2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
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.fts.service.pdb.PDBFTSPanel;
30 import jalview.fts.service.uniprot.UniprotFTSPanel;
31 import jalview.io.FileFormatI;
32 import jalview.io.gff.SequenceOntologyI;
33 import jalview.util.DBRefUtils;
34 import jalview.util.MessageManager;
35 import jalview.util.Platform;
36 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
37 import jalview.ws.seqfetcher.DbSourceProxy;
39 import java.awt.BorderLayout;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.KeyAdapter;
44 import java.awt.event.KeyEvent;
45 import java.util.ArrayList;
46 import java.util.Arrays;
47 import java.util.Iterator;
48 import java.util.List;
50 import javax.swing.JButton;
51 import javax.swing.JCheckBox;
52 import javax.swing.JInternalFrame;
53 import javax.swing.JLabel;
54 import javax.swing.JOptionPane;
55 import javax.swing.JPanel;
56 import javax.swing.JScrollPane;
57 import javax.swing.JTextArea;
58 import javax.swing.SwingConstants;
59 import javax.swing.tree.DefaultMutableTreeNode;
61 public class SequenceFetcher extends JPanel implements Runnable
63 JLabel dbeg = new JLabel();
65 JDatabaseTree database;
69 JLabel jLabel1 = new JLabel();
71 JCheckBox replacePunctuation = new JCheckBox();
73 JButton ok = new JButton();
75 JButton clear = new JButton();
77 JButton example = new JButton();
79 JButton close = new JButton();
81 JPanel jPanel1 = new JPanel();
83 JTextArea textArea = new JTextArea();
85 JScrollPane jScrollPane1 = new JScrollPane();
87 JPanel jPanel2 = new JPanel();
89 JPanel jPanel3 = new JPanel();
91 JPanel jPanel4 = new JPanel();
93 BorderLayout borderLayout1 = new BorderLayout();
95 BorderLayout borderLayout2 = new BorderLayout();
97 BorderLayout borderLayout3 = new BorderLayout();
101 IProgressIndicator guiWindow;
103 AlignFrame alignFrame;
107 final String noDbSelected = "-- Select Database --";
109 private static jalview.ws.SequenceFetcher sfetch = null;
111 private static long lastDasSourceRegistry = -3;
113 private static DasSourceRegistryI dasRegistry = null;
115 private static boolean _initingFetcher = false;
117 private static Thread initingThread = null;
119 int debounceTrap = 0;
121 public JTextArea getTextArea()
127 * Blocking method that initialises and returns the shared instance of the
128 * SequenceFetcher client
131 * - where the initialisation delay message should be shown
132 * @return the singleton instance of the sequence fetcher client
134 public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
135 final IProgressIndicator guiWindow)
137 if (_initingFetcher && initingThread != null && initingThread.isAlive())
139 if (guiWindow != null)
144 .getString("status.waiting_sequence_database_fetchers_init"),
145 Thread.currentThread().hashCode());
147 // initting happening on another thread - so wait around to see if it
149 while (_initingFetcher && initingThread != null
150 && initingThread.isAlive())
155 } catch (Exception e)
160 if (guiWindow != null)
165 .getString("status.waiting_sequence_database_fetchers_init"),
166 Thread.currentThread().hashCode());
170 || dasRegistry != Cache.getDasSourceRegistry()
171 || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
172 .getDasRegistryURL() + Cache
173 .getDasSourceRegistry().getLocalSourceString())
176 _initingFetcher = true;
177 initingThread = Thread.currentThread();
179 * give a visual indication that sequence fetcher construction is occuring
181 if (guiWindow != null)
183 guiWindow.setProgressBar(MessageManager
184 .getString("status.init_sequence_database_fetchers"),
185 Thread.currentThread().hashCode());
187 dasRegistry = Cache.getDasSourceRegistry();
188 dasRegistry.refreshSources();
190 jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
