import java.util.List;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.ws.params.ParamManager;
import jalview.ws2.actions.alignment.AlignmentAction;
+import jalview.ws2.actions.annotation.AnnotationAction;
import jalview.ws2.api.WebService;
import jalview.ws2.client.api.AbstractWebServiceDiscoverer;
import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
} catch (IOException e)
{
- Cache.log.error("slivka could not retrieve services from " + url, e);
+ Console.error("slivka could not retrieve services from " + url, e);
return STATUS_INVALID;
}
}
}
allServices.add(msaService);
}
+ else if (serviceClass == SERVICE_CLASS_PROT_SEQ_ANALYSIS)
+ {
+ var wsb = WebService.<AnnotationAction> newBuilder();
+ initServiceBuilder(slivkaService, wsb);
+ wsb.category("Protein Disorder");
+ wsb.interactive(false);
+ wsb.actionClass(AnnotationAction.class);
+ var psaService = wsb.build();
+ var client = new SlivkaAnnotationWSClient(slivkaService);
+ var actionBuilder = AnnotationAction.newBuilder(client);
+ actionBuilder.webService(psaService);
+ actionBuilder.name("Analysis");
+ psaService.addAction(actionBuilder.build());
+ allServices.add(psaService);
+ }
+ else if (serviceClass == SERVICE_CLASS_CONSERVATION)
+ {
+ var wsb = WebService.<AnnotationAction> newBuilder();
+ initServiceBuilder(slivkaService, wsb);
+ wsb.category("Conservation");
+ wsb.interactive(true);
+ wsb.actionClass(AnnotationAction.class);
+ var conService = wsb.build();
+ var client = new SlivkaAnnotationWSClient(slivkaService);
+ var actionBuilder = AnnotationAction.newBuilder(client);
+ actionBuilder.webService(conService);
+ actionBuilder.name("");
+ actionBuilder.alignmentAnalysis(true);
+ actionBuilder.requireAlignedSequences(true);
+ actionBuilder.filterSymbols(true);
+ conService.addAction(actionBuilder.build());
+ allServices.add(conService);
+ }
+ else if (serviceClass == SERVICE_CLASS_RNA_SEC_STR_PRED)
+ {
+ var wsb = WebService.<AnnotationAction> newBuilder();
+ initServiceBuilder(slivkaService, wsb);
+ wsb.category("Secondary Structure Prediction");
+ wsb.interactive(true);
+ wsb.actionClass(AnnotationAction.class);
+ var predService = wsb.build();
+ var client = new SlivkaAnnotationWSClient(slivkaService);
+ var actionBuilder = AnnotationAction.newBuilder(client);
+ actionBuilder.webService(predService);
+ actionBuilder.name("Prediction");
+ actionBuilder.minSequences(2);
+ actionBuilder.allowNucleotide(true);
+ actionBuilder.allowProtein(false);
+ actionBuilder.alignmentAnalysis(true);
+ actionBuilder.requireAlignedSequences(true);
+ actionBuilder.filterSymbols(false);
+ predService.addAction(actionBuilder.build());
+ allServices.add(predService);
+ }
else
{
continue;
{
try
{
- wsBuilder.url(service.getUrl().toURL());
+ wsBuilder.url(service.getClient().getUrl().toURL());
} catch (MalformedURLException e)
{
e.printStackTrace();