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

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

import org.apache.commons.lang3.StringUtils;
import org.opencb.biodata.models.clinical.Disorder;
import org.opencb.commons.utils.ListUtils;

import java.util.*;

public class PedigreeManager {

    private Pedigree pedigree;
    private List withoutParents;
    private List withOneParent;
    private List withoutChildren;
    private Map individualMap;
    private Map> partner;
    private Map> children;

    public PedigreeManager(Pedigree pedigree) {
        this.pedigree = pedigree;

        withoutParents = new ArrayList<>();
        withOneParent = new ArrayList<>();
        withoutChildren = new ArrayList<>();
        individualMap = new HashMap<>();
        partner = new HashMap<>();
        children = new HashMap<>();

        for (Member member : pedigree.getMembers()) {
            individualMap.put(member.getId(), member);

            // Parent and partner management
            if (member.getFather() == null && member.getMother() == null) {
                withoutParents.add(member);
            } else if (member.getFather() == null || member.getMother() == null) {
                withOneParent.add(member);
            } else {
                if (!partner.containsKey(member.getFather().getId())) {
                    partner.put(member.getFather().getId(), new ArrayList<>());
                }
                partner.get(member.getFather().getId()).add(member.getMother());

                if (!partner.containsKey(member.getMother().getId())) {
                    partner.put(member.getMother().getId(), new ArrayList<>());
                }
                partner.get(member.getMother().getId()).add(member.getFather());
            }

            // Children management
            if (member.getFather() != null) {
                if (!children.containsKey(member.getFather().getId())) {
                    children.put(member.getFather().getId(), new ArrayList<>());
                }
                children.get(member.getFather().getId()).add(member);
            }
            if (member.getMother() != null) {
                if (!children.containsKey(member.getMother().getId())) {
                    children.put(member.getMother().getId(), new ArrayList<>());
                }
                children.get(member.getMother().getId()).add(member);
            }
        }

        // Without children management
        for (Member member : pedigree.getMembers()) {
            if (!children.containsKey(member.getId())) {
                withoutChildren.add(member);
            }
        }
    }

    public Set getAffectedIndividuals(Disorder disorder) {
        Set members = new HashSet<>();
        for (Member member : pedigree.getMembers()) {
            if (ListUtils.isNotEmpty(member.getDisorders())) {
                for (Disorder tmpDisorder: member.getDisorders()) {
                    if (StringUtils.isNotEmpty(tmpDisorder.getId()) && tmpDisorder.getId().equals(disorder.getId())) {
                        members.add(member);
                        break;
                    }
                }
            }
        }
        return members;
    }

    public Set getUnaffectedIndividuals(Disorder disorder) {
        Set members = new HashSet<>();
        for (Member member : pedigree.getMembers()) {
            boolean affected = false;
            if (ListUtils.isNotEmpty(member.getDisorders())) {
                for (Disorder tmpDisorder: member.getDisorders()) {
                    if (StringUtils.isNotEmpty(tmpDisorder.getId()) && tmpDisorder.getId().equals(disorder.getId())) {
                        affected = true;
                        break;
                    }
                }
            }
            if (!affected) {
                members.add(member);
            }
        }
        return members;
    }

    public Pedigree getPedigree() {
        return pedigree;
    }

    public List getWithoutParents() {
        return withoutParents;
    }

    public List getWithOneParent() {
        return withOneParent;
    }

    public List getWithoutChildren() {
        return withoutChildren;
    }

    public Map getIndividualMap() {
        return individualMap;
    }

    public Map> getPartner() {
        return partner;
    }

    public Map> getChildren() {
        return children;
    }
}