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Merged
bioinsilico merged 3 commits into from
Mar 31, 2026
Merged

Js/dev genome features #9

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4e6b3ab
features map bug fixed
bioinsilico Mar 30, 2026
2860ee4
genome map fixed
bioinsilico Mar 31, 2026
303c39d
props
bioinsilico Mar 31, 2026
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2 changes: 1 addition & 1 deletion ...n/java/org/rcsb/rcsbsequencecoordinates/collectors/alignments/GenomeAlignmentsHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ private static int getIncrement(Document genomeAlignment){
return genomeAlignment.getInteger(SchemaConstants.Field.ORIENTATION);
}

private static List<Integer> mapToGenomeIndex(int proteinIndex, Range proteinRange, Range genomeRange){
public static List<Integer> mapToGenomeIndex(int proteinIndex, Range proteinRange, Range genomeRange){
if(!proteinRange.contains(proteinIndex))
return List.of();
int begin = 3 * (proteinIndex - proteinRange.bottom()) + genomeRange.bottom();
Expand Down
44 changes: 18 additions & 26 deletions ...in/java/org/rcsb/rcsbsequencecoordinates/collectors/annotations/AnnotationsCollector.java
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Expand Up @@ -5,10 +5,9 @@
package org.rcsb.rcsbsequencecoordinates.collectors.annotations;

import org.bson.Document;
import org.rcsb.rcsbsequencecoordinates.collectors.alignments.AlignmentsCollector;
import org.rcsb.rcsbsequencecoordinates.collectors.alignments.SequenceAlignmentsCollector;
import org.rcsb.rcsbsequencecoordinates.collectors.utils.AnnotationFilterOperator;
import org.rcsb.rcsbsequencecoordinates.collectors.utils.AnnotationRangeIntersection;
import org.rcsb.rcsbsequencecoordinates.collectors.utils.RangeIntersectionOperator;
import org.rcsb.graphqlschema.params.AnnotationFilter;
import org.rcsb.graphqlschema.reference.AnnotationReference;
import org.rcsb.graphqlschema.reference.GroupReference;
Expand Down Expand Up @@ -46,10 +45,10 @@ public Flux<Document> getAnnotations(
List<AnnotationFilter> annotationFilters,
List<Integer> range
) {
RangeIntersectionOperator annotationRangeIntersection = new RangeIntersectionOperator(range, new AnnotationRangeIntersection());
return getAnnotations(queryId, sequenceReference, annotationReferences, annotationFilters)
.filter(annotationRangeIntersection::isConnected)
.map(annotationRangeIntersection::applyRange);
return Flux.fromIterable(annotationReferences)
.flatMap(
annotationReference -> getAnnotations(queryId, sequenceReference, annotationReference, annotationFilters, range)
);
}

public Flux<Document> getAnnotations(
Expand All @@ -59,25 +58,13 @@ public Flux<Document> getAnnotations(
List<AnnotationFilter> annotationFilters
){
if(groupReference.equals(GroupReference.MATCHING_UNIPROT_ACCESSION))
return getAnnotations(groupId, SequenceReference.UNIPROT, annotationReferences, annotationFilters);
return getAnnotations(groupId, SequenceReference.UNIPROT, annotationReferences, annotationFilters, null);
return Flux.fromIterable(annotationReferences)
.flatMap(
annotationReference -> getAnnotations(groupId, groupReference, annotationReference, annotationFilters)
);
}

private Flux<Document> getAnnotations(
String queryId,
SequenceReference sequenceReference,
List<AnnotationReference> annotationReferences,
List<AnnotationFilter> annotationFilters
) {
return Flux.fromIterable(annotationReferences)
.flatMap(
annotationReference -> getAnnotations(queryId, sequenceReference, annotationReference, annotationFilters)
);
}

private Flux<Document> getAnnotations(
String groupId,
GroupReference groupReference,
Expand Down Expand Up @@ -126,14 +113,18 @@ private Flux<Document> getAnnotations(
String queryId,
SequenceReference sequenceReference,
AnnotationReference annotationReference,
List<AnnotationFilter> annotationFilters
List<AnnotationFilter> annotationFilters,
List<Integer> range
) {
return sequenceAlignmentsCollector
AlignmentsCollector alignmentsCollector = sequenceAlignmentsCollector
.request(
queryId,
sequenceReference,
annotationReference.toSequenceReference()
)
queryId,
sequenceReference,
annotationReference.toSequenceReference()
);
if(range != null)
alignmentsCollector.range(range);
return alignmentsCollector
.get()
.flatMap(
alignment -> getAnnotations(annotationReference, annotationFilters, alignment)
Expand All @@ -152,7 +143,8 @@ private Flux<Document> getAnnotations(
.filter(filter::targetCheck)
.map(filter::applyFilterToFeatures)
.filter(AnnotationsHelper::hasFeatures)
.map(annotations -> mapAnnotations(annotations, alignment));
.map(annotations -> mapAnnotations(annotations, alignment))
.filter(annotations -> !annotations.isEmpty());
}

