package jalview.ws.slivkaws;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.ws.ServiceChangeListener;
import jalview.ws.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
+import javajs.http.HttpClientFactory;
+
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
private List<ServiceWithParameters> reloadServices()
{
- Cache.log.info("Reloading Slivka services");
+ Console.info("Reloading Slivka services");
notifyServiceListeners(Collections.emptyList());
ArrayList<ServiceWithParameters> instances = new ArrayList<>();
{
switch (path[path.length - 1].toLowerCase())
{
+ case "rna secondary structure prediction":
+ newInstance = new RNAalifoldServiceInstance(client,
+ service, "Secondary Structure Prediction");
+ break;
case "sequence alignment analysis (conservation)":
newInstance = new SlivkaAnnotationServiceInstance(client,
service, Category.CATEGORY_CONSERVATION);
service, Category.CATEGORY_DISORDER);
break;
case "protein secondary structure prediction":
- newInstance = new SlivkaJPredServiceInstance(client,
+ newInstance = new SlivkaAnnotationServiceInstance(client,
service, "Secondary Structure Prediction");
break;
case "multiple sequence alignment":
}
services = instances;
- Cache.log.info("Slivka services reloading finished");
+ Console.info("Slivka services reloading finished");
notifyServiceListeners(instances);
return instances;
}
valid.add(url);
} catch (MalformedURLException e)
{
- Cache.log.warn("Problem whilst trying to make a URL from '"
+ Console.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- Cache.log.warn(
+ Console.warn(
"This was probably due to a malformed comma separated list"
+ " in the " + SLIVKA_HOST_URLS
+ " entry of $(HOME)/.jalview_properties)");
- Cache.log.debug("Exception was ", e);
+ Console.debug("Exception was ", e);
}
}
return valid;
{
List<?> services = new SlivkaClient(url).getServices();
return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
- } catch (IOException e)
+ } catch (IOException | org.json.JSONException e)
{
- Cache.log.error("Slivka could not retrieve services list", e);
+ Console.error("Slivka could not retrieve services list", e);
return STATUS_INVALID;
}
}