/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.io;\r
\r
-import jalview.datamodel.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import org.apache.axis.client.*;\r
-\r
-import java.awt.*;\r
-\r
import java.util.*;\r
\r
import javax.swing.*;\r
\r
-import javax.xml.namespace.QName;\r
-\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
+import uk.ac.ebi.www.*;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class WSWUBlastClient\r
{\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- int jobsRunning = 0;\r
-\r
- /**\r
- * Creates a new WSWUBlastClient object.\r
- *\r
- * @param al DOCUMENT ME!\r
- * @param ids DOCUMENT ME!\r
- */\r
- public WSWUBlastClient(AlignmentI al, ArrayList ids)\r
+ AlignmentPanel ap;\r
+ AlignmentI al;\r
+ CutAndPasteTransfer output = new CutAndPasteTransfer();\r
+ int jobsRunning = 0;\r
+\r
+ Vector suggestedIds = new Vector();\r
+ /**\r
+ * Creates a new WSWUBlastClient object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ * @param ids DOCUMENT ME!\r
+ */\r
+ public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)\r
+ {\r
+ this.ap = ap;\r
+ this.al = al;\r
+ output.setText(\r
+ "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."\r
+ + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."\r
+ + "\n\nRunning WSWUBlast at EBI."\r
+ + "\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."\r
+ +\r
+ "\nSOAP-based services provided by the European Bioinformatics Institute."\r
+ + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");\r
+\r
+ Desktop.addInternalFrame(output,\r
+ "BLASTing for unidentified sequences ", 800, 300);\r
+\r
+ for (int i = 0; i < ids.size(); i++)\r
{\r
- output.setText(\r
- "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +\r
- "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
- Desktop.addInternalFrame(output,\r
- "BLASTing for unidentified sequences ", 800, 300);\r
-\r
- for (int i = 0; i < ids.size(); i++)\r
- {\r
- SequenceI sequence = al.findName(ids.get(i).toString());\r
- StringBuffer nonGapped = new StringBuffer();\r
+ Sequence sequence = (Sequence) ids.get(i);\r
+ System.out.println(sequence.getName());\r
\r
- for (int n = 0; n < sequence.getSequence().length(); n++)\r
- {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
- {\r
- nonGapped.append(sequence.getCharAt(n));\r
- }\r
- }\r
-\r
- BlastThread thread = new BlastThread(ids.get(i).toString(),\r
- nonGapped.toString());\r
- thread.start();\r
- jobsRunning++;\r
- }\r
-\r
- ImageTwirler thread = new ImageTwirler();\r
- thread.start();\r
+ BlastThread thread = new BlastThread(sequence);\r
+ thread.start();\r
+ jobsRunning++;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param id1 DOCUMENT ME!\r
- * @param res DOCUMENT ME!\r
- */\r
- void parseResult(String id1, String res)\r
+ ImageTwirler thread = new ImageTwirler();\r
+ thread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param id1 DOCUMENT ME!\r
+ * @param res DOCUMENT ME!\r
+ */\r
+ void parseResult(Sequence seq, String res)\r
+ {\r
+ StringTokenizer st = new StringTokenizer(res, "\n");\r
+ String data;\r
+ String id2;\r
+ int maxFound = 90;\r
+ StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");\r
+\r
+ while (st.hasMoreTokens())\r
{\r
- StringTokenizer st = new StringTokenizer(res, "\n");\r
- String data;\r
- String id2;\r
- int maxFound = 90;\r
- StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");\r
+ data = st.nextToken();\r
+\r
+ if (data.indexOf(">UNIPROT") > -1)\r
+ {\r
+ int index = data.indexOf(">UNIPROT") + 9;\r
+ id2 = data.substring(index, data.indexOf(" ", index));\r
\r
- while (st.hasMoreTokens())\r
+ boolean identitiesFound = false;\r
