Examples with DNAFeature org.jbei.ice.lib.dto.DNAFeature used on opensource projects

Example 1 with DNAFeature

use of org.jbei.ice.lib.dto.DNAFeature in project ice by JBEI.

the class ICESBOLParserVisitor method createDNAFeature.

static DNAFeature createDNAFeature(SequenceAnnotation annotation, Pair pair) {
    DNAFeature feature = new DNAFeature();
    // set feature location
    DNAFeatureLocation location = new DNAFeatureLocation();
    location.setGenbankStart(pair.getFirst());
    location.setEnd(pair.getSecond());
    // get sequence strand type and uri
    feature.setStrand(pair.getStrand());
    feature.setUri(annotation.getURI().toString());
    // get sequence annotation type and start and end sequence
    DnaComponent subComponent = annotation.getSubComponent();
    if (subComponent != null) {
        location.setUri(subComponent.getURI().toString());
        String name = subComponent.getName();
        if (name == null || name.trim().isEmpty())
            name = subComponent.getDisplayId();
        feature.setName(name);
        feature.setIdentifier(subComponent.getDisplayId());
        String featureType = getFeatureType(subComponent.getTypes());
        feature.setType(featureType);
    }
    feature.getLocations().add(location);
    return feature;
}

Example 2 with DNAFeature

use of org.jbei.ice.lib.dto.DNAFeature in project ice by JBEI.

the class ICESBOLParserVisitor method walkTree.

private void walkTree(SequenceAnnotation parent, Pair relativePair) {
    List<SequenceAnnotation> annotations = parent.getSubComponent().getAnnotations();
    if (!annotations.isEmpty()) {
        for (SequenceAnnotation sequenceAnnotation : annotations) {
            int strand;
            if (sequenceAnnotation.getStrand() == null) {
                strand = relativePair.getStrand();
            } else {
                strand = sequenceAnnotation.getStrand() == StrandType.POSITIVE ? relativePair.getStrand() : relativePair.getStrand() * -1;
            }
            Pair newRelativePair;
            if (strand > 0)
                newRelativePair = calculatePairForPositiveStrand(sequenceAnnotation, relativePair);
            else
                newRelativePair = calculatePairForNegativeStrand(sequenceAnnotation, relativePair);
            walkTree(sequenceAnnotation, newRelativePair);
            DNAFeature feature = createDNAFeature(sequenceAnnotation, newRelativePair);
            DNAFeatureLocation location = feature.getLocations().get(0);
            featuredDNASequence.getFeatures().add(feature);
            Logger.debug("Adding feature " + strand + "[" + location.getGenbankStart() + ", " + location.getEnd() + "] for " + feature.getIdentifier());
        }
    }
}

Example 3 with DNAFeature

use of org.jbei.ice.lib.dto.DNAFeature in project ice by JBEI.

the class Annotations method generate.

/**
     * Using existing and potentially curated annotations on this ICE instance,
     * this generates matching features for the passed sequence
     *
     * @param sequence wrapper around dna sequence
     * @return wrapper around passed sequence and now with list if annotations for that sequence
     */
public FeaturedDNASequence generate(FeaturedDNASequence sequence) {
    BlastQuery query = new BlastQuery();
    query.setSequence(sequence.getSequence());
    try {
        List<DNAFeature> features = BlastPlus.runCheckFeatures(query);
        sequence.getFeatures().addAll(features);
        return sequence;
    } catch (BlastException e) {
        Logger.error(e);
        return null;
    }
}

Example 4 with DNAFeature

use of org.jbei.ice.lib.dto.DNAFeature in project ice by JBEI.

the class BlastPlus method processFeaturesBlastOutput.

/**
     * Process the output of the blast run for features
     * into a list of feature objects
     * <br>
     * Expected format for the output (per line) is
     * <code>feature_id, label, type, qstart, qend, sstart, send, sstrand</code>
     * Therefore line[0] is feature_id, line[1] is label etc
     * <br>Since we are only interested in features that have a full match (covers entire feature) some matches are
     * manually eliminated. The results returned by blast can cover only a subset of the sequence. e.g.
     * given query = 'ATGC' and feature1 = 'ATG' and feature2 = 'TATGT', the query will return
     * 1,3,1,3 and 1,3,2,4.
     *
     * @param blastOutput blast program output
     * @return list of feature objects resulting from processing the blast output
     */
public static List<DNAFeature> processFeaturesBlastOutput(String blastOutput) {
    List<DNAFeature> hashMap = new ArrayList<>();
    HashSet<String> duplicates = new HashSet<>();
    try (CSVReader reader = new CSVReader(new StringReader(blastOutput))) {
        List<String[]> lines = reader.readAll();
        for (String[] line : lines) {
            if (line.length != 9) {
                continue;
            }
            long id = Long.decode(line[0]);
            String label = line[1];
            String type = line[2];
            int strand = Integer.decode(line[3]);
            int queryStart = Integer.decode(line[4]);
            int queryEnd = Integer.decode(line[5]);
            int subjectStart = Integer.decode(line[6]);
            int subjectEnd = Integer.decode(line[7]);
            if (!duplicates.add(label + ":" + queryStart + ":" + queryEnd + ":" + strand)) {
                continue;
            }
            if (subjectStart != 1 && (queryEnd - queryStart) + 1 != subjectEnd)
                continue;
            // check for full feature coverage
            DNAFeature dnaFeature = new DNAFeature();
            dnaFeature.setId(id);
            dnaFeature.setName(label);
            dnaFeature.setType(type);
            DNAFeatureLocation location = new DNAFeatureLocation();
            location.setGenbankStart(queryStart);
            location.setEnd(queryEnd);
            dnaFeature.getLocations().add(location);
            dnaFeature.setStrand(strand);
            hashMap.add(dnaFeature);
        }
        return hashMap;
    } catch (IOException e) {
        Logger.error(e);
        return null;
    }
}

Example 5 with DNAFeature

use of org.jbei.ice.lib.dto.DNAFeature in project ice by JBEI.

the class AnnotationResource method curate.

/**
     * Curate available annotations to include or exclude them from auto-annotation feature
     *
     * @param list list of annotations each with specified curate
     */
@PUT
@Produces(MediaType.APPLICATION_JSON)
public Response curate(List<DNAFeature> list) {
    String userId = requireUserId();
    Annotations annotations = new Annotations(userId);
    try {
        final Type fooType = new TypeToken<ArrayList<DNAFeature>>() {
        }.getType();
        final Gson gson = new GsonBuilder().create();
        final ArrayList<DNAFeature> features = gson.fromJson(gson.toJsonTree(list), fooType);
        annotations.curate(features);
        return super.respond(true);
    } catch (PermissionException e) {
        Logger.error(e);
        throw new WebApplicationException(Response.Status.FORBIDDEN);
    }
}