import jalview.api.FeatureColourI;
import jalview.api.PollableAlignCalcWorkerI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
if (seqs == null || !checkValidInputSeqs(seqs))
{
- jalview.bin.Cache.log.debug(
+ jalview.bin.Console.debug(
"Sequences for analysis service were null or not valid");
return;
}
guiProgress.setProgressBar(service.getActionText(),
progressId = System.currentTimeMillis());
}
- jalview.bin.Cache.log.debug("submitted " + seqs.size()
+ jalview.bin.Console.debug("submitted " + seqs.size()
+ " sequences to " + service.getActionText());
rslt = annotService.submitToService(seqs, getPreset(),
return;
}
// TODO: handle job submission error reporting here.
- Cache.log.debug("Service " + service.getUri() + "\nSubmitted job ID: "
+ Console.debug("Service " + service.getUri() + "\nSubmitted job ID: "
+ rslt);
// ///
// otherwise, construct WsJob and any UI handlers
{
boolean finished = false;
- Cache.log.debug("Updating status for annotation service.");
+ Console.debug("Updating status for annotation service.");
annotService.updateStatus(running);
job.updateJobPanelState(info, "", running);
if (running.isSubjobComplete())
{
- Cache.log.debug(
+ Console.debug(
"Finished polling analysis service job: status reported is "
+ running.getState());
finished = true;
}
else
{
- Cache.log.debug("Status now " + running.getState());
+ Console.debug("Status now " + running.getState());
}
// pull any stats - some services need to flush log output before
// results are available
- Cache.log.debug("Updating progress log for annotation service.");
+ Console.debug("Updating progress log for annotation service.");
try
{
annotService.updateJobProgress(running);
} catch (Throwable thr)
{
- Cache.log.debug("Ignoring exception during progress update.",
+ Console.debug("Ignoring exception during progress update.",
thr);
}
- Cache.log.debug("Result of poll: " + running.getStatus());
+ Console.debug("Result of poll: " + running.getStatus());
if (finished)
{
- Cache.log.debug("Job poll loop exited. Job is " + running.getState());
+ Console.debug("Job poll loop exited. Job is " + running.getState());
if (running.isFinished())
{
// expect there to be results to collect
// features automatically according to user preferences
running.setFeatureRenderer(
((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
- Cache.log.debug("retrieving job results.");
+ Console.debug("retrieving job results.");
final Map<String, FeatureColourI> featureColours = new HashMap<>();
final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
List<AlignmentAnnotation> returnedAnnot = annotService
.getAnnotationResult(running.getJobHandle(), seqs,
featureColours, featureFilters);
- Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
+ Console.debug("Obtained " + (returnedAnnot == null ? "no rows"
: ("" + returnedAnnot.size())));
- Cache.log.debug("There were " + featureColours.size()
+ Console.debug("There were " + featureColours.size()
+ " feature colours and " + featureFilters.size()
+ " filters defined.");
if (running.hasResults())
{
- jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ jalview.bin.Console.debug("Updating result annotation from Job "
+ rslt + " at " + service.getUri());
updateResultAnnotation(true);
if (running.isTransferSequenceFeatures())
// regions
// not annotated due to gapMap/column visibility
- jalview.bin.Cache.log.debug(
+ jalview.bin.Console.debug(
"Updating feature display settings and transferring features from Job "
+ rslt + " at " + service.getUri());
// TODO: consider merge rather than apply here
ap.adjustAnnotationHeight();
}
}
- Cache.log.debug("Annotation Service Worker thread finished.");
+ Console.debug("Annotation Service Worker thread finished.");
}