package jalview.ws.slivkaws;
+import java.io.IOError;
+import java.io.IOException;
+import java.rmi.ServerError;
+import java.util.List;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;
-
-import java.io.IOError;
-import java.io.IOException;
-import java.rmi.ServerError;
-import java.util.List;
-
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
{
- SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
- super(client, service, "Sequence Alignment");
+ SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
+ super(client, service, category);
style = ServiceClient.MSAWSCLIENT;
}
files = client.getJobResults(jobId.getJobId());
for (RemoteFile f : files)
{
- if (f.getMimeType().equals("application/clustal"))
- {
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
- }
- else if (f.getMimeType().equals("application/fasta"))
- {
- return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
- }
+ return readAlignment(f);
}
} catch (IOException e)
{