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.gff.SequenceOntologyI;
32 import jalview.util.DBRefUtils;
33 import jalview.util.MessageManager;
34 import jalview.util.Platform;
35 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
36 import jalview.ws.seqfetcher.DbSourceProxy;
38 import java.awt.BorderLayout;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.event.KeyAdapter;
43 import java.awt.event.KeyEvent;
44 import java.util.ArrayList;
45 import java.util.Arrays;
46 import java.util.Iterator;
47 import java.util.List;
49 import javax.swing.JButton;
50 import javax.swing.JCheckBox;
51 import javax.swing.JInternalFrame;
52 import javax.swing.JLabel;
53 import javax.swing.JOptionPane;
54 import javax.swing.JPanel;
55 import javax.swing.JScrollPane;
56 import javax.swing.JTextArea;
57 import javax.swing.SwingConstants;
58 import javax.swing.tree.DefaultMutableTreeNode;
60 public class SequenceFetcher extends JPanel implements Runnable
62 JLabel dbeg = new JLabel();
64 JDatabaseTree database;
68 JLabel jLabel1 = new JLabel();
70 JCheckBox replacePunctuation = new JCheckBox();
72 JButton ok = new JButton();
74 JButton clear = new JButton();
76 JButton example = new JButton();
78 JButton close = new JButton();
80 JPanel jPanel1 = new JPanel();
82 JTextArea textArea = new JTextArea();
84 JScrollPane jScrollPane1 = new JScrollPane();
86 JPanel jPanel2 = new JPanel();
88 JPanel jPanel3 = new JPanel();
90 JPanel jPanel4 = new JPanel();
92 BorderLayout borderLayout1 = new BorderLayout();
94 BorderLayout borderLayout2 = new BorderLayout();
96 BorderLayout borderLayout3 = new BorderLayout();
100 IProgressIndicator guiWindow;
102 AlignFrame alignFrame;
106 final String noDbSelected = "-- Select Database --";
108 private static jalview.ws.SequenceFetcher sfetch = null;
110 private static long lastDasSourceRegistry = -3;
112 private static DasSourceRegistryI dasRegistry = null;
114 private static boolean _initingFetcher = false;
116 private static Thread initingThread = null;
118 int debounceTrap = 0;
120 public JTextArea getTextArea()
126 * Blocking method that initialises and returns the shared instance of the
127 * SequenceFetcher client
130 * - where the initialisation delay message should be shown
131 * @return the singleton instance of the sequence fetcher client
133 public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
134 final IProgressIndicator guiWindow)
136 if (_initingFetcher && initingThread != null && initingThread.isAlive())
138 if (guiWindow != null)
143 .getString("status.waiting_sequence_database_fetchers_init"),
144 Thread.currentThread().hashCode());
146 // initting happening on another thread - so wait around to see if it
148 while (_initingFetcher && initingThread != null
149 && initingThread.isAlive())
154 } catch (Exception e)
159 if (guiWindow != null)
164 .getString("status.waiting_sequence_database_fetchers_init"),
165 Thread.currentThread().hashCode());
169 || dasRegistry != Cache.getDasSourceRegistry()
170 || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
171 .getDasRegistryURL() + Cache
172 .getDasSourceRegistry().getLocalSourceString())
175 _initingFetcher = true;
176 initingThread = Thread.currentThread();
178 * give a visual indication that sequence fetcher construction is occuring
180 if (guiWindow != null)
182 guiWindow.setProgressBar(MessageManager
183 .getString("status.init_sequence_database_fetchers"),
184 Thread.currentThread().hashCode());
186 dasRegistry = Cache.getDasSourceRegistry();
187 dasRegistry.refreshSources();
189 jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
190 if (guiWindow != null)
192 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
194 lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
