From 6c11e006bd51aa10ba5e1379d96752cd567ed7bc Mon Sep 17 00:00:00 2001
From: imedina <igmecas@gmail.com>
Date: Mon, 11 Mar 2024 03:12:56 +0000
Subject: [PATCH 1/3] Add new SNP classes to store dbSNP

---
 .../org/opencb/biodata/models/core/Snp.java   | 147 ++++++++++++++++++
 .../biodata/models/core/SnpAnnotation.java    |  90 +++++++++++
 2 files changed, 237 insertions(+)
 create mode 100644 biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java
 create mode 100644 biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java b/biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java
new file mode 100644
index 00000000..c2d079ba
--- /dev/null
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java
@@ -0,0 +1,147 @@
+/*
+ * <!--
+ *   ~ 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.core;
+
+import java.util.List;
+
+public class Snp {
+    private String id;
+    private String chromosome;
+    private int position;
+    private String reference;
+    private List<String> alleles;
+    private String type;
+    private String source;
+    private String version;
+    private SnpAnnotation annotation;
+
+    public Snp() {
+    }
+
+    public Snp(String id, String chromosome, int position, String reference, List<String> alleles, String type,
+               String source, String version, SnpAnnotation annotation) {
+        this.id = id;
+        this.chromosome = chromosome;
+        this.position = position;
+        this.reference = reference;
+        this.alleles = alleles;
+        this.type = type;
+        this.source = source;
+        this.version = version;
+        this.annotation = annotation;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("Snp{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", chromosome='").append(chromosome).append('\'');
+        sb.append(", position=").append(position);
+        sb.append(", reference='").append(reference).append('\'');
+        sb.append(", alleles=").append(alleles);
+        sb.append(", type='").append(type).append('\'');
+        sb.append(", source='").append(source).append('\'');
+        sb.append(", version='").append(version).append('\'');
+        sb.append(", annotation=").append(annotation);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public Snp setId(String id) {
+        this.id = id;
+        return this;
+    }
+
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    public Snp setChromosome(String chromosome) {
+        this.chromosome = chromosome;
+        return this;
+    }
+
+    public int getPosition() {
+        return position;
+    }
+
+    public Snp setPosition(int position) {
+        this.position = position;
+        return this;
+    }
+
+    public String getReference() {
+        return reference;
+    }
+
+    public Snp setReference(String reference) {
+        this.reference = reference;
+        return this;
+    }
+
+    public List<String> getAlleles() {
+        return alleles;
+    }
+
+    public Snp setAlleles(List<String> alleles) {
+        this.alleles = alleles;
+        return this;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public Snp setType(String type) {
+        this.type = type;
+        return this;
+    }
+
+    public String getSource() {
+        return source;
+    }
+
+    public Snp setSource(String source) {
+        this.source = source;
+        return this;
+    }
+
+    public String getVersion() {
+        return version;
+    }
+
+    public Snp setVersion(String version) {
+        this.version = version;
+        return this;
+    }
+
+    public SnpAnnotation getAnnotation() {
+        return annotation;
+    }
+
+    public Snp setAnnotation(SnpAnnotation annotation) {
+        this.annotation = annotation;
+        return this;
+    }
+}
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java b/biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java
new file mode 100644
index 00000000..215341ad
--- /dev/null
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java
@@ -0,0 +1,90 @@
+/*
+ * <!--
+ *   ~ 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.core;
+
+import org.opencb.biodata.models.variant.avro.EvidenceEntry;
+import org.opencb.biodata.models.variant.avro.PopulationFrequency;
+
+import java.util.List;
+
+public class SnpAnnotation {
+
+    private List<String> flags;
+    private String gene;
+    private List<PopulationFrequency> populationFrequencies;
+    private List<EvidenceEntry> traitAssociation;
+
+    public SnpAnnotation() {
+    }
+
+    public SnpAnnotation(List<String> flags, String gene, List<PopulationFrequency> populationFrequencies, List<EvidenceEntry> traitAssociation) {
+        this.flags = flags;
+        this.gene = gene;
+        this.populationFrequencies = populationFrequencies;
+        this.traitAssociation = traitAssociation;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("SnpAnnotation{");
+        sb.append("flags=").append(flags);
+        sb.append(", gene='").append(gene).append('\'');
+        sb.append(", populationFrequencies=").append(populationFrequencies);
+        sb.append(", traitAssociation=").append(traitAssociation);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public List<String> getFlags() {
+        return flags;
+    }
+
+    public SnpAnnotation setFlags(List<String> flags) {
+        this.flags = flags;
+        return this;
+    }
+
+    public String getGene() {
+        return gene;
+    }
+
+    public SnpAnnotation setGene(String gene) {
+        this.gene = gene;
+        return this;
+    }
+
+    public List<PopulationFrequency> getPopulationFrequencies() {
+        return populationFrequencies;
+    }
+
+    public SnpAnnotation setPopulationFrequencies(List<PopulationFrequency> populationFrequencies) {
+        this.populationFrequencies = populationFrequencies;
+        return this;
+    }
+
+    public List<EvidenceEntry> getTraitAssociation() {
+        return traitAssociation;
+    }
+
+    public SnpAnnotation setTraitAssociation(List<EvidenceEntry> traitAssociation) {
+        this.traitAssociation = traitAssociation;
+        return this;
+    }
+}

