import jalview.ws.params.ParamManager;
import jalview.ws2.actions.NullAction;
import jalview.ws2.actions.api.ActionI;
+import jalview.ws2.actions.hmmer.PhmmerAction;
import jalview.ws2.api.WebService;
import jalview.ws2.client.api.AbstractWebServiceDiscoverer;
import uk.ac.dundee.compbio.hmmerclient.PhmmerClient;
@Override
protected List<WebService<?>> fetchServices(URL url) throws IOException
{
- PhmmerClient client;
+ PhmmerClient phmmerClient;
try {
- client = new PhmmerClient(url);
+ phmmerClient = new PhmmerClient(url);
}
catch (URISyntaxException e) {
throw new MalformedURLException(e.getMessage());
}
- if (!client.testEndpoint())
+ if (!phmmerClient.testEndpoint())
throw new IOException(
"unable to reach dispatcher server at " + url);
// TODO change once a concrete action is implemented
- var wsBuilder = WebService.<NullAction> newBuilder();
+ var wsBuilder = WebService.<PhmmerAction> newBuilder();
wsBuilder.url(url);
wsBuilder.clientName("job dispatcher");
wsBuilder.category("Database search");
wsBuilder.description("Hmmer3 phmmer is used to search one or more query sequences against a sequence database.");
wsBuilder.interactive(false);
wsBuilder.paramDatastore(ParamStores.newPhmmerDatastore(url, paramManager));
- wsBuilder.actionClass(NullAction.class);
+ wsBuilder.actionClass(PhmmerAction.class);
var webService = wsBuilder.build();
- var actionBuilder = NullAction.newBuilder();
+ var client = new PhmmerWSClient(phmmerClient);
+ var actionBuilder = PhmmerAction.newBuilder(client);
actionBuilder.webService(webService);
actionBuilder.name("");
webService.addAction(actionBuilder.build());