import java.util.List;
import java.util.Map;
-import jalview.analysis.AlignmentAnnotationUtils;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.ws2.api.JobStatus;
import jalview.ws2.client.api.AnnotationWebServiceClientI;
-public class AnnotationTask extends BaseTask<AnnotationJob, AnnotationResult>
+public class AnnotationTask
+ extends BaseTask<AnnotationJob, AnnotationResult>
{
private AnnotationWebServiceClientI client;
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;
* 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
{
- 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 ? selectionGroup : null;
- if (inputSeqs == null || inputSeqs.getWidth() <= 0 ||
- inputSeqs.getSequences() == null || inputSeqs.getSequences().size() < 1)
+ 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
udpateCalcId(returnedAnnot);
for (AlignmentAnnotation ala : returnedAnnot)
{
- SequenceI aseq = null;
- if (ala.sequenceRef != null)
+ 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)
{
- SequenceI seq = job.seqNames.get(ala.sequenceRef.getName());
- aseq = seq.getRootDatasetSequence();
+ int startRes = seq.findPosition(job.regionStart);
+ ala.createSequenceMapping(seq, startRes, false);
}
- ala.sequenceRef = aseq;
- Annotation[] gappedAnnots = createGappedAnnotations(ala.annotations, job.start, job.gapMap);
- ala.annotations = gappedAnnots;
}
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(returnedAnnot, 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();
+ annotation.autoCalculated = action.isAlignmentAnalysis()
+ && action.getWebService().isInteractive();
}
}
- private Annotation[] createGappedAnnotations(Annotation[] annotations, int start, boolean[] gapMap)
+ private Annotation[] createGappedAnnotations(Annotation[] annotations,
+ boolean[] gapMap)
{
- var size = Math.max(alignment.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
git://source.jalview.org / jalview.git / blobdiff