195 .getLocalSourceString()).hashCode();
197 _initingFetcher = false;
198 initingThread = null;
203 private IProgressIndicator progressIndicator;
205 public SequenceFetcher(IProgressIndicator guiIndic)
207 this.progressIndicator = guiIndic;
208 final SequenceFetcher us = this;
209 // launch initialiser thread
210 Thread sf = new Thread(new Runnable()
216 if (getSequenceFetcherSingleton(progressIndicator) != null)
218 us.initGui(progressIndicator);
222 javax.swing.SwingUtilities.invokeLater(new Runnable()
228 .showInternalMessageDialog(
231 .getString("warn.couldnt_create_sequence_fetcher_client"),
233 .getString("label.couldnt_create_sequence_fetcher"),
234 JOptionPane.ERROR_MESSAGE);
238 // raise warning dialog
245 private class DatabaseAuthority extends DefaultMutableTreeNode
250 private class DatabaseSource extends DefaultMutableTreeNode
256 * called by thread spawned by constructor
260 private void initGui(IProgressIndicator guiWindow)
262 this.guiWindow = guiWindow;
263 if (guiWindow instanceof AlignFrame)
265 alignFrame = (AlignFrame) guiWindow;
267 database = new JDatabaseTree(sfetch);
271 } catch (Exception ex)
273 ex.printStackTrace();
276 frame = new JInternalFrame();
277 frame.setContentPane(this);
278 if (Platform.isAMac())
280 Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240);
284 Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180);
288 private String getFrameTitle()
290 return ((alignFrame == null) ? MessageManager
291 .getString("label.new_sequence_fetcher") : MessageManager
292 .getString("label.additional_sequence_fetcher"));
295 private void jbInit() throws Exception
297 this.setLayout(borderLayout2);
299 database.setFont(JvSwingUtils.getLabelFont());
300 dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
301 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
302 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
303 jLabel1.setText(MessageManager
304 .getString("label.separate_multiple_accession_ids"));
306 replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
308 .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
309 replacePunctuation.setText(MessageManager
310 .getString("label.replace_commas_semicolons"));
311 ok.setText(MessageManager.getString("action.ok"));
312 ok.addActionListener(new ActionListener()
315 public void actionPerformed(ActionEvent e)
317 ok_actionPerformed();
320 clear.setText(MessageManager.getString("action.clear"));
321 clear.addActionListener(new ActionListener()
324 public void actionPerformed(ActionEvent e)
326 clear_actionPerformed();
330 example.setText(MessageManager.getString("label.example"));
331 example.addActionListener(new ActionListener()
334 public void actionPerformed(ActionEvent e)
336 example_actionPerformed();
339 close.setText(MessageManager.getString("action.close"));
340 close.addActionListener(new ActionListener()
343 public void actionPerformed(ActionEvent e)
345 close_actionPerformed(e);
348 textArea.setFont(JvSwingUtils.getLabelFont());
349 textArea.setLineWrap(true);
350 textArea.addKeyListener(new KeyAdapter()
353 public void keyPressed(KeyEvent e)
355 if (e.getKeyCode() == KeyEvent.VK_ENTER)
357 ok_actionPerformed();
361 jPanel3.setLayout(borderLayout1);
362 borderLayout1.setVgap(5);
364 jPanel1.add(example);
367 jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
368 jPanel2.setLayout(borderLayout3);
369 databaseButt = /*database.getDatabaseSelectorButton();
370 final JButton viewdbs =*/new JButton(
371 MessageManager.getString("action.select_ddbb"));
372 databaseButt.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent arg0)
379 database.showDialog();
382 databaseButt.setFont(JvSwingUtils.getLabelFont());
