From f5787de92ea097f38925250dbac5058365f25a60 Mon Sep 17 00:00:00 2001
From: Philip Tzou <philiptz@stanford.edu>
Date: Wed, 21 Nov 2018 17:40:18 -0800
Subject: [PATCH] Use hiv-aapcnt 2018.11-2

---
 DrugResistance/build.gradle                                 | 2 +-
 .../drugresistance/scripts/TypedMutationsExporter.java      | 2 +-
 Utilities/build.gradle                                      | 2 +-
 .../main/java/edu/stanford/hivdb/mutations/Mutation.java    | 2 +-
 .../main/java/edu/stanford/hivdb/graphql/MutationDef.java   | 6 ++++++
 5 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/DrugResistance/build.gradle b/DrugResistance/build.gradle
index f7e73cb7..880dc94b 100644
--- a/DrugResistance/build.gradle
+++ b/DrugResistance/build.gradle
@@ -34,7 +34,7 @@ dependencies {
     compile 'com.google.code.gson:gson:2.6.2'
     compile project(':Aligner')
     compile 'org.fstrf.stanfordAsiInterpreter.resistance:resistance:1.0'
-    compile 'edu.stanford.hivdb.aapcnt:hiv-aapcnt-java:2018.11'
+    compile 'edu.stanford.hivdb.aapcnt:hiv-aapcnt-java:2018.11-2'
     testCompile 'junit:junit:4.12'
     testCompile 'org.mockito:mockito-core:1.9.5'
     testCompile project(':Utilities')
diff --git a/DrugResistance/src/main/java/edu/stanford/hivdb/drugresistance/scripts/TypedMutationsExporter.java b/DrugResistance/src/main/java/edu/stanford/hivdb/drugresistance/scripts/TypedMutationsExporter.java
index 2b1d84db..b96f2a6e 100644
--- a/DrugResistance/src/main/java/edu/stanford/hivdb/drugresistance/scripts/TypedMutationsExporter.java
+++ b/DrugResistance/src/main/java/edu/stanford/hivdb/drugresistance/scripts/TypedMutationsExporter.java
@@ -42,7 +42,7 @@ public static void main(String[] args) {
 	}
 
 	private static void exportUnusuals() {
-		HIVAminoAcidPercents allAAPcnts = HIVAminoAcidPercents.getInstance("naive", "All"); 
+		HIVAminoAcidPercents allAAPcnts = HIVAminoAcidPercents.getInstance("all", "All"); 
 
 		// Map<GenePosition, Map<Character, Boolean>>
 		// 	unusuals = UnusualMutations.getUnusualMuts();
diff --git a/Utilities/build.gradle b/Utilities/build.gradle
index 968c38f8..709f531e 100644
--- a/Utilities/build.gradle
+++ b/Utilities/build.gradle
@@ -38,7 +38,7 @@ dependencies {
     compile 'org.apache.httpcomponents:httpclient:4.5.6'
     compile 'org.apache.httpcomponents:httpcore:4.4.10'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
-    compile 'edu.stanford.hivdb.aapcnt:hiv-aapcnt-java:2018.11'
+    compile 'edu.stanford.hivdb.aapcnt:hiv-aapcnt-java:2018.11-2'
     compile project(':TestResources')
 }
 
diff --git a/Utilities/src/main/java/edu/stanford/hivdb/mutations/Mutation.java b/Utilities/src/main/java/edu/stanford/hivdb/mutations/Mutation.java
index dd24f8f0..580978a5 100644
--- a/Utilities/src/main/java/edu/stanford/hivdb/mutations/Mutation.java
+++ b/Utilities/src/main/java/edu/stanford/hivdb/mutations/Mutation.java
@@ -43,7 +43,7 @@ public class Mutation implements Comparable<Mutation> {
 		"([AC-IK-NP-TV-Z.*]+(?:[#_]?[AC-IK-NP-TV-Z.*]+)?|[id_#~-]|[iI]ns(?:ertion)?|[dD]el(?:etion)?)" +
 		"(?::([ACGTRYMWSKBDHVN-]{3})?)?" +
 		"\\s*$");
-	private static final HIVAminoAcidPercents allAAPcnts = HIVAminoAcidPercents.getInstance("naive", "All");
+	private static final HIVAminoAcidPercents allAAPcnts = HIVAminoAcidPercents.getInstance("all", "All");
 
 	private Gene gene;
 	private String cons;
diff --git a/WebApplications/src/main/java/edu/stanford/hivdb/graphql/MutationDef.java b/WebApplications/src/main/java/edu/stanford/hivdb/graphql/MutationDef.java
index e0fad18a..26aef9f1 100644
--- a/WebApplications/src/main/java/edu/stanford/hivdb/graphql/MutationDef.java
+++ b/WebApplications/src/main/java/edu/stanford/hivdb/graphql/MutationDef.java
@@ -131,6 +131,12 @@ public Object get(DataFetchingEnvironment environment) {
 			.description(
 				"If the mutation is from unsequenced region.")
 			.build())
+		.field(newFieldDefinition()
+				.type(GraphQLBoolean)
+				.name("isDRM")
+				.description(
+					"If the mutation is a drug resistance mutation (DRM) or not.")
+				.build())
 		.field(newFieldDefinition()
 			.type(GraphQLBoolean)
 			.name("hasStop")