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.SequenceI;
28 import jalview.fts.core.GFTSPanel;
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.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.HashSet;
47 import java.util.Iterator;
48 import java.util.List;
50 import javax.swing.JButton;
51 import javax.swing.JCheckBox;
52 import javax.swing.JComboBox;
53 import javax.swing.JInternalFrame;
54 import javax.swing.JLabel;
55 import javax.swing.JPanel;
56 import javax.swing.JScrollPane;
57 import javax.swing.JTextArea;
58 import javax.swing.SwingConstants;
61 * A panel where the use may choose a database source, and enter one or more
62 * accessions, to retrieve entries from the database.
64 * If the selected source is Uniprot or PDB, a free text search panel is opened
65 * instead to perform the search and selection.
67 public class SequenceFetcher extends JPanel implements Runnable
69 private static jalview.ws.SequenceFetcher sfetch = null;
71 JLabel exampleAccession;
73 JComboBox<String> database;
75 JCheckBox replacePunctuation;
89 IProgressIndicator guiWindow;
91 AlignFrame alignFrame;
93 GFTSPanel parentSearchPanel;
95 IProgressIndicator progressIndicator;
97 volatile boolean _isConstructing = false;
100 * Returns the shared instance of the SequenceFetcher client
104 public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
108 sfetch = new jalview.ws.SequenceFetcher();
114 * Constructor given a client to receive any status or progress messages
115 * (currently either the Desktop, or an AlignFrame panel)
119 public SequenceFetcher(IProgressIndicator guiIndic)
121 this(guiIndic, null, null);
125 * Constructor with specified database and accession(s) to retrieve
131 public SequenceFetcher(IProgressIndicator guiIndic,
132 final String selectedDb, final String queryString)
134 this.progressIndicator = guiIndic;
135 getSequenceFetcherSingleton();
136 this.guiWindow = progressIndicator;
138 if (progressIndicator instanceof AlignFrame)
140 alignFrame = (AlignFrame) progressIndicator;
144 textArea.setText(queryString);
146 frame = new JInternalFrame();
147 frame.setContentPane(this);
148 Desktop.addInternalFrame(frame, getFrameTitle(), Desktop.FRAME_MAKE_VISIBLE, 400,
149 Platform.isAMacAndNotJS() ? 240 : 180, Desktop.FRAME_ALLOW_RESIZE, Desktop.FRAME_SET_MIN_SIZE_300);
152 private String getFrameTitle()
154 return ((alignFrame == null)
155 ? MessageManager.getString("label.new_sequence_fetcher")
157 .getString("label.additional_sequence_fetcher"));
160 private void jbInit(String selectedDb)
162 this.setLayout(new BorderLayout());
164 database = new JComboBox<>();
165 database.setFont(JvSwingUtils.getLabelFont());
166 database.setPrototypeDisplayValue("ENSEMBLGENOMES ");
167 String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
168 Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
169 database.addItem(MessageManager.getString("action.select_ddbb"));
170 for (String source : sources)
172 database.addItem(source);
174 database.setSelectedItem(selectedDb);
175 if (database.getSelectedIndex() == -1)
177 database.setSelectedIndex(0);
179 database.setMaximumRowCount(database.getItemCount());
180 database.addActionListener(new ActionListener()
183 public void actionPerformed(ActionEvent e)
185 String currentSelection = (String) database.getSelectedItem();
186 updateExampleQuery(currentSelection);
188 if ("pdb".equalsIgnoreCase(currentSelection))
191 new PDBFTSPanel(SequenceFetcher.this);
193 else if ("uniprot".equalsIgnoreCase(currentSelection))
196 new UniprotFTSPanel(SequenceFetcher.this);
205 exampleAccession = new JLabel("");
206 exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11));
207 JLabel jLabel1 = new JLabel(MessageManager
208 .getString("label.separate_multiple_accession_ids"));
209 jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11));
210 jLabel1.setHorizontalAlignment(SwingConstants.LEFT);
212 replacePunctuation = new JCheckBox(
213 MessageManager.getString("label.replace_commas_semicolons"));
214 replacePunctuation.setHorizontalAlignment(SwingConstants.LEFT);
215 replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11));
216 okBtn = new JButton(MessageManager.getString("action.ok"));
217 okBtn.addActionListener(new ActionListener()
220 public void actionPerformed(ActionEvent e)
222 ok_actionPerformed();
