Examples with SequenceProviderIndexOutOfBoundsException com.milaboratory.core.sequence.provider.SequenceProviderIndexOutOfBoundsException used on opensource projects

Example 1 with SequenceProviderIndexOutOfBoundsException

use of com.milaboratory.core.sequence.provider.SequenceProviderIndexOutOfBoundsException in project repseqio by repseqio.

the class CompileAction method compile.

public static void compile(Path source, Path destination, int surroundings) throws IOException {
    VDJCLibraryRegistry.resetDefaultRegistry();
    VDJCLibraryRegistry reg = VDJCLibraryRegistry.getDefault();
    reg.registerLibraries(source, "lib");
    List<VDJCLibraryData> result = new ArrayList<>();
    for (VDJCLibrary lib : reg.getLoadedLibraries()) {
        VDJCDataUtils.FragmentsBuilder fragmentsBuilder = new VDJCDataUtils.FragmentsBuilder();
        for (KnownSequenceFragmentData fragment : lib.getData().getSequenceFragments()) fragmentsBuilder.addRegion(fragment);
        for (VDJCGene gene : lib.getGenes()) {
            if (!gene.getData().getBaseSequence().isPureOriginalSequence())
                throw new IllegalArgumentException("Don't support mutated sequences yet.");
            URI uri = gene.getData().getBaseSequence().getOrigin();
            Range region = gene.getPartitioning().getContainingRegion();
            region = region.expand(surroundings);
            NucleotideSequence seq;
            try {
                seq = gene.getSequenceProvider().getRegion(region);
            } catch (SequenceProviderIndexOutOfBoundsException e) {
                region = e.getAvailableRange();
                if (region == null)
                    throw new IllegalArgumentException("Wrong anchor points for " + gene.getName() + " ?");
                seq = gene.getSequenceProvider().getRegion(region);
            }
            fragmentsBuilder.addRegion(uri, region, seq);
        }
        result.add(new VDJCLibraryData(lib.getTaxonId(), lib.getData().getSpeciesNames(), lib.getData().getGenes(), lib.getData().getMeta(), fragmentsBuilder.getFragments()));
    }
    VDJCDataUtils.writeToFile(result, destination, true);
    log.info("{} compiled successfully.", source);
}