383 database.addActionListener(new ActionListener()
386 public void actionPerformed(ActionEvent e)
389 String currentSelection = database.getSelectedItem();
390 if (currentSelection == null)
392 close_actionPerformed(null);
397 if (currentSelection.equalsIgnoreCase("pdb")
398 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
402 else if (currentSelection.equalsIgnoreCase("uniprot")
403 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
405 uniprotSourceAction();
411 database.action = -1;
416 jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
417 jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
418 JPanel jPanel2a = new JPanel(new BorderLayout());
419 jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
420 jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
421 jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
422 // jPanel2.setPreferredSize(new Dimension())
423 jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
424 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
425 this.add(jPanel3, java.awt.BorderLayout.CENTER);
426 this.add(jPanel2, java.awt.BorderLayout.NORTH);
427 jScrollPane1.getViewport().add(textArea);
430 * open the database tree
432 database.waitForInput();
435 private void pdbSourceAction()
437 databaseButt.setText(database.getSelectedItem());
438 new PDBFTSPanel(this);
442 private void uniprotSourceAction()
444 databaseButt.setText(database.getSelectedItem());
445 new UniprotFTSPanel(this);
448 private void otherSourceAction()
452 databaseButt.setText(database.getSelectedItem()
453 + (database.getSelectedSources().size() > 1 ? " (and "
454 + database.getSelectedSources().size() + " others)"
456 String eq = database.getExampleQueries();
457 dbeg.setText(MessageManager.formatMessage(
458 "label.example_query_param", new String[] { eq }));
459 boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
460 for (DbSourceProxy dbs : database.getSelectedSources())
462 if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
468 replacePunctuation.setEnabled(enablePunct);
470 } catch (Exception ex)
473 replacePunctuation.setEnabled(true);
478 protected void example_actionPerformed()
480 DbSourceProxy db = null;
483 textArea.setText(database.getExampleQueries());
484 } catch (Exception ex)
490 protected void clear_actionPerformed()
492 textArea.setText("");
496 public void close_actionPerformed(ActionEvent e)
500 frame.setClosed(true);
501 } catch (Exception ex)
506 public void ok_actionPerformed()
508 databaseButt.setEnabled(false);
509 example.setEnabled(false);
510 textArea.setEnabled(false);
511 ok.setEnabled(false);
512 close.setEnabled(false);
514 Thread worker = new Thread(this);
518 private void resetDialog()
520 databaseButt.setEnabled(true);
521 example.setEnabled(true);
522 textArea.setEnabled(true);
524 close.setEnabled(true);
531 if (!database.hasSelection())
533 error += "Please select the source database\n";
535 // TODO: make this transformation more configurable
536 com.stevesoft.pat.Regex empty;
537 if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
539 empty = new com.stevesoft.pat.Regex(
540 // replace commas and spaces with a semicolon
541 "(\\s|[,; ])+", ";");
545 // just turn spaces and semicolons into single semicolons
546 empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
548 textArea.setText(empty.replaceAll(textArea.getText()));
549 // see if there's anthing to search with
550 if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
553 error += "Please enter a (semi-colon separated list of) database id(s)";
555 if (error.length() > 0)
557 showErrorMessage(error);
561 // TODO: Refactor to GUI independent code and write tests.
562 // indicate if successive sources should be merged into one alignment.
