import jalview.util.MessageManager;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
-import java.util.LinkedHashSet;
+import java.util.ArrayList;
import java.util.List;
-import java.util.Set;
public abstract class AWSThread extends Thread
{
/**
* dataset sequence relationships to be propagated onto new results
*/
- protected Set<AlignedCodonFrame> codonframe = null;
+ protected List<AlignedCodonFrame> codonframe = null;
/**
* are there jobs still running in this thread.
{
// Deal with Transaction exceptions
wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
- .formatMessage("info.server_exception", new Object[] {
- WebServiceName, ex.getMessage() }));
+ .formatMessage("info.server_exception", new Object[]
+ { WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
WebserviceInfo.STATE_STOPPED_ERROR);
Cache.log.error("Out of memory when retrieving Job " + j
+ " id:" + WsUrl + "/" + jobs[j].jobId, er);
- new jalview.gui.OOMWarning("retrieving result for "
- + WebServiceName, er);
+ new jalview.gui.OOMWarning(
+ "retrieving result for " + WebServiceName, er);
System.gc();
}
}
Thread.sleep(5000);
} catch (InterruptedException e)
{
- Cache.log
- .debug("Interrupted sleep waiting for next job poll.", e);
+ Cache.log.debug("Interrupted sleep waiting for next job poll.",
+ e);
}
// System.out.println("I'm alive "+alTitle);
}
}
else
{
- Cache.log
- .debug("WebServiceJob poll loop finished with no jobs created.");
+ Cache.log.debug(
+ "WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(MessageManager
- .getString("info.no_jobs_ran"));
+ wsInfo.appendProgressText(
+ MessageManager.getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
}
.getCodonFrames();
if (cf != null)
{
- codonframe = new LinkedHashSet<AlignedCodonFrame>();
+ codonframe = new ArrayList<AlignedCodonFrame>();
codonframe.addAll(cf);
}
}