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.ws.dbsources.das.api.DasSourceRegistryI;
35 import jalview.ws.seqfetcher.DbSourceProxy;
37 import java.awt.BorderLayout;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.awt.event.KeyAdapter;
42 import java.awt.event.KeyEvent;
43 import java.util.ArrayList;
44 import java.util.Arrays;
45 import java.util.Iterator;
46 import java.util.List;
48 import javax.swing.JButton;
49 import javax.swing.JCheckBox;
50 import javax.swing.JInternalFrame;
51 import javax.swing.JLabel;
52 import javax.swing.JOptionPane;
53 import javax.swing.JPanel;
54 import javax.swing.JScrollPane;
55 import javax.swing.JTextArea;
56 import javax.swing.SwingConstants;
57 import javax.swing.tree.DefaultMutableTreeNode;
59 public class SequenceFetcher extends JPanel implements Runnable
61 JLabel dbeg = new JLabel();
63 JDatabaseTree database;
67 JLabel jLabel1 = new JLabel();
69 JCheckBox replacePunctuation = new JCheckBox();
71 JButton ok = new JButton();
73 JButton clear = new JButton();
75 JButton example = new JButton();
77 JButton close = new JButton();
79 JPanel jPanel1 = new JPanel();
81 JTextArea textArea = new JTextArea();
83 JScrollPane jScrollPane1 = new JScrollPane();
85 JPanel jPanel2 = new JPanel();
87 JPanel jPanel3 = new JPanel();
89 JPanel jPanel4 = new JPanel();
91 BorderLayout borderLayout1 = new BorderLayout();
93 BorderLayout borderLayout2 = new BorderLayout();
95 BorderLayout borderLayout3 = new BorderLayout();
99 IProgressIndicator guiWindow;
101 AlignFrame alignFrame;
105 final String noDbSelected = "-- Select Database --";
107 private static jalview.ws.SequenceFetcher sfetch = null;
109 private static long lastDasSourceRegistry = -3;
111 private static DasSourceRegistryI dasRegistry = null;
113 private static boolean _initingFetcher = false;
115 private static Thread initingThread = null;
117 int debounceTrap = 0;
119 public JTextArea getTextArea()
125 * Blocking method that initialises and returns the shared instance of the
126 * SequenceFetcher client
129 * - where the initialisation delay message should be shown
130 * @return the singleton instance of the sequence fetcher client
132 public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
133 final IProgressIndicator guiWindow)
135 if (_initingFetcher && initingThread != null && initingThread.isAlive())
137 if (guiWindow != null)
142 .getString("status.waiting_sequence_database_fetchers_init"),
143 Thread.currentThread().hashCode());
145 // initting happening on another thread - so wait around to see if it
147 while (_initingFetcher && initingThread != null
148 && initingThread.isAlive())
153 } catch (Exception e)
158 if (guiWindow != null)
163 .getString("status.waiting_sequence_database_fetchers_init"),
164 Thread.currentThread().hashCode());
168 || dasRegistry != Cache.getDasSourceRegistry()
169 || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
170 .getDasRegistryURL() + Cache
171 .getDasSourceRegistry().getLocalSourceString())
174 _initingFetcher = true;
175 initingThread = Thread.currentThread();
177 * give a visual indication that sequence fetcher construction is occuring
179 if (guiWindow != null)
181 guiWindow.setProgressBar(MessageManager
182 .getString("status.init_sequence_database_fetchers"),
183 Thread.currentThread().hashCode());
185 dasRegistry = Cache.getDasSourceRegistry();
186 dasRegistry.refreshSources();
188 jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
189 if (guiWindow != null)
191 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
193 lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
194 .getLocalSourceString()).hashCode();
196 _initingFetcher = false;
197 initingThread = null;
202 private IProgressIndicator progressIndicator;
204 public SequenceFetcher(IProgressIndicator guiIndic)
206 this.progressIndicator = guiIndic;
207 final SequenceFetcher us = this;
208 // launch initialiser thread
209 Thread sf = new Thread(new Runnable()
215 if (getSequenceFetcherSingleton(progressIndicator) != null)
217 us.initGui(progressIndicator);
221 javax.swing.SwingUtilities.invokeLater(new Runnable()
227 .showInternalMessageDialog(
230 .getString("warn.couldnt_create_sequence_fetcher_client"),
232 .getString("label.couldnt_create_sequence_fetcher"),
233 JOptionPane.ERROR_MESSAGE);
237 // raise warning dialog
244 private class DatabaseAuthority extends DefaultMutableTreeNode
249 private class DatabaseSource extends DefaultMutableTreeNode
255 * called by thread spawned by constructor
259 private void initGui(IProgressIndicator guiWindow)
261 this.guiWindow = guiWindow;
262 if (guiWindow instanceof AlignFrame)
264 alignFrame = (AlignFrame) guiWindow;
266 database = new JDatabaseTree(sfetch);
270 } catch (Exception ex)
272 ex.printStackTrace();
275 frame = new JInternalFrame();
276 frame.setContentPane(this);
277 if (new jalview.util.Platform().isAMac())
279 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
283 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
287 private String getFrameTitle()
289 return ((alignFrame == null) ? MessageManager
290 .getString("label.new_sequence_fetcher") : MessageManager
291 .getString("label.additional_sequence_fetcher"));
294 private void jbInit() throws Exception
296 this.setLayout(borderLayout2);
298 database.setFont(JvSwingUtils.getLabelFont());
