2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 import java.awt.event.*;
30 import jalview.datamodel.*;
31 import jalview.datamodel.xdb.embl.*;
34 import jalview.ws.DBRefFetcher;
35 import jalview.ws.ebi.EBIFetchClient;
36 import jalview.ws.seqfetcher.ASequenceFetcher;
37 import jalview.ws.seqfetcher.DbSourceProxy;
39 import java.awt.Rectangle;
40 import java.awt.BorderLayout;
41 import java.awt.Dimension;
43 public class SequenceFetcher extends JPanel implements Runnable
45 // ASequenceFetcher sfetch;
48 IProgressIndicator guiWindow;
50 AlignFrame alignFrame;
54 final String noDbSelected = "-- Select Database --";
56 Hashtable sources = new Hashtable();
58 private static jalview.ws.SequenceFetcher sfetch = null;
60 private static String dasRegistry = null;
62 public SequenceFetcher(IProgressIndicator guiIndic)
64 final IProgressIndicator guiWindow = guiIndic;
65 final SequenceFetcher us = this;
66 // launch initialiser thread
67 Thread sf = new Thread(new Runnable()
73 || dasRegistry != DasSourceBrowser.getDasRegistryURL())
76 * give a visual indication that sequence fetcher construction is
79 if (guiWindow != null)
81 guiWindow.setProgressBar(
82 "Initialising Sequence Database Fetchers", this
85 dasRegistry = DasSourceBrowser.getDasRegistryURL();
86 jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
87 if (guiWindow != null)
89 guiWindow.setProgressBar(
90 "Initialising Sequence Database Fetchers", this
96 us.initGui(guiWindow);
103 * called by thread spawned by constructor
107 private void initGui(IProgressIndicator guiWindow)
109 this.guiWindow = guiWindow;
110 if (guiWindow instanceof AlignFrame)
112 alignFrame = (AlignFrame) guiWindow;
115 database.addItem(noDbSelected);
117 * Dynamically generated database list will need a translation function from
118 * internal source to externally distinct names. UNIPROT and UP_NAME are
119 * identical DB sources, and should be collapsed.
122 String dbs[] = sfetch.getOrderedSupportedSources();
123 for (int i = 0; i < dbs.length; i++)
125 if (!sources.containsValue(dbs[i]))
127 String name = sfetch.getSourceProxy(dbs[i]).getDbName();
128 // duplicate source names are thrown away, here.
129 if (!sources.containsKey(name))
131 database.addItem(name);
133 // overwrite with latest version of the retriever for this source
134 sources.put(name, dbs[i]);
140 } catch (Exception ex)
142 ex.printStackTrace();
145 frame = new JInternalFrame();
146 frame.setContentPane(this);
147 if (new jalview.util.Platform().isAMac())
149 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
153 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
157 private String getFrameTitle()
159 return ((alignFrame == null) ? "New " : "Additional ")
160 + "Sequence Fetcher";
163 private void jbInit() throws Exception
165 this.setLayout(borderLayout2);
167 database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
168 dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
169 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
170 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
172 .setText("Separate multiple accession ids with semi colon \";\"");
174 ok.addActionListener(new ActionListener()
176 public void actionPerformed(ActionEvent e)
178 ok_actionPerformed();
181 clear.setText("Clear");
182 clear.addActionListener(new ActionListener()
184 public void actionPerformed(ActionEvent e)
186 clear_actionPerformed();
190 example.setText("Example");
191 example.addActionListener(new ActionListener()
193 public void actionPerformed(ActionEvent e)
195 example_actionPerformed();
198 close.setText("Close");
199 close.addActionListener(new ActionListener()
201 public void actionPerformed(ActionEvent e)
203 close_actionPerformed(e);
206 textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
207 textArea.setLineWrap(true);
208 textArea.addKeyListener(new KeyAdapter()
210 public void keyPressed(KeyEvent e)
212 if (e.getKeyCode() == KeyEvent.VK_ENTER)
213 ok_actionPerformed();
216 jPanel3.setLayout(borderLayout1);
217 borderLayout1.setVgap(5);
219 jPanel1.add(example);
222 jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
223 jPanel2.setLayout(borderLayout3);
225 database.addActionListener(new ActionListener()
228 public void actionPerformed(ActionEvent e)
230 DbSourceProxy db = null;
233 db = sfetch.getSourceProxy((String) sources.get(database
234 .getSelectedItem()));
235 dbeg.setText("Example query: " + db.getTestQuery());
236 } catch (Exception ex)
244 jPanel2.add(database, java.awt.BorderLayout.NORTH);
245 jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
246 jPanel2.add(jLabel1, java.awt.BorderLayout.SOUTH);
247 // jPanel2.setPreferredSize(new Dimension())
248 jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
249 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
250 this.add(jPanel3, java.awt.BorderLayout.CENTER);
251 this.add(jPanel2, java.awt.BorderLayout.NORTH);
252 jScrollPane1.getViewport().add(textArea);
256 protected void example_actionPerformed()
258 DbSourceProxy db = null;
261 db = sfetch.getSourceProxy((String) sources.get(database
262 .getSelectedItem()));
263 textArea.setText(db.getTestQuery());
264 } catch (Exception ex)
270 protected void clear_actionPerformed()
272 textArea.setText("");
276 JLabel dbeg = new JLabel();
278 JComboBox database = new JComboBox();
280 JLabel jLabel1 = new JLabel();
282 JButton ok = new JButton();
284 JButton clear = new JButton();
286 JButton example = new JButton();
288 JButton close = new JButton();
