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 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;
@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"))
+ var aln = readAlignment(f);
+ if (aln != null)
{
- 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 aln;
}
}
} catch (IOException e)