191 if (guiWindow != null)
193 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
195 lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
196 .getLocalSourceString()).hashCode();
198 _initingFetcher = false;
199 initingThread = null;
204 private IProgressIndicator progressIndicator;
206 public SequenceFetcher(IProgressIndicator guiIndic)
208 this.progressIndicator = guiIndic;
209 final SequenceFetcher us = this;
210 // launch initialiser thread
211 Thread sf = new Thread(new Runnable()
217 if (getSequenceFetcherSingleton(progressIndicator) != null)
219 us.initGui(progressIndicator);
223 javax.swing.SwingUtilities.invokeLater(new Runnable()
229 .showInternalMessageDialog(
232 .getString("warn.couldnt_create_sequence_fetcher_client"),
234 .getString("label.couldnt_create_sequence_fetcher"),
235 JOptionPane.ERROR_MESSAGE);
239 // raise warning dialog
246 private class DatabaseAuthority extends DefaultMutableTreeNode
251 private class DatabaseSource extends DefaultMutableTreeNode
257 * called by thread spawned by constructor
261 private void initGui(IProgressIndicator guiWindow)
263 this.guiWindow = guiWindow;
264 if (guiWindow instanceof AlignFrame)
266 alignFrame = (AlignFrame) guiWindow;
268 database = new JDatabaseTree(sfetch);
272 } catch (Exception ex)
274 ex.printStackTrace();
277 frame = new JInternalFrame();
278 frame.setContentPane(this);
279 if (Platform.isAMac())
281 Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240);
285 Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180);
289 private String getFrameTitle()
291 return ((alignFrame == null) ? MessageManager
292 .getString("label.new_sequence_fetcher") : MessageManager
293 .getString("label.additional_sequence_fetcher"));
296 private void jbInit() throws Exception
298 this.setLayout(borderLayout2);
300 database.setFont(JvSwingUtils.getLabelFont());
301 dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
302 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
303 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
304 jLabel1.setText(MessageManager
305 .getString("label.separate_multiple_accession_ids"));
307 replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
309 .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
310 replacePunctuation.setText(MessageManager
311 .getString("label.replace_commas_semicolons"));
312 ok.setText(MessageManager.getString("action.ok"));
313 ok.addActionListener(new ActionListener()
316 public void actionPerformed(ActionEvent e)
318 ok_actionPerformed();
321 clear.setText(MessageManager.getString("action.clear"));
322 clear.addActionListener(new ActionListener()
325 public void actionPerformed(ActionEvent e)
327 clear_actionPerformed();
331 example.setText(MessageManager.getString("label.example"));
332 example.addActionListener(new ActionListener()
335 public void actionPerformed(ActionEvent e)
337 example_actionPerformed();
340 close.setText(MessageManager.getString("action.close"));
341 close.addActionListener(new ActionListener()
344 public void actionPerformed(ActionEvent e)
346 close_actionPerformed(e);
349 textArea.setFont(JvSwingUtils.getLabelFont());
350 textArea.setLineWrap(true);
351 textArea.addKeyListener(new KeyAdapter()
354 public void keyPressed(KeyEvent e)
356 if (e.getKeyCode() == KeyEvent.VK_ENTER)
358 ok_actionPerformed();
362 jPanel3.setLayout(borderLayout1);
363 borderLayout1.setVgap(5);
365 jPanel1.add(example);
368 jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
369 jPanel2.setLayout(borderLayout3);
370 databaseButt = /*database.getDatabaseSelectorButton();
371 final JButton viewdbs =*/new JButton(
372 MessageManager.getString("action.select_ddbb"));
373 databaseButt.addActionListener(new ActionListener()
377 public void actionPerformed(ActionEvent arg0)
380 database.showDialog();
