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

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/*
 * 
 *
 */

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

import org.apache.commons.collections4.CollectionUtils;
import org.opencb.biodata.models.clinical.Phenotype;

import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import static org.opencb.biodata.models.clinical.ClinicalProperty.*;

public class ClinicalVariantEvidence {

    private String interpretationMethodName;

    private List phenotypes;
    private GenomicFeature genomicFeature;
    private List modeOfInheritances;
    private String panelId;
    private VariantClassification classification;
    private Penetrance penetrance;
    private double score;
    private boolean fullyExplainPhenotypes;
    private List compoundHeterozygousVariantIds;
    /***************************************************************************
     * IMPORTANT
     * roleInCancer is deprecated but it is kept by backward compatibility,
     * and it is set in the function setRolesInCancer:
     *
     *     public ClinicalVariantEvidence setRolesInCancer(List rolesInCancer) {
     *         this.rolesInCancer = rolesInCancer;
     *         if (CollectionUtils.isNotEmpty(rolesInCancer)) {
     *             this.setRoleInCancer(rolesInCancer.get(0));
     *         }
     *         return this;
     *     }
     *  FIXME (29/09/22) This has been added to keep backward compatibility. To be removed in 1 year.
     ********************************************************************************/
    @Deprecated
    private RoleInCancer roleInCancer;
    private List rolesInCancer;
    @Deprecated
    private boolean actionable;

    private ClinicalEvidenceReview review;

    private Map attributes;

    public ClinicalVariantEvidence() {
        phenotypes = Collections.emptyList();
        compoundHeterozygousVariantIds = Collections.emptyList();
        fullyExplainPhenotypes = false;
        actionable = false;
        review = new ClinicalEvidenceReview();
        attributes = new HashMap<>();
    }


    @Deprecated
    public ClinicalVariantEvidence(String interpretationMethodName, List phenotypes, GenomicFeature genomicFeature,
                                   List modeOfInheritances, String panelId, VariantClassification classification,
                                   Penetrance penetrance, double score, boolean fullyExplainPhenotypes,
                                   List compoundHeterozygousVariantIds, RoleInCancer roleInCancer, boolean actionable,
                                   ClinicalEvidenceReview review) {
        this(interpretationMethodName, phenotypes, genomicFeature, modeOfInheritances, panelId, classification, penetrance, score,
                fullyExplainPhenotypes, compoundHeterozygousVariantIds, roleInCancer, null, actionable, review, new HashMap<>());
    }

    @Deprecated
    public ClinicalVariantEvidence(String interpretationMethodName, List phenotypes, GenomicFeature genomicFeature,
                                   List modeOfInheritances, String panelId, VariantClassification classification,
                                   Penetrance penetrance, double score, boolean fullyExplainPhenotypes,
                                   List compoundHeterozygousVariantIds, RoleInCancer roleInCancer, List rolesInCancer,
                                   boolean actionable, ClinicalEvidenceReview review) {
        this(interpretationMethodName, phenotypes, genomicFeature, modeOfInheritances, panelId, classification, penetrance, score,
                fullyExplainPhenotypes, compoundHeterozygousVariantIds, roleInCancer, rolesInCancer, actionable, review, new HashMap<>());
    }

    public ClinicalVariantEvidence(String interpretationMethodName, List phenotypes, GenomicFeature genomicFeature,
                                   List modeOfInheritances, String panelId, VariantClassification classification,
                                   Penetrance penetrance, double score, boolean fullyExplainPhenotypes,
                                   List compoundHeterozygousVariantIds, RoleInCancer roleInCancer, List rolesInCancer,
                                   boolean actionable, ClinicalEvidenceReview review, Map attributes) {
        this.interpretationMethodName = interpretationMethodName;
        this.phenotypes = phenotypes;
        this.genomicFeature = genomicFeature;
        this.modeOfInheritances = modeOfInheritances;
        this.panelId = panelId;
        this.classification = classification;
        this.penetrance = penetrance;
        this.score = score;
        this.fullyExplainPhenotypes = fullyExplainPhenotypes;
        this.compoundHeterozygousVariantIds = compoundHeterozygousVariantIds;
        this.roleInCancer = roleInCancer;
        this.rolesInCancer = rolesInCancer;
        this.actionable = actionable;
        this.review = review;
        this.attributes = attributes;
    }

    @Deprecated
    public ClinicalVariantEvidence(String interpretationMethodName, List phenotypes, GenomicFeature genomicFeature,
                                   List modeOfInheritances, String panelId, VariantClassification classification,
                                   Penetrance penetrance, double score, boolean fullyExplainPhenotypes,
                                   List compoundHeterozygousVariantIds, RoleInCancer roleInCancer,
                                   ClinicalEvidenceReview review) {
        this.interpretationMethodName = interpretationMethodName;
        this.phenotypes = phenotypes;
        this.genomicFeature = genomicFeature;
        this.modeOfInheritances = modeOfInheritances;
        this.panelId = panelId;
        this.classification = classification;
        this.penetrance = penetrance;
        this.score = score;
        this.fullyExplainPhenotypes = fullyExplainPhenotypes;
        this.compoundHeterozygousVariantIds = compoundHeterozygousVariantIds;
        this.roleInCancer = roleInCancer;
        this.review = review;
        this.attributes = new HashMap<>();
    }