225 JButton clear = new JButton(MessageManager.getString("action.clear"));
226 clear.addActionListener(new ActionListener()
229 public void actionPerformed(ActionEvent e)
231 clear_actionPerformed();
235 exampleBtn = new JButton(MessageManager.getString("label.example"));
236 exampleBtn.addActionListener(new ActionListener()
239 public void actionPerformed(ActionEvent e)
241 example_actionPerformed();
244 closeBtn = new JButton(MessageManager.getString("action.cancel"));
245 closeBtn.addActionListener(new ActionListener()
248 public void actionPerformed(ActionEvent e)
250 close_actionPerformed(e);
253 backBtn = new JButton(MessageManager.getString("action.back"));
254 backBtn.addActionListener(new ActionListener()
257 public void actionPerformed(ActionEvent e)
259 parentSearchPanel.btn_back_ActionPerformed();
262 // back not visible unless embedded
263 backBtn.setVisible(false);
265 textArea = new JTextArea();
266 textArea.setFont(JvSwingUtils.getLabelFont());
267 textArea.setLineWrap(true);
268 textArea.addKeyListener(new KeyAdapter()
271 public void keyPressed(KeyEvent e)
273 if (e.getKeyCode() == KeyEvent.VK_ENTER)
275 ok_actionPerformed();
280 JPanel actionPanel = new JPanel();
281 actionPanel.add(backBtn);
282 actionPanel.add(exampleBtn);
283 actionPanel.add(clear);
284 actionPanel.add(okBtn);
285 actionPanel.add(closeBtn);
287 JPanel databasePanel = new JPanel();
288 databasePanel.setLayout(new BorderLayout());
289 databasePanel.add(database, BorderLayout.NORTH);
290 databasePanel.add(exampleAccession, BorderLayout.CENTER);
291 JPanel jPanel2a = new JPanel(new BorderLayout());
292 jPanel2a.add(jLabel1, BorderLayout.NORTH);
293 jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
294 databasePanel.add(jPanel2a, BorderLayout.SOUTH);
296 JPanel idsPanel = new JPanel();
297 idsPanel.setLayout(new BorderLayout(0, 5));
298 JScrollPane jScrollPane1 = new JScrollPane();
299 jScrollPane1.getViewport().add(textArea);
300 idsPanel.add(jScrollPane1, BorderLayout.CENTER);
302 this.add(actionPanel, BorderLayout.SOUTH);
303 this.add(idsPanel, BorderLayout.CENTER);
304 this.add(databasePanel, BorderLayout.NORTH);
308 * Answers a semi-colon-delimited string with the example query or queries for
309 * the selected database
314 protected String getExampleQueries(String db)
316 StringBuilder sb = new StringBuilder();
317 HashSet<String> hs = new HashSet<>();
318 for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
320 String tq = dbs.getTestQuery();
321 if (hs.add(tq)) // not a duplicate source
330 return sb.toString();
334 * Action on selecting a database other than Uniprot or PDB is to enable or
335 * disable 'Replace commas', and await input in the query field
337 protected void otherSourceAction()
341 String eq = exampleAccession.getText();
342 // TODO this should be a property of the SequenceFetcher whether commas
343 // are allowed in the IDs...
345 boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
346 replacePunctuation.setEnabled(enablePunct);
348 } catch (Exception ex)
350 exampleAccession.setText("");
351 replacePunctuation.setEnabled(true);
357 * Sets the text of the example query to incorporate the example accession
358 * provided by the selected database source
360 * @param selectedDatabase
363 protected String updateExampleQuery(String selectedDatabase)
365 String eq = getExampleQueries(selectedDatabase);
366 exampleAccession.setText(MessageManager
367 .formatMessage("label.example_query_param", new String[]
373 * Action on clicking the 'Example' button is to write the example accession
374 * as the query text field value
376 protected void example_actionPerformed()
378 String eq = getExampleQueries((String) database.getSelectedItem());
379 textArea.setText(eq);
384 * Clears the query input field
386 protected void clear_actionPerformed()
388 textArea.setText("");
393 * Action on Close button is to close this frame, and also (if it is embedded
394 * in a search panel) to close the search panel
398 protected void close_actionPerformed(ActionEvent e)
402 frame.setClosed(true);
403 if (parentSearchPanel != null)
405 parentSearchPanel.btn_cancel_ActionPerformed();
407 } catch (Exception ex)
413 * Action on OK is to start the fetch for entered accession(s)
415 public void ok_actionPerformed()
