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

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/*
 * 
 *
 */

package org.opencb.biodata.models.pedigree;


import java.util.*;

/**
 * @author Alejandro Aleman Ramos <[email protected]>
 */
public class Pedigree {

    private Map individuals;
    private Map> families;
    private Map fields;

    public Pedigree() {
        individuals = new LinkedHashMap<>(100);
        families = new LinkedHashMap<>(100);
        fields = new LinkedHashMap<>(5);
    }

    public Set getFamily(String familyId) {
        return families.get(familyId);
    }

    public Individual getIndividual(String id) {
        return individuals.get(id);
    }

    public Map getIndividuals() {
        return individuals;
    }

    public void setIndividuals(Map individuals) {
        this.individuals = individuals;
    }

    public Map> getFamilies() {
        return families;
    }

    public void setFamilies(Map> families) {
        this.families = families;
    }

    public Map getFields() {
        return fields;
    }

    public void setFields(Map fields) {
        this.fields = fields;
    }

    public void addIndividual(Individual ind) {
        this.individuals.put(ind.getId(), ind);
    }

    public void addIndividualToFamily(String familyId, Individual ind) {

        this.families.get(familyId).add(ind);

    }

    public void addFamily(String familyId, Set family) {
        this.getFamilies().put(familyId, family);
    }


    @Override
    public String toString() {
        StringBuilder sb = new StringBuilder();
        sb.append("Pedigree\n");
        if (fields.size() > 0) {
            sb.append("fields = " + fields.keySet().toString() + "\n");
        }

        for (Map.Entry> elem : this.families.entrySet()) {
            sb.append(elem.getKey() + "\n");
            for (Individual ind : elem.getValue()) {
                sb.append("\t" + ind.toString() + "\n");
            }
        }
        return sb.toString();
    }

    public List getFamiliesTDT() {

        List families = new ArrayList<>();
        Individual ind;

        for (Map.Entry entry : this.individuals.entrySet()) {
            ind = entry.getValue();
            if (ind.getFather() != null && ind.getMother() != null) {
                addIndividualToFamily(ind, ind.getFather(), ind.getMother(), families);
            }
        }
        return families;
    }

    private void addIndividualToFamily(Individual ind, Individual father, Individual mother, List families) {
        boolean b = false;

        Iterator it = families.iterator();
        Family fam;

        while (it.hasNext() && !b) {
            fam = it.next();
            if (fam.getFather().equals(father) && fam.getMother().equals(mother)) {
                fam.addChild(ind);
                b = true;
            }
        }
        if (!b) {
            fam = new Family(father, mother);
            fam.addChild(ind);
            families.add(fam);
        }
    }
}