299 dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
300 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
301 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
302 jLabel1.setText(MessageManager
303 .getString("label.separate_multiple_accession_ids"));
305 replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
307 .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
308 replacePunctuation.setText(MessageManager
309 .getString("label.replace_commas_semicolons"));
310 ok.setText(MessageManager.getString("action.ok"));
311 ok.addActionListener(new ActionListener()
314 public void actionPerformed(ActionEvent e)
316 ok_actionPerformed();
319 clear.setText(MessageManager.getString("action.clear"));
320 clear.addActionListener(new ActionListener()
323 public void actionPerformed(ActionEvent e)
325 clear_actionPerformed();
329 example.setText(MessageManager.getString("label.example"));
330 example.addActionListener(new ActionListener()
333 public void actionPerformed(ActionEvent e)
335 example_actionPerformed();
338 close.setText(MessageManager.getString("action.close"));
339 close.addActionListener(new ActionListener()
342 public void actionPerformed(ActionEvent e)
344 close_actionPerformed(e);
347 textArea.setFont(JvSwingUtils.getLabelFont());
348 textArea.setLineWrap(true);
349 textArea.addKeyListener(new KeyAdapter()
352 public void keyPressed(KeyEvent e)
354 if (e.getKeyCode() == KeyEvent.VK_ENTER)
356 ok_actionPerformed();
360 jPanel3.setLayout(borderLayout1);
361 borderLayout1.setVgap(5);
363 jPanel1.add(example);
366 jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
367 jPanel2.setLayout(borderLayout3);
368 databaseButt = database.getDatabaseSelectorButton();
369 databaseButt.setFont(JvSwingUtils.getLabelFont());
370 database.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
376 String currentSelection = database.getSelectedItem();
378 if (currentSelection.equalsIgnoreCase("pdb")
379 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
383 // else if (currentSelection.equalsIgnoreCase("uniprot")
384 // && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) ==
387 // uniprotSourceAction();
393 database.action = -1;
398 jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
399 jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
400 JPanel jPanel2a = new JPanel(new BorderLayout());
401 jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
402 jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
403 jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
404 // jPanel2.setPreferredSize(new Dimension())
405 jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
406 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
407 this.add(jPanel3, java.awt.BorderLayout.CENTER);
408 this.add(jPanel2, java.awt.BorderLayout.NORTH);
409 jScrollPane1.getViewport().add(textArea);
413 private void pdbSourceAction()
415 databaseButt.setText(database.getSelectedItem());
416 new PDBFTSPanel(this);
420 private void uniprotSourceAction()
422 databaseButt.setText(database.getSelectedItem());
423 new UniprotFTSPanel(this);
426 private void otherSourceAction()
430 databaseButt.setText(database.getSelectedItem()
431 + (database.getSelectedSources().size() > 1 ? " (and "
432 + database.getSelectedSources().size() + " others)"
434 String eq = database.getExampleQueries();
435 dbeg.setText(MessageManager.formatMessage(
436 "label.example_query_param", new String[] { eq }));
437 boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
438 for (DbSourceProxy dbs : database.getSelectedSources())
440 if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
446 replacePunctuation.setEnabled(enablePunct);
448 } catch (Exception ex)
451 replacePunctuation.setEnabled(true);
456 protected void example_actionPerformed()
458 DbSourceProxy db = null;
461 textArea.setText(database.getExampleQueries());
462 } catch (Exception ex)
468 protected void clear_actionPerformed()
470 textArea.setText("");
474 public void close_actionPerformed(ActionEvent e)
478 frame.setClosed(true);
479 } catch (Exception ex)
484 public void ok_actionPerformed()
486 databaseButt.setEnabled(false);
487 example.setEnabled(false);
488 textArea.setEnabled(false);
489 ok.setEnabled(false);
490 close.setEnabled(false);
492 Thread worker = new Thread(this);
496 private void resetDialog()
498 databaseButt.setEnabled(true);
499 example.setEnabled(true);
500 textArea.setEnabled(true);
502 close.setEnabled(true);
509 if (!database.hasSelection())
511 error += "Please select the source database\n";
513 // TODO: make this transformation more configurable
514 com.stevesoft.pat.Regex empty;
515 if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
517 empty = new com.stevesoft.pat.Regex(
518 // replace commas and spaces with a semicolon
519 "(\\s|[,; ])+", ";");
523 // just turn spaces and semicolons into single semicolons
524 empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
526 textArea.setText(empty.replaceAll(textArea.getText()));
527 // see if there's anthing to search with
528 if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
531 error += "Please enter a (semi-colon separated list of) database id(s)";
533 if (error.length() > 0)
535 showErrorMessage(error);
539 // TODO: Refactor to GUI independent code and write tests.