418 * tidy inputs and check there is something to search for
420 String t0 = textArea.getText();
421 String text = t0.trim();
422 if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
424 text = text.replace(",", ";");
426 text = text.replaceAll("(\\s|[; ])+", ";");
427 if (!t0.equals(text))
429 textArea.setText(text);
435 "Please enter a (semi-colon separated list of) database id(s)");
439 if (database.getSelectedIndex() == 0)
442 showErrorMessage("Please choose a database");
447 exampleBtn.setEnabled(false);
448 textArea.setEnabled(false);
449 okBtn.setEnabled(false);
450 closeBtn.setEnabled(false);
451 backBtn.setEnabled(false);
453 Thread worker = new Thread(this);
457 private void resetDialog()
459 exampleBtn.setEnabled(true);
460 textArea.setEnabled(true);
461 okBtn.setEnabled(true);
462 closeBtn.setEnabled(true);
463 backBtn.setEnabled(parentSearchPanel != null);
469 boolean addToLast = false;
470 List<String> aresultq = new ArrayList<>();
471 List<String> presultTitle = new ArrayList<>();
472 List<AlignmentI> presult = new ArrayList<>();
473 List<AlignmentI> aresult = new ArrayList<>();
474 List<DbSourceProxy> sources = sfetch
475 .getSourceProxy((String) database.getSelectedItem());
476 Iterator<DbSourceProxy> proxies = sources.iterator();
477 String[] qries = textArea.getText().trim().split(";");
478 List<String> nextFetch = Arrays.asList(qries);
479 Iterator<String> en = Arrays.asList(new String[0]).iterator();
480 int nqueries = qries.length;
482 FeatureSettingsModelI preferredFeatureColours = null;
483 while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
485 if (!en.hasNext() && nextFetch.size() > 0)
487 en = nextFetch.iterator();
488 nqueries = nextFetch.size();
489 // save the remaining queries in the original array
490 qries = nextFetch.toArray(new String[nqueries]);
491 nextFetch = new ArrayList<>();
494 DbSourceProxy proxy = proxies.next();
498 guiWindow.setProgressBar(MessageManager.formatMessage(
499 "status.fetching_sequence_queries_from", new String[]
500 { Integer.valueOf(nqueries).toString(),
501 proxy.getDbName() }),
502 Thread.currentThread().hashCode());
503 if (proxy.getMaximumQueryCount() == 1)
506 * proxy only handles one accession id at a time
510 String acc = en.next();
511 if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
520 * proxy can fetch multiple accessions at one time
522 fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
524 } catch (Exception e)
526 showErrorMessage("Error retrieving " + textArea.getText() + " from "
527 + database.getSelectedItem());
529 // +="Couldn't retrieve sequences from "+database.getSelectedItem();
530 System.err.println("Retrieval failed for source ='"
531 + database.getSelectedItem() + "' and query\n'"
532 + textArea.getText() + "'\n");
534 } catch (OutOfMemoryError e)
536 showErrorMessage("Out of Memory when retrieving "
537 + textArea.getText() + " from " + database.getSelectedItem()
538 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
542 showErrorMessage("Serious Error retrieving " + textArea.getText()
543 + " from " + database.getSelectedItem());
547 // Stack results ready for opening in alignment windows
548 if (aresult != null && aresult.size() > 0)
550 FeatureSettingsModelI proxyColourScheme = proxy
551 .getFeatureColourScheme();
552 if (proxyColourScheme != null)
554 preferredFeatureColours = proxyColourScheme;
557 AlignmentI ar = null;
558 if (proxy.isAlignmentSource())
561 // new window for each result
562 while (aresult.size() > 0)
564 presult.add(aresult.remove(0));
566 aresultq.remove(0) + " " + getDefaultRetrievalTitle());
572 if (addToLast && presult.size() > 0)
574 ar = presult.remove(presult.size() - 1);
575 titl = presultTitle.remove(presultTitle.size() - 1);
577 // concatenate all results in one window
578 while (aresult.size() > 0)
582 ar = aresult.remove(0);
586 ar.append(aresult.remove(0));
591 presultTitle.add(titl);
594 guiWindow.setProgressBar(
595 MessageManager.getString("status.finshed_querying"),
596 Thread.currentThread().hashCode());
602 .getString("status.parsing_results")
603 : MessageManager.getString("status.processing"),
604 Thread.currentThread().hashCode());
606 while (presult.size() > 0)
608 parseResult(presult.remove(0), presultTitle.remove(0), null,
609 preferredFeatureColours);
611 // only remove visual delay after we finished parsing.
612 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
613 if (nextFetch.size() > 0)
615 StringBuffer sb = new StringBuffer();
616 sb.append("Didn't retrieve the following "
617 + (nextFetch.size() == 1 ? "query"
618 : nextFetch.size() + " queries")
620 int l = sb.length(), lr = 0;
621 for (String s : nextFetch)
623 if (l != sb.length())
627 if (lr - sb.length() > 40)
633 showErrorMessage(sb.toString());
639 * Tries to fetch one or more accession ids from the database proxy
643 * the queries to fetch
645 * a successful queries list to add to
647 * a list of retrieved alignments to add to
649 * failed queries are added to this list
652 void fetchMultipleAccessions(DbSourceProxy proxy,
653 Iterator<String> accessions, List<String> aresultq,
654 List<AlignmentI> aresult, List<String> nextFetch) throws Exception
656 StringBuilder multiacc = new StringBuilder();
657 List<String> tosend = new ArrayList<>();
658 while (accessions.hasNext())
660 String nel = accessions.next();
662 multiacc.append(nel);
663 if (accessions.hasNext())
665 multiacc.append(proxy.getAccessionSeparator());
671 String query = multiacc.toString();
672 AlignmentI rslt = proxy.getSequenceRecords(query);
673 if (rslt == null || rslt.getHeight() == 0)
675 // no results - pass on all queries to next source
676 nextFetch.addAll(tosend);
682 if (tosend.size() > 1)
684 checkResultForQueries(rslt, tosend, nextFetch, proxy);
687 } catch (OutOfMemoryError oome)
689 new OOMWarning("fetching " + multiacc + " from "
690 + database.getSelectedItem(), oome, this);
695 * Query for a single accession id via the database proxy
700 * a list of successful queries to add to
702 * a list of retrieved alignments to add to
703 * @return true if the fetch was successful, else false
705 boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
706 List<String> aresultq, List<AlignmentI> aresult)
708 boolean success = false;
715 // give the server a chance to breathe
717 } catch (Exception e)
723 AlignmentI indres = null;
726 indres = proxy.getSequenceRecords(accession);
727 } catch (OutOfMemoryError oome)
730 "fetching " + accession + " from " + proxy.getDbName(),
735 aresultq.add(accession);
739 } catch (Exception e)
741 Cache.log.info("Error retrieving " + accession + " from "
742 + proxy.getDbName(), e);
748 * Checks which of the queries were successfully retrieved by searching the
749 * DBRefs of the retrieved sequences for a match. Any not found are added to
750 * the 'nextFetch' list.
757 void checkResultForQueries(AlignmentI rslt, List<String> queries,
758 List<String> nextFetch, DbSourceProxy proxy)
760 SequenceI[] rs = rslt.getSequencesArray();
762 for (String q : queries)
764 // BH 2019.01.25 dbr is never used.
765 // DBRefEntry dbr = new DBRefEntry();
766 // dbr.setSource(proxy.getDbSource());
767 // dbr.setVersion(null);
768 String accId = proxy.getAccessionIdFromQuery(q);
769 // dbr.setAccessionId(accId);
770 boolean rfound = false;
771 for (int r = 0, nr = rs.length; r < nr; r++)
775 List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
777 if (!found.isEmpty())
793 * @return a standard title for any results retrieved using the currently
794 * selected source and settings
796 public String getDefaultRetrievalTitle()
798 return "Retrieved from " + database.getSelectedItem();
801 AlignmentI parseResult(AlignmentI al, String title,
802 FileFormatI currentFileFormat,
803 FeatureSettingsModelI preferredFeatureColours)
806 if (al != null && al.getHeight() > 0)
810 title = getDefaultRetrievalTitle();
812 if (alignFrame == null)
814 AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
815 AlignFrame.DEFAULT_HEIGHT);
816 if (currentFileFormat != null)
818 af.currentFileFormat = currentFileFormat;
821 List<SequenceI> alsqs = al.getSequences();
824 for (SequenceI sq : alsqs)
826 if (sq.getFeatures().hasFeatures())
828 af.setShowSeqFeatures(true);
834 if (preferredFeatureColours != null)
836 af.getViewport().applyFeaturesStyle(preferredFeatureColours);
838 if (Cache.getDefault("HIDE_INTRONS", true))
840 af.hideFeatureColumns(SequenceOntologyI.EXON, false);
842 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
843 AlignFrame.DEFAULT_HEIGHT);
845 af.setStatus(MessageManager
846 .getString("label.successfully_pasted_alignment_file"));
850 af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
851 } catch (Exception ex)
857 alignFrame.viewport.addAlignment(al, title);
863 void showErrorMessage(final String error)
866 javax.swing.SwingUtilities.invokeLater(new Runnable()
871 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), error,
872 MessageManager.getString("label.error_retrieving_data"),
873 JvOptionPane.WARNING_MESSAGE);
878 public IProgressIndicator getProgressIndicator()
880 return progressIndicator;
883 public void setProgressIndicator(IProgressIndicator progressIndicator)
885 this.progressIndicator = progressIndicator;
889 * Hide this panel (on clicking the database button to open the database
894 frame.setVisible(false);
897 public void setQuery(String ids)
899 textArea.setText(ids);
903 * Called to modify the search panel for embedding as an alternative tab of a
904 * free text search panel. The database choice list is hidden (since the
905 * choice has been made), and a Back button is made visible (which reopens the
906 * Sequence Fetcher panel).
910 public void embedIn(GFTSPanel parentPanel)
912 database.setVisible(false);
913 backBtn.setVisible(true);
914 parentSearchPanel = parentPanel;