Examples with AnnotationLocation org.jbei.ice.storage.model.AnnotationLocation used on opensource projects

Example 1 with AnnotationLocation

use of org.jbei.ice.storage.model.AnnotationLocation in project ice by JBEI.

the class GenbankFormatter method format.

@Override
public void format(Sequence sequence, OutputStream outputStream) throws FormatterException, IOException {
    if (sequence == null || outputStream == null || sequence.getSequence().isEmpty()) {
        return;
    }
    SimpleRichSequence simpleRichSequence = null;
    try {
        simpleRichSequence = new SimpleRichSequence(getNamespace(), normalizeLocusName(name), accessionNumber, version, DNATools.createDNA(sequence.getSequence()), seqVersion);
        simpleRichSequence.setCircular(getCircular());
        if (getDescription() != null && !getDescription().isEmpty()) {
            simpleRichSequence.setDescription(getDescription());
        }
        if (getDivision() != null && !getDivision().isEmpty()) {
            simpleRichSequence.setDivision(getDivision());
        }
        if (getIdentifier() != null && !getIdentifier().isEmpty()) {
            simpleRichSequence.setIdentifier(getIdentifier());
        }
        if (sequence.getSequenceFeatures() != null && sequence.getSequenceFeatures().size() > 0) {
            Set<Feature> featureSet = new LinkedHashSet<>();
            for (SequenceFeature sequenceFeature : sequence.getSequenceFeatures()) {
                if (sequenceFeature.getFeature() == null) {
                    Logger.warn("In sequence with id: " + sequence.getId() + "; SequenceFeature object has no feature assigned to it.");
                    continue;
                }
                RichFeature.Template featureTemplate = new RichFeature.Template();
                featureTemplate.annotation = getAnnotations(sequenceFeature);
                Set<AnnotationLocation> locations = sequenceFeature.getAnnotationLocations();
                if (locations == null || locations.size() == 0)
                    continue;
                if (locations.size() == 1) {
                    featureTemplate.location = new SimpleRichLocation(new SimplePosition(sequenceFeature.getUniqueGenbankStart()), new SimplePosition(sequenceFeature.getUniqueEnd()), 1, getStrand(sequenceFeature));
                } else {
                    ArrayList<Location> members = new ArrayList<>();
                    for (AnnotationLocation location : locations) {
                        members.add(new SimpleRichLocation(new SimplePosition(location.getGenbankStart()), new SimplePosition(location.getEnd()), 1, getStrand(sequenceFeature)));
                    }
                    featureTemplate.location = new CompoundRichLocation(members);
                }
                featureTemplate.source = getDefaultFeatureSource();
                featureTemplate.type = getFeatureType(sequenceFeature);
                featureTemplate.rankedCrossRefs = new TreeSet<>();
                SimpleRichFeature simpleRichFeature = new SimpleRichFeature(simpleRichSequence, featureTemplate);
                featureSet.add(simpleRichFeature);
            }
            simpleRichSequence.setFeatureSet(featureSet);
        }
    } catch (Exception e) {
        throw new FormatterException("Failed to create generate genbank file", e);
    }
    RichSequence.IOTools.writeGenbank(outputStream, simpleRichSequence, getNamespace());
}

Example 2 with AnnotationLocation

use of org.jbei.ice.storage.model.AnnotationLocation in project ice by JBEI.

the class SBOLVisitor method visit.

public void visit(SequenceFeature feature) {
    SequenceAnnotation annotation = SBOLFactory.createSequenceAnnotation();
    String uri = feature.getUri();
    if (uri == null || uri.isEmpty()) {
        uri = UUID.randomUUID().toString();
        annotation.setURI(URI.create(uriString + "/sa#" + uri));
    } else {
        if (uris.contains(uri))
            return;
        uris.add(uri);
        annotation.setURI(URI.create(uri));
    }
    AnnotationLocation location = null;
    if (feature.getAnnotationLocations() != null && !feature.getAnnotationLocations().isEmpty()) {
        location = (AnnotationLocation) feature.getAnnotationLocations().toArray()[0];
        if (location.getGenbankStart() <= location.getEnd()) {
            annotation.setBioStart(location.getGenbankStart());
            annotation.setBioEnd(location.getEnd());
        }
    }
    annotation.setStrand(feature.getStrand() == 1 ? StrandType.POSITIVE : StrandType.NEGATIVE);
    DnaComponent subComponent = SBOLFactory.createDnaComponent();
    String dcUri = feature.getFeature().getUri();
    if (dcUri == null || dcUri.isEmpty()) {
        dcUri = UUID.randomUUID().toString();
        subComponent.setURI(URI.create(uriString + "/dc#" + dcUri));
        subComponent.setDisplayId(dcUri);
    } else {
        if (uris.contains(dcUri))
            return;
        uris.add(dcUri);
        subComponent.setURI(URI.create(dcUri));
        String displayId = StringUtils.isBlank(feature.getFeature().getIdentification()) ? dcUri.substring(dcUri.lastIndexOf("/") + 1) : feature.getFeature().getIdentification();
        subComponent.setDisplayId(displayId);
    }
    subComponent.setName(feature.getName());
    subComponent.addType(IceSequenceOntology.getURI(feature.getGenbankType()));
    annotation.setSubComponent(subComponent);
    // add a dna sequence for cases where the feature wraps around the origin
    if (location != null && location.getGenbankStart() > location.getEnd()) {
        DnaSequence subComponentSequence = SBOLFactory.createDnaSequence();
        String sequence = location.getSequenceFeature().getSequence().getSequence();
        StringBuilder builder = new StringBuilder();
        int start = location.getGenbankStart() - 1;
        if (start < sequence.length()) {
            builder.append(sequence.substring(start, sequence.length()));
        } else {
            Logger.warn("Encountered feature with start " + location.getGenbankStart() + " and sequence length of " + sequence.length());
            return;
        }
        builder.append(sequence.substring(0, location.getEnd()));
        subComponentSequence.setNucleotides(builder.toString());
        subComponentSequence.setURI(URI.create(uriString + "/ds#" + UUID.randomUUID().toString()));
        subComponent.setDnaSequence(subComponentSequence);
    }
    dnaComponent.addAnnotation(annotation);
}