org.opencb.biodata.models.clinical.pedigree.Pedigree Maven / Gradle / Ivy

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/*
 * 
 *
 */

package org.opencb.biodata.models.clinical.pedigree;

import com.fasterxml.jackson.databind.ObjectMapper;
import org.opencb.biodata.models.clinical.Disorder;
import org.opencb.biodata.models.clinical.Phenotype;

import java.util.*;

/**
 * Created by imedina on 10/10/16.
 */
public class Pedigree {
    private String name;

    private List phenotypes;
    private List disorders;

    private List members;

    private Member proband;

    private Map attributes;

    /**
     * Empty constructor.
     */
    public Pedigree() {
    }

    /**
     * Constructor.
     *
     * @param name          Family name
     * @param members       Individuals belonging to this family
     * @param attributes    Family attributes
     */
    public Pedigree(String name, List members, Map attributes) {
        this(name, members, null, Collections.emptyList(), Collections.emptyList(), attributes);
    }

    /**
     * Constructor.
     *  @param name          Family name
     * @param members       Individuals belonging to this family
     * @param phenotypes    List of phenotypes present in the members of the family
     * @param disorders     List of disorders present in the members of the family
     * @param attributes    Family attributes
     */
    public Pedigree(String name, List members, List phenotypes, List disorders,
                    Map attributes) {
        this(name, members, null, phenotypes, disorders, attributes);
    }

    /**
     * Constructor.
     *  @param name          Family name
     * @param members       Individuals belonging to this family
     * @param proband       Proband individual
     * @param phenotypes    List of phenotypes present in the members of the family
     * @param disorders     List of disorders present in the members of the family
     * @param attributes    Family attributes
     */
    public Pedigree(String name, List members, Member proband, List phenotypes, List disorders,
                    Map attributes) {
        this.name = name;
        this.members = members;
        this.proband = proband;
        this.phenotypes = phenotypes;
        this.disorders = disorders;
        this.attributes = attributes;
    }

    @Override
    public String toString() {
        final StringBuilder sb = new StringBuilder("Pedigree{");
        sb.append("name='").append(name).append('\'');
        sb.append(", phenotypes=").append(phenotypes);
        sb.append(", disorders=").append(disorders);
        sb.append(", members=").append(members);
        sb.append(", proband=").append(proband);
        sb.append(", attributes=").append(attributes);
        sb.append('}');
        return sb.toString();
    }

    public String getName() {
        return name;
    }

    public Pedigree setName(String name) {
        this.name = name;
        return this;
    }

    public List getPhenotypes() {
        return phenotypes;
    }

    public Pedigree setPhenotypes(List phenotypes) {
        this.phenotypes = phenotypes;
        return this;
    }

    public List getDisorders() {
        return disorders;
    }

    public Pedigree setDisorders(List disorders) {
        this.disorders = disorders;
        return this;
    }

    public List getMembers() {
        return members;
    }

    public Pedigree setMembers(List members) {
        this.members = members;
        return this;
    }

    public Member getProband() {
        return proband;
    }

    public Pedigree setProband(Member proband) {
        this.proband = proband;
        return this;
    }

    public Map getAttributes() {
        return attributes;
    }

    public Pedigree setAttributes(Map attributes) {
        this.attributes = attributes;
        return this;
    }

    public String toJSON() {
        try {
            ObjectMapper mapper = new ObjectMapper();
            return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(this).toString();
        } catch (Exception e) {
            return "";
        }
    }
}