package jalview.gui; import javax.swing.*; import java.awt.*; import java.awt.event.*; import jalview.io.EBIFetchClient; import MCview.*; import jalview.datamodel.*; import jalview.analysis.AlignSeq; import java.io.File; import jalview.io.*; import java.util.*; public class SequenceFetcher extends JPanel implements Runnable { JInternalFrame frame; AlignFrame alignFrame; StringBuffer result; public SequenceFetcher(AlignFrame af) { alignFrame = af; database.addItem("-- Select Database --"); database.addItem("Uniprot"); database.addItem("EMBL"); database.addItem("EMBLCDS"); database.addItem("PDB"); try { jbInit(); } catch (Exception ex) { ex.printStackTrace(); } frame = new JInternalFrame(); frame.setContentPane(this); if(System.getProperty("os.name").startsWith("Mac")) Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 140); else Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 120); } private void jbInit() throws Exception { this.setLayout(gridBagLayout1); database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); jLabel1.setText( "Separate multiple accession ids with semi colon \";\""); ok.setText("OK"); ok.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); } }); cancel.setText("Cancel"); cancel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { cancel_actionPerformed(e); } }); textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); textfield.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); } }); jPanel1.add(ok); jPanel1.add(cancel); this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0 , GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(7, 4, 0, 6), 77, 6)); this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 6), 221, 1)); this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0 , GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(7, -2, 7, 12), 241, -2)); this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0 , GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(0, 4, 0, 0), 1, 0)); } JComboBox database = new JComboBox(); JLabel jLabel1 = new JLabel(); JButton ok = new JButton(); JButton cancel = new JButton(); JPanel jPanel1 = new JPanel(); JTextField textfield = new JTextField(); GridBagLayout gridBagLayout1 = new GridBagLayout(); public void cancel_actionPerformed(ActionEvent e) { try { frame.setClosed(true); } catch (Exception ex) {} } public void ok_actionPerformed(ActionEvent e) { frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence..."); database.setEnabled(false); textfield.setEnabled(false); ok.setEnabled(false); cancel.setEnabled(false); Thread worker = new Thread(this); worker.start(); } public void run() { result = new StringBuffer(); if (database.getSelectedItem().equals("Uniprot")) { getUniprotFile(textfield.getText()); } else if (database.getSelectedItem().equals("EMBL") || database.getSelectedItem().equals("EMBLCDS")) { EBIFetchClient dbFetch = new EBIFetchClient(); String[] reply = dbFetch.fetchData( database.getSelectedItem().toString().toLowerCase( ) + ":" + textfield.getText(), "fasta", "raw"); for (int i = 0; i < reply.length; i++) result.append(reply[i] + "\n"); parseResult(result.toString()); } else if (database.getSelectedItem().equals("PDB")) { result = getPDBFile(textfield.getText().toUpperCase()); parseResult(result.toString()); } if (result == null || result.length() == 0) showErrorMessage("Error retrieving " + textfield.getText() + " from " + database.getSelectedItem()); database.setEnabled(true); textfield.setEnabled(true); ok.setEnabled(true); cancel.setEnabled(true); frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)"); } void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient(); File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null); SequenceFeatureFetcher sff = new SequenceFeatureFetcher(); Vector entries = sff.getUniprotEntries(file); if(entries!=null) { //First, make the new sequences Enumeration en = entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry = (UniprotEntry) en.nextElement(); StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" ); Enumeration en2 = entry.getAccession().elements(); while(en2.hasMoreElements()) { name.append("|"); name.append(en2.nextElement()); } en2 = entry.getName().elements(); while(en2.hasMoreElements()) { name.append("|"); name.append(en2.nextElement()); } if(entry.getProteinName()!=null) name.append(" "+entry.getProteinName().elementAt(0)); result.append(name +"\n"+entry.getUniprotSequence().getContent()); } //Then read in the features and apply them to the dataset SequenceI [] sequence = parseResult(result.toString()); for(int i=0; i -1) { chain = id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); } EBIFetchClient ebi = new EBIFetchClient(); String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw"); try { PDBfile pdbfile = new PDBfile(reply); for (int i = 0; i < pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain) pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) result.append("\n>PDB|" + id + "|" + ( (PDBChain) pdbfile.chains.elementAt(i)).sequence. getName() + "\n" + ( (PDBChain) pdbfile.chains.elementAt(i)).sequence. getSequence()); } } catch (Exception ex) // Problem parsing PDB file { showErrorMessage("Error retrieving " + textfield.getText() + " from " + database.getSelectedItem()); return null; } return result; } SequenceI[] parseResult(String result) { String format = IdentifyFile.Identify(result, "Paste"); SequenceI[] sequences = null; if (FormatAdapter.formats.contains(format)) { sequences = new FormatAdapter().readFile(result.toString(), "Paste", format); if (sequences != null && sequences.length>0) { if(alignFrame==null) { AlignFrame af = new AlignFrame(new Alignment(sequences)); af.currentFileFormat = format; Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(), AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT); af.statusBar.setText("Successfully pasted alignment file"); try { af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (Exception ex) {} } else { for (int i = 0; i < sequences.length; i++) { alignFrame.viewport.alignment.addSequence(sequences[i]); //////////////////////////// //Datset needs extension; ///////////////////////////// Sequence ds = new Sequence(sequences[i].getName(), AlignSeq.extractGaps("-. ", sequences[i].getSequence()), sequences[i].getStart(), sequences[i].getEnd()); sequences[i].setDatasetSequence(ds); alignFrame.viewport.alignment.getDataset().addSequence(ds); } alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment. getHeight()); alignFrame.viewport.alignment.getWidth(); alignFrame.viewport.firePropertyChange("alignment", null, alignFrame.viewport.getAlignment().getSequences()); } if (database.getSelectedItem().equals("PDB")) { for (int i = 0; i < sequences.length; i++) { PDBEntry entry = new PDBEntry(); entry.setId(textfield.getText()); sequences[i].getDatasetSequence().addPDBId(entry); } } } else showErrorMessage( "Error retrieving "+textfield.getText() +" from "+database.getSelectedItem()); } return sequences; } void showErrorMessage(String error) { JOptionPane.showInternalMessageDialog(Desktop.desktop, error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE); } }