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.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;
35 import java.awt.BorderLayout;
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;
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;
57 import com.stevesoft.pat.Regex;
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 * Blocking method that initialises and returns the shared instance of the
120 * SequenceFetcher client
123 * - where the initialisation delay message should be shown
124 * @return the singleton instance of the sequence fetcher client
126 public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
127 final IProgressIndicator guiWindow)
129 if (_initingFetcher && initingThread != null && initingThread.isAlive())
131 if (guiWindow != null)
133 guiWindow.setProgressBar(
134 MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
135 Thread.currentThread().hashCode());
137 // initting happening on another thread - so wait around to see if it
139 while (_initingFetcher && initingThread != null
140 && initingThread.isAlive())
145 } catch (Exception e)
150 if (guiWindow != null)
152 guiWindow.setProgressBar(
153 MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
154 Thread.currentThread().hashCode());
158 || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
159 || lastDasSourceRegistry != (jalview.bin.Cache
160 .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
161 .getDasSourceRegistry().getLocalSourceString())
164 _initingFetcher = true;
165 initingThread = Thread.currentThread();
167 * give a visual indication that sequence fetcher construction is occuring
169 if (guiWindow != null)
171 guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
172 Thread.currentThread().hashCode());
174 dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
175 dasRegistry.refreshSources();
177 jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
178 if (guiWindow != null)
180 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
182 lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
183 .getLocalSourceString()).hashCode();
185 _initingFetcher = false;
186 initingThread = null;
191 private IProgressIndicator progressIndicator;
192 public SequenceFetcher(IProgressIndicator guiIndic)
194 this.progressIndicator = guiIndic;
195 final SequenceFetcher us = this;
196 // launch initialiser thread
197 Thread sf = new Thread(new Runnable()
203 if (getSequenceFetcherSingleton(progressIndicator) != null)
205 us.initGui(progressIndicator);
209 javax.swing.SwingUtilities.invokeLater(new Runnable()
215 .showInternalMessageDialog(
217 MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
218 MessageManager.getString("label.couldnt_create_sequence_fetcher"),
219 JOptionPane.ERROR_MESSAGE);
223 // raise warning dialog
230 private class DatabaseAuthority extends DefaultMutableTreeNode
235 private class DatabaseSource extends DefaultMutableTreeNode
241 * called by thread spawned by constructor
245 private void initGui(IProgressIndicator guiWindow)
247 this.guiWindow = guiWindow;
248 if (guiWindow instanceof AlignFrame)
250 alignFrame = (AlignFrame) guiWindow;
252 database = new JDatabaseTree(sfetch);
256 } catch (Exception ex)
258 ex.printStackTrace();
261 frame = new JInternalFrame();
262 frame.setContentPane(this);
263 if (new jalview.util.Platform().isAMac())
265 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
269 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
273 private String getFrameTitle()
275 return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
278 private void jbInit() throws Exception
280 this.setLayout(borderLayout2);
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"));
289 replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
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()
298 public void actionPerformed(ActionEvent e)
300 ok_actionPerformed();
303 clear.setText(MessageManager.getString("action.clear"));
304 clear.addActionListener(new ActionListener()
307 public void actionPerformed(ActionEvent e)
309 clear_actionPerformed();
313 example.setText(MessageManager.getString("label.example"));
314 example.addActionListener(new ActionListener()
317 public void actionPerformed(ActionEvent e)
319 example_actionPerformed();
322 close.setText(MessageManager.getString("action.close"));
323 close.addActionListener(new ActionListener()
326 public void actionPerformed(ActionEvent e)
328 close_actionPerformed(e);
331 textArea.setFont(JvSwingUtils.getLabelFont());
332 textArea.setLineWrap(true);
333 textArea.addKeyListener(new KeyAdapter()
336 public void keyPressed(KeyEvent e)
338 if (e.getKeyCode() == KeyEvent.VK_ENTER)
340 ok_actionPerformed();
344 jPanel3.setLayout(borderLayout1);
345 borderLayout1.setVgap(5);
347 jPanel1.add(example);
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()
357 public void actionPerformed(ActionEvent e)
360 String currentSelection = database.getSelectedItem();
362 if (!currentSelection.equalsIgnoreCase("pdb"))
366 if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
374 jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
375 jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
376 JPanel jPanel2a = new JPanel(new BorderLayout());
377 jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
378 jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
379 jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
380 // jPanel2.setPreferredSize(new Dimension())
381 jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
382 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
383 this.add(jPanel3, java.awt.BorderLayout.CENTER);