+ while (!identitiesFound)\r
{\r
- data = st.nextToken();\r
+ data = st.nextToken();\r
+\r
+ if (data.indexOf("Identities") > -1)\r
+ {\r
+ identitiesFound = true;\r
+\r
+ int value = Integer.parseInt(data.substring(data.indexOf(\r
+ "(") + 1,\r
+ data.indexOf("%")));\r
\r
- if (data.indexOf("database=\"uniprot\" id=") > -1)\r
+ if (value >= maxFound)\r
{\r
- int index = data.indexOf("database=\"uniprot\" id=") + 23;\r
- id2 = data.substring(index, data.indexOf("\"", index));\r
-\r
- while (data.indexOf("</alignment>") == -1)\r
- {\r
- data = st.nextToken();\r
-\r
- if (data.indexOf("<identity>") > -1)\r
- {\r
- int value = Integer.parseInt(data.substring(data.indexOf(\r
- "<identity>") + 10,\r
- data.indexOf("</identity>")));\r
-\r
- if (value >= maxFound)\r
- {\r
- maxFound = value;\r
- buffer.append(" " + id2 + " " + value + "%; ");\r
- }\r
- }\r
- }\r
+ maxFound = value;\r
+ buffer.append(" " + id2 + " " + value + "%; ");\r
+ suggestedIds.addElement(new Object[]\r
+ {seq, id2});\r
}\r
+ }\r
}\r
-\r
- output.setText(output.getText() + buffer.toString());\r
+ }\r
}\r
\r
- class ImageTwirler extends Thread\r
+ output.appendText(buffer.toString());\r
+ }\r
+\r
+ void updateIds()\r
+ {\r
+ // This must be outside the run() body as java 1.5\r
+ // will not return any value from the OptionPane to the expired thread.\r
+ int reply = JOptionPane.showConfirmDialog(\r
+ Desktop.desktop, "Automatically update suggested ids?",\r
+ "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
{\r
- ImageIcon[] imageIcon;\r
- int imageIndex = 0;\r
+ Enumeration keys = suggestedIds.elements();\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object[] object = (Object[]) keys.nextElement();\r
\r
- public ImageTwirler()\r
- {\r
- imageIcon = new ImageIcon[9];\r
+ Sequence oldseq = (Sequence) object[0];\r
\r
- for (int i = 0; i < 9; i++)\r
- {\r
- java.net.URL url = getClass().getResource("/images/dna" +\r
- (i + 1) + ".gif");\r
+ oldseq.setName(object[1].toString());\r
\r
- if (url != null)\r
- {\r
- imageIcon[i] = new ImageIcon(url);\r
- }\r
- }\r
+ // Oldseq is actually in the dataset, we must find the\r
+ // Visible seq and change its name also.\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ if (al.getSequenceAt(i).getDatasetSequence() == oldseq)\r
+ {\r
+ al.getSequenceAt(i).setName(oldseq.getName());\r
+ break;\r
+ }\r
}\r
\r
- public void run()\r
+ DBRefEntry[] entries = oldseq.getDBRef();\r
+ if (entries != null)\r
{\r
- while (jobsRunning > 0)\r
- {\r
- try\r
- {\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %= 9;\r
- output.setFrameIcon(imageIcon[imageIndex]);\r
- output.setTitle("BLASTing for unidentified sequences - " +\r
- jobsRunning + " jobs running.");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
+ oldseq.addDBRef(new jalview.datamodel.\r
+ DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,\r
+ "0",\r
+ entries[0].getAccessionId()));\r
}\r
+ }\r
}\r
+ ap.paintAlignment(true);\r
+\r
+ }\r
+\r
+ class ImageTwirler\r
+ extends Thread\r
+ {\r
+ ImageIcon[] imageIcon;\r
+ int imageIndex = 0;\r
\r
- class BlastThread extends Thread\r
+ public ImageTwirler()\r
{\r
- String sequence;\r
- String seqid;\r
- String jobid;\r
- boolean jobComplete = false;\r
+ imageIcon = new ImageIcon[9];\r
\r
- BlastThread(String id, String sequence)\r
+ for (int i = 0; i < 9; i++)\r
+ {\r
+ java.net.URL url = getClass().getResource("/images/dna" +\r
+ (i + 1) + ".gif");\r
+\r
+ if (url != null)\r
{\r
- this.sequence = sequence;\r
- seqid = id;\r
+ imageIcon[i] = new ImageIcon(url);\r
}\r
+ }\r
+ }\r
\r
- public void run()\r
+ public void run()\r
+ {\r