563 boolean addToLast = false;
564 List<String> aresultq = new ArrayList<String>();
565 List<String> presultTitle = new ArrayList<String>();
566 List<AlignmentI> presult = new ArrayList<AlignmentI>();
567 List<AlignmentI> aresult = new ArrayList<AlignmentI>();
568 Iterator<DbSourceProxy> proxies = database.getSelectedSources()
571 List<String> nextFetch = Arrays.asList(qries = textArea.getText()
573 Iterator<String> en = Arrays.asList(new String[0]).iterator();
574 int nqueries = qries.length;
576 FeatureSettingsModelI preferredFeatureColours = null;
577 while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
579 if (!en.hasNext() && nextFetch.size() > 0)
581 en = nextFetch.iterator();
582 nqueries = nextFetch.size();
583 // save the remaining queries in the original array
584 qries = nextFetch.toArray(new String[nqueries]);
585 nextFetch = new ArrayList<String>();
588 DbSourceProxy proxy = proxies.next();
593 .setProgressBar(MessageManager.formatMessage(
594 "status.fetching_sequence_queries_from",
596 Integer.valueOf(nqueries).toString(),
597 proxy.getDbName() }), Thread.currentThread()
599 if (proxy.getMaximumQueryCount() == 1)
602 * proxy only handles one accession id at a time
606 String acc = en.next();
607 if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
616 * proxy can fetch multiple accessions at one time
618 fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
620 } catch (Exception e)
622 showErrorMessage("Error retrieving " + textArea.getText()
623 + " from " + database.getSelectedItem());
625 // +="Couldn't retrieve sequences from "+database.getSelectedItem();
626 System.err.println("Retrieval failed for source ='"
627 + database.getSelectedItem() + "' and query\n'"
628 + textArea.getText() + "'\n");
630 } catch (OutOfMemoryError e)
632 showErrorMessage("Out of Memory when retrieving "
635 + database.getSelectedItem()
636 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
640 showErrorMessage("Serious Error retrieving " + textArea.getText()
641 + " from " + database.getSelectedItem());
645 // Stack results ready for opening in alignment windows
646 if (aresult != null && aresult.size() > 0)
648 FeatureSettingsModelI proxyColourScheme = proxy
649 .getFeatureColourScheme();
650 if (proxyColourScheme != null)
652 preferredFeatureColours = proxyColourScheme;
655 AlignmentI ar = null;
656 if (proxy.isAlignmentSource())
659 // new window for each result
660 while (aresult.size() > 0)
662 presult.add(aresult.remove(0));
663 presultTitle.add(aresultq.remove(0) + " "
664 + getDefaultRetrievalTitle());
670 if (addToLast && presult.size() > 0)
672 ar = presult.remove(presult.size() - 1);
673 titl = presultTitle.remove(presultTitle.size() - 1);
675 // concatenate all results in one window
676 while (aresult.size() > 0)
680 ar = aresult.remove(0);
684 ar.append(aresult.remove(0));
689 presultTitle.add(titl);
692 guiWindow.setProgressBar(MessageManager
693 .getString("status.finshed_querying"), Thread.currentThread()
696 guiWindow.setProgressBar(
697 (presult.size() > 0) ? MessageManager
698 .getString("status.parsing_results") : MessageManager
699 .getString("status.processing"), Thread.currentThread()
702 while (presult.size() > 0)
704 parseResult(presult.remove(0), presultTitle.remove(0), null,
705 preferredFeatureColours);
707 // only remove visual delay after we finished parsing.
708 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
709 if (nextFetch.size() > 0)
711 StringBuffer sb = new StringBuffer();
712 sb.append("Didn't retrieve the following "
713 + (nextFetch.size() == 1 ? "query" : nextFetch.size()
714 + " queries") + ": \n");
715 int l = sb.length(), lr = 0;
716 for (String s : nextFetch)
718 if (l != sb.length())
722 if (lr - sb.length() > 40)
728 showErrorMessage(sb.toString());
734 * Tries to fetch one or more accession ids from the database proxy
738 * the queries to fetch
740 * a successful queries list to add to
742 * a list of retrieved alignments to add to
744 * failed queries are added to this list
747 void fetchMultipleAccessions(DbSourceProxy proxy,
748 Iterator<String> accessions, List<String> aresultq,
749 List<AlignmentI> aresult, List<String> nextFetch)
752 StringBuilder multiacc = new StringBuilder();
753 List<String> tosend = new ArrayList<String>();
754 while (accessions.hasNext())
756 String nel = accessions.next();
758 multiacc.append(nel);
759 if (accessions.hasNext())
761 multiacc.append(proxy.getAccessionSeparator());
767 String query = multiacc.toString();
768 AlignmentI rslt = proxy.getSequenceRecords(query);
769 if (rslt == null || rslt.getHeight() == 0)
771 // no results - pass on all queries to next source
772 nextFetch.addAll(tosend);
778 if (tosend.size() > 1)
780 checkResultForQueries(rslt, tosend, nextFetch, proxy);
783 } catch (OutOfMemoryError oome)
785 new OOMWarning("fetching " + multiacc + " from "
786 + database.getSelectedItem(), oome, this);
791 * Query for a single accession id via the database proxy
796 * a list of successful queries to add to
798 * a list of retrieved alignments to add to
799 * @return true if the fetch was successful, else false
801 boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
802 List<String> aresultq, List<AlignmentI> aresult)
804 boolean success = false;
811 // give the server a chance to breathe
813 } catch (Exception e)
819 AlignmentI indres = null;
822 indres = proxy.getSequenceRecords(accession);
823 } catch (OutOfMemoryError oome)
825 new OOMWarning("fetching " + accession + " from "
826 + proxy.getDbName(), oome, this);
830 aresultq.add(accession);
834 } catch (Exception e)
837 "Error retrieving " + accession
838 + " from " + proxy.getDbName(), e);
846 * Checks which of the queries were successfully retrieved by searching the
847 * DBRefs of the retrieved sequences for a match. Any not found are added to
848 * the 'nextFetch' list.
