de.charite.compbio.jannovar.pedigree.Pedigree Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of jannovar-core Show documentation
jannovar-core is a library for the functional annotation of genomic variants
There is a newer version: 0.41
package de.charite.compbio.jannovar.pedigree;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;

import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;

import de.charite.compbio.jannovar.Immutable;

// TODO(holtgrem): Test me!

/**
 * Represent one pedigree from a PED file.
 *
 * @author Peter N Robinson
 * @author Manuel Holtgrewe
 */
@Immutable
public final class Pedigree {

	/** the pedigree's name */
	private final String name;

	/** the pedigree's members */
	private final ImmutableList members;

	/** mapping from member name to member */
	private final ImmutableMap nameToMember;

	/**
	 * Initialize the object with the given values
	 *
	 * @param name
	 *            the name of the pedigree/family
	 * @param members
	 *            list of the members
	 */
	public Pedigree(String name, Collection members) {
		this.name = name;
		this.members = ImmutableList.copyOf(members);

		ImmutableMap.Builder mapBuilder = new ImmutableMap.Builder();
		int i = 0;
		for (Person person : members)
			mapBuilder.put(person.getName(), new IndexedPerson(i++, person));
		this.nameToMember = mapBuilder.build();
	}

	/**
	 * Initialize the object with the members of contents that have the pedigree name equal to
	 * pedigreeName.
	 *
	 * @param contents
	 *            contents from the pedigree file
	 * @param pedigreeName
	 *            name of the pedigree to extract
	 * @throws PedParseException
	 *             in the case of problems with references to individuals for mother and father
	 */
	public Pedigree(PedFileContents contents, String pedigreeName) throws PedParseException {
		this(pedigreeName, new PedigreeExtractor(pedigreeName, contents).run());
	}
	
	/** @return number of members in pedigree */
	public int getNMembers() {
		return members.size();
	}

	/** @return the pedigree's name */
	public String getName() {
		return name;
	}

	/** @return the pedigree's members */
	public ImmutableList getMembers() {
		return members;
	}

	/** @return mapping from member name to member */
	public ImmutableMap getNameToMember() {
		return nameToMember;
	}

	/**
	 * Obtain subset of members in a pedigree or change order.
	 *
	 * If a {@link Person} is selected that has parents in this but the parent's name is not in
	 * name then the {@link Person} will have null as the parent object.
	 *
	 * @return Pedigree with the members from names in the given order
	 */
	public Pedigree subsetOfMembers(Collection names) {
		HashSet nameSet = new HashSet();
		nameSet.addAll(names);

		ArrayList tmpMembers = new ArrayList();
		for (String name : names)
			if (hasPerson(name)) {
				Person p = nameToMember.get(name).getPerson();
				Person father = nameSet.contains(p.getFather().getName()) ? p.getFather() : null;
				Person mother = nameSet.contains(p.getMother().getName()) ? p.getMother() : null;

				tmpMembers.add(new Person(p.getName(), father, mother, p.getSex(), p.getDisease(), p.getExtraFields()));
			}
		return new Pedigree(name, tmpMembers);
	}

	/**
	 * @return a pedigree with one affected sample
	 */
	public static Pedigree constructSingleSamplePedigree(String sampleName) {
		final Person person = new Person(sampleName, null, null, Sex.UNKNOWN, Disease.AFFECTED);
		return new Pedigree("pedigree", ImmutableList.of(person));
	}

	/**
	 * @return true if the pedigree contains a sample with the given name.
	 */
	public boolean hasPerson(String name) {
		return nameToMember.containsKey(name);
	}

	/**
	 * @return list of members, in the same order as in {@link #members}.
	 */
	public ImmutableList getNames() {
		ImmutableList.Builder builder = new ImmutableList.Builder();
		for (Person p : members)
			builder.add(p.getName());
		return builder.build();
	}

	@Override
	public String toString() {
		return "Pedigree [name=" + name + ", members=" + members + ", nameToMember=" + nameToMember + "]";
	}

	/**
	 * Helper class, used in the name to member map.
	 */
	public static class IndexedPerson {
		private final int idx;
		private final Person person;

		public IndexedPerson(int idx, Person person) {
			this.idx = idx;
			this.person = person;
		}

		/** @return numeric index of person in pedigree */
		public int getIdx() {
			return idx;
		}

		/** @return the wrapped {@link Person} */
		public Person getPerson() {
			return person;
		}
	}

}