290 JPanel jPanel1 = new JPanel();
292 JTextArea textArea = new JTextArea();
294 JScrollPane jScrollPane1 = new JScrollPane();
296 JPanel jPanel2 = new JPanel();
298 JPanel jPanel3 = new JPanel();
300 JPanel jPanel4 = new JPanel();
302 BorderLayout borderLayout1 = new BorderLayout();
304 BorderLayout borderLayout2 = new BorderLayout();
306 BorderLayout borderLayout3 = new BorderLayout();
308 public void close_actionPerformed(ActionEvent e)
312 frame.setClosed(true);
313 } catch (Exception ex)
318 public void ok_actionPerformed()
320 database.setEnabled(false);
321 textArea.setEnabled(false);
322 ok.setEnabled(false);
323 close.setEnabled(false);
325 Thread worker = new Thread(this);
329 private void resetDialog()
331 database.setEnabled(true);
332 textArea.setEnabled(true);
334 close.setEnabled(true);
340 if (database.getSelectedItem().equals(noDbSelected))
342 error += "Please select the source database\n";
344 com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
345 textArea.setText(empty.replaceAll(textArea.getText()));
346 if (textArea.getText().length() == 0)
348 error += "Please enter a (semi-colon separated list of) database id(s)";
350 if (error.length() > 0)
352 showErrorMessage(error);
356 AlignmentI aresult = null;
359 guiWindow.setProgressBar("Fetching Sequences from "
360 + database.getSelectedItem(), Thread.currentThread()
362 aresult = sfetch.getSourceProxy(
363 (String) sources.get(database.getSelectedItem()))
364 .getSequenceRecords(textArea.getText());
366 } catch (Exception e)
368 showErrorMessage("Error retrieving " + textArea.getText() + " from "
369 + database.getSelectedItem());
370 // error +="Couldn't retrieve sequences from "+database.getSelectedItem();
371 System.err.println("Retrieval failed for source ='"
372 + database.getSelectedItem() + "' and query\n'"
373 + textArea.getText() + "'\n");
375 } catch (OutOfMemoryError e)
377 showErrorMessage("Out of Memory when retrieving "
380 + database.getSelectedItem()
381 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
385 showErrorMessage("Serious Error retrieving " + textArea.getText()
386 + " from " + database.getSelectedItem());
389 guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
392 parseResult(aresult, null, null);
398 * result = new StringBuffer(); if
399 * (database.getSelectedItem().equals("Uniprot")) {
400 * getUniprotFile(textArea.getText()); } else if
401 * (database.getSelectedItem().equals("EMBL") ||
402 * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource =
403 * database.getSelectedItem().equals("EMBLCDS") ?
404 * jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
406 * StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
407 * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch =
408 * new EBIFetchClient(); String qry =
409 * database.getSelectedItem().toString().toLowerCase( ) + ":" +
410 * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
412 * jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
413 * reply.exists()) { efile =
414 * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null) {
415 * for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
416 * entry = (EmblEntry) i.next(); SequenceI[] seqparts =
417 * entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
418 * SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
419 * SequenceI[seqparts.length]; } else { newseqs = new
420 * SequenceI[seqs.length+seqparts.length];
422 * for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
423 * for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
424 * seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
426 * } } } else { result.append("# no response for "+qry); } } if (seqs!=null &&
427 * seqs.length>0) { if (parseResult(new Alignment(seqs), null, null)!=null) {
428 * result.append("# Successfully parsed the "+database.getSelectedItem()+"
429 * Queries into an Alignment"); } } } else if
430 * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
431 * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
432 * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
433 * SequenceI[] seqparts = getPDBFile(query.toUpperCase()); if (seqparts !=
434 * null) { if (seqs == null) { seqs = seqparts; } else { SequenceI[] newseqs =
435 * new SequenceI[seqs.length+seqparts.length]; int i=0; for (; i <
436 * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int j=0;j<seqparts.length;
437 * i++, j++) { newseqs[i] = seqparts[j]; } seqs=newseqs; } result.append("#
438 * Success for "+query.toUpperCase()+"\n"); } } if (seqs != null &&
439 * seqs.length > 0) { if (parseResult(new Alignment(seqs), null, null)!=null) {
440 * result.append( "# Successfully parsed the PDB File Queries into an
441 * Alignment"); } } } else if( database.getSelectedItem().equals("PFAM")) {
442 * try { result.append(new FastaFile(
443 * "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
444 * textArea.getText().toUpperCase(), "URL").print() );
446 * if(result.length()>0) { parseResult( result.toString(),
447 * textArea.getText().toUpperCase() ); }
448 * } catch (java.io.IOException ex) { result = null; } }
450 * if (result == null || result.length() == 0) { showErrorMessage("Error
451 * retrieving " + textArea.getText() + " from " + database.getSelectedItem()); }
453 * resetDialog(); return; }
455 * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient();
456 * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
458 * DBRefFetcher dbref = new DBRefFetcher(); Vector entries =
