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 compbio.data.msa.Category;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
files = client.getJobResults(jobId.getJobId());
for (RemoteFile f : files)
{
- return readAlignment(f);
+ 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);
+ }
}
} catch (IOException e)
{