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.io.DataSourceType;
10 import jalview.io.JPredFile;
11 import jalview.ws.api.JPredMutlipleAlignmentServiceI;
12 import jalview.ws.api.JobId;
13 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
14 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
15 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
17 public class SlivkaJPredServiceInstance extends SlivkaWSInstance
18 implements JPredMutlipleAlignmentServiceI
21 public SlivkaJPredServiceInstance(SlivkaClient client,
22 SlivkaService service, String action)
24 super(client, service, action);
25 style = ServiceClient.JPREDWSCLIENT;
29 public JobId align(List<SequenceI> sequences) throws Throwable
31 return super.submit(sequences, null, null);
35 public AlignmentI getAlignment(JobId jobId) throws Exception
37 List<RemoteFile> files;
39 files = client.getJobResults(jobId.getJobId());
40 for (RemoteFile f : files) {
41 var alignment = readAlignment(f);
42 if (alignment != null)
48 catch (IOException e) {
55 public JPredFile getPrediction(JobId jobId) throws Exception
57 List<RemoteFile> files = client.getJobResults(jobId.getJobId());
58 for (RemoteFile f : files)
60 if (f.getLabel().equals("concise"))
62 return new JPredFile(f.getURL(), DataSourceType.URL);