383 databaseButt.setFont(JvSwingUtils.getLabelFont());
384 database.addActionListener(new ActionListener()
387 public void actionPerformed(ActionEvent e)
390 String currentSelection = database.getSelectedItem();
391 if (currentSelection == null)
393 close_actionPerformed(null);
398 if (currentSelection.equalsIgnoreCase("pdb")
399 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
403 else if (currentSelection.equalsIgnoreCase("uniprot")
404 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
406 uniprotSourceAction();
412 database.action = -1;
417 jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
418 jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
419 JPanel jPanel2a = new JPanel(new BorderLayout());
420 jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
421 jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
422 jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
423 // jPanel2.setPreferredSize(new Dimension())
424 jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
425 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
426 this.add(jPanel3, java.awt.BorderLayout.CENTER);
427 this.add(jPanel2, java.awt.BorderLayout.NORTH);
428 jScrollPane1.getViewport().add(textArea);
431 * open the database tree
433 database.waitForInput();
436 private void pdbSourceAction()
438 databaseButt.setText(database.getSelectedItem());
439 new PDBFTSPanel(this);
443 private void uniprotSourceAction()
445 databaseButt.setText(database.getSelectedItem());
446 new UniprotFTSPanel(this);
449 private void otherSourceAction()
453 databaseButt.setText(database.getSelectedItem()
454 + (database.getSelectedSources().size() > 1 ? " (and "
455 + database.getSelectedSources().size() + " others)"
457 String eq = database.getExampleQueries();
458 dbeg.setText(MessageManager.formatMessage(
459 "label.example_query_param", new String[] { eq }));
460 boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
461 for (DbSourceProxy dbs : database.getSelectedSources())
463 if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
469 replacePunctuation.setEnabled(enablePunct);
471 } catch (Exception ex)
474 replacePunctuation.setEnabled(true);
479 protected void example_actionPerformed()
481 DbSourceProxy db = null;
484 textArea.setText(database.getExampleQueries());
485 } catch (Exception ex)
491 protected void clear_actionPerformed()
493 textArea.setText("");
497 public void close_actionPerformed(ActionEvent e)
501 frame.setClosed(true);
502 } catch (Exception ex)
507 public void ok_actionPerformed()
509 databaseButt.setEnabled(false);
510 example.setEnabled(false);
511 textArea.setEnabled(false);
512 ok.setEnabled(false);
513 close.setEnabled(false);
515 Thread worker = new Thread(this);
519 private void resetDialog()
521 databaseButt.setEnabled(true);
522 example.setEnabled(true);
523 textArea.setEnabled(true);
525 close.setEnabled(true);
532 if (!database.hasSelection())
534 error += "Please select the source database\n";
536 // TODO: make this transformation more configurable
537 com.stevesoft.pat.Regex empty;
538 if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
540 empty = new com.stevesoft.pat.Regex(
541 // replace commas and spaces with a semicolon
542 "(\\s|[,; ])+", ";");
546 // just turn spaces and semicolons into single semicolons
547 empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
549 textArea.setText(empty.replaceAll(textArea.getText()));
550 // see if there's anthing to search with
551 if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
554 error += "Please enter a (semi-colon separated list of) database id(s)";
556 if (error.length() > 0)
558 showErrorMessage(error);
562 // TODO: Refactor to GUI independent code and write tests.
563 // indicate if successive sources should be merged into one alignment.
