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>
+public class AnnotationTask
+ extends BaseTask<AnnotationJob, AnnotationResult>
{
private AnnotationWebServiceClientI client;
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,
- AlignViewportI viewport)
+ AnnotationAction action, List<ArgumentI> args,
+ Credentials credentials, AlignViewportI viewport)
{
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
* in a field and started separately.
- *
+ *
* @return list of annotation jobs
* @throws ServiceInputInvalidException
* input data is not valid
*/
@Override
- public List<AnnotationJob> prepareJobs() throws ServiceInputInvalidException
+ 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");
- if (alignment.isNucleotide() && !action.doAllowNucleotide())
+ if (alignment == null || alignment.getWidth() <= 0
+ || alignment.getSequences() == null)
throw new ServiceInputInvalidException(
- action.getFullName() + " does not allow nucleotide sequences");
+ "Alignment does not contain sequences");
+ if (alignment.isNucleotide() && !action.doAllowNucleotide())
+ throw new ServiceInputInvalidException(action.getFullName()
+ + " does not allow nucleotide sequences");
if (!alignment.isNucleotide() && !action.doAllowProtein())
throw new ServiceInputInvalidException(
- action.getFullName() + " does not allow protein sequences");
+ action.getFullName() + " does not allow protein sequences");
boolean bySequence = !action.isAlignmentAnalysis();
- AnnotatedCollectionI inputSeqs = bySequence ? viewport.getSelectionGroup() : null;
- if (inputSeqs == null || inputSeqs.getWidth() <= 0 ||
- inputSeqs.getSequences() == null || inputSeqs.getSequences().size() < 1)
+ AnnotatedCollectionI inputSeqs = bySequence ? selectionGroup : null;
+ if (inputSeqs == null || inputSeqs.getWidth() <= 0
+ || inputSeqs.getSequences() == null
+ || inputSeqs.getSequences().size() < 1)
inputSeqs = alignment;
boolean submitGaps = action.isAlignmentAnalysis();
boolean requireAligned = action.getRequireAlignedSequences();
boolean filterSymbols = action.getFilterSymbols();
int minSize = action.getMinSequences();
AnnotationJob job = AnnotationJob.create(inputSeqs, bySequence,
- submitGaps, requireAligned, filterSymbols, minSize);
+ submitGaps, requireAligned, filterSymbols, minSize);
if (!job.isInputValid())
{
job.setStatus(JobStatus.INVALID);
- throw new ServiceInputInvalidException("Annotation job has invalid input");
+ throw new ServiceInputInvalidException(
+ "Annotation job has invalid input");
}
job.setStatus(JobStatus.READY);
return List.of(job);
}
@Override
- protected AnnotationResult collectResult(List<AnnotationJob> jobs) throws IOException
+ protected AnnotationResult collectResult(List<AnnotationJob> jobs)
+ throws IOException
{
final Map<String, FeatureColourI> featureColours = new HashMap<>();
final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
var job = jobs.get(0);
List<AlignmentAnnotation> returnedAnnot = client.attachAnnotations(
- job.getServerJob(), job.getInputSequences(), featureColours,
- featureFilters);
+ job.getServerJob(), job.getInputSequences(), featureColours,
+ featureFilters);
/* TODO
* copy over each annotation row returned and also defined on each
* sequence, excluding regions not annotated due to gapMap/column
* visibility */
udpateCalcId(returnedAnnot);
- int graphGroup = viewport.getAlignment().getLastGraphGroup();
- shiftGraphGroup(returnedAnnot, graphGroup);
- 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);
- ala.sequenceRef = aseq;
- ala.annotations = gappedAnnots;
-
- AlignmentAnnotation newAnnot = viewport.getAlignment()
- .updateFromOrCopyAnnotation(ala);
- if (aseq != null) // I suspect it's always true
