Examples with Cluster com.milaboratory.core.clustering.Cluster used on opensource projects

Example 1 with Cluster

use of com.milaboratory.core.clustering.Cluster in project mixcr by milaboratory.

the class CloneAssembler method runClustering.

public void runClustering() {
    if (clusteredClonesAccumulators != null)
        throw new IllegalStateException("Already clustered.");
    if (!preClusteringDone)
        throw new IllegalStateException("No preclustering done.");
    @SuppressWarnings("unchecked") Clustering clustering = new Clustering(cloneList, new SequenceExtractor<CloneAccumulator, NucleotideSequence>() {

        @Override
        public NucleotideSequence getSequence(CloneAccumulator object) {
            return object.getSequence().getConcatenated().getSequence();
        }
    }, new CloneClusteringStrategy(parameters.getCloneClusteringParameters(), this));
    this.progressReporter = clustering;
    List<Cluster<CloneAccumulator>> clusters = clustering.performClustering();
    clusteredClonesAccumulators = new ArrayList<>(clusters.size());
    idMapping = new TIntIntHashMap(cloneList.size());
    for (int i = 0; i < clusters.size(); ++i) {
        final Cluster<CloneAccumulator> cluster = clusters.get(i);
        final CloneAccumulator head = cluster.getHead();
        idMapping.put(head.getCloneIndex(), i);
        head.setCloneIndex(i);
        final int k = ~i;
        cluster.processAllChildren(new TObjectProcedure<Cluster<CloneAccumulator>>() {

            @Override
            public boolean execute(Cluster<CloneAccumulator> object) {
                onClustered(head, object.getHead());
                if (parameters.isAddReadsCountOnClustering())
                    head.mergeCounts(object.getHead());
                idMapping.put(object.getHead().getCloneIndex(), k);
                return true;
            }
        });
        clusteredClonesAccumulators.add(head);
    }
    this.progressReporter = null;
}