models: add ClinicalVariantSummary, #TASK-5611, #TASK-5610

biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java

@@ -40,6 +40,8 @@ public class ClinicalVariant extends Variant {
     private ClinicalVariantConfidence confidence;
     private List<String> tags;
 
+    private ClinicalVariantSummary summary;
+
     private Status status;
 
     // TODO maybe this parameter should be in Variant
@@ -95,6 +97,7 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
         this.attributes = attributes;
     }
 
+    @Deprecated
     public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
                            Map<String, Object> filters, String recommendation, List<MiniPubmed> references,
                            ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, Status status,
@@ -113,6 +116,26 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
         this.attributes = attributes;
     }
 
+    public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
+                           Map<String, Object> filters, String recommendation, List<MiniPubmed> references,
+                           ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, ClinicalVariantSummary summary,
+                           Status status, List<String> tags, Map<String, Object> attributes) {
+        super(avro);
+
+        this.evidences = evidences;
+        this.comments = comments;
+        this.filters = filters;
+        this.recommendation = recommendation;
+        this.references = references;
+        this.discussion = discussion;
+        this.summary = summary;
+        this.status = status;
+        this.tags = tags;
+        this.confidence = confidence;
+        this.attributes = attributes;
+    }
+
+
     @Override
     public String toString() {
         return super.toString();
@@ -181,6 +204,15 @@ public ClinicalVariant setConfidence(ClinicalVariantConfidence confidence) {
         return this;
     }
 
+    public ClinicalVariantSummary getSummary() {
+        return summary;
+    }
+
+    public ClinicalVariant setSummary(ClinicalVariantSummary summary) {
+        this.summary = summary;
+        return this;
+    }
+
     public Status getStatus() {
         return status;
     }

biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariantSummary.java

@@ -0,0 +1,190 @@
+/*
+ * <!--
+ *   ~ Copyright 2015-2017 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.biodata.models.clinical.interpretation;
+
+import org.opencb.biodata.models.clinical.ClinicalProperty;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class ClinicalVariantSummary {
+
+    private int numCases;
+    private int numPrimaryInterpretations;
+    private int numSecondaryInterpretations;
+    private Map<String, Integer> evidencePhenotypeCounts;
+    private Map<String, Integer> evidenceTierCounts;
+    private Map<String, Integer> evidenceAcmgCounts;
+    private Map<ClinicalProperty.ClinicalSignificance, Integer> evidenceClinicalSignificanceCounts;
+    private Map<VariantClassification.DrugResponse, Integer> drugResponseCounts;
+    private Map<VariantClassification.TraitAssociation, Integer> evidenceTraitAssociationCounts;
+    private Map<VariantClassification.FunctionalEffect, Integer> evidenceFunctionalEffectCounts;
+    private Map<VariantClassification.Tumorigenesis, Integer> evidenceTumorigenesisCounts;
+
+    public ClinicalVariantSummary() {
+        this.evidencePhenotypeCounts = new HashMap<>();
+        this.evidenceTierCounts = new HashMap<>();
+        this.evidenceAcmgCounts = new HashMap<>();
+        this.evidenceClinicalSignificanceCounts = new HashMap<>();
+        this.drugResponseCounts = new HashMap<>();
+        this.evidenceTraitAssociationCounts = new HashMap<>();
+        this.evidenceFunctionalEffectCounts = new HashMap<>();
+        this.evidenceTumorigenesisCounts = new HashMap<>();
+    }
+
+    public ClinicalVariantSummary(int numCases, int numPrimaryInterpretations, int numSecondaryInterpretations,
+                                  Map<String, Integer> evidencePhenotypeCounts,
+                                  Map<String, Integer> evidenceTierCounts,
+                                  Map<String, Integer> evidenceAcmgCounts,
+                                  Map<ClinicalProperty.ClinicalSignificance, Integer> evidenceClinicalSignificanceCounts,
+                                  Map<VariantClassification.DrugResponse, Integer> drugResponseCounts,
+                                  Map<VariantClassification.TraitAssociation, Integer> evidenceTraitAssociationCounts,
+                                  Map<VariantClassification.FunctionalEffect, Integer> evidenceFunctionalEffectCounts,
+                                  Map<VariantClassification.Tumorigenesis, Integer> evidenceTumorigenesisCounts) {
+        this.numCases = numCases;
+        this.numPrimaryInterpretations = numPrimaryInterpretations;
+        this.numSecondaryInterpretations = numSecondaryInterpretations;
+        this.evidencePhenotypeCounts = evidencePhenotypeCounts;
+        this.evidenceTierCounts = evidenceTierCounts;
+        this.evidenceAcmgCounts = evidenceAcmgCounts;
+        this.evidenceClinicalSignificanceCounts = evidenceClinicalSignificanceCounts;
+        this.drugResponseCounts = drugResponseCounts;
+        this.evidenceTraitAssociationCounts = evidenceTraitAssociationCounts;
+        this.evidenceFunctionalEffectCounts = evidenceFunctionalEffectCounts;
+        this.evidenceTumorigenesisCounts = evidenceTumorigenesisCounts;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalVariantSummary{");
+        sb.append("numCases=").append(numCases);
+        sb.append(", numPrimaryInterpretations=").append(numPrimaryInterpretations);
+        sb.append(", numSecondaryInterpretations=").append(numSecondaryInterpretations);
+        sb.append(", evidencePhenotypeCounts=").append(evidencePhenotypeCounts);
+        sb.append(", evidenceTierCounts=").append(evidenceTierCounts);
+        sb.append(", evidenceAcmgCounts=").append(evidenceAcmgCounts);
+        sb.append(", evidenceClinicalSignificanceCounts=").append(evidenceClinicalSignificanceCounts);
+        sb.append(", drugResponseCounts=").append(drugResponseCounts);
+        sb.append(", evidenceTraitAssociationCounts=").append(evidenceTraitAssociationCounts);
+        sb.append(", evidenceFunctionalEffectCounts=").append(evidenceFunctionalEffectCounts);
+        sb.append(", evidenceTumorigenesisCounts=").append(evidenceTumorigenesisCounts);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public int getNumCases() {
+        return numCases;
+    }
+
+    public ClinicalVariantSummary setNumCases(int numCases) {
+        this.numCases = numCases;
+        return this;
+    }
+
+    public int getNumPrimaryInterpretations() {
+        return numPrimaryInterpretations;
+    }
+
+    public ClinicalVariantSummary setNumPrimaryInterpretations(int numPrimaryInterpretations) {
+        this.numPrimaryInterpretations = numPrimaryInterpretations;
+        return this;
+    }
+
+    public int getNumSecondaryInterpretations() {
+        return numSecondaryInterpretations;
+    }
+
+    public ClinicalVariantSummary setNumSecondaryInterpretations(int numSecondaryInterpretations) {
+        this.numSecondaryInterpretations = numSecondaryInterpretations;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidencePhenotypeCounts() {
+        return evidencePhenotypeCounts;
+    }
+
+    public ClinicalVariantSummary setEvidencePhenotypeCounts(Map<String, Integer> evidencePhenotypeCounts) {
+        this.evidencePhenotypeCounts = evidencePhenotypeCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceTierCounts() {
+        return evidenceTierCounts;
+    }
+
+    public ClinicalVariantSummary setEvidenceTierCounts(Map<String, Integer> evidenceTierCounts) {
+        this.evidenceTierCounts = evidenceTierCounts;
+        return this;
+    }
+
+    public Map<String, Integer> getEvidenceAcmgCounts() {
+        return evidenceAcmgCounts;
+    }
+
+    public ClinicalVariantSummary setEvidenceAcmgCounts(Map<String, Integer> evidenceAcmgCounts) {
+        this.evidenceAcmgCounts = evidenceAcmgCounts;
+        return this;
+    }
+
+    public Map<ClinicalProperty.ClinicalSignificance, Integer> getEvidenceClinicalSignificanceCounts() {
+        return evidenceClinicalSignificanceCounts;
+    }
+
+    public ClinicalVariantSummary setEvidenceClinicalSignificanceCounts(Map<ClinicalProperty.ClinicalSignificance, Integer> evidenceClinicalSignificanceCounts) {
+        this.evidenceClinicalSignificanceCounts = evidenceClinicalSignificanceCounts;
+        return this;
+    }
+
+    public Map<VariantClassification.DrugResponse, Integer> getDrugResponseCounts() {
+        return drugResponseCounts;
+    }
+
+    public ClinicalVariantSummary setDrugResponseCounts(Map<VariantClassification.DrugResponse, Integer> drugResponseCounts) {
+        this.drugResponseCounts = drugResponseCounts;
+        return this;
+    }
+
+    public Map<VariantClassification.TraitAssociation, Integer> getEvidenceTraitAssociationCounts() {
+        return evidenceTraitAssociationCounts;
+    }
+
+    public ClinicalVariantSummary setEvidenceTraitAssociationCounts(Map<VariantClassification.TraitAssociation, Integer> evidenceTraitAssociationCounts) {
+        this.evidenceTraitAssociationCounts = evidenceTraitAssociationCounts;
+        return this;
+    }
+
+    public Map<VariantClassification.FunctionalEffect, Integer> getEvidenceFunctionalEffectCounts() {
+        return evidenceFunctionalEffectCounts;
+    }
+
+    public ClinicalVariantSummary setEvidenceFunctionalEffectCounts(Map<VariantClassification.FunctionalEffect, Integer> evidenceFunctionalEffectCounts) {
+        this.evidenceFunctionalEffectCounts = evidenceFunctionalEffectCounts;
+        return this;
+    }
+
+    public Map<VariantClassification.Tumorigenesis, Integer> getEvidenceTumorigenesisCounts() {
+        return evidenceTumorigenesisCounts;
+    }
+
+    public ClinicalVariantSummary setEvidenceTumorigenesisCounts(Map<VariantClassification.Tumorigenesis, Integer> evidenceTumorigenesisCounts) {
+        this.evidenceTumorigenesisCounts = evidenceTumorigenesisCounts;
+        return this;
+    }
+}