org.opencb.biodata.models.clinical.interpretation.CancerPanel Maven / Gradle / Ivy

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

import com.fasterxml.jackson.annotation.JsonIgnore;
import org.apache.commons.collections4.CollectionUtils;
import org.opencb.biodata.models.clinical.ClinicalProperty.RoleInCancer;

import java.util.Collections;
import java.util.List;

public class CancerPanel {

    private boolean somatic;
    private boolean germline;
    private List roles;
    private List tissues;
    private List somaticTumourTypes;
    private List germlineTumourTypes;
    private List fusionPartners;

    public CancerPanel() {
    }

    @Deprecated
    public CancerPanel(boolean somatic, boolean germline, RoleInCancer role, List tissues,
                       List somaticTumourTypes, List germlineTumourTypes, List fusionPartners) {
        this.somatic = somatic;
        this.germline = germline;
        this.roles = role != null ? Collections.singletonList(role) : null;
        this.tissues = tissues;
        this.somaticTumourTypes = somaticTumourTypes;
        this.germlineTumourTypes = germlineTumourTypes;
        this.fusionPartners = fusionPartners;
    }

    public CancerPanel(boolean somatic, boolean germline, List roles, List tissues,
                       List somaticTumourTypes, List germlineTumourTypes, List fusionPartners) {
        this.somatic = somatic;
        this.germline = germline;
        this.roles = roles;
        this.tissues = tissues;
        this.somaticTumourTypes = somaticTumourTypes;
        this.germlineTumourTypes = germlineTumourTypes;
        this.fusionPartners = fusionPartners;
    }

    @Override
    public String toString() {
        final StringBuilder sb = new StringBuilder("Cancer{");
        sb.append("somatic=").append(somatic);
        sb.append(", germline=").append(germline);
        sb.append(", roles=").append(roles);
        sb.append(", tissues=").append(tissues);
        sb.append(", somaticTumourTypes=").append(somaticTumourTypes);
        sb.append(", germlineTumourTypes=").append(germlineTumourTypes);
        sb.append(", fusionPartners=").append(fusionPartners);
        sb.append('}');
        return sb.toString();
    }

    public boolean isSomatic() {
        return somatic;
    }

    public CancerPanel setSomatic(boolean somatic) {
        this.somatic = somatic;
        return this;
    }

    public boolean isGermline() {
        return germline;
    }

    public CancerPanel setGermline(boolean germline) {
        this.germline = germline;
        return this;
    }

    @Deprecated
    @JsonIgnore
    public RoleInCancer getRole() {
        return CollectionUtils.isNotEmpty(roles) ? roles.get(0) : null;
    }

    @Deprecated
    @JsonIgnore
    public CancerPanel setRole(RoleInCancer role) {
        this.roles = role != null ? Collections.singletonList(role) : null;
        return this;
    }

    public List getRoles() {
        return roles;
    }

    public CancerPanel setRoles(List roles) {
        this.roles = roles;
        return this;
    }

    public List getTissues() {
        return tissues;
    }

    public CancerPanel setTissues(List tissues) {
        this.tissues = tissues;
        return this;
    }

    public List getSomaticTumourTypes() {
        return somaticTumourTypes;
    }

    public CancerPanel setSomaticTumourTypes(List somaticTumourTypes) {
        this.somaticTumourTypes = somaticTumourTypes;
        return this;
    }

    public List getGermlineTumourTypes() {
        return germlineTumourTypes;
    }

    public CancerPanel setGermlineTumourTypes(List germlineTumourTypes) {
        this.germlineTumourTypes = germlineTumourTypes;
        return this;
    }

    public List getFusionPartners() {
        return fusionPartners;
    }

    public CancerPanel setFusionPartners(List fusionPartners) {
        this.fusionPartners = fusionPartners;
        return this;
    }
}