1 package jalview.ws.slivkaws;
3 import java.io.IOError;
4 import java.io.IOException;
5 import java.rmi.ServerError;
8 import jalview.datamodel.AlignmentI;
9 import jalview.datamodel.SequenceI;
10 import jalview.ws.api.JobId;
11 import jalview.ws.api.MultipleSequenceAlignmentI;
12 import jalview.ws.params.ArgumentI;
13 import jalview.ws.params.InvalidArgumentException;
14 import jalview.ws.params.WsParamSetI;
15 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
16 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
17 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
19 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
21 SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
22 super(client, service, category);
23 style = ServiceClient.MSAWSCLIENT;
27 public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
29 return super.submit(toalign, parameters, list);
33 public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
35 List<RemoteFile> files;
38 files = client.getJobResults(jobId.getJobId());
39 for (RemoteFile f : files)
41 return readAlignment(f);
43 } catch (IOException e)