+ if ((result.indexOf("JOB PENDING") == -1) &&\r
+ (result.indexOf("JOB RUNNING") == -1)) {\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
+ } catch (Exception ex) {\r
+ }\r
+ }\r
+ }\r
+\r
+ void StartJob() {\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
+ 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
+ params, seqbytes\r
+ });\r
+ jobid = result;\r
+ System.out.println(\r
+ "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +\r
+ jobid + "'");\r
+ } catch (Exception exp) {\r
+ System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
+ exp.printStackTrace();\r
+ }\r
+ }\r
+ }\r