564 boolean addToLast = false;
565 List<String> aresultq = new ArrayList<String>();
566 List<String> presultTitle = new ArrayList<String>();
567 List<AlignmentI> presult = new ArrayList<AlignmentI>();
568 List<AlignmentI> aresult = new ArrayList<AlignmentI>();
569 Iterator<DbSourceProxy> proxies = database.getSelectedSources()
572 List<String> nextFetch = Arrays.asList(qries = textArea.getText()
574 Iterator<String> en = Arrays.asList(new String[0]).iterator();
575 int nqueries = qries.length;
577 FeatureSettingsModelI preferredFeatureColours = null;
578 while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
580 if (!en.hasNext() && nextFetch.size() > 0)
582 en = nextFetch.iterator();
583 nqueries = nextFetch.size();
584 // save the remaining queries in the original array
585 qries = nextFetch.toArray(new String[nqueries]);
586 nextFetch = new ArrayList<String>();
589 DbSourceProxy proxy = proxies.next();
594 .setProgressBar(MessageManager.formatMessage(
595 "status.fetching_sequence_queries_from",
597 Integer.valueOf(nqueries).toString(),
598 proxy.getDbName() }), Thread.currentThread()
600 if (proxy.getMaximumQueryCount() == 1)
603 * proxy only handles one accession id at a time
607 String acc = en.next();
608 if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
617 * proxy can fetch multiple accessions at one time
619 fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
621 } catch (Exception e)
623 showErrorMessage("Error retrieving " + textArea.getText()
624 + " from " + database.getSelectedItem());
626 // +="Couldn't retrieve sequences from "+database.getSelectedItem();
627 System.err.println("Retrieval failed for source ='"
628 + database.getSelectedItem() + "' and query\n'"
629 + textArea.getText() + "'\n");
631 } catch (OutOfMemoryError e)
633 showErrorMessage("Out of Memory when retrieving "
636 + database.getSelectedItem()
637 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
641 showErrorMessage("Serious Error retrieving " + textArea.getText()
642 + " from " + database.getSelectedItem());
646 // Stack results ready for opening in alignment windows
647 if (aresult != null && aresult.size() > 0)
649 FeatureSettingsModelI proxyColourScheme = proxy
650 .getFeatureColourScheme();
651 if (proxyColourScheme != null)
653 preferredFeatureColours = proxyColourScheme;
656 AlignmentI ar = null;
657 if (proxy.isAlignmentSource())
660 // new window for each result
661 while (aresult.size() > 0)
663 presult.add(aresult.remove(0));
664 presultTitle.add(aresultq.remove(0) + " "
665 + getDefaultRetrievalTitle());
671 if (addToLast && presult.size() > 0)
673 ar = presult.remove(presult.size() - 1);
674 titl = presultTitle.remove(presultTitle.size() - 1);
676 // concatenate all results in one window
677 while (aresult.size() > 0)
681 ar = aresult.remove(0);
685 ar.append(aresult.remove(0));
690 presultTitle.add(titl);
693 guiWindow.setProgressBar(MessageManager
694 .getString("status.finshed_querying"), Thread.currentThread()
697 guiWindow.setProgressBar(
698 (presult.size() > 0) ? MessageManager
699 .getString("status.parsing_results") : MessageManager
700 .getString("status.processing"), Thread.currentThread()
703 while (presult.size() > 0)
705 parseResult(presult.remove(0), presultTitle.remove(0), null,
706 preferredFeatureColours);
708 // only remove visual delay after we finished parsing.
709 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
710 if (nextFetch.size() > 0)
712 StringBuffer sb = new StringBuffer();
713 sb.append("Didn't retrieve the following "
714 + (nextFetch.size() == 1 ? "query" : nextFetch.size()
715 + " queries") + ": \n");
716 int l = sb.length(), lr = 0;
717 for (String s : nextFetch)
719 if (l != sb.length())
723 if (lr - sb.length() > 40)
729 showErrorMessage(sb.toString());
735 * Tries to fetch one or more accession ids from the database proxy
739 * the queries to fetch
741 * a successful queries list to add to
743 * a list of retrieved alignments to add to
745 * failed queries are added to this list
748 void fetchMultipleAccessions(DbSourceProxy proxy,
749 Iterator<String> accessions, List<String> aresultq,
750 List<AlignmentI> aresult, List<String> nextFetch)
753 StringBuilder multiacc = new StringBuilder();
754 List<String> tosend = new ArrayList<String>();
755 while (accessions.hasNext())
757 String nel = accessions.next();
759 multiacc.append(nel);
760 if (accessions.hasNext())
762 multiacc.append(proxy.getAccessionSeparator());
768 String query = multiacc.toString();
769 AlignmentI rslt = proxy.getSequenceRecords(query);
770 if (rslt == null || rslt.getHeight() == 0)
772 // no results - pass on all queries to next source
773 nextFetch.addAll(tosend);
779 if (tosend.size() > 1)
781 checkResultForQueries(rslt, tosend, nextFetch, proxy);
784 } catch (OutOfMemoryError oome)
786 new OOMWarning("fetching " + multiacc + " from "
787 + database.getSelectedItem(), oome, this);
792 * Query for a single accession id via the database proxy
797 * a list of successful queries to add to
799 * a list of retrieved alignments to add to
800 * @return true if the fetch was successful, else false
802 boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
803 List<String> aresultq, List<AlignmentI> aresult)
805 boolean success = false;
812 // give the server a chance to breathe
814 } catch (Exception e)
820 AlignmentI indres = null;
823 indres = proxy.getSequenceRecords(accession);
824 } catch (OutOfMemoryError oome)
826 new OOMWarning("fetching " + accession + " from "
827 + proxy.getDbName(), oome, this);
831 aresultq.add(accession);
835 } catch (Exception e)
838 "Error retrieving " + accession
839 + " from " + proxy.getDbName(), e);
845 * Checks which of the queries were successfully retrieved by searching the
846 * DBRefs of the retrieved sequences for a match. Any not found are added to
847 * the 'nextFetch' list.
854 void checkResultForQueries(AlignmentI rslt, List<String> queries,
855 List<String> nextFetch, DbSourceProxy proxy)
857 SequenceI[] rs = rslt.getSequencesArray();
859 for (String q : queries)
861 DBRefEntry dbr = new DBRefEntry();
862 dbr.setSource(proxy.getDbSource());
863 dbr.setVersion(null);
864 String accId = proxy.getAccessionIdFromQuery(q);
865 dbr.setAccessionId(accId);
866 boolean rfound = false;
867 for (int r = 0; r < rs.length; r++)
871 List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
873 if (!found.isEmpty())
889 * @return a standard title for any results retrieved using the currently
890 * selected source and settings
892 public String getDefaultRetrievalTitle()
894 return "Retrieved from " + database.getSelectedItem();
897 AlignmentI parseResult(AlignmentI al, String title,
898 FileFormatI currentFileFormat,
899 FeatureSettingsModelI preferredFeatureColours)
902 if (al != null && al.getHeight() > 0)
906 title = getDefaultRetrievalTitle();
908 if (alignFrame == null)
910 AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
911 AlignFrame.DEFAULT_HEIGHT);
912 if (currentFileFormat != null)
914 af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
916 // NON-FormatAdapter Sourced
920 SequenceFeature[] sfs = null;
921 List<SequenceI> alsqs;
922 synchronized (alsqs = al.getSequences())
924 for (SequenceI sq : alsqs)
926 if ((sfs = sq.getSequenceFeatures()) != null)
930 af.setShowSeqFeatures(true);
938 if (preferredFeatureColours != null)
940 af.getViewport().applyFeaturesStyle(preferredFeatureColours);
942 if (Cache.getDefault("HIDE_INTRONS", true))
944 af.hideFeatureColumns(SequenceOntologyI.EXON, false);
947 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
948 AlignFrame.DEFAULT_HEIGHT);
950 af.statusBar.setText(MessageManager
951 .getString("label.successfully_pasted_alignment_file"));
955 af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
957 } catch (Exception ex)
963 alignFrame.viewport.addAlignment(al, title);
969 void showErrorMessage(final String error)
972 javax.swing.SwingUtilities.invokeLater(new Runnable()
977 JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
978 MessageManager.getString("label.error_retrieving_data"),
979 JOptionPane.WARNING_MESSAGE);
984 public IProgressIndicator getProgressIndicator()
986 return progressIndicator;
989 public void setProgressIndicator(IProgressIndicator progressIndicator)
991 this.progressIndicator = progressIndicator;
995 * Make this panel visible (after a selection has been made in the database
1000 frame.setVisible(true);
1004 * Hide this panel (on clicking the database button to open the database
1009 frame.setVisible(false);