1 package jalview.ws.slivkaws;
3 import java.io.IOError;
4 import java.io.IOException;
7 import jalview.datamodel.AlignmentI;
8 import jalview.datamodel.SequenceI;
9 import jalview.ws.api.JPredMutlipleAlignmentServiceI;
10 import jalview.ws.api.JobId;
11 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
12 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
13 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
15 public class SlivkaJPredServiceInstance extends SlivkaWSInstance
16 implements JPredMutlipleAlignmentServiceI
19 public SlivkaJPredServiceInstance(SlivkaClient client,
20 SlivkaService service, String action)
22 super(client, service, action);
23 style = ServiceClient.JPREDWSCLIENT;
27 public JobId align(List<SequenceI> sequences) throws Throwable
29 return super.submit(sequences, null, null);
33 public AlignmentI getResult(JobId jobId) throws Exception
35 List<RemoteFile> files;
37 files = client.getJobResults(jobId.getJobId());
38 for (RemoteFile f : files) {
39 if (f.getMimeType().equals("application/clustal")
40 || f.getMimeType().equals("application/fasta"))
42 return readAlignment(f);
46 catch (IOException e) {