459 * dbref.getUniprotEntries(file);
461 * if (entries != null) { //First, make the new sequences Enumeration en =
462 * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry =
463 * (UniprotEntry) en.nextElement();
465 * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration
466 * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) {
467 * name.append("|"); name.append(en2.nextElement()); } en2 =
468 * entry.getName().elements(); while (en2.hasMoreElements()) {
469 * name.append("|"); name.append(en2.nextElement()); }
471 * if (entry.getProtein() != null) { name.append(" " +
472 * entry.getProtein().getName().elementAt(0)); }
474 * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
478 * //Then read in the features and apply them to the dataset Alignment al =
479 * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
480 * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
481 * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries =
482 * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry)
483 * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; }
485 * onlyPdbEntries.addElement(pdb); }
487 * Enumeration en2 = entry.getAccession().elements(); while
488 * (en2.hasMoreElements()) {
489 * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
490 * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); }
495 * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if
496 * (entry.getFeature() != null) { e = entry.getFeature().elements(); while
497 * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
498 * e.nextElement(); sf.setFeatureGroup("Uniprot");
499 * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } } }
501 * SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
502 * chain = null; if (id.indexOf(":") > -1) { chain =
503 * id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
505 * EBIFetchClient ebi = new EBIFetchClient(); String file =
506 * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file ==
507 * null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
508 * jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
509 * pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
510 * pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) { PDBChain
511 * pdbchain = (PDBChain) pdbfile.chains.elementAt(i); // Get the Chain's
512 * Sequence - who's dataset includes any special features added from the PDB
513 * file SequenceI sq = pdbchain.sequence; // Specially formatted name for the
514 * PDB chain sequences retrieved from the PDB
515 * sq.setName("PDB|"+id+"|"+sq.getName()); // Might need to add more metadata
516 * to the PDBEntry object // like below /* PDBEntry entry = new PDBEntry(); //
517 * Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
518 * entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
519 * pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
520 * sq.getDatasetSequence().addPDBId(entry);
521 * // Add PDB DB Refs // We make a DBRefEtntry because we have obtained the
522 * PDB file from a verifiable source // JBPNote - PDB DBRefEntry should also
523 * carry the chain and mapping information DBRefEntry dbentry = new
524 * DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
525 * sq.addDBRef(dbentry); // and add seuqence to the retrieved set
526 * result.addElement(sq.deriveSequence()); } }
528 * if (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
529 * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file {
530 * jalview.bin.Cache.log.warn("Exception when retrieving " +
531 * textArea.getText() + " from " + database.getSelectedItem(), ex); return
535 * SequenceI[] results = new SequenceI[result.size()]; for (int i = 0, j =
536 * result.size(); i < j; i++) { results[i] = (SequenceI) result.elementAt(i);
537 * result.setElementAt(null,i); } return results; }
539 AlignmentI parseResult(String result, String title)
541 String format = new IdentifyFile().Identify(result, "Paste");
542 Alignment sequences = null;
543 if (FormatAdapter.isValidFormat(format))
548 sequences = new FormatAdapter().readFile(result.toString(),
550 } catch (Exception ex)
554 if (sequences != null)
556 return parseResult(sequences, title, format);
561 showErrorMessage("Error retrieving " + textArea.getText() + " from "
562 + database.getSelectedItem());
568 AlignmentI parseResult(AlignmentI al, String title,
569 String currentFileFormat)
572 if (al != null && al.getHeight() > 0)
574 if (alignFrame == null)
576 AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
577 AlignFrame.DEFAULT_HEIGHT);
578 if (currentFileFormat != null)
580 af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
582 // NON-FormatAdapter Sourced
588 title = "Retrieved from " + database.getSelectedItem();
591 Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
592 AlignFrame.DEFAULT_HEIGHT);
594 af.statusBar.setText("Successfully pasted alignment file");
598 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
600 } catch (Exception ex)
606 for (int i = 0; i < al.getHeight(); i++)
608 alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
615 alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
617 alignFrame.viewport.alignment.getWidth();
618 alignFrame.viewport.firePropertyChange("alignment", null,
619 alignFrame.viewport.getAlignment().getSequences());
625 void showErrorMessage(final String error)
628 javax.swing.SwingUtilities.invokeLater(new Runnable()
632 JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
633 "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);