From fb3421aab7c9acef5152f324f8dd2abc83e09d63 Mon Sep 17 00:00:00 2001
From: bbimber <M0ndayBlu>
Date: Wed, 12 Jun 2019 10:30:40 -0700
Subject: [PATCH] Refactor VariantEval methods to allow subclass to override

---
 .../walkers/varianteval/VariantEval.java      | 14 +++++++--
 .../evaluators/VariantEvaluator.java          |  4 +++
 .../varianteval/util/EvaluationContext.java   | 29 +++++++++++++++----
 3 files changed, 40 insertions(+), 7 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
index 765e34fb0cd..084bf89ef70 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
@@ -414,7 +414,7 @@ private void checkForIncompatibleEvaluatorsAndStratifiers( final List<VariantStr
             for ( Class<? extends VariantEvaluator> ec : evaluationClasses )
                 if ( vs.getIncompatibleEvaluators().contains(ec) )
                     throw new CommandLineException.BadArgumentValue("ST and ET",
-                            "The selected stratification " + vs.getName() + 
+                            "The selected stratification " + vs.getName() +
                                     " and evaluator " + ec.getSimpleName() +
                                     " are incompatible due to combinatorial memory requirements." +
                                     " Please disable one");
@@ -427,11 +427,21 @@ final void createStratificationStates(final List<VariantStratifier> stratificati
 
         logger.info("Creating " + stratManager.size() + " combinatorial stratification states");
         for ( int i = 0; i < stratManager.size(); i++ ) {
-            EvaluationContext ec = new EvaluationContext(this, evaluationObjects);
+            EvaluationContext ec = createEvaluationContext(evaluationObjects);
             stratManager.set(i, ec);
         }
     }
 
+    /**
+     * Create the EvaluationContext (new instance) for the provided set of VariantEvaluators.
+     *
+     * @param evaluationObjects The list of VariantEvaluator classes
+     * @return The EvaluationContext for this set of VariantEvaluator classes
+     */
+    protected EvaluationContext createEvaluationContext(final Set<Class<? extends VariantEvaluator>> evaluationObjects) {
+        return new EvaluationContext(this, evaluationObjects);
+    }
+
     private class PositionAggregator {
         private SimpleInterval i = null;
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java
index e14398c9aec..020caf6394e 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java
@@ -11,6 +11,10 @@ public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
     private VariantEval walker;
     private final String simpleName;
 
+    protected VariantEvaluator(String simpleName) {
+        this.simpleName = simpleName;
+    }
+
     protected VariantEvaluator() {
         this.simpleName = getClass().getSimpleName();
     }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java
index 60b3656fcdf..1078e6dd134 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java
@@ -10,13 +10,14 @@
 import org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager;
 
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
 
-public final class EvaluationContext {
+public class EvaluationContext {
     // NOTE: must be hashset to avoid O(log n) cost of iteration in the very frequently called apply function
     final VariantEval walker;
-    private final ArrayList<VariantEvaluator> evaluationInstances;
+    private final List<VariantEvaluator> evaluationInstances;
     private final Set<Class<? extends VariantEvaluator>> evaluationClasses;
 
     public EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses) {
@@ -26,7 +27,7 @@ public EvaluationContext(final VariantEval walker, final Set<Class<? extends Var
     private EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses, final boolean doInitialize) {
         this.walker = walker;
         this.evaluationClasses = evaluationClasses;
-        this.evaluationInstances = new ArrayList<VariantEvaluator>(evaluationClasses.size());
+        this.evaluationInstances = new ArrayList<>(evaluationClasses.size());
 
         for ( final Class<? extends VariantEvaluator> c : evaluationClasses ) {
             try {
@@ -41,13 +42,31 @@ private EvaluationContext(final VariantEval walker, final Set<Class<? extends Va
         }
     }
 
+    /**
+     * Return a list of instances of each VariantEvaluator (see getEvaluationClasses).  Note: elements of this list can be null.
+     *
+     * @return The list of VariantEvaluator instances
+     */
+    public List<VariantEvaluator> getEvaluationInstances() {
+        return evaluationInstances;
+    }
+
+    /**
+     * Returns a set of VariantEvaluator classes to be used
+     *
+     * @return The set of VariantEvaluator classes to be used
+     */
+    public Set<Class<? extends VariantEvaluator>> getEvaluationClasses() {
+        return evaluationClasses;
+    }
+
     /**
      * Returns a sorted set of VariantEvaluators
      *
-     * @return
+     * @return A sorted set of VariantEvaluator instances
      */
     public final TreeSet<VariantEvaluator> getVariantEvaluators() {
-        return new TreeSet<VariantEvaluator>(evaluationInstances);
+        return new TreeSet<>(evaluationInstances);
     }
 
     public final void apply(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext, VariantContext comp, VariantContext eval) {