From 426ec383af0b0fb76929e410751d4dfcc5ae11cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Tue, 1 Sep 2020 10:29:52 +0200
Subject: [PATCH] models: update ClinicalVariantEvidence object, #189

---
 .../ClinicalVariantEvidence.java              | 23 ++++-----------
 .../interpretation/GenomicFeature.java        | 28 ++++++++++++++++++-
 2 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariantEvidence.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariantEvidence.java
index 458c5e3a8..805d44704 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariantEvidence.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariantEvidence.java
@@ -32,7 +32,6 @@ public class ClinicalVariantEvidence {
     private String interpretationMethodName;
 
     private List<Phenotype> phenotypes;
-    private List<SequenceOntologyTerm> consequenceTypes;
     private GenomicFeature genomicFeature;
     private ModeOfInheritance modeOfInheritance;
     private String panelId;
@@ -47,20 +46,18 @@ public class ClinicalVariantEvidence {
 
     public ClinicalVariantEvidence() {
         phenotypes = Collections.emptyList();
-        consequenceTypes = Collections.emptyList();
         compoundHeterozygousVariantIds = Collections.emptyList();
         fullyExplainPhenotypes = false;
         actionable = false;
     }
 
-    public ClinicalVariantEvidence(String interpretationMethodName, List<Phenotype> phenotypes, List<SequenceOntologyTerm> consequenceTypes,
-                                   GenomicFeature genomicFeature, ModeOfInheritance modeOfInheritance, String panelId,
-                                   VariantClassification classification, Penetrance penetrance, double score,
-                                   boolean fullyExplainPhenotypes, List<String> compoundHeterozygousVariantIds, RoleInCancer roleInCancer,
-                                   boolean actionable, String justification) {
+    public ClinicalVariantEvidence(String interpretationMethodName, List<Phenotype> phenotypes, GenomicFeature genomicFeature,
+                                   ModeOfInheritance modeOfInheritance, String panelId, VariantClassification classification,
+                                   Penetrance penetrance, double score, boolean fullyExplainPhenotypes,
+                                   List<String> compoundHeterozygousVariantIds, RoleInCancer roleInCancer, boolean actionable,
+                                   String justification) {
         this.interpretationMethodName = interpretationMethodName;
         this.phenotypes = phenotypes;
-        this.consequenceTypes = consequenceTypes;
         this.genomicFeature = genomicFeature;
         this.modeOfInheritance = modeOfInheritance;
         this.panelId = panelId;
@@ -79,7 +76,6 @@ public String toString() {
         final StringBuilder sb = new StringBuilder("ClinicalVariantEvidence{");
         sb.append("interpretationMethodName='").append(interpretationMethodName).append('\'');
         sb.append(", phenotypes=").append(phenotypes);
-        sb.append(", consequenceTypes=").append(consequenceTypes);
         sb.append(", genomicFeature=").append(genomicFeature);
         sb.append(", modeOfInheritance=").append(modeOfInheritance);
         sb.append(", panelId='").append(panelId).append('\'');
@@ -113,15 +109,6 @@ public ClinicalVariantEvidence setPhenotypes(List<Phenotype> phenotypes) {
         return this;
     }
 
-    public List<SequenceOntologyTerm> getConsequenceTypes() {
-        return consequenceTypes;
-    }
-
-    public ClinicalVariantEvidence setConsequenceTypes(List<SequenceOntologyTerm> consequenceTypes) {
-        this.consequenceTypes = consequenceTypes;
-        return this;
-    }
-
     public GenomicFeature getGenomicFeature() {
         return genomicFeature;
     }
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/GenomicFeature.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/GenomicFeature.java
index 9a855cf48..daaf99cb9 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/GenomicFeature.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/GenomicFeature.java
@@ -20,6 +20,7 @@
 package org.opencb.biodata.models.clinical.interpretation;
 
 import org.opencb.biodata.models.core.Xref;
+import org.opencb.biodata.models.variant.avro.SequenceOntologyTerm;
 
 import java.util.List;
 
@@ -28,19 +29,35 @@ public class GenomicFeature {
     private String type; // GENE, VARIANT, REGION,...
     private String transcriptId;
     private String geneName;
+    private List<SequenceOntologyTerm> consequenceTypes;
     private List<Xref> xrefs;
 
     public GenomicFeature() {
     }
 
-    public GenomicFeature(String id, String type, String transcriptId, String geneName, List<Xref> xrefs) {
+    public GenomicFeature(String id, String type, String transcriptId, String geneName, List<SequenceOntologyTerm> consequenceTypes,
+                          List<Xref> xrefs) {
         this.id = id;
         this.type = type;
         this.transcriptId = transcriptId;
         this.geneName = geneName;
+        this.consequenceTypes = consequenceTypes;
         this.xrefs = xrefs;
     }
 
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("GenomicFeature{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", type='").append(type).append('\'');
+        sb.append(", transcriptId='").append(transcriptId).append('\'');
+        sb.append(", geneName='").append(geneName).append('\'');
+        sb.append(", consequenceTypes=").append(consequenceTypes);
+        sb.append(", xrefs=").append(xrefs);
+        sb.append('}');
+        return sb.toString();
+    }
+
     public String getId() {
         return id;
     }
@@ -77,6 +94,15 @@ public GenomicFeature setGeneName(String geneName) {
         return this;
     }
 
+    public List<SequenceOntologyTerm> getConsequenceTypes() {
+        return consequenceTypes;
+    }
+
+    public GenomicFeature setConsequenceTypes(List<SequenceOntologyTerm> consequenceTypes) {
+        this.consequenceTypes = consequenceTypes;
+        return this;
+    }
+
     public List<Xref> getXrefs() {
         return xrefs;
     }