.getAccessionValidator() != null)
630                 {
631                   Regex vgr = proxy.getAccessionValidator();
632                   vgr.search(q);
633                   if (vgr.numSubs() > 0)
634                   {
635                     dbr.setAccessionId(vgr.stringMatched(1));
636                   }
637                   else
638                   {
639                     dbr.setAccessionId(vgr.stringMatched());
640                   }
641                 }
642                 else
643                 {
644                   dbr.setAccessionId(q);
645                 }
646                 boolean rfound = false;
647                 for (int r = 0; r < rs.length; r++)
648                 {
649                   if (rs[r] != null
650                           && (found = DBRefUtils.searchRefs(
651                                   rs[r].getDBRef(), dbr)) != null
652                           && found.length > 0)
653                   {
654                     rfound = true;
655                     rs[r] = null;
656                     continue;
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         AlignmentI ar = null;
701         if (isAliSource)
702         {
703           addToLast = false;
704           // new window for each result
705           while (aresult.size() > 0)
706           {
707             presult.add(aresult.remove(0));
708             presultTitle.add(aresultq.remove(0) + " "
709                     + getDefaultRetrievalTitle());
710           }
711         }
712         else
713         {
714           String titl = null;
715           if (addToLast && presult.size() > 0)
716           {
717             ar = presult.remove(presult.size() - 1);
718             titl = presultTitle.remove(presultTitle.size() - 1);
719           }
720           // concatenate all results in one window
721           while (aresult.size() > 0)
722           {
723             if (ar == null)
724             {
725               ar = aresult.remove(0);
726             }
727             else
728             {
729               ar.append(aresult.remove(0));
730             }
731             ;
732           }
733           addToLast = true;
734           presult.add(ar);
735           presultTitle.add(titl);
736         }
737       }
738       guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
739               .hashCode());
740     }
741     guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
742             : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
743     // process results
744     while (presult.size() > 0)
745     {
746       parseResult(presult.remove(0), presultTitle.remove(0), null);
747     }
748     // only remove visual delay after we finished parsing.
749     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
750     if (nextfetch.size() > 0)
751     {
752       StringBuffer sb = new StringBuffer();
753       sb.append("Didn't retrieve the following "
754               + (nextfetch.size() == 1 ? "query" : nextfetch.size()
755                       + " queries") + ": \n");
756       int l = sb.length(), lr = 0;
757       for (String s : nextfetch)
758       {
759         if (l != sb.length())
760         {
761           sb.append("; ");
762         }
763         if (lr - sb.length() > 40)
764         {
765           sb.append("\n");
766         }
767         sb.append(s);
768       }
769       showErrorMessage(sb.toString());
770     }
771     resetDialog();
772   }
773
774   AlignmentI parseResult(String result, String title)
775   {
776     String format = new IdentifyFile().Identify(result, "Paste");
777     AlignmentI sequences = null;
778     if (FormatAdapter.isValidFormat(format))
779     {
780       sequences = null;
781       try
782       {
783         sequences = new FormatAdapter().readFile(result.toString(),
784                 "Paste", format);
785       } catch (Exception ex)
786       {
787       }
788
789       if (sequences != null)
790       {
791         return parseResult(sequences, title, format);
792       }
793     }
794     else
795     {
796       showErrorMessage("Error retrieving " + textArea.getText() + " from "
797               + database.getSelectedItem());
798     }
799
800     return null;
801   }
802
803   /**
804    * 
805    * @return a standard title for any results retrieved using the currently
806    *         selected source and settings
807    */
808   public String getDefaultRetrievalTitle()
809   {
810     return "Retrieved from " + database.getSelectedItem();
811   }
812
813   AlignmentI parseResult(AlignmentI al, String title,
814           String currentFileFormat)
815   {
816
817     if (al != null && al.getHeight() > 0)
818     {
819       if (title == null)
820       {
821         title = getDefaultRetrievalTitle();
822       }
823       if (alignFrame == null)
824       {
825         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
826                 AlignFrame.DEFAULT_HEIGHT);
827         if (currentFileFormat != null)
828         {
829           af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
830           // FORMAT FOR
831           // NON-FormatAdapter Sourced
832           // Alignments?
833         }
834
835         SequenceFeature[] sfs = null;
836         List<SequenceI> alsqs;
837         synchronized (alsqs = al.getSequences())
838         {
839           for (SequenceI sq : alsqs)
840           {
841             if ((sfs = sq.getSequenceFeatures()) != null)
842             {
843               if (sfs.length > 0)
844               {
845                 af.setShowSeqFeatures(true);
846                 break;
847               }
848             }
849
850           }
851         }
852         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
853                 AlignFrame.DEFAULT_HEIGHT);
854
855         af.statusBar.setText(MessageManager
856                 .getString("label.successfully_pasted_alignment_file"));
857
858         try
859         {
860           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
861                   false));
862         } catch (Exception ex)
863         {
864         }
865       }
866       else
867       {
868         alignFrame.viewport.addAlignment(al, title);
869       }
870     }
871     return al;
872   }
873
874   void showErrorMessage(final String error)
875   {
876     resetDialog();
877     javax.swing.SwingUtilities.invokeLater(new Runnable()
878     {
879       @Override
880       public void run()
881       {
882         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
883                 MessageManager.getString("label.error_retrieving_data"),
884                 JOptionPane.WARNING_MESSAGE);
885       }
886     });
887   }
888
889   public IProgressIndicator getProgressIndicator()
890   {
891     return progressIndicator;
892   }
893
894
895
896   public void setProgressIndicator(IProgressIndicator progressIndicator)
897   {
898     this.progressIndicator = progressIndicator;
899   }
900 }