de.charite.compbio.jannovar.pedigree.PedPerson 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 com.google.common.collect.ImmutableList;

import de.charite.compbio.jannovar.Immutable;

/**
 * Representation of a line from a pedigree (.ped) file.
 *
 * A pedigree file is a TSV file and contains information about multiple indivdidual. Each line is a record and
 * describes an individual. The files have six core columns that have to be present:
 *
 * 
 * {@link #pedigree}
 * the name of the pedigree
 * {@link #name}
 * the name of the individual
 * {@link #father}
 * the name of the individual's father
 * {@link #mother}
 * the name of the individual's mother
 * {@link #sex}
 * the sex of the individual
 * {@link #disease}
 * the disease status of the individual
 * 
 *
 * The remaining columns are stored in {@link #extraFields}.
 *
 * The PedPerson class describes a record from a pedigree file. This introduces some limitations. For
 * example, the record stores the id of the parents but not references to the parent objects. The class {@link Person}
 * provides a more Java-programmer oriented version of this information.
 *
 * @author Manuel Holtgrewe
 */
@Immutable
public final class PedPerson {

	/** pedigree name */
	private final String pedigree;

	/** name of the individual */
	private final String name;

	/** individual's father's name, "0" if father not in pedigree */
	private final String father;

	/** individual's mother's name, "0" if father not in pedigree */
	private final String mother;

	/** invidual's sex */
	private final Sex sex;

	/** individual's disease status */
	private final Disease disease;

	/** the additional fields stored for this person */
	private final ImmutableList extraFields;

	/**
	 * Initialize object with the given data.
	 */
	public PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease,
			Collection extraFields) {
		this.pedigree = pedigree;
		this.name = name;
		this.father = father;
		this.mother = mother;
		this.sex = sex;
		this.disease = disease;
		this.extraFields = ImmutableList.copyOf(extraFields);
	}

	/**
	 * Initialize object with the given data.
	 */
	public PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease) {
		this(pedigree, name, father, mother, sex, disease, new ArrayList());
	}

	/** @return pedigree name */
	public String getPedigree() {
		return pedigree;
	}

	/** @return name of the individual */
	public String getName() {
		return name;
	}

	/** @return individual's father's name, "0" if father not in pedigree */
	public String getFather() {
		return father;
	}

	/** @return individual's mother's name, "0" if father not in pedigree */
	public String getMother() {
		return mother;
	}

	/** @return invidual's sex */
	public Sex getSex() {
		return sex;
	}

	/** @return individual's disease status */
	public Disease getDisease() {
		return disease;
	}

	/** @return the additional fields stored for this person */
	public ImmutableList getExtraFields() {
		return extraFields;
	}

	/**
	 * @return true if the person is a founder (both mother and father are "0")
	 */
	public boolean isFounder() {
		return (father.equals("0") && mother.equals("0"));
	}

	@Override
	public String toString() {
		return "PedPerson [pedigree=" + pedigree + ", name=" + name + ", father=" + father + ", mother=" + mother
				+ ", sex=" + sex + ", disease=" + disease + ", extraFields=" + extraFields + "]";
	}

	@Override
	public int hashCode() {
		final int prime = 31;
		int result = 1;
		result = prime * result + ((disease == null) ? 0 : disease.hashCode());
		result = prime * result + ((extraFields == null) ? 0 : extraFields.hashCode());
		result = prime * result + ((father == null) ? 0 : father.hashCode());
		result = prime * result + ((mother == null) ? 0 : mother.hashCode());
		result = prime * result + ((name == null) ? 0 : name.hashCode());
		result = prime * result + ((pedigree == null) ? 0 : pedigree.hashCode());
		result = prime * result + ((sex == null) ? 0 : sex.hashCode());
		return result;
	}

	@Override
	public boolean equals(Object obj) {
		if (this == obj)
			return true;
		if (obj == null)
			return false;
		if (getClass() != obj.getClass())
			return false;
		PedPerson other = (PedPerson) obj;
		if (disease != other.disease)
			return false;
		if (extraFields == null) {
			if (other.extraFields != null)
				return false;
		} else if (!extraFields.equals(other.extraFields))
			return false;
		if (father == null) {
			if (other.father != null)
				return false;
		} else if (!father.equals(other.father))
			return false;
		if (mother == null) {
			if (other.mother != null)
				return false;
		} else if (!mother.equals(other.mother))
			return false;
		if (name == null) {
			if (other.name != null)
				return false;
		} else if (!name.equals(other.name))
			return false;
		if (pedigree == null) {
			if (other.pedigree != null)
				return false;
		} else if (!pedigree.equals(other.pedigree))
			return false;
		if (sex != other.sex)
			return false;
		return true;
	}

}