private Flux<Document> switchAlignmentEntityIdToReference(Document alignment, SequenceReference reference){
Expand Down
24 changes: 17 additions & 7 deletions src/main/java/org/rcsb/rcsbsequencecoordinates/collectors/annotations/AnnotationsHelper.java
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Expand Up @@ -23,6 +23,7 @@
import static com.mongodb.client.model.Filters.eq;
import static com.mongodb.client.model.Filters.or;
import static com.mongodb.client.model.Projections.*;
import static org.rcsb.rcsbsequencecoordinates.collectors.alignments.GenomeAlignmentsHelper.mapToGenomeIndex;
import static org.rcsb.rcsbsequencecoordinates.collectors.map.MapHelper.parseAsymFromInstance;
import static org.rcsb.rcsbsequencecoordinates.collectors.map.MapHelper.parseEntryFromInstance;
import static org.rcsb.utils.RangeMethods.intersection;
Expand Down Expand Up @@ -69,12 +70,15 @@ public static List<Bson> getAggregation(List<String> ids){
}

public static Document mapAnnotations(Document annotations, Document alignment){
List<Document> features = annotations.getList(SequenceCoordinatesConstants.FEATURES, Document.class).stream()
.map(feature-> mapFeature(feature, alignment))
.filter(d->!d.getList(SequenceCoordinatesConstants.FEATURE_POSITIONS, Document.class).isEmpty())
.toList();
if (features.isEmpty())
return new Document();
annotations.put(
SchemaConstants.Field.FEATURES,
annotations.getList(SequenceCoordinatesConstants.FEATURES, Document.class).stream()
.map(feature-> mapFeature(feature, alignment))
.filter(d->!d.getList(SequenceCoordinatesConstants.FEATURE_POSITIONS, Document.class).isEmpty())
.toList()
features
);
return annotations;
}
Expand Down Expand Up @@ -164,7 +168,9 @@ private static Document valuesIntersection(Document featureRegion, Document alig
alignmentRegion.getInteger(SequenceCoordinatesConstants.QUERY_END)
);
return new Document(Map.of(
SchemaConstants.Field.BEG_SEQ_ID, mapIndex(intersection.bottom(), targetRange, queryRange),
SchemaConstants.Field.BEG_SEQ_ID, alignmentRegion.containsKey(SequenceCoordinatesConstants.EXON_SHIFT) ?
mapToGenomeIndex(intersection.bottom(), targetRange, queryRange).get(0) :
mapIndex(intersection.bottom(), targetRange, queryRange),
SchemaConstants.Field.BEG_ORI_ID, intersection.bottom(),
SchemaConstants.Field.VALUES, featureValues.subList(
intersection.bottom() - featureRange.bottom(),
Expand Down Expand Up @@ -195,8 +201,12 @@ private static Document regionIntersection(Document featureRegion, Document alig
alignmentRegion.getInteger(SequenceCoordinatesConstants.QUERY_END)
);
return new Document(Map.of(
SchemaConstants.Field.BEG_SEQ_ID, mapIndex(intersection.bottom(), targetRange, queryRange),
SchemaConstants.Field.END_SEQ_ID, mapIndex(intersection.top(), targetRange, queryRange),
SchemaConstants.Field.BEG_SEQ_ID, alignmentRegion.containsKey(SequenceCoordinatesConstants.EXON_SHIFT) ?
mapToGenomeIndex(intersection.bottom(), targetRange, queryRange).get(0) :
mapIndex(intersection.bottom(), targetRange, queryRange),
SchemaConstants.Field.END_SEQ_ID, alignmentRegion.containsKey(SequenceCoordinatesConstants.EXON_SHIFT) ?
mapToGenomeIndex(intersection.top(), targetRange, queryRange).get(2) :
mapIndex(intersection.top(), targetRange, queryRange),
SchemaConstants.Field.BEG_ORI_ID, intersection.bottom(),
SchemaConstants.Field.END_ORI_ID, intersection.top(),
SchemaConstants.Field.OPEN_BEGIN, intersection.bottom() != featureRegion.getInteger(SequenceCoordinatesConstants.BEG_SEQ_ID),
Expand Down
4 changes: 3 additions & 1 deletion src/main/resources/static/graphiql/index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,9 @@
<!DOCTYPE html>
<html lang="en">
<head>
<title>GraphiQL</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>RCSB PDB Sequence Coordinates - GraphiQL</title>
<style>
body {
height: 100%;
Expand Down
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