2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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23 import javax.swing.*;
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25 import jalview.analysis.*;
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26 import jalview.datamodel.*;
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27 import jalview.gui.*;
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28 import uk.ac.ebi.www.*;
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34 * @version $Revision$
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36 public class WSWUBlastClient
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40 CutAndPasteTransfer output = new CutAndPasteTransfer();
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41 int jobsRunning = 0;
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43 Vector suggestedIds = new Vector();
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45 * Creates a new WSWUBlastClient object.
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47 * @param al DOCUMENT ME!
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48 * @param ids DOCUMENT ME!
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50 public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
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55 "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
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56 + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
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57 + "\n\nRunning WSWUBlast at EBI."
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58 + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
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60 "\nSOAP-based services provided by the European Bioinformatics Institute."
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61 + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
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63 Desktop.addInternalFrame(output,
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64 "BLASTing for unidentified sequences ", 800, 300);
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66 for (int i = 0; i < ids.size(); i++)
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68 Sequence sequence = (Sequence) ids.get(i);
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69 System.out.println(sequence.getName());
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71 BlastThread thread = new BlastThread(sequence);
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76 ImageTwirler thread = new ImageTwirler();
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83 * @param id1 DOCUMENT ME!
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84 * @param res DOCUMENT ME!
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86 void parseResult(Sequence seq, String res)
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88 StringTokenizer st = new StringTokenizer(res, "\n");
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92 StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
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94 while (st.hasMoreTokens())
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96 data = st.nextToken();
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98 if (data.indexOf(">UNIPROT") > -1)
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100 int index = data.indexOf(">UNIPROT") + 9;
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101 id2 = data.substring(index, data.indexOf(" ", index));
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103 boolean identitiesFound = false;
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104 while (!identitiesFound)
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106 data = st.nextToken();
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108 if (data.indexOf("Identities") > -1)
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110 identitiesFound = true;
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112 int value = Integer.parseInt(data.substring(data.indexOf(
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114 data.indexOf("%")));
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116 if (value >= maxFound)
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119 buffer.append(" " + id2 + " " + value + "%; ");
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120 suggestedIds.addElement(new Object[]
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128 output.appendText(buffer.toString());
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133 // This must be outside the run() body as java 1.5
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134 // will not return any value from the OptionPane to the expired thread.
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135 int reply = JOptionPane.showConfirmDialog(
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136 Desktop.desktop, "Automatically update suggested ids?",
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137 "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
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139 if (reply == JOptionPane.YES_OPTION)
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141 Enumeration keys = suggestedIds.elements();
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142 while (keys.hasMoreElements())
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144 Object[] object = (Object[]) keys.nextElement();
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146 Sequence oldseq = (Sequence) object[0];
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148 oldseq.setName(object[1].toString());
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150 // Oldseq is actually in the dataset, we must find the
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151 // Visible seq and change its name also.
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152 for (int i = 0; i < al.getHeight(); i++)
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154 if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
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156 al.getSequenceAt(i).setName(oldseq.getName());
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161 DBRefEntry[] entries = oldseq.getDBRef();
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162 if (entries != null)
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164 oldseq.addDBRef(new jalview.datamodel.
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165 DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
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167 entries[0].getAccessionId()));
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171 ap.paintAlignment(true);
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178 ImageIcon[] imageIcon;
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179 int imageIndex = 0;
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181 public ImageTwirler()
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183 imageIcon = new ImageIcon[9];
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185 for (int i = 0; i < 9; i++)
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187 java.net.URL url = getClass().getResource("/images/dna" +
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192 imageIcon[i] = new ImageIcon(url);
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199 while (jobsRunning > 0)
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206 output.setFrameIcon(imageIcon[imageIndex]);
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207 output.setTitle("BLASTing for unidentified sequences - " +
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208 jobsRunning + " jobs running.");
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210 catch (Exception ex)
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215 if (jobsRunning == 0)
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227 boolean jobComplete = false;
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229 BlastThread(Sequence sequence)
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231 System.out.println("blasting for: " + sequence.getName());
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232 this.sequence = sequence;
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239 while (!jobComplete)
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243 WSWUBlastService service = new WSWUBlastServiceLocator();
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244 WSWUBlast wublast = service.getWSWUBlast();
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245 WSFile[] results = wublast.getResults(jobid);
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247 if (results != null)
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249 String result = new String(wublast.poll(jobid, "tooloutput"));
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250 parseResult(sequence, result);
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251 jobComplete = true;
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256 Thread.sleep(10000);
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257 System.out.println("WSWuBlastClient: I'm alive " +
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258 sequence.getName() + " " + jobid); // log.debug
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261 catch (Exception ex)
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269 InputParams params = new InputParams();
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271 params.setProgram("blastp");
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272 params.setDatabase("uniprot");
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273 params.setMatrix("pam10");
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275 params.setNumal(5);
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276 params.setSensitivity("low");
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277 params.setSort("totalscore");
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278 params.setOutformat("txt");
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279 params.setAsync(true);
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283 Data inputs[] = new Data[1];
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284 Data input = new Data();
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285 input.setType("sequence");
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286 input.setContent(AlignSeq.extractGaps("-. ",
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287 sequence.getSequenceAsString()));
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290 WSWUBlastService service = new WSWUBlastServiceLocator();
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291 WSWUBlast wublast = service.getWSWUBlast();
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292 jobid = wublast.runWUBlast(params, inputs);
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294 catch (Exception exp)
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296 jobComplete = true;
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298 System.err.println("WSWUBlastClient error:\n" + exp.toString());
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299 exp.printStackTrace();
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