Add Mutation.isSDRM to GraphQL; release v2.2.2

hivdb · Jan 19, 2018 · 4791ff5 · 4791ff5
1 parent 122798c
commit 4791ff5
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Showing 12 changed files with 190,456 additions and 184,934 deletions.
diff --git a/Aligner/build.gradle b/Aligner/build.gradle
@@ -6,7 +6,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '2.2.1-1'
+version = '2.2.2'
 
 description = """Aligner"""
 

diff --git a/DrugResistance/build.gradle b/DrugResistance/build.gradle
@@ -6,7 +6,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '2.2.1-1'
+version = '2.2.2'
 
 description = """DrugResistance"""
 

diff --git a/TestResources/build.gradle b/TestResources/build.gradle
@@ -5,7 +5,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '2.2.1-1'
+version = '2.2.2'
 
 description = """Test resources"""
 

diff --git a/Utilities/build.gradle b/Utilities/build.gradle
@@ -6,7 +6,7 @@ plugins {
 }
 
 group = 'edu.stanford.hivdb'
-version = '2.2.1-1'
+version = '2.2.2'
 
 description = """Utilities"""
 

diff --git a/Utilities/src/main/java/edu/stanford/hivdb/mutations/Mutation.java b/Utilities/src/main/java/edu/stanford/hivdb/mutations/Mutation.java
@@ -338,6 +338,7 @@ public static Mutation parseString(String mutText) {
 	public boolean hasConsensus () { return aas.split("_", 2)[0].contains(gene.getConsensus(pos));}
 	public boolean hasStop() { return getAAs().contains("*"); }
 	public boolean isUnusual() { return UnusualMutations.containsUnusualMut(this); }
+	public boolean isSDRM() { return Sdrms.isSDRM(this); }
 	public boolean hasBDHVN() {
 		// TODO: what if BDHVN doesn't affect the amimo acid?
 		return triplet.contains("B") || triplet.contains("D") || triplet.contains("H") ||

diff --git a/Utilities/src/main/java/edu/stanford/hivdb/mutations/Sdrms.java b/Utilities/src/main/java/edu/stanford/hivdb/mutations/Sdrms.java
@@ -19,14 +19,13 @@
 package edu.stanford.hivdb.mutations;
 
 import java.sql.SQLException;
-import java.util.Collection;
 
 import edu.stanford.hivdb.utilities.JdbcDatabase;
 import edu.stanford.hivdb.utilities.Cachable;
 
 public class Sdrms {
 	@Cachable.CachableField
-	private static Collection<Mutation> sdrms;
+	private static MutationSet sdrms;
 	private static final JdbcDatabase db;
 
 	static {
@@ -48,16 +47,22 @@ public class Sdrms {
 	public static MutationSet getSdrms(MutationSet seqMuts) {
 		return seqMuts.intersectsWith(sdrms);
 	}
+
+	public static boolean isSDRM(Mutation mut) {
+		return sdrms.hasSharedAAMutation(mut);
+	}
 
 	private static void populateSDRMs() throws SQLException {
 		final String sqlStatement =
 			"SELECT Gene, Pos, AAs FROM tblSDRMs ORDER BY Gene, Pos, AAs";
 
-		sdrms = db.iterate(sqlStatement, rs -> {
-			return new Mutation(
-				Gene.valueOf(rs.getString("Gene")),
-				rs.getInt("Pos"),
-				rs.getString("AAs"));
-		});
+		sdrms = new MutationSet(
+			db.iterate(sqlStatement, rs -> {
+				return new Mutation(
+						Gene.valueOf(rs.getString("Gene")),
+						rs.getInt("Pos"),
+						rs.getString("AAs"));
+			})
+		);
 	}
 }