540 // indicate if successive sources should be merged into one alignment.
541 boolean addToLast = false;
542 List<String> aresultq = new ArrayList<String>();
543 List<String> presultTitle = new ArrayList<String>();
544 List<AlignmentI> presult = new ArrayList<AlignmentI>();
545 List<AlignmentI> aresult = new ArrayList<AlignmentI>();
546 Iterator<DbSourceProxy> proxies = database.getSelectedSources()
549 List<String> nextFetch = Arrays.asList(qries = textArea.getText()
551 Iterator<String> en = Arrays.asList(new String[0]).iterator();
552 int nqueries = qries.length;
554 FeatureSettingsModelI preferredFeatureColours = null;
555 while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
557 if (!en.hasNext() && nextFetch.size() > 0)
559 en = nextFetch.iterator();
560 nqueries = nextFetch.size();
561 // save the remaining queries in the original array
562 qries = nextFetch.toArray(new String[nqueries]);
563 nextFetch = new ArrayList<String>();
566 DbSourceProxy proxy = proxies.next();
571 .setProgressBar(MessageManager.formatMessage(
572 "status.fetching_sequence_queries_from",
574 Integer.valueOf(nqueries).toString(),
575 proxy.getDbName() }), Thread.currentThread()
577 if (proxy.getMaximumQueryCount() == 1)
580 * proxy only handles one accession id at a time
584 String acc = en.next();
585 if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
594 * proxy can fetch multiple accessions at one time
596 fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
598 } catch (Exception e)
600 showErrorMessage("Error retrieving " + textArea.getText()
601 + " from " + database.getSelectedItem());
603 // +="Couldn't retrieve sequences from "+database.getSelectedItem();
604 System.err.println("Retrieval failed for source ='"
605 + database.getSelectedItem() + "' and query\n'"
606 + textArea.getText() + "'\n");
608 } catch (OutOfMemoryError e)
610 showErrorMessage("Out of Memory when retrieving "
613 + database.getSelectedItem()
614 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
618 showErrorMessage("Serious Error retrieving " + textArea.getText()
619 + " from " + database.getSelectedItem());
623 // Stack results ready for opening in alignment windows
624 if (aresult != null && aresult.size() > 0)
626 FeatureSettingsModelI proxyColourScheme = proxy
627 .getFeatureColourScheme();
628 if (proxyColourScheme != null)
630 preferredFeatureColours = proxyColourScheme;
633 AlignmentI ar = null;
634 if (proxy.isAlignmentSource())
637 // new window for each result
638 while (aresult.size() > 0)
640 presult.add(aresult.remove(0));
641 presultTitle.add(aresultq.remove(0) + " "
642 + getDefaultRetrievalTitle());
648 if (addToLast && presult.size() > 0)
650 ar = presult.remove(presult.size() - 1);
651 titl = presultTitle.remove(presultTitle.size() - 1);
653 // concatenate all results in one window
654 while (aresult.size() > 0)
658 ar = aresult.remove(0);
662 ar.append(aresult.remove(0));
667 presultTitle.add(titl);
670 guiWindow.setProgressBar(MessageManager
671 .getString("status.finshed_querying"), Thread.currentThread()
674 guiWindow.setProgressBar(
675 (presult.size() > 0) ? MessageManager
676 .getString("status.parsing_results") : MessageManager
677 .getString("status.processing"), Thread.currentThread()
680 while (presult.size() > 0)
682 parseResult(presult.remove(0), presultTitle.remove(0), null,
683 preferredFeatureColours);
685 // only remove visual delay after we finished parsing.
