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

Example 11 with DNAFeature

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

the class Annotations method generate.

/**
     * Auto generate annotations for specified entry
     *
     * @param entryId       unique (local) identifier for entry
     * @param ownerFeatures whether to only include the features created by the requesting user
     * @return wrapper around generated annotations, if any are found
     */
public FeaturedDNASequence generate(long entryId, boolean ownerFeatures) {
    Entry entry = entryDAO.get(entryId);
    if (entry == null)
        throw new IllegalArgumentException("Could not retrieve entry with id \"" + entryId + "\"");
    Sequence sequence = sequenceDAO.getByEntry(entry);
    if (sequence == null)
        return null;
    String sequenceString = sequence.getSequence();
    BlastQuery query = new BlastQuery();
    query.setSequence(sequenceString);
    try {
        List<DNAFeature> features = BlastPlus.runCheckFeatures(query);
        FeaturedDNASequence dnaSequence = new FeaturedDNASequence();
        // check permissions
        Account account = accountDAO.getByEmail(userId);
        List<Group> groups = this.groupDAO.retrieveMemberGroups(account);
        for (DNAFeature dnaFeature : features) {
            Feature feature = this.featureDAO.get(dnaFeature.getId());
            if (feature == null)
                continue;
            List<Long> entries = this.sequenceFeatureDAO.getEntryIdsByFeature(feature);
            if (entries.isEmpty())
                continue;
            if (!isAdministrator()) {
                entries = this.permissionDAO.getCanReadEntries(account, groups, entries);
                if (entries.isEmpty())
                    continue;
            }
            if (ownerFeatures) {
                entries = this.entryDAO.filterByUserId(this.userId, entries);
            }
            if (entries != null && !entries.isEmpty()) {
                dnaFeature.getEntries().addAll(entries);
                dnaSequence.getFeatures().add(dnaFeature);
            }
        }
        dnaSequence.setLength(sequenceString.length());
        return dnaSequence;
    } catch (BlastException e) {
        Logger.error(e);
        return null;
    }
}

Example 12 with DNAFeature

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

the class Annotations method get.

/**
     * Retrieves list of annotations that are available
     *
     * @param offset paging start
     * @param limit  maximum number of annotations to return
     * @param sort   paging sort
     * @return available annotations that conform to parameters along with the total number that are available
     * @throws PermissionException if the requesting user's account does not have administrative privileges
     */
public Results<DNAFeatures> get(int offset, int limit, String sort) {
    if (!isAdministrator())
        throw new PermissionException("Administrative privileges required to retrieve features");
    long count = this.featureDAO.getFeaturesGroupByCount();
    Results<DNAFeatures> results = new Results<>();
    results.setResultCount(count);
    Map<String, List<Feature>> map = this.featureDAO.getFeaturesGroupBy(offset, limit);
    for (String key : map.keySet()) {
        DNAFeatures features = new DNAFeatures(key);
        for (Feature feature : map.get(key)) {
            DNAFeature dnaFeature = feature.toDataTransferObject();
            dnaFeature.setSequence(feature.getSequence());
            List<Long> entries = this.sequenceFeatureDAO.getEntryIdsByFeature(feature);
            if (entries != null)
                dnaFeature.getEntries().addAll(entries);
            features.getFeatures().add(dnaFeature);
        }
        results.getData().add(features);
    }
    return results;
}

Example 13 with DNAFeature

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

the class Annotations method filter.

public Results<DNAFeature> filter(int offset, int limit, String filter) {
    Account account = accountDAO.getByEmail(userId);
    List<Group> groups = new GroupController().getAllGroups(account);
    List<SequenceFeature> features = sequenceFeatureDAO.getSequenceFeatures(this.userId, groups, filter, offset, limit);
    int count = sequenceFeatureDAO.getSequenceFeaturesCount(this.userId, groups, filter);
    Results<DNAFeature> results = new Results<>();
    results.setResultCount(count);
    for (SequenceFeature feature : features) {
        DNAFeature dnaFeature = feature.toDataTransferObject();
        Entry entry = feature.getSequence().getEntry();
        dnaFeature.setIdentifier(entry.getPartNumber());
        DNAFeatureLocation location = new DNAFeatureLocation();
        location.setGenbankStart(feature.getUniqueGenbankStart());
        location.setEnd(feature.getUniqueEnd());
        dnaFeature.getLocations().add(location);
        dnaFeature.getEntries().add(entry.getId());
        results.getData().add(dnaFeature);
    }
    return results;
}