+ while (jobsRunning > 0)\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(100);\r
+ imageIndex++;\r
+ imageIndex %= 9;\r
+ output.setFrameIcon(imageIcon[imageIndex]);\r
+ output.setTitle("BLASTing for unidentified sequences - " +\r
+ jobsRunning + " jobs running.");\r
+ }\r
+ catch (Exception ex)\r
{\r
- StartJob();\r
-\r
- while (!jobComplete)\r
- {\r
- try\r
- {\r
- Call call = (Call) new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
- call.setOperationName(new QName("WSWUBlast", "polljob"));\r
-\r
- String result = (String) call.invoke(new Object[]\r
- {\r
- jobid, "xml"\r
- });\r
-\r
- if ((result.indexOf("JOB PENDING") == -1) &&\r
- (result.indexOf("JOB RUNNING") == -1))\r
- {\r
- parseResult(seqid, result);\r
- jobComplete = true;\r
- jobsRunning--;\r
- }\r
-\r
- Thread.sleep(5000);\r
-\r
- // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
}\r
+ }\r
+\r
+ if (jobsRunning == 0)\r
+ {\r
+ updateIds();\r
+ }\r
+ }\r
+ }\r
+\r
+ class BlastThread\r
+ extends Thread\r
+ {\r
+ Sequence sequence;\r
+ String jobid;\r
+ boolean jobComplete = false;\r
\r
- void StartJob()\r
+ BlastThread(Sequence sequence)\r
+ {\r
+ System.out.println("blasting for: " + sequence.getName());\r
+ this.sequence = sequence;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ StartJob();\r
+\r
+ while (!jobComplete)\r
+ {\r
+ try\r
+ {\r
+ WSWUBlastService service = new WSWUBlastServiceLocator();\r
+ WSWUBlast wublast = service.getWSWUBlast();\r
+ WSFile[] results = wublast.getResults(jobid);\r
+\r
+ if (results != null)\r
+ {\r
+ String result = new String(wublast.poll(jobid, "tooloutput"));\r
+ parseResult(sequence, result);\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ }\r
+ else\r
+ {\r
+ Thread.sleep(10000);\r
+ System.out.println("WSWuBlastClient: I'm alive " +\r
+ sequence.getName() + " " + jobid); // log.debug\r
+ }\r
+ }\r
+ catch (Exception ex)\r
{\r
- HashMap params = new HashMap();\r
- params.put("database", "uniprot");\r
- params.put("sensitivity", "low");\r
- params.put("sort", "totalscore");\r
- params.put("matrix", "pam10");\r
- params.put("program", "blastp");\r
- params.put("alignments", "5");\r
- params.put("outformat", "xml");\r
- params.put("searchtype", "1");\r
-\r
- byte[] seqbytes = sequence.getBytes();\r
-\r
- try\r
- {\r
- Call call = (Call) new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
- call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
-\r
- String result = (String) call.invoke(new Object[]\r
- {\r
- params, seqbytes\r
- });\r
- jobid = result;\r
- System.out.println(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +\r
- jobid + "'");\r
- }\r
- catch (Exception exp)\r
- {\r
- System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
- exp.printStackTrace();\r
- }\r
}\r
+ }\r
+ }\r
+\r
+ void StartJob()\r
+ {\r
+ InputParams params = new InputParams();\r
+\r
+ params.setProgram("blastp");\r
+ params.setDatabase("uniprot");\r
+ params.setMatrix("pam10");\r
+\r
+ params.setNumal(5);\r
+ params.setSensitivity("low");\r
+ params.setSort("totalscore");\r
+ params.setOutformat("txt");\r
+ params.setAsync(true);\r
+\r
+ try\r
+ {\r
+ Data inputs[] = new Data[1];\r
+ Data input = new Data();\r
+ input.setType("sequence");\r
+ input.setContent(AlignSeq.extractGaps("-. ",\r
+ sequence.getSequenceAsString()));\r
+ inputs[0] = input;\r
+\r
+ WSWUBlastService service = new WSWUBlastServiceLocator();\r
+ WSWUBlast wublast = service.getWSWUBlast();\r
+ jobid = wublast.runWUBlast(params, inputs);\r
+ }\r
+ catch (Exception exp)\r
+ {\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
+ exp.printStackTrace();\r
+ }\r
}\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff