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.analysis.AlignSeq;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.datamodel.Sequence;
27 import jalview.gui.AlignmentPanel;
28 import jalview.gui.CutAndPasteTransfer;
29 import jalview.gui.Desktop;
30 import jalview.util.MessageManager;
32 import java.util.ArrayList;
33 import java.util.Enumeration;
34 import java.util.StringTokenizer;
35 import java.util.Vector;
37 import javax.swing.ImageIcon;
38 import javax.swing.JOptionPane;
40 import uk.ac.ebi.www.Data;
41 import uk.ac.ebi.www.InputParams;
42 import uk.ac.ebi.www.WSFile;
43 import uk.ac.ebi.www.WSWUBlast;
44 import uk.ac.ebi.www.WSWUBlastService;
45 import uk.ac.ebi.www.WSWUBlastServiceLocator;
53 public class WSWUBlastClient
59 CutAndPasteTransfer output = new CutAndPasteTransfer();
63 Vector suggestedIds = new Vector();
66 * Creates a new WSWUBlastClient object.
73 public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
77 output.setText(MessageManager
78 .getString("label.wswublast_client_credits"));
80 Desktop.addInternalFrame(output, MessageManager
81 .getString("label.blasting_for_unidentified_sequence"), 800,
84 for (int i = 0; i < ids.size(); i++)
86 Sequence sequence = (Sequence) ids.get(i);
87 System.out.println(sequence.getName());
89 BlastThread thread = new BlastThread(sequence);
94 ImageTwirler thread = new ImageTwirler();
106 void parseResult(Sequence seq, String res)
108 StringTokenizer st = new StringTokenizer(res, "\n");
112 StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
114 while (st.hasMoreTokens())
116 data = st.nextToken();
118 if (data.indexOf(">UNIPROT") > -1)
120 int index = data.indexOf(">UNIPROT") + 9;
121 id2 = data.substring(index, data.indexOf(" ", index));
123 boolean identitiesFound = false;
124 while (!identitiesFound)
126 data = st.nextToken();
128 if (data.indexOf("Identities") > -1)
130 identitiesFound = true;
132 int value = Integer.parseInt(data.substring(
133 data.indexOf("(") + 1, data.indexOf("%")));
135 if (value >= maxFound)
138 buffer.append(" " + id2 + " " + value + "%; ");
139 suggestedIds.addElement(new Object[] { seq, id2 });
146 output.appendText(buffer.toString());
151 // This must be outside the run() body as java 1.5
152 // will not return any value from the OptionPane to the expired thread.
153 int reply = JOptionPane.showConfirmDialog(Desktop.desktop,
154 "Automatically update suggested ids?",
155 "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
157 if (reply == JOptionPane.YES_OPTION)
159 Enumeration keys = suggestedIds.elements();
160 while (keys.hasMoreElements())
162 Object[] object = (Object[]) keys.nextElement();
164 Sequence oldseq = (Sequence) object[0];
166 oldseq.setName(object[1].toString());
168 // Oldseq is actually in the dataset, we must find the
169 // Visible seq and change its name also.
170 for (int i = 0; i < al.getHeight(); i++)
172 if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
174 al.getSequenceAt(i).setName(oldseq.getName());
179 DBRefEntry[] entries = oldseq.getDBRef();
182 oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
183 jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
188 ap.paintAlignment(true);
192 class ImageTwirler extends Thread
194 ImageIcon[] imageIcon;
198 public ImageTwirler()
200 imageIcon = new ImageIcon[9];
202 for (int i = 0; i < 9; i++)
204 java.net.URL url = getClass().getResource(
205 "/images/dna" + (i + 1) + ".gif");
209 imageIcon[i] = new ImageIcon(url);
216 while (jobsRunning > 0)
223 output.setFrameIcon(imageIcon[imageIndex]);
224 output.setTitle(MessageManager.formatMessage(
225 "label.blasting_for_unidentified_sequence_jobs_running",
226 new String[] { Integer.valueOf(jobsRunning).toString() }));
227 } catch (Exception ex)
232 if (jobsRunning == 0)
239 class BlastThread extends Thread
245 boolean jobComplete = false;
247 BlastThread(Sequence sequence)
249 System.out.println("blasting for: " + sequence.getName());
250 this.sequence = sequence;
261 WSWUBlastService service = new WSWUBlastServiceLocator();
262 WSWUBlast wublast = service.getWSWUBlast();
263 WSFile[] results = wublast.getResults(jobid);
267 String result = new String(wublast.poll(jobid, "tooloutput"));
268 parseResult(sequence, result);
275 System.out.println("WSWuBlastClient: I'm alive "
276 + sequence.getName() + " " + jobid); // log.debug
278 } catch (Exception ex)
286 InputParams params = new InputParams();
288 params.setProgram("blastp");
289 params.setDatabase("uniprot");
290 params.setMatrix("pam10");
293 params.setSensitivity("low");
294 params.setSort("totalscore");
295 params.setOutformat("txt");
296 params.setAsync(true);
300 Data inputs[] = new Data[1];
301 Data input = new Data();
302 input.setType("sequence");
303 input.setContent(AlignSeq.extractGaps("-. ",
304 sequence.getSequenceAsString()));
307 WSWUBlastService service = new WSWUBlastServiceLocator();
308 WSWUBlast wublast = service.getWSWUBlast();
309 jobid = wublast.runWUBlast(params, inputs);
310 } catch (Exception exp)
314 System.err.println("WSWUBlastClient error:\n" + exp.toString());
315 exp.printStackTrace();