Class Family

src/main/java/com/rtg/relation/Family.java:53–494

Represents a nuclear family (father, mother, and at least one child).

 * Represents a nuclear family (father, mother, and at least one child).
 */
public class Family {

  /** Position of the first child in model array. */
  public static final int FIRST_CHILD_INDEX = 2;
  /** Position of the mother in model array. */
  public static final int MOTHER_INDEX = 1;
  /** Position of the father in model array. */
  public static final int FATHER_INDEX = 0;

  final String mFather;
  final String mMother;
  final Set<String> mChildren = new TreeSet<>();
  final GenomeRelationships mPedigree;
  private final String[] mMembers;
  private final boolean[] mIsDiseased;
  private final int[] mSampleIds;
  private int mFatherFamilyId;
  private int mFatherDistinctMates = 1;
  private int mMotherFamilyId;
  private int mMotherDistinctMates = 1;



  /**
   * Constructs a family from the provided pedigree.
   * The file must contain only parent-child relationships
   * Each child must share the same two parents.
   * @param pedigree the GenomeRelationships which describes the family
   * @return the identified family
   * @throws PedigreeException if the genome file doesn't describe a simple family
   */
  public static Family getFamily(GenomeRelationships pedigree) throws PedigreeException {
    String firstParent = null;
    String secondParent = null;
    final String father;
    final String mother;
    final Set<String> children = new TreeSet<>();
    for (final String name : pedigree.genomes()) {
      boolean found = false;
      for (final Relationship r : pedigree.relationships(name, new RelationshipTypeFilter(RelationshipType.PARENT_CHILD))) {
        if (r.first().equals(name)) {
          if (!found) {
            if (firstParent != null) {
              throw new PedigreeException("There are more than two parents specified");
            }
            firstParent = secondParent;
            secondParent = name;
          }
          found = true;
        } else {
          children.add(name);
        }
      }
    }
    if (firstParent == null) {
      throw new PedigreeException("There are fewer than two parents specified");
    }
    if ((pedigree.getSex(firstParent) == Sex.FEMALE) || (pedigree.getSex(secondParent) == Sex.MALE)) {