Examples with SequenceResolver io.repseq.seqbase.SequenceResolver used on opensource projects

Example 1 with SequenceResolver

use of io.repseq.seqbase.SequenceResolver in project repseqio by repseqio.

the class VDJCLibraryRegistry method registerLibrary.

/**
 * Creates and registers single library from VDJCLibraryData
 *
 * @param context context to use for resolution of sequences
 * @param name    library name
 * @param data    library data
 * @return created library
 */
public synchronized VDJCLibrary registerLibrary(Path context, String name, VDJCLibraryData data) {
    // Creating library object
    VDJCLibrary library = new VDJCLibrary(data, name, this, context);
    // Getting library id
    VDJCLibraryId rootId = library.getLibraryIdWithoutChecksum();
    // Check if such library is already registered
    if (libraries.containsKey(rootId))
        throw new RuntimeException("Duplicate library: " + rootId);
    // Loading known sequence fragments from VDJCLibraryData to current SequenceResolver
    SequenceResolver resolver = getSequenceResolver();
    for (KnownSequenceFragmentData fragment : data.getSequenceFragments()) resolver.resolve(new SequenceAddress(context, fragment.getUri())).setRegion(fragment.getRange(), fragment.getSequence());
    // Adding genes
    for (VDJCGeneData gene : data.getGenes()) VDJCLibrary.addGene(library, gene);
    // Adding common species names
    Long taxonId = data.getTaxonId();
    for (String speciesName : data.getSpeciesNames()) {
        String cSpeciesName = canonicalizeSpeciesName(speciesName);
        if (speciesNames.containsKey(cSpeciesName) && !speciesNames.get(cSpeciesName).equals(taxonId))
            throw new IllegalArgumentException("Mismatch in common species name between several libraries. " + "(Library name = " + name + "; name = " + speciesName + ").");
        speciesNames.put(cSpeciesName, taxonId);
        List<String> names = speciesNamesReverse.get(taxonId);
        if (names == null)
            speciesNamesReverse.put(taxonId, names = new ArrayList<>());
        names.add(speciesName);
    }
    // Adding this library to collection
    libraries.put(library.getLibraryIdWithoutChecksum(), library);
    return library;
}