1 package jalview.ws.slivkaws;
3 import jalview.bin.Cache;
4 import jalview.datamodel.AlignmentI;
5 import jalview.datamodel.SequenceI;
6 import jalview.io.DataSourceType;
7 import jalview.io.FileFormat;
8 import jalview.io.FormatAdapter;
9 import jalview.ws.api.JobId;
10 import jalview.ws.api.MultipleSequenceAlignmentI;
11 import jalview.ws.params.ArgumentI;
12 import jalview.ws.params.InvalidArgumentException;
13 import jalview.ws.params.WsParamSetI;
15 import java.io.IOError;
16 import java.io.IOException;
17 import java.rmi.ServerError;
18 import java.util.Collection;
19 import java.util.List;
21 import compbio.data.msa.Category;
22 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
23 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
24 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
26 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
28 SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
29 super(client, service, category);
30 style = ServiceClient.MSAWSCLIENT;
34 public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
36 return super.submit(toalign, parameters, list);
40 public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
42 Collection<RemoteFile> files;
45 var slivkaJob = client.getJob(jobId.getJobId());
46 files = slivkaJob.getResults();
47 for (RemoteFile f : files)
49 if (f.getMediaType().equals("application/clustal"))
51 return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
53 else if (f.getMediaType().equals("application/fasta"))
55 return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
58 } catch (IOException e)