models: update models to support clinical variant summary stats, #TAS…

…K-5611, #TASK-5610

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

@@ -21,6 +21,7 @@
 
 import org.opencb.biodata.models.clinical.ClinicalComment;
 import org.opencb.biodata.models.clinical.ClinicalDiscussion;
+import org.opencb.biodata.models.clinical.interpretation.stats.ClinicalVariantSummaryStats;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 
@@ -40,7 +41,7 @@ public class ClinicalVariant extends Variant {
     private ClinicalVariantConfidence confidence;
     private List<String> tags;
 
-    private ClinicalVariantSummary summary;
+    private ClinicalVariantSummaryStats summary;
 
     private Status status;
 
@@ -118,7 +119,7 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
 
     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,
+                           ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, ClinicalVariantSummaryStats summary,
                            Status status, List<String> tags, Map<String, Object> attributes) {
         super(avro);
 
@@ -204,11 +205,11 @@ public ClinicalVariant setConfidence(ClinicalVariantConfidence confidence) {
         return this;
     }
 
-    public ClinicalVariantSummary getSummary() {
+    public ClinicalVariantSummaryStats getSummary() {
         return summary;
     }
 
-    public ClinicalVariant setSummary(ClinicalVariantSummary summary) {
+    public ClinicalVariant setSummary(ClinicalVariantSummaryStats summary) {
         this.summary = summary;
         return this;
     }

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

@@ -0,0 +1,100 @@
+/*
+ * <!--
+ *   ~ 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.stats;
+
+public class ClinicalVariantSummaryStats {
+
+    private int numCases;
+    private int numPrimaryInterpretations;
+    private int numSecondaryInterpretations;
+    private InterpretationSummaryStats primaryInterpretationSummary;
+    private InterpretationSummaryStats secondaryInterpretationsSummary;
+
+    public ClinicalVariantSummaryStats() {
+        primaryInterpretationSummary = new InterpretationSummaryStats();
+        secondaryInterpretationsSummary = new InterpretationSummaryStats();
+    }
+
+    public ClinicalVariantSummaryStats(int numCases, int numPrimaryInterpretations, int numSecondaryInterpretations,
+                                       InterpretationSummaryStats primaryInterpretationSummary, InterpretationSummaryStats secondaryInterpretationsSummary) {
+        this.numCases = numCases;
+        this.numPrimaryInterpretations = numPrimaryInterpretations;
+        this.numSecondaryInterpretations = numSecondaryInterpretations;
+        this.primaryInterpretationSummary = primaryInterpretationSummary;
+        this.secondaryInterpretationsSummary = secondaryInterpretationsSummary;
+    }
+
+    @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(", primaryInterpretationSummary=").append(primaryInterpretationSummary);
+        sb.append(", secondaryInterpretationsSummary=").append(secondaryInterpretationsSummary);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public int getNumCases() {
+        return numCases;
+    }
+
+    public ClinicalVariantSummaryStats setNumCases(int numCases) {
+        this.numCases = numCases;
+        return this;
+    }
+
+    public int getNumPrimaryInterpretations() {
+        return numPrimaryInterpretations;
+    }
+
+    public ClinicalVariantSummaryStats setNumPrimaryInterpretations(int numPrimaryInterpretations) {
+        this.numPrimaryInterpretations = numPrimaryInterpretations;
+        return this;
+    }
+
+    public int getNumSecondaryInterpretations() {
+        return numSecondaryInterpretations;
+    }
+
+    public ClinicalVariantSummaryStats setNumSecondaryInterpretations(int numSecondaryInterpretations) {
+        this.numSecondaryInterpretations = numSecondaryInterpretations;
+        return this;
+    }
+
+    public InterpretationSummaryStats getPrimaryInterpretationSummary() {
+        return primaryInterpretationSummary;
+    }
+
+    public ClinicalVariantSummaryStats setPrimaryInterpretationSummary(InterpretationSummaryStats primaryInterpretationSummary) {
+        this.primaryInterpretationSummary = primaryInterpretationSummary;
+        return this;
+    }
+
+    public InterpretationSummaryStats getSecondaryInterpretationsSummary() {
+        return secondaryInterpretationsSummary;
+    }
+
+    public ClinicalVariantSummaryStats setSecondaryInterpretationsSummary(InterpretationSummaryStats secondaryInterpretationsSummary) {
+        this.secondaryInterpretationsSummary = secondaryInterpretationsSummary;
+        return this;
+    }
+}