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

Example 6 with DNAFeature

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

the class Feature method toDataTransferObject.

@Override
public DNAFeature toDataTransferObject() {
    DNAFeature dnaFeature = new DNAFeature();
    dnaFeature.setId(this.id);
    dnaFeature.setAnnotationType(this.genbankType);
    dnaFeature.setName(this.name);
    dnaFeature.setUri(this.uri);
    if (this.curation != null) {
        dnaFeature.setCuration(this.curation.toDataTransferObject());
    }
    return dnaFeature;
}

Example 7 with DNAFeature

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

the class AnnotationsTest method testCurate.

@Test
public void testCurate() throws Exception {
    Account account = AccountCreator.createTestAccount("AnnotationsTest.testCurate", true);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    SequenceDAO sequenceDAO = new SequenceDAO();
    Assert.assertFalse(sequenceDAO.hasSequence(plasmid.getId()));
    DNASequence dnaSequence = GeneralParser.getInstance().parse(sequenceString);
    Sequence sequence = SequenceController.dnaSequenceToSequence(dnaSequence);
    sequence.setEntry(plasmid);
    sequence = sequenceDAO.saveSequence(sequence);
    Assert.assertNotNull(sequence);
    SequenceFeatureDAO sequenceFeatureDAO = new SequenceFeatureDAO();
    List<SequenceFeature> sequenceFeatures = sequenceFeatureDAO.getEntrySequenceFeatures(plasmid);
    Assert.assertEquals(1, sequenceFeatures.size());
    Feature feature = sequenceFeatures.get(0).getFeature();
    DNAFeature dnaFeature = feature.toDataTransferObject();
    Curation curation = new Curation();
    curation.setExclude(true);
    dnaFeature.setCuration(curation);
    List<DNAFeature> features = new ArrayList<>();
    features.add(dnaFeature);
    Annotations annotations = new Annotations(account.getEmail());
    annotations.curate(features);
    sequenceFeatures = sequenceFeatureDAO.getEntrySequenceFeatures(plasmid);
    feature = sequenceFeatures.get(0).getFeature();
    Assert.assertTrue(feature.getCuration().isExclude());
}

Example 8 with DNAFeature

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

the class ICESBOLParserVisitor method visit.

@Override
public void visit(DnaComponent component) {
    if (featuredDNASequence == null) {
        featuredDNASequence = new FeaturedDNASequence();
        if (update != null) {
            String name = component.getName();
            if (name == null || name.trim().isEmpty())
                update.getKeyValue().put(EntryField.NAME, name);
            else {
                update.getKeyValue().put(EntryField.NAME, name);
                update.getKeyValue().put(EntryField.ALIAS, component.getDisplayId());
            }
            update.getKeyValue().put(EntryField.SUMMARY, component.getDescription());
        }
        featuredDNASequence.setName(component.getName());
        featuredDNASequence.setIdentifier(component.getDisplayId());
        featuredDNASequence.setDescription(component.getDescription());
        featuredDNASequence.setDcUri(component.getURI().toString());
        DnaSequence sequence = component.getDnaSequence();
        if (sequence != null) {
            featuredDNASequence.setSequence(sequence.getNucleotides());
            featuredDNASequence.setUri(sequence.getURI().toString());
        }
    }
    List<SequenceAnnotation> annotations = component.getAnnotations();
    Logger.debug("Encountered DC " + component.getDisplayId());
    if (!annotations.isEmpty()) {
        // iterate sorted annotations for top level
        for (SequenceAnnotation sequenceAnnotation : annotations) {
            int strand;
            if (sequenceAnnotation.getStrand() == null) {
                strand = 1;
            } else {
                strand = sequenceAnnotation.getStrand() == StrandType.POSITIVE ? 1 : -1;
            }
            Pair relative = new Pair(sequenceAnnotation.getBioStart(), sequenceAnnotation.getBioEnd(), strand);
            walkTree(sequenceAnnotation, relative);
            DNAFeature feature = createDNAFeature(sequenceAnnotation, relative);
            DNAFeatureLocation location = feature.getLocations().get(0);
            featuredDNASequence.getFeatures().add(feature);
            Logger.debug("Adding feature [" + location.getGenbankStart() + ", " + location.getEnd() + "] for " + feature.getIdentifier());
        }
    }
}

Example 9 with DNAFeature

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

the class SequenceFeature method toDataTransferObject.

@Override
public DNAFeature toDataTransferObject() {
    DNAFeature dnaFeature = new DNAFeature();
    dnaFeature.setName(this.name);
    dnaFeature.setType(this.genbankType);
    return dnaFeature;
}

Example 10 with DNAFeature

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

the class Annotations method curate.

/**
     * Curates a specified set of annotations. The curation properties are contained in each annotation (feature)
     * object
     *
     * @param features set of features to be curated
     */
public void curate(List<DNAFeature> features) {
    if (!isAdministrator())
        throw new PermissionException("Administrative privileges required to curate features");
    for (DNAFeature dnaFeature : features) {
        if (dnaFeature.getCuration() == null)
            continue;
        Feature feature = featureDAO.get(dnaFeature.getId());
        if (feature == null)
            continue;
        FeatureCurationModel curationModel = feature.getCuration();
        if (feature.getCuration() == null) {
            if (dnaFeature.getCuration().isExclude()) {
                curationModel = new FeatureCurationModel();
                curationModel.setFeature(feature);
                curationModel.setExclude(true);
                curationModel = curationModelDAO.create(curationModel);
            }
        } else {
            curationModel.setExclude(dnaFeature.getCuration().isExclude());
            curationModel = curationModelDAO.update(curationModel);
        }
        if (curationModel != null) {
            feature.setCuration(curationModel);
            featureDAO.update(feature);
        }
    }
}