    @Override
    public String toString() {
        final StringBuilder sb = new StringBuilder("ClinicalVariantEvidence{");
        sb.append("interpretationMethodName='").append(interpretationMethodName).append('\'');
        sb.append(", phenotypes=").append(phenotypes);
        sb.append(", genomicFeature=").append(genomicFeature);
        sb.append(", modeOfInheritances=").append(modeOfInheritances);
        sb.append(", panelId='").append(panelId).append('\'');
        sb.append(", classification=").append(classification);
        sb.append(", penetrance=").append(penetrance);
        sb.append(", score=").append(score);
        sb.append(", fullyExplainPhenotypes=").append(fullyExplainPhenotypes);
        sb.append(", compoundHeterozygousVariantIds=").append(compoundHeterozygousVariantIds);
        sb.append(", roleInCancer=").append(roleInCancer);
        sb.append(", rolesInCancer=").append(rolesInCancer);
        sb.append(", actionable=").append(actionable);
        sb.append(", review=").append(review);
        sb.append(", attributes=").append(attributes);
        sb.append('}');
        return sb.toString();
    }

    public String getInterpretationMethodName() {
        return interpretationMethodName;
    }

    public ClinicalVariantEvidence setInterpretationMethodName(String interpretationMethodName) {
        this.interpretationMethodName = interpretationMethodName;
        return this;
    }

    public List getPhenotypes() {
        return phenotypes;
    }

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

    public GenomicFeature getGenomicFeature() {
        return genomicFeature;
    }

    public ClinicalVariantEvidence setGenomicFeature(GenomicFeature genomicFeature) {
        this.genomicFeature = genomicFeature;
        return this;
    }

    public List getModeOfInheritances() {
        return modeOfInheritances;
    }

    public ClinicalVariantEvidence setModeOfInheritances(List modeOfInheritances) {
        this.modeOfInheritances = modeOfInheritances;
        return this;
    }

    public String getPanelId() {
        return panelId;
    }

    public ClinicalVariantEvidence setPanelId(String panelId) {
        this.panelId = panelId;
        return this;
    }

    public VariantClassification getClassification() {
        return classification;
    }

    public ClinicalVariantEvidence setClassification(VariantClassification classification) {
        this.classification = classification;
        return this;
    }

    public Penetrance getPenetrance() {
        return penetrance;
    }

    public ClinicalVariantEvidence setPenetrance(Penetrance penetrance) {
        this.penetrance = penetrance;
        return this;
    }

    public double getScore() {
        return score;
    }

    public ClinicalVariantEvidence setScore(double score) {
        this.score = score;
        return this;
    }

    public boolean isFullyExplainPhenotypes() {
        return fullyExplainPhenotypes;
    }

    public ClinicalVariantEvidence setFullyExplainPhenotypes(boolean fullyExplainPhenotypes) {
        this.fullyExplainPhenotypes = fullyExplainPhenotypes;
        return this;
    }

    public List getCompoundHeterozygousVariantIds() {
        return compoundHeterozygousVariantIds;
    }

    public ClinicalVariantEvidence setCompoundHeterozygousVariantIds(List compoundHeterozygousVariantIds) {
        this.compoundHeterozygousVariantIds = compoundHeterozygousVariantIds;
        return this;
    }

    @Deprecated
    public RoleInCancer getRoleInCancer() {
        return roleInCancer;
    }

    @Deprecated
    public ClinicalVariantEvidence setRoleInCancer(RoleInCancer roleInCancer) {
        this.roleInCancer = roleInCancer;
        return this;
    }

    public List getRolesInCancer() {
        return rolesInCancer;
    }

    public ClinicalVariantEvidence setRolesInCancer(List rolesInCancer) {
        this.rolesInCancer = rolesInCancer;
        // FIXME (29/09/22) This has been added to keep backward compatibility. To be removed in 1 year.
        if (CollectionUtils.isNotEmpty(rolesInCancer)) {
            this.setRoleInCancer(rolesInCancer.get(0));
        }
        return this;
    }

    public boolean isActionable() {
        return actionable;
    }

    public ClinicalVariantEvidence setActionable(boolean actionable) {
        this.actionable = actionable;
        return this;
    }

    public ClinicalEvidenceReview getReview() {
        return review;
    }

    public ClinicalVariantEvidence setReview(ClinicalEvidenceReview review) {
        this.review = review;
        return this;
    }

    public Map getAttributes() {
        return attributes;
    }

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