package jalview.ws.slivkaws;
-import jalview.datamodel.SequenceI;
-import jalview.gui.WebserviceInfo;
-import jalview.ws.api.JalviewServiceEndpointProviderI;
-import jalview.ws.api.JalviewWebServiceI;
-import jalview.ws.api.JobId;
-import jalview.ws.api.ServiceWithParameters;
-import jalview.ws.gui.WsJob;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParamManager;
-import jalview.ws.params.WsParamSetI;
-
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOError;
import java.util.Optional;
import java.util.Set;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.WebserviceInfo;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
+import jalview.ws.api.JalviewWebServiceI;
+import jalview.ws.api.JobId;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.gui.WsJob;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
import uk.ac.dundee.compbio.slivkaclient.FieldType;
import uk.ac.dundee.compbio.slivkaclient.FormField;
import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
- stateMap.put(JobState.INTERRUPED, WsJob.JobState.CANCELLED);
+ stateMap.put(JobState.INTERRUPTED, WsJob.JobState.CANCELLED);
stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
{
- super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
+ super(action, action, service.getLabel(), "Slivka", client.getUrl().toString());
this.client = client;
this.service = service;
}
}
return store;
}
+
+ public static AlignmentI readAlignment(RemoteFile f) throws IOException
+ {
+ final var mimetype = f.getMimeType();
+ FileFormat format;
+ if (mimetype.equals("application/clustal"))
+ format = FileFormat.Clustal;
+ else if (mimetype.equals("application/fasta"))
+ format = FileFormat.Fasta;
+ else
+ return null;
+ return new FormatAdapter().readFile(f.getURL().toString(),
+ DataSourceType.URL, format);
+ }
}