import java.io.IOException;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import jalview.analysis.AlignmentAnnotationUtils;
-import jalview.api.AlignCalcManagerI2;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
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;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
-import jalview.schemes.FeatureSettingsAdapter;
-import jalview.util.ArrayUtils;
import jalview.util.MapList;
-import jalview.util.MathUtils;
-import jalview.util.Pair;
-import jalview.workers.AlignCalcWorker;
import jalview.ws.params.ArgumentI;
-import jalview.ws2.actions.BaseJob;
import jalview.ws2.actions.BaseTask;
import jalview.ws2.actions.ServiceInputInvalidException;
-import jalview.ws2.actions.api.JobI;
-import jalview.ws2.actions.api.TaskEventListener;
-import jalview.ws2.actions.api.TaskI;
import jalview.ws2.api.Credentials;
import jalview.ws2.api.JobStatus;
-import jalview.ws2.api.WebServiceJobHandle;
import jalview.ws2.client.api.AnnotationWebServiceClientI;
-import jalview.ws2.helpers.DelegateJobEventListener;
-import jalview.ws2.helpers.TaskEventSupport;
public class AnnotationTask extends BaseTask<AnnotationJob, AnnotationResult>
{
private final AlignViewportI viewport;
- private JobStatus taskStatus = null;
-
- private AlignCalcWorkerAdapter worker = null;
-
- private DelegateJobEventListener<AnnotationResult> jobEventHandler;
-
public AnnotationTask(AnnotationWebServiceClientI client,
AnnotationAction action, List<ArgumentI> args, Credentials credentials,
AlignViewportI viewport)
this.viewport = viewport;
}
- // public void start(AlignCalcManagerI2 calcManager)
- // {
- // if (this.worker != null)
- // throw new IllegalStateException("task already started");
- // this.worker = new AlignCalcWorkerAdapter(calcManager);
- // if (taskStatus != JobStatus.CANCELLED)
- // {
- // List<AlignCalcWorkerI> oldWorkers = calcManager.getWorkersOfClass(
- // AlignCalcWorkerAdapter.class);
- // for (var worker : oldWorkers)
- // {
- // if (action.getWebService().getName().equalsIgnoreCase(
- // ((AlignCalcWorkerAdapter) worker).getServiceName()))
- // {
- // // remove interactive workers for the same service.
- // calcManager.removeWorker(worker);
- // calcManager.cancelWorker(worker);
- // }
- // }
- // if (action.getWebService().isInteractive())
- // calcManager.registerWorker(worker);
- // else
- // calcManager.startWorker(worker);
- // }
- // }
-
/**
* Create and return a list of annotation jobs from the current state of the
* viewport. Returned job are not started by this method and should be stored
List<AlignmentAnnotation> annotations = new ArrayList<>();
for (AlignmentAnnotation ala : returnedAnnot)
{
- SequenceI seq = job.seqNames.get(ala.sequenceRef.getName());
- SequenceI aseq = seq.getRootDatasetSequence();
- Annotation[] gappedAnnots = createGappedAnnotations(ala.annotations, job.start, job.gapMap);
+ SequenceI aseq = null;
+ if (ala.sequenceRef != null) {
+ SequenceI seq = job.seqNames.get(ala.sequenceRef.getName());
+ aseq = seq.getRootDatasetSequence();
+ }
ala.sequenceRef = aseq;
+ Annotation[] gappedAnnots = createGappedAnnotations(ala.annotations, job.start, job.gapMap);
ala.annotations = gappedAnnots;
AlignmentAnnotation newAnnot = viewport.getAlignment()
.updateFromOrCopyAnnotation(ala);
- if (aseq != null) // I suspect it's always true
+ if (aseq != null)
{
aseq.addAlignmentAnnotation(newAnnot);
newAnnot.adjustForAlignment();