From 0d4dd8e9e9f97bcfee556adf3a1f63a046e8136a Mon Sep 17 00:00:00 2001
From: Peter Robinson <peter.robinson@jax.org>
Date: Wed, 27 Aug 2025 15:24:10 +0200
Subject: [PATCH] first commit BOQA prioritizer

---
 exomiser-core/pom.xml                         |  5 ++
 .../core/prioritisers/BoqaPriority.java       | 64 +++++++++++++++++++
 .../core/prioritisers/BoqaPriorityResult.java | 23 +++++++
 .../core/prioritisers/PriorityType.java       |  2 +
 4 files changed, 94 insertions(+)
 create mode 100644 exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriority.java
 create mode 100644 exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriorityResult.java

diff --git a/exomiser-core/pom.xml b/exomiser-core/pom.xml
index 54ea8b457..608d34a43 100644
--- a/exomiser-core/pom.xml
+++ b/exomiser-core/pom.xml
@@ -36,6 +36,11 @@
         <arrow.version>18.2.0</arrow.version>
     </properties>
     <dependencies>
+        <dependency>
+            <groupId>com.github.p2gx.boqa</groupId>
+            <artifactId>boqa-core</artifactId>
+            <version>0.1.0-SNAPSHOT</version>
+        </dependency>
         <!--Jannovar is used for providing known gene annotations on variants -->
         <dependency>
             <groupId>de.charite.compbio</groupId>
diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriority.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriority.java
new file mode 100644
index 000000000..1b2759aa5
--- /dev/null
+++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriority.java
@@ -0,0 +1,64 @@
+package org.monarchinitiative.exomiser.core.prioritisers;
+
+import com.github.p2gx.boqa.core.DiseaseData;
+import org.monarchinitiative.exomiser.core.model.Gene;
+import org.monarchinitiative.exomiser.core.prioritisers.service.PriorityService;
+
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Stream;
+
+public class BoqaPriority implements Prioritiser<BoqaPriorityResult> {
+
+    public static class ExomiserDiseaseData implements DiseaseData {
+        private final PriorityService priorityService;
+
+        public ExomiserDiseaseData(PriorityService priorityService) {
+            this.priorityService = priorityService;
+        }
+
+        @Override
+        public int size() {
+            return 0;
+        }
+
+        @Override
+        public Set<String> getDiseaseIds() {
+            return Set.of();
+        }
+
+        @Override
+        public Set<String> getIncludedDiseaseFeatures(String diseaseTermId) {
+            return new HashSet<>(this.priorityService.getHpoIdsForDiseaseId(diseaseTermId));
+        }
+
+        @Override
+        public Set<String> getDiseaseGeneIds(String s) {
+            return Set.of();
+        }
+
+        @Override
+        public Set<String> getDiseaseGeneSymbols(String s) {
+            return Set.of();
+        }
+    }
+
+
+
+
+   public BoqaPriority(PriorityService priorityService, Path hpOboPath){
+       DiseaseData diseaseData = new ExomiserDiseaseData(priorityService);
+   }
+
+    @Override
+    public Stream<BoqaPriorityResult> prioritise(List<String> hpoIds, List<Gene> genes) {
+        return Stream.empty();
+    }
+
+    @Override
+    public PriorityType priorityType() {
+        return PriorityType.BOQA_PRIORITY;
+    }
+}
diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriorityResult.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriorityResult.java
new file mode 100644
index 000000000..9e7699719
--- /dev/null
+++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/BoqaPriorityResult.java
@@ -0,0 +1,23 @@
+package org.monarchinitiative.exomiser.core.prioritisers;
+
+public record BoqaPriorityResult() implements PriorityResult{
+    @Override
+    public int geneId() {
+        return 0;
+    }
+
+    @Override
+    public String geneSymbol() {
+        return "";
+    }
+
+    @Override
+    public double score() {
+        return 0;
+    }
+
+    @Override
+    public PriorityType priorityType() {
+        return null;
+    }
+}
diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/PriorityType.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/PriorityType.java
index 9b2800922..f4f41f9df 100644
--- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/PriorityType.java
+++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/PriorityType.java
@@ -36,6 +36,8 @@ public enum PriorityType {
     PHIVE_PRIORITY,
     //Prioritises against OMIM data
     OMIM_PRIORITY,
+    // Bayesian Ontology Query Algorithm
+    BOQA_PRIORITY,
     //None - for when you don't want to run any prioritisation
     NONE