Resolve conflicts

opencb · Jan 28, 2019 · 2d56be1 · 2d56be1
2 parents 158bdc6 + 5df970d
commit 2d56be1
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Showing 8 changed files with 465 additions and 16 deletions.
diff --git a/bionetdb-core/pom.xml b/bionetdb-core/pom.xml
@@ -22,7 +22,8 @@
         </dependency>
         <dependency>
             <groupId>org.opencb.biodata</groupId>
-            <artifactId>biodata-models</artifactId>
+            <artifactId>biodata-tools</artifactId>
+            <version>${biodata.version}</version>
         </dependency>
         <dependency>
             <groupId>org.opencb.commons</groupId>
@@ -73,11 +74,6 @@
             <artifactId>junit</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.opencb.biodata</groupId>
-            <artifactId>biodata-tools</artifactId>
-            <version>1.4.0-SNAPSHOT</version>
-        </dependency>
     </dependencies>
 
     <build>

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDbManager.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDbManager.java
@@ -16,10 +16,7 @@
 import org.opencb.bionetdb.core.neo4j.Neo4JBioPaxLoader;
 import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor;
 import org.opencb.bionetdb.core.neo4j.Neo4JVariantLoader;
-import org.opencb.bionetdb.core.network.Network;
-import org.opencb.bionetdb.core.network.NetworkManager;
-import org.opencb.bionetdb.core.network.NetworkPath;
-import org.opencb.bionetdb.core.network.Node;
+import org.opencb.bionetdb.core.network.*;
 import org.opencb.cellbase.client.config.ClientConfiguration;
 import org.opencb.cellbase.client.config.RestConfig;
 import org.opencb.cellbase.client.rest.CellBaseClient;
@@ -307,6 +304,30 @@ public QueryResult getSummaryStats(Query query, QueryOptions queryOptions) throw
         return null;
     }
 
+    public List<Variant> getMatchingDominantVariants(String child, String father, String mother, QueryOptions options) {
+        return networkDBAdaptor.getMatchingDominantVariants(child, father, mother, options);
+    }
+
+    public List<Variant> getMatchingRecessiveVariants(String child, String father, String mother, QueryOptions options) {
+        return networkDBAdaptor.getMatchingRecessiveVariants(child, father, mother, options);
+    }
+
+    public List<Variant> getMatchingDeNovoVariants(String child, String father, String mother, QueryOptions options) {
+        return networkDBAdaptor.getMatchingDeNovoVariants(child, father, mother, options);
+    }
+
+    public List<Variant> getMatchingXLinkedVariants(String child, String father, String mother, QueryOptions options) {
+        return networkDBAdaptor.getMatchingXLinkedVariants(child, father, mother, options);
+    }
+
+    public List<VariantsPair> getMatchingVariantsInSameGen(String child, String father, String mother, int limit) {
+        return networkDBAdaptor.getMatchingVariantsInSameGen(child, father, mother, limit);
+    }
+
+    public List<String> getSpecificBurdenTest(List<String> gene) {
+        return networkDBAdaptor.getSpecificBurdenTest(gene);
+    }
+
     //-------------------------------------------------------------------------
     // P R I V A T E     M E T H O D S
     //-------------------------------------------------------------------------

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/VariantsPair.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/VariantsPair.java
@@ -0,0 +1,45 @@
+package org.opencb.bionetdb.core;
+
+import org.opencb.biodata.models.variant.Variant;
+
+public class VariantsPair {
+    private Variant variant1;
+    private Variant variant2;
+    private String gene;
+
+    public VariantsPair() {
+    }
+
+    public VariantsPair(Variant variant1, Variant variant2, String gene) {
+        this.variant1 = variant1;
+        this.variant2 = variant2;
+        this.gene = gene;
+    }
+
+    public Variant getVariant1() {
+        return variant1;
+    }
+
+    public VariantsPair setVariant1(Variant variant1) {
+        this.variant1 = variant1;
+        return this;
+    }
+
+    public Variant getVariant2() {
+        return variant2;
+    }
+
+    public VariantsPair setVariant2(Variant variant2) {
+        this.variant2 = variant2;
+        return this;
+    }
+
+    public String getGene() {
+        return gene;
+    }
+
+    public VariantsPair setGene(String gene) {
+        this.gene = gene;
+        return this;
+    }
+}
diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java
@@ -1,5 +1,7 @@
 package org.opencb.bionetdb.core.api;
 
+import org.opencb.biodata.models.variant.Variant;
+import org.opencb.bionetdb.core.VariantsPair;
 import org.opencb.bionetdb.core.api.query.NetworkPathQuery;
 import org.opencb.bionetdb.core.api.query.NodeQuery;
 import org.opencb.bionetdb.core.exceptions.BioNetDBException;
@@ -124,18 +126,27 @@ enum NetworkQueryParams implements QueryParam {
     QueryResult<Network> networkQueryByPaths(List<NetworkPathQuery> pathQueries, QueryOptions queryOptions) throws BioNetDBException;
     QueryResult<Network> networkQuery(String cypher) throws BioNetDBException;
 
-
     //-------------------------------------------------------------------------
-    // T E S T S
+    // A N A L Y S I S
     //-------------------------------------------------------------------------
 
-    void loadTest();
+    List<Variant> getMatchingDominantVariants(String child, String father, String mother, QueryOptions options);
+
+    List<Variant> getMatchingRecessiveVariants(String child, String father, String mother, QueryOptions options);
 
+    List<Variant> getMatchingDeNovoVariants(String child, String father, String mother, QueryOptions options);
 
+    List<Variant> getMatchingXLinkedVariants(String child, String father, String mother, QueryOptions options);
 
+    List<VariantsPair> getMatchingVariantsInSameGen(String child, String father, String mother, int limit);
 
+    List<String> getSpecificBurdenTest(List<String> genes);
 
+    //-------------------------------------------------------------------------
+    // T E S T S
+    //-------------------------------------------------------------------------
 
+    void loadTest();
 
 //    QueryResult<Node> queryNodes(Query query, QueryOptions queryOptions) throws BioNetDBException;
 //