From ef752abc04d234ee16e4a68169c32d8d55d28fcb Mon Sep 17 00:00:00 2001
From: imedina <igmecas@gmail.com>
Date: Tue, 12 Mar 2024 02:30:43 +0000
Subject: [PATCH 2/3] Update SnpAnnotation data model

---
 .../biodata/models/core/SnpAnnotation.java    | 27 ++++++-------------
 1 file changed, 8 insertions(+), 19 deletions(-)

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java b/biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java
index 215341ad..16fab718 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java
@@ -19,37 +19,26 @@
 
 package org.opencb.biodata.models.core;
 
-import org.opencb.biodata.models.variant.avro.EvidenceEntry;
 import org.opencb.biodata.models.variant.avro.PopulationFrequency;
 
 import java.util.List;
+import java.util.Map;
 
 public class SnpAnnotation {
 
     private List<String> flags;
     private String gene;
     private List<PopulationFrequency> populationFrequencies;
-    private List<EvidenceEntry> traitAssociation;
+    private Map<String, Object> additionalAttributes;
 
     public SnpAnnotation() {
     }
 
-    public SnpAnnotation(List<String> flags, String gene, List<PopulationFrequency> populationFrequencies, List<EvidenceEntry> traitAssociation) {
+    public SnpAnnotation(List<String> flags, String gene, List<PopulationFrequency> populationFrequencies, Map<String, Object> additionalAttributes) {
         this.flags = flags;
         this.gene = gene;
         this.populationFrequencies = populationFrequencies;
-        this.traitAssociation = traitAssociation;
-    }
-
-    @Override
-    public String toString() {
-        final StringBuilder sb = new StringBuilder("SnpAnnotation{");
-        sb.append("flags=").append(flags);
-        sb.append(", gene='").append(gene).append('\'');
-        sb.append(", populationFrequencies=").append(populationFrequencies);
-        sb.append(", traitAssociation=").append(traitAssociation);
-        sb.append('}');
-        return sb.toString();
+        this.additionalAttributes = additionalAttributes;
     }
 
     public List<String> getFlags() {
@@ -79,12 +68,12 @@ public SnpAnnotation setPopulationFrequencies(List<PopulationFrequency> populati
         return this;
     }
 
-    public List<EvidenceEntry> getTraitAssociation() {
-        return traitAssociation;
+    public Map<String, Object> getAdditionalAttributes() {
+        return additionalAttributes;
     }
 
-    public SnpAnnotation setTraitAssociation(List<EvidenceEntry> traitAssociation) {
-        this.traitAssociation = traitAssociation;
+    public SnpAnnotation setAdditionalAttributes(Map<String, Object> additionalAttributes) {
+        this.additionalAttributes = additionalAttributes;
         return this;
     }
 }

From 9ea6c147b64917ff95fed4b8335bd89eae109176 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, 12 Mar 2024 11:28:15 +0100
Subject: [PATCH 3/3] models: rename alleles to alternates, #TASK-5813,
 #TASK-5789

---
 .../java/org/opencb/biodata/models/core/Snp.java | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java b/biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java
index c2d079ba..8f8cc712 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java
@@ -26,7 +26,7 @@ public class Snp {
     private String chromosome;
     private int position;
     private String reference;
-    private List<String> alleles;
+    private List<String> alternates;
     private String type;
     private String source;
     private String version;
@@ -35,13 +35,13 @@ public class Snp {
     public Snp() {
     }
 
-    public Snp(String id, String chromosome, int position, String reference, List<String> alleles, String type,
+    public Snp(String id, String chromosome, int position, String reference, List<String> alternates, String type,
                String source, String version, SnpAnnotation annotation) {
         this.id = id;
         this.chromosome = chromosome;
         this.position = position;
         this.reference = reference;
-        this.alleles = alleles;
+        this.alternates = alternates;
         this.type = type;
         this.source = source;
         this.version = version;
@@ -55,7 +55,7 @@ public String toString() {
         sb.append(", chromosome='").append(chromosome).append('\'');
         sb.append(", position=").append(position);
         sb.append(", reference='").append(reference).append('\'');
-        sb.append(", alleles=").append(alleles);
+        sb.append(", alternates=").append(alternates);
         sb.append(", type='").append(type).append('\'');
         sb.append(", source='").append(source).append('\'');
         sb.append(", version='").append(version).append('\'');
@@ -100,12 +100,12 @@ public Snp setReference(String reference) {
         return this;
     }
 
-    public List<String> getAlleles() {
-        return alleles;
+    public List<String> getAlternates() {
+        return alternates;
     }
 
-    public Snp setAlleles(List<String> alleles) {
-        this.alleles = alleles;
+    public Snp setAlternates(List<String> alternates) {
+        this.alternates = alternates;
         return this;
     }