import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.WsJobParameters;
import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
import jalview.util.MathUtils;
import jalview.util.MessageManager;
+import jalview.workers.AlignCalcManager2;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import jalview.ws2.MenuEntryProviderI;
}
@Override
+ public boolean isAlignmentAnalysis()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean getFilterNonStandardSymbols()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean getNeedsAlignedSequences()
+ {
+ return false;
+ }
+
+ @Override
public MenuEntryProviderI getMenuBuilder()
{
return this::buildMenu;
{
final var calcName = service.getName();
PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
+ final var calcManager = frame.getViewport().getCalcManager();
{
var item = new JMenuItem(MessageManager.formatMessage(
"label.calcname_with_default_settings", calcName));
item.addActionListener((event) -> {
- WebServiceWorkerI worker = new AnnotationWorker();
- wsExecutor.submit(worker);
+ AlignViewport viewport = frame.getCurrentView();
+ AlignmentViewPanel alignPanel = frame.alignPanel;
+ var worker = new AnnotationServiceWorker(this, service,
+ Collections.emptyList(), viewport, alignPanel, frame, frame,
+ calcManager);
+ calcManager.startWorker(worker);
+ // TODO create and submit AnnotataionServiceWorker
});
parent.add(item);
}
.thenAcceptAsync((arguments) -> {
if (arguments != null)
{
-
+ AlignViewport viewport = frame.getCurrentView();
+ AlignmentViewPanel alignPanel = frame.alignPanel;
+ var worker = new AnnotationServiceWorker(
+ AnnotationOperation.this, service, arguments, viewport,
+ alignPanel, frame, frame, calcManager);
+ calcManager.startWorker(worker);
}
});
});
});
}
- private class AnnotationWorker implements WebServiceWorkerI
- {
- private long uid = MathUtils.getUID();
-
- private WSJobList jobs = new WSJobList();
-
- private HashMap<Long, Integer> exceptionCount = new HashMap<>();
-
- private static final int MAX_RETRY = 5;
-
- @Override
- public long getUID()
- {
- return uid;
- }
-
- @Override
- public WebServiceI getWebService()
- {
- return service;
- }
-
- @Override
- public List<WSJob> getJobs()
- {
- return Collections.unmodifiableList(jobs);
- }
-
- @Override
- public void start() throws IOException
- {
-
- }
-
- @Override
- public boolean poll() throws IOException
- {
- boolean done = true;
- for (WSJob job : getJobs())
- {
- if (!job.getStatus().isDone() && !job.getStatus().isFailed())
- {
- Cache.log.debug(format("Polling job %s", job));
- try
- {
- service.updateProgress(job);
- exceptionCount.remove(job.getUid());
- } catch (IOException e)
- {
- Cache.log.error(format("Polling job %s failed.", job), e);
- int count = exceptionCount.getOrDefault(job.getUid(),
- MAX_RETRY);
- if (--count <= 0)
- {
- job.setStatus(WSJobStatus.SERVER_ERROR);
- Cache.log.warn(format(
- "Attempts limit exceeded. Droping job %s.", job));
- }
- exceptionCount.put(job.getUid(), count);
- } catch (OutOfMemoryError e)
- {
- job.setStatus(WSJobStatus.BROKEN);
- Cache.log.error(
- format("Out of memory when retrieving job %s", job), e);
- }
- Cache.log.debug(
- format("Job %s status is %s", job, job.getStatus()));
- }
- done &= job.getStatus().isDone() || job.getStatus().isFailed();
- }
- return done;
- }
-
- @Override
- public void done()
- {
- // TODO Auto-generated method stub
-
- }
-
- }
}