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Interpretation.java
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Interpretation.java
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/*
* Copyright 2015-2020 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.opencb.opencga.core.models.clinical;
import org.opencb.biodata.models.clinical.ClinicalAnalyst;
import org.opencb.biodata.models.clinical.ClinicalComment;
import org.opencb.biodata.models.clinical.interpretation.ClinicalVariant;
import org.opencb.biodata.models.clinical.interpretation.InterpretationMethod;
import org.opencb.biodata.models.common.Status;
import org.opencb.commons.annotations.DataField;
import org.opencb.opencga.core.api.FieldConstants;
import org.opencb.opencga.core.models.IPrivateStudyUid;
import org.opencb.opencga.core.models.panel.Panel;
import java.util.Collections;
import java.util.List;
import java.util.Map;
public class Interpretation extends org.opencb.biodata.models.clinical.interpretation.Interpretation implements IPrivateStudyUid {
// Private fields
@DataField(id = "studyUid", indexed = true,
description = FieldConstants.INTERPRETATION_STUDY_UID)
private long studyUid;
@DataField(id = "uid", indexed = true,
description = FieldConstants.INTERPRETATION_UID)
private long uid;
@DataField(id = "panels", indexed = true,
description = FieldConstants.INTERPRETATION_PANELS)
private List<Panel> panels;
@DataField(id = "internal", indexed = true,
description = FieldConstants.GENERIC_INTERNAL)
private InterpretationInternal internal;
@DataField(id = "release", indexed = true,
description = FieldConstants.GENERIC_RELEASE_DESCRIPTION)
private int release;
public Interpretation() {
super();
}
public Interpretation(String id, String description, String clinicalAnalysisId, ClinicalAnalyst analyst,
InterpretationMethod method, String creationDate, String modificationDate, boolean locked,
List<ClinicalVariant> primaryFindings, List<ClinicalVariant> secondaryFindings, List<Panel> panels,
List<ClinicalComment> comments, Status status, Map<String, Object> attributes) {
super(id, "", description, clinicalAnalysisId, analyst, method, primaryFindings, secondaryFindings, comments, null, status,
creationDate, modificationDate, locked, 0, attributes);
this.panels = panels;
}
public Interpretation(org.opencb.biodata.models.clinical.interpretation.Interpretation interpretation) {
this(interpretation.getId(), interpretation.getDescription(), interpretation.getClinicalAnalysisId(), interpretation.getAnalyst(),
interpretation.getMethod(), interpretation.getCreationDate(), interpretation.getModificationDate(),
interpretation.isLocked(), interpretation.getPrimaryFindings(), interpretation.getSecondaryFindings(),
Collections.emptyList(), interpretation.getComments(), interpretation.getStatus(), interpretation.getAttributes());
}
@Override
public String toString() {
final StringBuilder sb = new StringBuilder("Interpretation{");
sb.append("studyUid=").append(studyUid);
sb.append(", uid=").append(uid);
sb.append(", panels=").append(panels);
sb.append(", internal=").append(internal);
sb.append(", release=").append(release);
sb.append('}');
return sb.toString();
}
@Override
public long getStudyUid() {
return studyUid;
}
@Override
public Interpretation setStudyUid(long studyUid) {
this.studyUid = studyUid;
return this;
}
@Override
public Interpretation setId(String id) {
super.setId(id);
return this;
}
@Override
public long getUid() {
return uid;
}
@Override
public Interpretation setUid(long uid) {
this.uid = uid;
return this;
}
public List<Panel> getPanels() {
return panels;
}
public Interpretation setPanels(List<Panel> panels) {
this.panels = panels;
return this;
}
public InterpretationInternal getInternal() {
return internal;
}
public Interpretation setInternal(InterpretationInternal internal) {
this.internal = internal;
return this;
}
public int getRelease() {
return release;
}
public Interpretation setRelease(int release) {
this.release = release;
return this;
}
@Override
public Interpretation setDescription(String description) {
super.setDescription(description);
return this;
}
@Override
public Interpretation setClinicalAnalysisId(String clinicalAnalysisId) {
super.setClinicalAnalysisId(clinicalAnalysisId);
return this;
}
@Override
public Interpretation setAnalyst(ClinicalAnalyst analyst) {
super.setAnalyst(analyst);
return this;
}
@Override
public Interpretation setMethod(InterpretationMethod method) {
super.setMethod(method);
return this;
}
@Override
public Interpretation setPrimaryFindings(List<ClinicalVariant> primaryFindings) {
super.setPrimaryFindings(primaryFindings);
return this;
}
@Override
public Interpretation setSecondaryFindings(List<ClinicalVariant> secondaryFindings) {
super.setSecondaryFindings(secondaryFindings);
return this;
}
@Override
public Interpretation setComments(List<ClinicalComment> comments) {
super.setComments(comments);
return this;
}
@Override
public Interpretation setStatus(Status status) {
super.setStatus(status);
return this;
}
@Override
public Interpretation setLocked(boolean locked) {
super.setLocked(locked);
return this;
}
}