Examples with TObjectLongHashMap gnu.trove.map.hash.TObjectLongHashMap used on opensource projects

Example 1 with TObjectLongHashMap

use of gnu.trove.map.hash.TObjectLongHashMap in project spf4j by zolyfarkas.

the class GCUsageSampler method start.

@JmxExport
public static synchronized void start(@JmxExport("sampleTimeMillis") final int sampleTime) {
    if (samplingFuture == null) {
        final MeasurementRecorder gcUsage = RecorderFactory.createDirectRecorder("gc-time", "ms", sampleTime);
        samplingFuture = DefaultScheduler.INSTANCE.scheduleWithFixedDelay(new AbstractRunnable() {

            private final TObjectLongMap lastValues = new TObjectLongHashMap();

            @Override
            public void doRun() {
                synchronized (lastValues) {
                    gcUsage.record(getGCTimeDiff(MBEANS, lastValues));
                }
            }
        }, sampleTime, sampleTime, TimeUnit.MILLISECONDS);
    } else {
        throw new IllegalStateException("GC usage sampling already started " + samplingFuture);
    }
}

Example 2 with TObjectLongHashMap

use of gnu.trove.map.hash.TObjectLongHashMap in project mixcr by milaboratory.

the class AlignedTarget method orderTargets.

public static List<AlignedTarget> orderTargets(List<AlignedTarget> targets) {
    // Selecting best gene by total score
    final EnumMap<GeneType, VDJCGene> bestGenes = new EnumMap<>(GeneType.class);
    for (GeneType geneType : GeneType.VDJC_REFERENCE) {
        TObjectLongMap<VDJCGene> scores = new TObjectLongHashMap<>();
        for (AlignedTarget target : targets) {
            for (VDJCHit hit : target.getAlignments().getHits(geneType)) {
                Alignment<NucleotideSequence> alignment = hit.getAlignment(target.getTargetId());
                if (alignment != null)
                    scores.adjustOrPutValue(hit.getGene(), (long) alignment.getScore(), (long) alignment.getScore());
            }
        }
        VDJCGene bestGene = null;
        long bestScore = Long.MIN_VALUE;
        TObjectLongIterator<VDJCGene> it = scores.iterator();
        while (it.hasNext()) {
            it.advance();
            if (bestScore < it.value()) {
                bestScore = it.value();
                bestGene = it.key();
            }
        }
        if (bestGene != null)
            bestGenes.put(geneType, bestGene);
    }
    // Class to facilitate comparison between targets
    final class Wrapper implements Comparable<Wrapper> {

        final AlignedTarget target;

        final EnumMap<GeneType, Alignment<NucleotideSequence>> alignments = new EnumMap<>(GeneType.class);

        Wrapper(AlignedTarget target) {
            this.target = target;
            for (VDJCGene gene : bestGenes.values()) for (VDJCHit hit : target.getAlignments().getHits(gene.getGeneType())) if (hit.getGene() == gene) {
                Alignment<NucleotideSequence> alignment = hit.getAlignment(target.targetId);
                if (alignment != null) {
                    alignments.put(gene.getGeneType(), alignment);
                    break;
                }
            }
        }

        GeneType firstAlignedGeneType() {
            for (GeneType geneType : GeneType.VDJC_REFERENCE) if (alignments.containsKey(geneType))
                return geneType;
            return null;
        }

        @Override
        public int compareTo(Wrapper o) {
            GeneType thisFirstGene = firstAlignedGeneType();
            GeneType otherFirstGene = o.firstAlignedGeneType();
            int cmp = Byte.compare(thisFirstGene.getOrder(), otherFirstGene.getOrder());
            return cmp != 0 ? cmp : Integer.compare(alignments.get(thisFirstGene).getSequence1Range().getLower(), o.alignments.get(thisFirstGene).getSequence1Range().getLower());
        }
    }
    // Creating wrappers and sorting list
    List<Wrapper> wrappers = new ArrayList<>(targets.size());
    for (AlignedTarget target : targets) {
        Wrapper wrapper = new Wrapper(target);
        if (wrapper.firstAlignedGeneType() == null)
            continue;
        wrappers.add(wrapper);
    }
    Collections.sort(wrappers);
    // Creating result
    List<AlignedTarget> result = new ArrayList<>(wrappers.size());
    for (Wrapper wrapper : wrappers) result.add(wrapper.target);
    return result;
}