2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import javax.swing.*;
\r
23 import java.awt.event.*;
\r
24 import jalview.io.EBIFetchClient;
\r
26 import jalview.datamodel.*;
\r
27 import jalview.analysis.AlignSeq;
\r
28 import java.io.File;
\r
29 import jalview.io.*;
\r
33 public class SequenceFetcher
\r
34 extends JPanel implements Runnable
\r
36 JInternalFrame frame;
\r
37 AlignFrame alignFrame;
\r
38 StringBuffer result;
\r
39 final String noDbSelected = "-- Select Database --";
\r
40 public SequenceFetcher(AlignFrame af)
\r
43 database.addItem(noDbSelected);
\r
44 database.addItem("Uniprot");
\r
45 database.addItem("EMBL");
\r
46 database.addItem("EMBLCDS");
\r
47 database.addItem("PDB");
\r
53 catch (Exception ex)
\r
55 ex.printStackTrace();
\r
58 frame = new JInternalFrame();
\r
59 frame.setContentPane(this);
\r
60 if(System.getProperty("os.name").startsWith("Mac"))
\r
61 Desktop.addInternalFrame(frame, ((af==null) ?
\r
62 "New " : "Additional ")+"Sequence Fetcher (WSDBfetch@EBI)", 400, 140);
\r
64 Desktop.addInternalFrame(frame, ((af==null) ?
\r
65 "New " : "Additional ")+"Sequence Fetcher (WSDBfetch@EBI)", 400, 125);
\r
68 private void jbInit()
\r
71 this.setLayout(gridBagLayout1);
\r
73 database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
74 database.setMinimumSize(new Dimension(160, 21));
\r
75 database.setPreferredSize(new Dimension(160, 21));
\r
76 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
\r
78 "Separate multiple accession ids with semi colon \";\"");
\r
80 ok.addActionListener(new ActionListener()
\r
82 public void actionPerformed(ActionEvent e)
\r
84 ok_actionPerformed(e);
\r
87 cancel.setText("Cancel");
\r
88 cancel.addActionListener(new ActionListener()
\r
90 public void actionPerformed(ActionEvent e)
\r
92 cancel_actionPerformed(e);
\r
95 textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
96 textfield.addActionListener(new ActionListener()
\r
98 public void actionPerformed(ActionEvent e)
\r
100 ok_actionPerformed(e);
\r
104 jPanel1.add(cancel);
\r
105 this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
\r
106 , GridBagConstraints.WEST,
\r
107 GridBagConstraints.NONE,
\r
108 new Insets(7, 4, 0, 6), 77, 6));
\r
109 this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
\r
110 , GridBagConstraints.WEST,
\r
111 GridBagConstraints.BOTH,
\r
112 new Insets(7, -2, 7, 12), 241, -2));
\r
113 this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
\r
114 , GridBagConstraints.WEST,
\r
115 GridBagConstraints.NONE,
\r
116 new Insets(0, 4, 0, 0), 1, 0));
\r
117 this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
\r
118 , GridBagConstraints.CENTER,
\r
119 GridBagConstraints.HORIZONTAL,
\r
120 new Insets(0, 0, 0, 6), 200, 1));
\r
123 JComboBox database = new JComboBox();
\r
124 JLabel jLabel1 = new JLabel();
\r
125 JButton ok = new JButton();
\r
126 JButton cancel = new JButton();
\r
127 JPanel jPanel1 = new JPanel();
\r
128 JTextField textfield = new JTextField();
\r
129 GridBagLayout gridBagLayout1 = new GridBagLayout();
\r
130 public void cancel_actionPerformed(ActionEvent e)
\r
134 frame.setClosed(true);
\r
136 catch (Exception ex)
\r
140 public void ok_actionPerformed(ActionEvent e)
\r
142 frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");
\r
143 database.setEnabled(false);
\r
144 textfield.setEnabled(false);
\r
145 ok.setEnabled(false);
\r
146 cancel.setEnabled(false);
\r
148 Thread worker = new Thread(this);
\r
152 private void resetDialog() {
\r
153 database.setEnabled(true);
\r
154 textfield.setEnabled(true);
\r
155 ok.setEnabled(true);
\r
156 cancel.setEnabled(true);
\r
157 frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");
\r
163 if (database.getSelectedItem().equals(noDbSelected))
\r
164 error += "Please select the source database\n";
\r
165 com.stevesoft.pat.Regex empty=new com.stevesoft.pat.Regex("\\s+","");
\r
166 textfield.setText(empty.replaceAll(textfield.getText()));
\r
167 if (textfield.getText().length()==0)
\r
168 error+="Please enter a (semi-colon separated list of) database id(s)";
\r
169 if (error.length()>0) {
\r
170 showErrorMessage(error);
\r
175 result = new StringBuffer();
\r
176 if (database.getSelectedItem().equals("Uniprot"))
\r
178 getUniprotFile(textfield.getText());
\r
180 else if (database.getSelectedItem().equals("EMBL")
\r
181 || database.getSelectedItem().equals("EMBLCDS"))
\r
183 EBIFetchClient dbFetch = new EBIFetchClient();
\r
184 String[] reply = dbFetch.fetchData(
\r
185 database.getSelectedItem().toString().toLowerCase(
\r
186 ) + ":" + textfield.getText(),
\r
189 for (int i = 0; i < reply.length; i++)
\r
190 result.append(reply[i] + "\n");
\r
192 parseResult(result.toString());
\r
194 else if (database.getSelectedItem().equals("PDB"))
\r
196 result = getPDBFile(textfield.getText().toUpperCase());
