How to use

ObjectArraySet

in

it.unimi.dsi.fastutil.objects

public AggregatedSoftmaxGenotypePrediction(BaseInformationRecords.BaseInformation record,
                      List<Prediction> individualOutputPredictions) {
  predictedAlleles = new ObjectArraySet<>();
  trueAlleles = new ObjectArraySet<>();
  set(record, (SoftmaxGenotypePrediction) individualOutputPredictions.get(0),
      (MetadataPrediction) individualOutputPredictions.get(1));
}

/**
 * Creates a new array set copying the contents of a given set.
 * 
 * @param c
 *            a collection.
 */
public ObjectArraySet(final Collection<? extends K> c) {
  this(c.size());
  addAll(c);
}
/**

@Override
public boolean contains(final Object k) {
  return findKey(k) != -1;
}
@Override

if (alleleIsCalled) predictedAlleles.add(allele);
if (alleleIsInTrueGenotype) trueAlleles.add(allele);

  public static Set<String> getGenotype(String genotype){
    Set<String> alleles = new ObjectArraySet<>();
    for (String allele : genotype.split("/")){
      alleles.add(allele);
    }
    alleles.remove("");
    alleles.remove("?");
    alleles.remove(".");
    return alleles;
  }
}

@Override
public boolean remove(final Object k) {
  final int pos = findKey(k);
  if (pos == -1)
    return false;
  final int tail = size - pos - 1;
  for (int i = 0; i < tail; i++)
    a[pos + i] = a[pos + i + 1];
  size--;
  a[size] = null;
  return true;
}
@Override

/**
 * Creates a new array set copying the contents of a given collection.
 * 
 * @param c
 *            a collection.
 */
public ObjectArraySet(ObjectCollection<K> c) {
  this(c.size());
  addAll(c);
}
/**

public static Set<String> fromTosToAlleles(Set<Variant.FromTo> alleles) {
  Set<String> toSet = new ObjectArraySet<>(alleles.size());
  for (Variant.FromTo allele : alleles) {
    toSet.add(allele.getTo());
  }
  return toSet;
}

@Override
public boolean add(final K k) {
  final int pos = findKey(k);
  if (pos != -1)
    return false;
  if (size == a.length) {
    final Object[] b = new Object[size == 0 ? 2 : size * 2];
    for (int i = size; i-- != 0;)
      b[i] = a[i];
    a = b;
  }
  a[size++] = k;
  return true;
}
@Override

public SegmentLabelMapper(int ploidy) {
  this.ploidy = ploidy;
  this.labels = new ObjectArraySet<>();
  this.labels.addAll(this.buildLabels(ploidy));
  this.numberOfLabelsPerBase = this.labels.size();
  this.indexedLabels = this.buildLabelMap();
}

private int[] assignSelectedIndices(String[] inputNames, Set<String> inputNamesToExport) {
  if (inputNamesToExport == null) {
    inputNamesToExport = new ObjectArraySet<>();
    inputNamesToExport.addAll(ObjectArrayList.wrap(inputNames));
  }
  int[] inputIndicesSelected = new int[inputNames.length];
  if (!inputNamesToExport.isEmpty()) {
    // the none keyword makes it possible to export no inputs.
    inputNamesToExport.remove("none");
    inputIndicesSelected = new int[inputNamesToExport.size()];
    Arrays.fill(inputIndicesSelected, -1);
    int i = 0;
    for (int j = 0; j < inputNames.length; j++) {
      if (inputNamesToExport.contains(inputNames[j])) {
        inputIndicesSelected[i++] = j;
      }
    }
    for (int index : inputIndicesSelected) {
      if (index == -1) {
        System.err.printf("An argument to --export-inputs/outputs does not match actual inputs/outputs.");
        System.exit(1);
      }
    }
  }
  return inputIndicesSelected;
}

public static Set<String> alleles(String genotype) {
  genotype = genotype.toUpperCase();
  ObjectSet<String> result = new ObjectArraySet<>();
  Collections.addAll(result, genotype.split("[|/]"));
  result.remove("|");
  result.remove("/");
  result.remove("?");
  result.remove(".");
  result.remove("");
  return result;
}

public static Set<String> alleles(String genotype) {
  genotype = genotype.toUpperCase();
  ObjectSet<String> result = new ObjectArraySet<>();
  Collections.addAll(result, genotype.split("[|/]"));
  result.remove("|");
  result.remove("/");
  result.remove("?");
  result.remove(".");
  result.remove("");
  return result;
}

Set<Variant.FromTo> extendedTrueAlleles = new ObjectArraySet<>(trueAlleles);

@Override
public void execute()  {
  Set<String> testIDs = new ObjectArraySet<>(args().testChromosomes);
  Set<String> valIDs = new ObjectArraySet<>(args().valChromosomes);
  Map<String,Integer> testCounts = new Object2IntArrayMap<>(testIDs.size());
  Map<String,Integer> valCounts = new Object2IntArrayMap<>(valIDs.size());

  trueAlleles = new ObjectArraySet<Variant.FromTo>(1);
  trueAlleles.add(new Variant.FromTo(referenceBase,referenceBase));
} else if (isVariant && variant.isIndel() && (!indelsAsRef) && (!considerIndels)){

Set<Variant.FromTo> predictedFromTos = new ObjectArraySet<>(2);
Set<Variant.FromTo> trueFromTos = new ObjectArraySet<>(2);
for (BaseInformationRecords.CountInfo c : currentRecord.getSamples(0).getCountsList()) {
  if (predictedAlleles().contains(c.getToSequence())) {

final int indelMappedLength = indelSequenceLength;
Set<Integer> sampleIndices = new ObjectArraySet<>();
sampleIndices.add(germlineIndex);
sampleIndices.add(somaticIndex);

final int indelMappedLength= indelSequenceLength;
Set<Integer> sampleIndices = new ObjectArraySet<>();
sampleIndices.add(germlineIndex);
sampleIndices.add(somaticIndex);

String previousChr = "";
int previousAlignmentStart = -1;
ObjectSet<String> chromosomeSeen = new ObjectArraySet<String>();