import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.JobStatus;\r
import compbio.metadata.Option;\r
import compbio.metadata.Limit;\r
import compbio.metadata.Preset;\r
private static void listAllServices(String hostname) throws WebServiceException, IOException {\r
RegistryWS registry = connectToRegistry(hostname);\r
Set<Services> func_services = Collections.emptySet();\r
- Set<Services> nonfunc_services = Collections.emptySet();\r
+ //Set<Services> nonfunc_services = Collections.emptySet();\r
if (registry != null) {\r
func_services = registry.getSupportedServices();\r
- nonfunc_services = registry.getNonoperatedServices();\r
+ //nonfunc_services = registry.getNonoperatedServices();\r
FileUtil.closeSilently(((Closeable) registry));\r
} else {\r
System.out.println("Failed to connect to the registry! ");\r
String mess = "\n\rThe list:\n";\r
System.out.println(mess + Services.toString(func_services));\r
}\r
+ /*\r
if (!nonfunc_services.isEmpty()) {\r
System.out.println("There are " + nonfunc_services.size() + " non-available services at " + hostname + ":");\r
String mess = "The list (internal tests failed): ";\r
System.out.println(mess + Services.toString(nonfunc_services));\r
}\r
+ */\r
}\r
\r
/**\r
}\r
System.out.println("\n\rcalling predictor.........");\r
Thread.sleep(100);\r
+ JobStatus status = wsproxy.getJobStatus(jobId);\r
+ System.out.println("\njob " + jobId + " status: " + status);\r
scores = wsproxy.getAnnotation(jobId);\r
} catch (JobSubmissionException e) {\r
System.err.println("Exception while submitting job to a web server. Exception details are below:");\r
jobId = msaws.align(fastalist);\r
}\r
System.out.println("\ncalling program.........");\r
- Thread.sleep(100);\r
+ long startTime = System.nanoTime();\r
+ while (JobStatus.RUNNING == msaws.getJobStatus(jobId)) {\r
+ Thread.sleep(1000);\r
+ long endTime = System.nanoTime();\r
+ System.out.println("job " + jobId + " time executing: "+ (endTime - startTime) / 1000000 +" msec, status: " + msaws.getJobStatus(jobId));\r
+ }\r
alignment = msaws.getResult(jobId);\r
} catch (IOException e) {\r
System.err.println("Exception while reading the input file. Check that the input file is a FASTA file! "\r