384 this.add(jPanel2, java.awt.BorderLayout.NORTH);
385 jScrollPane1.getViewport().add(textArea);
389 private void pdbSourceAction()
391 databaseButt.setText(database.getSelectedItem());
392 new PDBSearchPanel(this);
396 private void otherSourceAction()
400 databaseButt.setText(database.getSelectedItem()
401 + (database.getSelectedSources().size() > 1 ? " (and "
402 + database.getSelectedSources().size() + " others)"
404 String eq = database.getExampleQueries();
405 dbeg.setText(MessageManager.formatMessage(
406 "label.example_query_param", new String[]
408 boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
409 for (DbSourceProxy dbs : database.getSelectedSources())
411 if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
417 replacePunctuation.setEnabled(enablePunct);
419 } catch (Exception ex)
422 replacePunctuation.setEnabled(true);
427 protected void example_actionPerformed()
429 DbSourceProxy db = null;
432 textArea.setText(database.getExampleQueries());
433 } catch (Exception ex)
439 protected void clear_actionPerformed()
441 textArea.setText("");
447 public void close_actionPerformed(ActionEvent e)
451 frame.setClosed(true);
452 } catch (Exception ex)
457 public void ok_actionPerformed()
459 databaseButt.setEnabled(false);
460 example.setEnabled(false);
461 textArea.setEnabled(false);
462 ok.setEnabled(false);
463 close.setEnabled(false);
465 Thread worker = new Thread(this);
469 private void resetDialog()
471 databaseButt.setEnabled(true);
472 example.setEnabled(true);
473 textArea.setEnabled(true);
475 close.setEnabled(true);
482 if (!database.hasSelection())
484 error += "Please select the source database\n";
486 // TODO: make this transformation more configurable
487 com.stevesoft.pat.Regex empty;
488 if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
490 empty = new com.stevesoft.pat.Regex(
491 // replace commas and spaces with a semicolon
492 "(\\s|[,; ])+", ";");
496 // just turn spaces and semicolons into single semicolons
497 empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
499 textArea.setText(empty.replaceAll(textArea.getText()));
500 // see if there's anthing to search with
501 if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
504 error += "Please enter a (semi-colon separated list of) database id(s)";
506 if (error.length() > 0)
508 showErrorMessage(error);
512 // indicate if successive sources should be merged into one alignment.
513 boolean addToLast = false;
514 ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
515 ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
516 Iterator<DbSourceProxy> proxies = database.getSelectedSources()
519 List<String> nextfetch = Arrays.asList(qries = textArea.getText()
521 Iterator<String> en = Arrays.asList(new String[0]).iterator();
522 int nqueries = qries.length;
523 while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
525 if (!en.hasNext() && nextfetch.size() > 0)
527 en = nextfetch.iterator();
528 nqueries = nextfetch.size();
529 // save the remaining queries in the original array
530 qries = nextfetch.toArray(new String[nqueries]);
531 nextfetch = new ArrayList<String>();
534 DbSourceProxy proxy = proxies.next();
535 boolean isAliSource = false;
539 guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
540 .currentThread().hashCode());
541 isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
542 if (proxy.getAccessionSeparator() == null)
546 String item = en.next();
553 // give the server a chance to breathe
555 } catch (Exception e)
562 AlignmentI indres = null;
565 indres = proxy.getSequenceRecords(item);
566 } catch (OutOfMemoryError oome)
568 new OOMWarning("fetching " + item + " from "
569 + proxy.getDbName(), oome, this);
580 } catch (Exception e)
582 jalview.bin.Cache.log.info("Error retrieving " + item
583 + " from " + proxy.getDbName(), e);
590 StringBuffer multiacc = new StringBuffer();
591 ArrayList<String> tosend = new ArrayList<String>();
594 String nel = en.next();
596 multiacc.append(nel);
599 multiacc.append(proxy.getAccessionSeparator());
606 List<String> nores = new ArrayList<String>();
607 rslt = proxy.getSequenceRecords(multiacc.toString());
608 if (rslt == null || rslt.getHeight() == 0)
610 // no results - pass on all queries to next source
611 nextfetch.addAll(tosend);
615 aresultq.add(multiacc.toString());
618 rs = rslt.getSequencesArray();
619 // search for each query in the dbrefs associated with each
622 // ones we do not find will be used to query next source (if any)
623 for (String q : tosend)
625 DBRefEntry dbr = new DBRefEntry(), found[] = null;
626 dbr.setSource(proxy.getDbSource());
627 dbr.setVersion(null);
628 if (proxy.getAccessionValidator() != null)
630 Regex vgr = proxy.getAccessionValidator();
632 if (vgr.numSubs() > 0)
634 dbr.setAccessionId(vgr.stringMatched(1));
638 dbr.setAccessionId(vgr.stringMatched());
643 dbr.setAccessionId(q);
645 boolean rfound = false;
646 for (int r = 0; r < rs.length; r++)
649 && (found = DBRefUtils.searchRefs(
650 rs[r].getDBRef(), dbr)) != null
664 } catch (OutOfMemoryError oome)
666 new OOMWarning("fetching " + multiacc + " from "
667 + database.getSelectedItem(), oome, this);
671 } catch (Exception e)
673 showErrorMessage("Error retrieving " + textArea.getText()
674 + " from " + database.getSelectedItem());
676 // +="Couldn't retrieve sequences from "+database.getSelectedItem();
677 System.err.println("Retrieval failed for source ='"
678 + database.getSelectedItem() + "' and query\n'"
679 + textArea.getText() + "'\n");
681 } catch (OutOfMemoryError e)
683 // resets dialog box - so we don't use OOMwarning here.
684 showErrorMessage("Out of Memory when retrieving "
687 + database.getSelectedItem()
688 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
692 showErrorMessage("Serious Error retrieving " + textArea.getText()
693 + " from " + database.getSelectedItem());
696 // Stack results ready for opening in alignment windows
697 if (aresult != null && aresult.size() > 0)
699 AlignmentI ar = null;
703 // new window for each result
704 while (aresult.size() > 0)
706 presult.add(aresult.remove(0));
707 presultTitle.add(aresultq.remove(0) + " "
708 + getDefaultRetrievalTitle());
714 if (addToLast && presult.size() > 0)
716 ar = presult.remove(presult.size() - 1);
717 titl = presultTitle.remove(presultTitle.size() - 1);
719 // concatenate all results in one window
720 while (aresult.size() > 0)
724 ar = aresult.remove(0);
728 ar.append(aresult.remove(0));
734 presultTitle.add(titl);
737 guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
740 guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
741 : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
743 while (presult.size() > 0)
745 parseResult(presult.remove(0), presultTitle.remove(0), null);
747 // only remove visual delay after we finished parsing.
748 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
749 if (nextfetch.size() > 0)
751 StringBuffer sb = new StringBuffer();
752 sb.append("Didn't retrieve the following "
753 + (nextfetch.size() == 1 ? "query" : nextfetch.size()
754 + " queries") + ": \n");
755 int l = sb.length(), lr = 0;
756 for (String s : nextfetch)
758 if (l != sb.length())
762 if (lr - sb.length() > 40)
768 showErrorMessage(sb.toString());
773 AlignmentI parseResult(String result, String title)
775 String format = new IdentifyFile().Identify(result, "Paste");
776 AlignmentI sequences = null;
777 if (FormatAdapter.isValidFormat(format))
782 sequences = new FormatAdapter().readFile(result.toString(),
784 } catch (Exception ex)
788 if (sequences != null)
790 return parseResult(sequences, title, format);
795 showErrorMessage("Error retrieving " + textArea.getText() + " from "
796 + database.getSelectedItem());
804 * @return a standard title for any results retrieved using the currently
805 * selected source and settings
807 public String getDefaultRetrievalTitle()
809 return "Retrieved from " + database.getSelectedItem();
812 AlignmentI parseResult(AlignmentI al, String title,
813 String currentFileFormat)
816 if (al != null && al.getHeight() > 0)
820 title = getDefaultRetrievalTitle();
822 if (alignFrame == null)
824 AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
825 AlignFrame.DEFAULT_HEIGHT);
826 if (currentFileFormat != null)
828 af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
830 // NON-FormatAdapter Sourced
834 SequenceFeature[] sfs = null;
835 List<SequenceI> alsqs;
836 synchronized (alsqs = al.getSequences())
838 for (SequenceI sq : alsqs)
840 if ((sfs = sq.getSequenceFeatures()) != null)
844 af.setShowSeqFeatures(true);
851 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
852 AlignFrame.DEFAULT_HEIGHT);
854 af.statusBar.setText(MessageManager
855 .getString("label.successfully_pasted_alignment_file"));
859 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
861 } catch (Exception ex)
867 alignFrame.viewport.addAlignment(al, title);
873 void showErrorMessage(final String error)
876 javax.swing.SwingUtilities.invokeLater(new Runnable()
881 JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
882 MessageManager.getString("label.error_retrieving_data"),
883 JOptionPane.WARNING_MESSAGE);
888 public IProgressIndicator getProgressIndicator()
890 return progressIndicator;
893 public void setProgressIndicator(IProgressIndicator progressIndicator)
895 this.progressIndicator = progressIndicator;