+ SequenceI seq = (ala.sequenceRef == null) ? null
+ : job.seqNames.get(ala.sequenceRef.getName());
+ if (job.gapMap != null && job.gapMap.length > 0)
+ ala.annotations = createGappedAnnotations(ala.annotations,
+ job.gapMap);
+ if (seq != null)
{
- aseq.addAlignmentAnnotation(newAnnot);
- newAnnot.adjustForAlignment();
- AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
- newAnnot, newAnnot.label, newAnnot.getCalcId());
+ int startRes = seq.findPosition(job.regionStart);
+ ala.createSequenceMapping(seq, startRes, false);
}
- annotations.add(newAnnot);
}
boolean hasFeatures = false;
for (SequenceI sq : job.getInputSequences())
{
- if (!sq.getFeatures().hasFeatures() && (sq.getDBRefs() == null || sq.getDBRefs().isEmpty()))
+ if (!sq.getFeatures().hasFeatures()
+ && (sq.getDBRefs() == null || sq.getDBRefs().isEmpty()))
continue;
hasFeatures = true;
SequenceI seq = job.seqNames.get(sq.getName());
SequenceI datasetSeq = seq.getRootDatasetSequence();
- List<ContiguousI> sourceRange = findContiguousRanges(datasetSeq, job.gapMap, job.start, job.end);
+ List<ContiguousI> sourceRange = findContiguousRanges(seq,
+ job.gapMap, job.regionStart, job.regionEnd);
int[] sourceStartEnd = ContiguousI.toStartEndArray(sourceRange);
- Mapping mp = new Mapping(new MapList(
- sourceStartEnd, new int[]
- { datasetSeq.getStart(), datasetSeq.getEnd() }, 1, 1));
+ Mapping mp = new Mapping(
+ new MapList(
+ sourceStartEnd,
+ new int[] { datasetSeq.getStart(), datasetSeq.getEnd() },
+ 1, 1));
datasetSeq.transferAnnotation(sq, mp);
}
- return new AnnotationResult(annotations, hasFeatures, featureColours, featureFilters);
+ return new AnnotationResult(returnedAnnot, hasFeatures, featureColours,
+ featureFilters);
}
/**
{
for (var annotation : annotations)
{
- if (annotation.getCalcId() == null || annotation.getCalcId().isEmpty())
+ if (annotation.getCalcId() == null
+ || annotation.getCalcId().isEmpty())
{
annotation.setCalcId(action.getFullName());
}
- annotation.autoCalculated = action.isAlignmentAnalysis() &&
- action.getWebService().isInteractive();
- }
- }
-
- private static void shiftGraphGroup(Iterable<AlignmentAnnotation> annotations, int shift)
- {
- for (AlignmentAnnotation ala : annotations)
- {
- if (ala.graphGroup > 0)
- {
- ala.graphGroup += shift;
- }
+ annotation.autoCalculated = action.isAlignmentAnalysis()
+ && action.getWebService().isInteractive();
}
}
- private Annotation[] createGappedAnnotations(Annotation[] annotations, int start, boolean[] gapMap)
+ // TODO: review and test
+ // may produce wrong output if annotations longer than gapMap
+ private Annotation[] createGappedAnnotations(Annotation[] annotations,
+ boolean[] gapMap)
{
- var size = Math.max(viewport.getAlignment().getWidth(), gapMap.length);
+ var size = Math.max(annotations.length, gapMap.length);
Annotation[] gappedAnnotations = new Annotation[size];
- for (int p = 0, ap = start; ap < size; ap++)
+ for (int p = 0, ap = 0; ap < size; ap++)
{
- if (gapMap != null && gapMap.length > ap && !gapMap[ap])
+ if (ap < gapMap.length && !gapMap[ap])
{
gappedAnnotations[ap] = new Annotation("", "", ' ', Float.NaN);
}
return gappedAnnotations;
}
- private List<ContiguousI> findContiguousRanges(SequenceI seq, boolean[] gapMap, int start, int end)
+ // TODO: review ant test!!!
+ private List<ContiguousI> findContiguousRanges(SequenceI seq,
+ boolean[] gapMap, int start, int end)
{
if (gapMap == null || gapMap.length < end)
- return List.of(seq.findPositions(start, end));
+ return List.of(seq.findPositions(start + 1, end + 1));
List<ContiguousI> ranges = new ArrayList<>();
int lastcol = start, col = start;
do
} 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