686 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
687 if (nextFetch.size() > 0)
689 StringBuffer sb = new StringBuffer();
690 sb.append("Didn't retrieve the following "
691 + (nextFetch.size() == 1 ? "query" : nextFetch.size()
692 + " queries") + ": \n");
693 int l = sb.length(), lr = 0;
694 for (String s : nextFetch)
696 if (l != sb.length())
700 if (lr - sb.length() > 40)
706 showErrorMessage(sb.toString());
712 * Tries to fetch one or more accession ids from the database proxy
716 * the queries to fetch
718 * a successful queries list to add to
720 * a list of retrieved alignments to add to
722 * failed queries are added to this list
725 void fetchMultipleAccessions(DbSourceProxy proxy,
726 Iterator<String> accessions, List<String> aresultq,
727 List<AlignmentI> aresult, List<String> nextFetch)
730 StringBuilder multiacc = new StringBuilder();
731 List<String> tosend = new ArrayList<String>();
732 while (accessions.hasNext())
734 String nel = accessions.next();
736 multiacc.append(nel);
737 if (accessions.hasNext())
739 multiacc.append(proxy.getAccessionSeparator());
745 String query = multiacc.toString();
746 AlignmentI rslt = proxy.getSequenceRecords(query);
747 if (rslt == null || rslt.getHeight() == 0)
749 // no results - pass on all queries to next source
750 nextFetch.addAll(tosend);
756 if (tosend.size() > 1)
758 checkResultForQueries(rslt, tosend, nextFetch, proxy);
761 } catch (OutOfMemoryError oome)
763 new OOMWarning("fetching " + multiacc + " from "
764 + database.getSelectedItem(), oome, this);
769 * Query for a single accession id via the database proxy
774 * a list of successful queries to add to
776 * a list of retrieved alignments to add to
777 * @return true if the fetch was successful, else false
779 boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
780 List<String> aresultq, List<AlignmentI> aresult)
782 boolean success = false;
789 // give the server a chance to breathe
791 } catch (Exception e)
797 AlignmentI indres = null;
800 indres = proxy.getSequenceRecords(accession);
801 } catch (OutOfMemoryError oome)
803 new OOMWarning("fetching " + accession + " from "
804 + proxy.getDbName(), oome, this);
808 aresultq.add(accession);
812 } catch (Exception e)
815 "Error retrieving " + accession
816 + " from " + proxy.getDbName(), e);
824 * Checks which of the queries were successfully retrieved by searching the
825 * DBRefs of the retrieved sequences for a match. Any not found are added to
826 * the 'nextFetch' list.
833 void checkResultForQueries(AlignmentI rslt, List<String> queries,
834 List<String> nextFetch, DbSourceProxy proxy)
836 SequenceI[] rs = rslt.getSequencesArray();
838 for (String q : queries)
840 DBRefEntry[] found = null;
841 DBRefEntry dbr = new DBRefEntry();
842 dbr.setSource(proxy.getDbSource());
843 dbr.setVersion(null);
844 String accId = proxy.getAccessionIdFromQuery(q);
845 dbr.setAccessionId(accId);
846 boolean rfound = false;
847 for (int r = 0; r < rs.length; r++)
851 found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
852 if (found != null && found.length > 0)
868 * @return a standard title for any results retrieved using the currently
869 * selected source and settings
871 public String getDefaultRetrievalTitle()
873 return "Retrieved from " + database.getSelectedItem();
876 AlignmentI parseResult(AlignmentI al, String title,
877 String currentFileFormat,
878 FeatureSettingsModelI preferredFeatureColours)
881 if (al != null && al.getHeight() > 0)
885 title = getDefaultRetrievalTitle();
887 if (alignFrame == null)
889 AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
890 AlignFrame.DEFAULT_HEIGHT);
891 if (currentFileFormat != null)
893 af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
895 // NON-FormatAdapter Sourced
899 SequenceFeature[] sfs = null;
900 List<SequenceI> alsqs;
901 synchronized (alsqs = al.getSequences())
903 for (SequenceI sq : alsqs)
905 if ((sfs = sq.getSequenceFeatures()) != null)
909 af.setShowSeqFeatures(true);
917 if (preferredFeatureColours != null)
919 af.getViewport().applyFeaturesStyle(preferredFeatureColours);
921 if (Cache.getDefault("HIDE_INTRONS", true))
923 hideIntronsIfPresent(af);
926 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
927 AlignFrame.DEFAULT_HEIGHT);
929 af.statusBar.setText(MessageManager
930 .getString("label.successfully_pasted_alignment_file"));
934 af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
936 } catch (Exception ex)
942 alignFrame.viewport.addAlignment(al, title);
949 * Hide columns not containing 'exon' features, provided there are exon
950 * features on the alignment
954 public void hideIntronsIfPresent(AlignFrame af)
956 boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
958 SequenceOntologyI.EXON);
961 af.avc.markColumnsContainingFeatures(true, false, true,
962 SequenceOntologyI.EXON);
963 af.getViewport().hideSelectedColumns();
967 void showErrorMessage(final String error)
970 javax.swing.SwingUtilities.invokeLater(new Runnable()
975 JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
976 MessageManager.getString("label.error_retrieving_data"),
977 JOptionPane.WARNING_MESSAGE);
982 public IProgressIndicator getProgressIndicator()
984 return progressIndicator;
987 public void setProgressIndicator(IProgressIndicator progressIndicator)
989 this.progressIndicator = progressIndicator;