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 AnnotationAction action;
- private final AlignViewportI viewport;
+ private final AlignmentI alignment;
- private JobStatus taskStatus = null;
-
- private AlignCalcWorkerAdapter worker = null;
-
- private DelegateJobEventListener<AnnotationResult> jobEventHandler;
+ private final AnnotatedCollectionI selectionGroup;
public AnnotationTask(AnnotationWebServiceClientI client,
AnnotationAction action, List<ArgumentI> args, Credentials credentials,
super(client, args, credentials);
this.client = client;
this.action = action;
- this.viewport = viewport;
+ this.alignment = viewport.getAlignment();
+ this.selectionGroup = viewport.getSelectionGroup();
}
- // 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
@Override
public List<AnnotationJob> prepareJobs() throws ServiceInputInvalidException
{
- AlignmentI alignment = viewport.getAlignment();
if (alignment == null || alignment.getWidth() <= 0 ||
alignment.getSequences() == null)
throw new ServiceInputInvalidException("Alignment does not contain sequences");
throw new ServiceInputInvalidException(
action.getFullName() + " does not allow protein sequences");
boolean bySequence = !action.isAlignmentAnalysis();
- AnnotatedCollectionI inputSeqs = bySequence ? viewport.getSelectionGroup() : null;
+ AnnotatedCollectionI inputSeqs = bySequence ? selectionGroup : null;
if (inputSeqs == null || inputSeqs.getWidth() <= 0 ||
inputSeqs.getSequences() == null || inputSeqs.getSequences().size() < 1)
inputSeqs = alignment;
* visibility */
udpateCalcId(returnedAnnot);
- int graphGroup = getNextGraphGroup(viewport.getAlignment());
- shiftGraphGroup(returnedAnnot, graphGroup);
- List<AlignmentAnnotation> annotations = new ArrayList<>();
for (AlignmentAnnotation ala : returnedAnnot)
{
- SequenceI seq = job.seqNames.get(ala.sequenceRef.getName());
- SequenceI aseq = getRootDatasetSequence(seq);
- Annotation[] gappedAnnots = createGappedAnnotations(ala.annotations, job.start, job.gapMap);
- ala.sequenceRef = aseq;
- ala.annotations = gappedAnnots;
-
- AlignmentAnnotation newAnnot = viewport.getAlignment()
- .updateFromOrCopyAnnotation(ala);
- if (aseq != null) // I suspect it's always true
+ SequenceI aseq = null;
+ if (ala.sequenceRef != null)
{
- aseq.addAlignmentAnnotation(newAnnot);
- newAnnot.adjustForAlignment();
- AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
- newAnnot, newAnnot.label, newAnnot.getCalcId());
+ SequenceI seq = job.seqNames.get(ala.sequenceRef.getName());
+ aseq = seq.getRootDatasetSequence();
}
- annotations.add(newAnnot);
+ ala.sequenceRef = aseq;
+ Annotation[] gappedAnnots = createGappedAnnotations(ala.annotations, job.start, job.gapMap);
+ ala.annotations = gappedAnnots;
}
boolean hasFeatures = false;
continue;
hasFeatures = true;
SequenceI seq = job.seqNames.get(sq.getName());
- SequenceI datasetSeq = getRootDatasetSequence(seq);
+ SequenceI datasetSeq = seq.getRootDatasetSequence();
List<ContiguousI> sourceRange = findContiguousRanges(datasetSeq, job.gapMap, job.start, job.end);
int[] sourceStartEnd = ContiguousI.toStartEndArray(sourceRange);
Mapping mp = new Mapping(new MapList(
datasetSeq.transferAnnotation(sq, mp);
}
- return new AnnotationResult(annotations, hasFeatures, featureColours, featureFilters);
+ return new AnnotationResult(returnedAnnot, hasFeatures, featureColours, featureFilters);
}
/**
}
}
- private static int getNextGraphGroup(AlignmentI alignment)
- {
- if (alignment == null || alignment.getAlignmentAnnotation() == null)
- return 1;
- int graphGroup = 1;
- for (AlignmentAnnotation ala : alignment.getAlignmentAnnotation())
- graphGroup = Math.max(graphGroup, ala.graphGroup);
- return graphGroup;
- }
-
- private static void shiftGraphGroup(Iterable<AlignmentAnnotation> annotations, int shift)
- {
- for (AlignmentAnnotation ala : annotations)
- {
- if (ala.graphGroup > 0)
- {
- ala.graphGroup += shift;
- }
- }
- }
-
- private static SequenceI getRootDatasetSequence(SequenceI sequence)
- {
- while (sequence.getDatasetSequence() != null)
- {
- sequence = sequence.getDatasetSequence();
- }
- return sequence;
- }
-
private Annotation[] createGappedAnnotations(Annotation[] annotations, int start, boolean[] gapMap)
{
- var size = Math.max(viewport.getAlignment().getWidth(), gapMap.length);
+ var size = Math.max(alignment.getWidth(), gapMap.length);
Annotation[] gappedAnnotations = new Annotation[size];
for (int p = 0, ap = start; ap < size; ap++)
{
} while (++col <= end);
return ranges;
}
-
- @Override
- public String toString()
- {
- var status = taskStatus != null ? taskStatus.name() : "UNSET";
- return String.format("%s(%x, %s)", getClass().getSimpleName(), uid, status);
- }
}
git://source.jalview.org / jalview.git / blobdiff