\r
198 parseResult(result.toString());
\r
202 if (result == null || result.length() == 0)
\r
203 showErrorMessage("Error retrieving " + textfield.getText()
\r
204 + " from " + database.getSelectedItem());
\r
206 textfield.setText("");
\r
210 void getUniprotFile(String id)
\r
212 EBIFetchClient ebi = new EBIFetchClient();
\r
213 File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);
\r
214 SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
\r
215 Vector entries = sff.getUniprotEntries(file);
\r
219 //First, make the new sequences
\r
220 Enumeration en = entries.elements();
\r
221 while (en.hasMoreElements())
\r
223 UniprotEntry entry = (UniprotEntry) en.nextElement();
\r
224 StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );
\r
225 Enumeration en2 = entry.getAccession().elements();
\r
226 while(en2.hasMoreElements())
\r
229 name.append(en2.nextElement());
\r
231 en2 = entry.getName().elements();
\r
232 while(en2.hasMoreElements())
\r
235 name.append(en2.nextElement());
\r
238 if(entry.getProteinName()!=null)
\r
239 name.append(" "+entry.getProteinName().elementAt(0));
\r
241 result.append(name +"\n"+entry.getUniprotSequence().getContent());
\r
245 //Then read in the features and apply them to the dataset
\r
246 SequenceI [] sequence = parseResult(result.toString());
\r
247 for(int i=0; i<entries.size(); i++)
\r
249 UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
\r
250 Enumeration e = entry.getDbReference().elements();
\r
251 Vector onlyPdbEntries = new Vector();
\r
252 while (e.hasMoreElements())
\r
254 PDBEntry pdb = (PDBEntry) e.nextElement();
\r
255 if (!pdb.getType().equals("PDB"))
\r
258 onlyPdbEntries.addElement(pdb);
\r
261 sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
\r
262 sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());
\r
268 StringBuffer getPDBFile(String id)
\r
270 StringBuffer result = new StringBuffer();
\r
271 String chain = null;
\r
272 if (id.indexOf(":") > -1)
\r
274 chain = id.substring(id.indexOf(":") + 1);
\r
275 id = id.substring(0, id.indexOf(":"));
\r
278 EBIFetchClient ebi = new EBIFetchClient();
\r
279 String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
\r
284 PDBfile pdbfile = new PDBfile(reply);
\r
285 for (int i = 0; i < pdbfile.chains.size(); i++)
\r
287 if (chain == null ||
\r
288 ( (PDBChain) pdbfile.chains.elementAt(i)).id.
\r
289 toUpperCase().equals(chain))
\r
290 result.append("\n>PDB|" + id + "|" +
\r
291 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
\r
295 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
\r
299 catch (Exception ex) // Problem parsing PDB file
\r
301 jalview.bin.Cache.log.warn("Exception when retrieving " + textfield.getText() + " from " +
\r
302 database.getSelectedItem(), ex);
\r
309 SequenceI[] parseResult(String result)
\r
311 String format = IdentifyFile.Identify(result, "Paste");
\r
312 SequenceI[] sequences = null;
\r
314 if (FormatAdapter.formats.contains(format))
\r
316 sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);
\r
317 if (sequences != null && sequences.length>0)
\r
319 if(alignFrame==null)
\r
321 AlignFrame af = new AlignFrame(new Alignment(sequences));
\r
322 af.currentFileFormat = format;
\r
323 Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),
\r
324 AlignFrame.NEW_WINDOW_WIDTH,
\r
325 AlignFrame.NEW_WINDOW_HEIGHT);
\r
326 af.statusBar.setText("Successfully pasted alignment file");
\r
329 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
\r
331 catch (Exception ex)
\r
336 for (int i = 0; i < sequences.length; i++)
\r
338 alignFrame.viewport.alignment.addSequence(sequences[i]);
\r
340 ////////////////////////////
\r
341 //Datset needs extension;
\r
342 /////////////////////////////
\r
343 Sequence ds = new Sequence(sequences[i].getName(),
\r
344 AlignSeq.extractGaps("-. ",
\r
345 sequences[i].getSequence()),
\r
346 sequences[i].getStart(),
\r
347 sequences[i].getEnd());
\r
348 sequences[i].setDatasetSequence(ds);
\r
349 alignFrame.viewport.alignment.getDataset().addSequence(ds);
\r
351 alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
\r
353 alignFrame.viewport.alignment.getWidth();
\r
354 alignFrame.viewport.firePropertyChange("alignment", null,
\r
355 alignFrame.viewport.getAlignment().getSequences());
\r
359 if (database.getSelectedItem().equals("PDB"))
\r
361 for (int i = 0; i < sequences.length; i++)
\r
363 PDBEntry entry = new PDBEntry();
\r
364 entry.setId(textfield.getText());
\r
365 sequences[i].getDatasetSequence().addPDBId(entry);
\r
371 showErrorMessage( "Error retrieving "+textfield.getText()
\r
372 +" from "+database.getSelectedItem());
\r
379 void showErrorMessage(String error)
\r
381 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
382 error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
\r