855 void checkResultForQueries(AlignmentI rslt, List<String> queries,
856 List<String> nextFetch, DbSourceProxy proxy)
858 SequenceI[] rs = rslt.getSequencesArray();
860 for (String q : queries)
862 DBRefEntry[] found = null;
863 DBRefEntry dbr = new DBRefEntry();
864 dbr.setSource(proxy.getDbSource());
865 dbr.setVersion(null);
866 String accId = proxy.getAccessionIdFromQuery(q);
867 dbr.setAccessionId(accId);
868 boolean rfound = false;
869 for (int r = 0; r < rs.length; r++)
873 found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
874 if (found != null && found.length > 0)
890 * @return a standard title for any results retrieved using the currently
891 * selected source and settings
893 public String getDefaultRetrievalTitle()
895 return "Retrieved from " + database.getSelectedItem();
898 AlignmentI parseResult(AlignmentI al, String title,
899 String currentFileFormat,
900 FeatureSettingsModelI preferredFeatureColours)
903 if (al != null && al.getHeight() > 0)
907 title = getDefaultRetrievalTitle();
909 if (alignFrame == null)
911 AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
912 AlignFrame.DEFAULT_HEIGHT);
913 if (currentFileFormat != null)
915 af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
917 // NON-FormatAdapter Sourced
921 SequenceFeature[] sfs = null;
922 List<SequenceI> alsqs;
923 synchronized (alsqs = al.getSequences())
925 for (SequenceI sq : alsqs)
927 if ((sfs = sq.getSequenceFeatures()) != null)
931 af.setShowSeqFeatures(true);
939 if (preferredFeatureColours != null)
941 af.getViewport().applyFeaturesStyle(preferredFeatureColours);
943 if (Cache.getDefault("HIDE_INTRONS", true))
945 af.hideFeatureColumns(SequenceOntologyI.EXON, false);
948 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
949 AlignFrame.DEFAULT_HEIGHT);
951 af.statusBar.setText(MessageManager
952 .getString("label.successfully_pasted_alignment_file"));
956 af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
958 } catch (Exception ex)
964 alignFrame.viewport.addAlignment(al, title);
970 void showErrorMessage(final String error)
973 javax.swing.SwingUtilities.invokeLater(new Runnable()
978 JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
979 MessageManager.getString("label.error_retrieving_data"),
980 JOptionPane.WARNING_MESSAGE);
985 public IProgressIndicator getProgressIndicator()
987 return progressIndicator;
990 public void setProgressIndicator(IProgressIndicator progressIndicator)
992 this.progressIndicator = progressIndicator;
996 * Make this panel visible (after a selection has been made in the database
1001 frame.setVisible(true);
1005 * Hide this panel (on clicking the database button to open the database
1010 frame.setVisible(false);