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.ByteArrayInputStream;
-import java.io.IOError;
-import java.io.IOException;
-import java.io.InputStream;
-import java.rmi.ServerError;
-import java.util.HashMap;
-import java.util.List;
-
-import uk.ac.dundee.compbio.slivkaclient.FormField;
import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
{
- SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
- super(client, service, "Alignment");
+ SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service, String category) {
+ super(client, service, category);
+ style = ServiceClient.MSAWSCLIENT;
}
@Override
public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
{
- StringBuilder builder = new StringBuilder();
- for (SequenceI seq : toalign)
- {
- builder.append(">").append(seq.getName()).append("\n");
- builder.append(seq.getSequence()).append("\n");
- }
- InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
- RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
- SlivkaForm form = service.getForm();
- HashMap<String, String> values = new HashMap<>(list != null ? list.size() : 0);
- if (list != null)
- {
- for (ArgumentI arg : list)
- {
- values.put(arg.getName(), arg.getValue());
- }
- }
- for (FormField field : form.getFields())
- {
- switch (field.getType()) {
- case FILE:
- form.insert(field.getName(), file);
- break;
- case BOOLEAN:
- String value = values.get(field.getName());
- form.insert(field.getName(), (value != null && !value.isBlank()) ? true : false);
- break;
- default:
- form.insert(field.getName(), field.valueOf(values.get(field.getName())));
- }
- }
- return new JobId(service.getName(), service.getName(), form.submit());
+ return super.submit(toalign, parameters, list);
}
@Override
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)
{