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;
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;
}
@Override
public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
{
- List<RemoteFile> files;
try
{
- files = client.getJobResults(jobId.getJobId());
+ List<RemoteFile> files = client.getJobResults(jobId.getJobId());
for (RemoteFile f : files)
{
- if (f.getMimeType().equals("application/clustal"))
+ if (f.getMimeType().equals("application/clustal")
+ || f.getMimeType().equals("application/fasta"))
{
- 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)